ChemWiki - User contributions [en]

Latex-guide

2015-08-25T12:00:12Z

Amckinle: Created page with "=A guide to using LaTeX in Chemistry= We have decided to compile this page as a 'ready reference' for those wishing to dip their toe into the murky waters of typesetting. It..."

=A guide to using LaTeX in Chemistry=

We have decided to compile this page as a 'ready reference' for those wishing to dip their toe into the murky waters of typesetting. It is not intended to be a comprehensive guide, it will not show you how to set up your own document class, it will not make you an expert in LaTeX and it certainly won't grant you the power of flight(!). What we hope it will do is give you an outline to starting to mark-up your documents in such a way that they may be run through a LaTeX processor to generate beautiful looking documents and to hopefully take away some of the stress associated with using run-of-the-mill word processing applications when trying to get your tables of contents or figures included.

==Why bother?==
Why not? If you haven't ever done any markup before (HTML, TeX, coding etc), LaTeX is a simple step into a mark-up environment that will yield quick results and will give you quick feedback on your mark-up skills. It is also an open platform - i.e. it is FREE software - which means that there are literally thousands of resources on the internet, and you should become used to putting the phrase "How do I show [THING] in latex" into your favourite internet search engine. (Try [https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=how%20do%20i%20do%20a%20pound%20sign%20in%20latex this], [https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=how+do+i+enter+a+plus+minus+in+latex this], or, more relevant to chemistry, [https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=how+do+i+show+the+standard+state+in+latex this]). It will also get you into the discipline of coding - making sure you close your parentheses, use the appropriate characters etc. It's not onerous, it just requires a bit of thought.

Basically, LaTeX is a way to get your documents looking "publication quality" without having to worry about margins, alignment of text with images, tables of contents, page numbers... it will save you ''days'' of time. Plus - you want a different layout? Columns, landscape, wider margins? No problem - just load the relevant document class (around 5 seconds work), process the document again (10-15 seconds depending on length of document), and bingo. Seriously, it will change your life. Or at least part of it.

Finally, LaTeX is mature software. That doesn't mean it is old (well, it sort of is; the current version 2e was released in 1994), but it means that it is very stable, reliable, and essentially bug free. So, in the event of it throwing an error, the chances are that the mistake has come from your input rather than a problem with the software. Far from being frustrating, it means that '''you can fix the problem''' - and that can be enormously calming!

==Getting started==

Py:python-ViCE-2015

2015-08-14T13:29:50Z

Amckinle: /* Download Anaconda Python Distribution */

=iPython notebooks for Data Analysis and Visualisation: a ViCE 2015 workshop=

This page is intended to have downloadable resources to support the 2015 Variety in Chemistry Education and Physics Higher Education Conference workshop, as well as guidance on how to install scientific python onto your own computer.

==Abstract==
'''IPython notebooks for data analysis and visualisation'''

''João Pedro Malhado, Clyde Fare, Andrew McKinley, Michael Bearpark''

Imperial College London

This workshop is based on a course on data analysis and visualisation taught at the Chemistry Department of Imperial College London as part of the first year undergraduate curriculum. The purpose of the course is to introduce the basic data analysis techniques required to interpret experimental (or otherwise) data collected in the laboratory, along with introducing the IPython notebook as an electronic, multi-media, interactive computing notebook that students are encouraged to use throughout their degree.

Whilst the focus of the course is not computer programming, it could serve as a pre-introduction to the subject. It introduces variables, data structures in the form of arrays, functions, and more generally a computing platform.

The course was designed as a series of self-learning interactive exercises using IPython notebooks. The first three notebooks introduce concepts interactively while the two exercise notebooks develop problem solving based on these concepts. The course material can be found at: [https://github.com/imperialchem/python-data-viz-intro]

The conference workshop will be a session encompassing an adumbrated version of the key parts of this student class. This will be a hands-on session for participants to explore the possibilities of this new notebook technology and how to use it in a teaching environment.

(Participants should bring or have access to a computer with the Scientific Python installed – installations instructions will be circulated prior to the conference.)

==Pre-workshop guidance==

===Preparations for the workshop===

We circulate this guide to help you in your preparation for our workshop. You will need to bring or have alternative access to a computer with the scientific python distribution installed; here we outline guidance for installation of Anaconda, the preferred distribution for using the iPython notebook.

NOTE: The download is reasonably large (ca. 290 Mb), so it is best to have this downloaded in advance of the workshop.

Please do get in touch if you have any questions - [mailto:python@imperial.ac.uk Email us]

===Download Anaconda Python Distribution===
[[File:Py-vice2015-prep1.png|thumb|alt=Anaconda Website|Figure 1: The Anaconda Website ([http://continuum.io/downloads link])]]

Visit [http://continuum.io/downloads the Anaconda website] in order to download the Anaconda Scientific Python distribution; it is available for Windows, Mac OSX and Linux. It will likely auto-detect your operating system and offer the appropriate downloader. This tutorial focuses on MacOS, but installation for Windows is as trivial.

NOTE on versions: for participation in this workshop please ensure you have installed version 3.x or higher.

Once downloaded, open the installer and follow the instructions.

===Launching the application===

The application will install in a variety of locations; you are looking for the application entitled "Launcher":

Windows: Start Menu --> Anaconda --> Launcher

MacOS: ~/anaconda/Launcher

Linux: ~/anaconda/Launcher

This will bring up the menu to launch the various aspects of the Anaconda distribution. We are interested in the ipython-notebook, so click "Launch"

[[File:Py-vice2015-prep2.png|thumb|alt=Screengrab of the Launcher application| Figure 2: Screengrab of the Launcher application]]

===Launching iPython notebooks===
Running the "Launch" script highlighted in Figure 2 will go through the motions of launching iPython, and will open your web browser to your computer's file structure. You may want to bookmark the file tree location ([http://localhost:8888/tree or click here]) for future reference.

Navigate through your file structure to wherever you wish to store your iPython workshop material, and open the appropriate file (extension *.ipynb). Note that the content of the notebook may take a second or two to appear.

You can also create a "New" ipython notebook from the menu in the upper right of your window.
[[File:Py-vice2015-prep3.png|thumb|alt=The file structure in web browser| Figure 3: The web browser-based file manager]]

===Your first iPython notebook===

Congratulations - you are now ready to do some Python coding. We have uploaded a preliminary notebook HERE which will allow you to verify your installation and go over the preliminary material for the course.

We look forward to seeing you at ViCE!

- João, Clyde, Andrew, Mike.

[[File:Py-vice2015-prep4.png|thumb|alt=Your first iPython notebook|Figure 4: What you should see upon successful loading of the first workshop script.]]

Py:python-ViCE-2015

2015-08-14T11:54:23Z

Amckinle: /* Download Anaconda Python Distribution */

=iPython notebooks for Data Analysis and Visualisation: a ViCE 2015 workshop=

This page is intended to have downloadable resources to support the 2015 Variety in Chemistry Education and Physics Higher Education Conference workshop, as well as guidance on how to install scientific python onto your own computer.

==Abstract==
'''IPython notebooks for data analysis and visualisation'''

''João Pedro Malhado, Clyde Fare, Andrew McKinley, Michael Bearpark''

Imperial College London

This workshop is based on a course on data analysis and visualisation taught at the Chemistry Department of Imperial College London as part of the first year undergraduate curriculum. The purpose of the course is to introduce the basic data analysis techniques required to interpret experimental (or otherwise) data collected in the laboratory, along with introducing the IPython notebook as an electronic, multi-media, interactive computing notebook that students are encouraged to use throughout their degree.

Whilst the focus of the course is not computer programming, it could serve as a pre-introduction to the subject. It introduces variables, data structures in the form of arrays, functions, and more generally a computing platform.

The course was designed as a series of self-learning interactive exercises using IPython notebooks. The first three notebooks introduce concepts interactively while the two exercise notebooks develop problem solving based on these concepts. The course material can be found at: [https://github.com/imperialchem/python-data-viz-intro]

The conference workshop will be a session encompassing an adumbrated version of the key parts of this student class. This will be a hands-on session for participants to explore the possibilities of this new notebook technology and how to use it in a teaching environment.

(Participants should bring or have access to a computer with the Scientific Python installed – installations instructions will be circulated prior to the conference.)

==Pre-workshop guidance==

===Preparations for the workshop===

We circulate this guide to help you in your preparation for our workshop. You will need to bring or have alternative access to a computer with the scientific python distribution installed; here we outline guidance for installation of Anaconda, the preferred distribution for using the iPython notebook.

NOTE: The download is reasonably large (ca. 290 Mb), so it is best to have this downloaded in advance of the workshop.

Please do get in touch if you have any questions - [mailto:python@imperial.ac.uk Email us]

===Download Anaconda Python Distribution===
[[File:Py-vice2015-prep1.png|thumb|alt=Anaconda Website|Figure 1: The Anaconda Website]]

Visit [http://continuum.io/downloads the Anaconda website] in order to download the Anaconda Scientific Python distribution; it is available for Windows, Mac OSX and Linux. It will likely auto-detect your operating system and offer the appropriate downloader. This tutorial focuses on MacOS, but installation for Windows is as trivial.

NOTE on versions: for participation in this workshop please ensure you have installed version 3.x or higher.

Once downloaded, open the installer and follow the instructions.

===Launching the application===

The application will install in a variety of locations; you are looking for the application entitled "Launcher":

Windows: Start Menu --> Anaconda --> Launcher

MacOS: ~/anaconda/Launcher

Linux: ~/anaconda/Launcher

This will bring up the menu to launch the various aspects of the Anaconda distribution. We are interested in the ipython-notebook, so click "Launch"

[[File:Py-vice2015-prep2.png|thumb|alt=Screengrab of the Launcher application| Figure 2: Screengrab of the Launcher application]]

===Launching iPython notebooks===
Running the "Launch" script highlighted in Figure 2 will go through the motions of launching iPython, and will open your web browser to your computer's file structure. You may want to bookmark the file tree location ([http://localhost:8888/tree or click here]) for future reference.

Navigate through your file structure to wherever you wish to store your iPython workshop material, and open the appropriate file (extension *.ipynb). Note that the content of the notebook may take a second or two to appear.

You can also create a "New" ipython notebook from the menu in the upper right of your window.
[[File:Py-vice2015-prep3.png|thumb|alt=The file structure in web browser| Figure 3: The web browser-based file manager]]

===Your first iPython notebook===

Congratulations - you are now ready to do some Python coding. We have uploaded a preliminary notebook HERE which will allow you to verify your installation and go over the preliminary material for the course.

We look forward to seeing you at ViCE!

- João, Clyde, Andrew, Mike.

[[File:Py-vice2015-prep4.png|thumb|alt=Your first iPython notebook|Figure 4: What you should see upon successful loading of the first workshop script.]]

Py:python-ViCE-2015

2015-08-14T11:53:47Z

Amckinle: /* Launching the application */

=iPython notebooks for Data Analysis and Visualisation: a ViCE 2015 workshop=

This page is intended to have downloadable resources to support the 2015 Variety in Chemistry Education and Physics Higher Education Conference workshop, as well as guidance on how to install scientific python onto your own computer.

==Abstract==
'''IPython notebooks for data analysis and visualisation'''

''João Pedro Malhado, Clyde Fare, Andrew McKinley, Michael Bearpark''

Imperial College London

This workshop is based on a course on data analysis and visualisation taught at the Chemistry Department of Imperial College London as part of the first year undergraduate curriculum. The purpose of the course is to introduce the basic data analysis techniques required to interpret experimental (or otherwise) data collected in the laboratory, along with introducing the IPython notebook as an electronic, multi-media, interactive computing notebook that students are encouraged to use throughout their degree.

Whilst the focus of the course is not computer programming, it could serve as a pre-introduction to the subject. It introduces variables, data structures in the form of arrays, functions, and more generally a computing platform.

The course was designed as a series of self-learning interactive exercises using IPython notebooks. The first three notebooks introduce concepts interactively while the two exercise notebooks develop problem solving based on these concepts. The course material can be found at: [https://github.com/imperialchem/python-data-viz-intro]

The conference workshop will be a session encompassing an adumbrated version of the key parts of this student class. This will be a hands-on session for participants to explore the possibilities of this new notebook technology and how to use it in a teaching environment.

(Participants should bring or have access to a computer with the Scientific Python installed – installations instructions will be circulated prior to the conference.)

==Pre-workshop guidance==

===Preparations for the workshop===

We circulate this guide to help you in your preparation for our workshop. You will need to bring or have alternative access to a computer with the scientific python distribution installed; here we outline guidance for installation of Anaconda, the preferred distribution for using the iPython notebook.

NOTE: The download is reasonably large (ca. 290 Mb), so it is best to have this downloaded in advance of the workshop.

Please do get in touch if you have any questions - [mailto:python@imperial.ac.uk Email us]

===Download Anaconda Python Distribution===
Visit [http://continuum.io/downloads the Anaconda website] in order to download the Anaconda Scientific Python distribution; it is available for Windows, Mac OSX and Linux. It will likely auto-detect your operating system and offer the appropriate downloader. This tutorial focuses on MacOS, but installation for Windows is as trivial.

NOTE on versions: for participation in this workshop please ensure you have installed version 3.x or higher.

Once downloaded, open the installer and follow the instructions.
[[File:Py-vice2015-prep1.png|thumb|alt=Anaconda Website|The Anaconda Website]]

===Launching the application===

The application will install in a variety of locations; you are looking for the application entitled "Launcher":

Windows: Start Menu --> Anaconda --> Launcher

MacOS: ~/anaconda/Launcher

Linux: ~/anaconda/Launcher

This will bring up the menu to launch the various aspects of the Anaconda distribution. We are interested in the ipython-notebook, so click "Launch"

[[File:Py-vice2015-prep2.png|thumb|alt=Screengrab of the Launcher application| Figure 2: Screengrab of the Launcher application]]

===Launching iPython notebooks===
Running the "Launch" script highlighted in Figure 2 will go through the motions of launching iPython, and will open your web browser to your computer's file structure. You may want to bookmark the file tree location ([http://localhost:8888/tree or click here]) for future reference.

Navigate through your file structure to wherever you wish to store your iPython workshop material, and open the appropriate file (extension *.ipynb). Note that the content of the notebook may take a second or two to appear.

You can also create a "New" ipython notebook from the menu in the upper right of your window.
[[File:Py-vice2015-prep3.png|thumb|alt=The file structure in web browser| Figure 3: The web browser-based file manager]]

===Your first iPython notebook===

Congratulations - you are now ready to do some Python coding. We have uploaded a preliminary notebook HERE which will allow you to verify your installation and go over the preliminary material for the course.

We look forward to seeing you at ViCE!

- João, Clyde, Andrew, Mike.

[[File:Py-vice2015-prep4.png|thumb|alt=Your first iPython notebook|Figure 4: What you should see upon successful loading of the first workshop script.]]

File:Py-vice2015-prep4.png

2015-08-14T11:53:04Z

Amckinle: Python workshop prep 4

Python workshop prep 4

File:Py-vice2015-prep3.png

2015-08-14T11:51:08Z

Amckinle: iPython prep 3

iPython prep 3

Py:python-ViCE-2015

2015-08-14T11:49:21Z

Amckinle: /* Launching the application */

=iPython notebooks for Data Analysis and Visualisation: a ViCE 2015 workshop=

This page is intended to have downloadable resources to support the 2015 Variety in Chemistry Education and Physics Higher Education Conference workshop, as well as guidance on how to install scientific python onto your own computer.

==Abstract==
'''IPython notebooks for data analysis and visualisation'''

''João Pedro Malhado, Clyde Fare, Andrew McKinley, Michael Bearpark''

Imperial College London

This workshop is based on a course on data analysis and visualisation taught at the Chemistry Department of Imperial College London as part of the first year undergraduate curriculum. The purpose of the course is to introduce the basic data analysis techniques required to interpret experimental (or otherwise) data collected in the laboratory, along with introducing the IPython notebook as an electronic, multi-media, interactive computing notebook that students are encouraged to use throughout their degree.

Whilst the focus of the course is not computer programming, it could serve as a pre-introduction to the subject. It introduces variables, data structures in the form of arrays, functions, and more generally a computing platform.

The course was designed as a series of self-learning interactive exercises using IPython notebooks. The first three notebooks introduce concepts interactively while the two exercise notebooks develop problem solving based on these concepts. The course material can be found at: [https://github.com/imperialchem/python-data-viz-intro]

The conference workshop will be a session encompassing an adumbrated version of the key parts of this student class. This will be a hands-on session for participants to explore the possibilities of this new notebook technology and how to use it in a teaching environment.

(Participants should bring or have access to a computer with the Scientific Python installed – installations instructions will be circulated prior to the conference.)

==Pre-workshop guidance==

===Preparations for the workshop===

We circulate this guide to help you in your preparation for our workshop. You will need to bring or have alternative access to a computer with the scientific python distribution installed; here we outline guidance for installation of Anaconda, the preferred distribution for using the iPython notebook.

NOTE: The download is reasonably large (ca. 290 Mb), so it is best to have this downloaded in advance of the workshop.

Please do get in touch if you have any questions - [mailto:python@imperial.ac.uk Email us]

===Download Anaconda Python Distribution===
Visit [http://continuum.io/downloads the Anaconda website] in order to download the Anaconda Scientific Python distribution; it is available for Windows, Mac OSX and Linux. It will likely auto-detect your operating system and offer the appropriate downloader. This tutorial focuses on MacOS, but installation for Windows is as trivial.

NOTE on versions: for participation in this workshop please ensure you have installed version 3.x or higher.

Once downloaded, open the installer and follow the instructions.
[[File:Py-vice2015-prep1.png|thumb|alt=Anaconda Website|The Anaconda Website]]

===Launching the application===

The application will install in a variety of locations; you are looking for the application entitled "Launcher":

Windows: Start Menu --> Anaconda --> Launcher

MacOS: ~/anaconda/Launcher

Linux: ~/anaconda/Launcher

This will bring up the menu to launch the various aspects of the Anaconda distribution. We are interested in the ipython-notebook, so click "Launch"

[[File:Py-vice2015-prep2.png|thumb|alt=Screengrab of the Launcher application|Screengrab of the Launcher application]]

Py:python-ViCE-2015

2015-08-14T11:48:43Z

Amckinle: /* Launching the application */

=iPython notebooks for Data Analysis and Visualisation: a ViCE 2015 workshop=

This page is intended to have downloadable resources to support the 2015 Variety in Chemistry Education and Physics Higher Education Conference workshop, as well as guidance on how to install scientific python onto your own computer.

==Abstract==
'''IPython notebooks for data analysis and visualisation'''

''João Pedro Malhado, Clyde Fare, Andrew McKinley, Michael Bearpark''

Imperial College London

This workshop is based on a course on data analysis and visualisation taught at the Chemistry Department of Imperial College London as part of the first year undergraduate curriculum. The purpose of the course is to introduce the basic data analysis techniques required to interpret experimental (or otherwise) data collected in the laboratory, along with introducing the IPython notebook as an electronic, multi-media, interactive computing notebook that students are encouraged to use throughout their degree.

Whilst the focus of the course is not computer programming, it could serve as a pre-introduction to the subject. It introduces variables, data structures in the form of arrays, functions, and more generally a computing platform.

The course was designed as a series of self-learning interactive exercises using IPython notebooks. The first three notebooks introduce concepts interactively while the two exercise notebooks develop problem solving based on these concepts. The course material can be found at: [https://github.com/imperialchem/python-data-viz-intro]

The conference workshop will be a session encompassing an adumbrated version of the key parts of this student class. This will be a hands-on session for participants to explore the possibilities of this new notebook technology and how to use it in a teaching environment.

(Participants should bring or have access to a computer with the Scientific Python installed – installations instructions will be circulated prior to the conference.)

==Pre-workshop guidance==

===Preparations for the workshop===

We circulate this guide to help you in your preparation for our workshop. You will need to bring or have alternative access to a computer with the scientific python distribution installed; here we outline guidance for installation of Anaconda, the preferred distribution for using the iPython notebook.

NOTE: The download is reasonably large (ca. 290 Mb), so it is best to have this downloaded in advance of the workshop.

Please do get in touch if you have any questions - [mailto:python@imperial.ac.uk Email us]

===Download Anaconda Python Distribution===
Visit [http://continuum.io/downloads the Anaconda website] in order to download the Anaconda Scientific Python distribution; it is available for Windows, Mac OSX and Linux. It will likely auto-detect your operating system and offer the appropriate downloader. This tutorial focuses on MacOS, but installation for Windows is as trivial.

NOTE on versions: for participation in this workshop please ensure you have installed version 3.x or higher.

Once downloaded, open the installer and follow the instructions.
[[File:Py-vice2015-prep1.png|thumb|alt=Anaconda Website|The Anaconda Website]]

===Launching the application===

The application will install in a variety of locations; you are looking for the application entitled "Launcher":

Windows: Start Menu --> Anaconda --> Launcher

MacOS: ~/anaconda/Launcher

Linux: ~/anaconda/Launcher

This will bring up the menu to launch the various aspects of the Anaconda distribution. We are interested in the ipython-notebook, so click "Launch"

[[File:Py-vice2015-prep2.png|Thumb|alt=Screengrab of the Launcher application|Screengrab of the Launcher application]]

File:Py-vice2015-prep2.png

2015-08-14T11:47:30Z

Amckinle: Python prepration 2

Python prepration 2

Py:python-ViCE-2015

2015-08-14T11:46:57Z

Amckinle: /* Download Anaconda Python Distribution */

Py:python-ViCE-2015

2015-08-14T11:20:59Z

Amckinle: /* Pre-workshop guidance */

File:Py-vice2015-prep1.png

2015-08-14T11:19:44Z

Amckinle: Installing python, slide 1

Installing python, slide 1

Py:python-ViCE-2015

2015-08-14T11:11:30Z

Amckinle: /* Abstract */

Py:python-ViCE-2015

2015-08-14T11:10:53Z

Amckinle: /* Abstract */

Py:python-ViCE-2015

2015-08-14T11:07:06Z

Amckinle: Created page with "=iPython notebooks for Data Analysis and Visualisation: a ViCE 2015 workshop= This page is intended to have downloadable resources to support the 2015 Variety in Chemistry Ed..."

It:lectures-2011

2014-11-12T09:54:49Z

Amckinle: /* Property based searches */

[[It:intro-2011|Go to Introduction]] | '''Go to Workshops''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
----

==Workshop material - Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

----
<references />
----

===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wok.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the '''only''' formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=Workshop Exercises - IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# [http://www.reaxys.com Reaxys]
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

=Extra Material for Future Reference - 3D Structure based searches=
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

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[[It:intro-2011|Go to Introduction]] | '''Go to Workshops''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-11-12T09:53:49Z

Amckinle: /* Other Search Engines */

[[It:intro-2011|Go to Introduction]] | '''Go to Workshops''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

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<references />
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==Workshop material - Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

----
<references />
----

===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wok.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the '''only''' formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=Workshop Exercises - IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

=Extra Material for Future Reference - 3D Structure based searches=
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

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[[It:intro-2011|Go to Introduction]] | '''Go to Workshops''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-11-12T09:51:31Z

Amckinle: /* Web of Science, WOS */

[[It:intro-2011|Go to Introduction]] | '''Go to Workshops''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
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==Workshop material - Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

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<references />
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===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wok.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the '''only''' formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=Workshop Exercises - IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

=Extra Material for Future Reference - 3D Structure based searches=
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

----
[[It:intro-2011|Go to Introduction]] | '''Go to Workshops''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:assignment-2011

2014-10-16T14:02:32Z

Amckinle: /* CIT Assignment 2014 */

It:coursework-2011

2014-10-15T16:23:41Z

Amckinle: /* Inserting the citations just found into Word using EndNote */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Overall Objectives of CIT workshops=

The Computer lab (formally booked for your group, A1, A2, B1, B2, C1, C2) is for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library. All "Chemistry Software" should be available also in the Library to your user account. If you find that something is not immediately available, please do get in touch with the ICT Helpdesk. During the lab time allocated for the IT course, you will be expected to achieve the following objectives:

# Accessing course and laboratory notes and using scientific journals to support lectures
# Using '''Word''' in combination with the '''EndNote''' bibliographic database and '''ChemDraw''' to write laboratory reports and essays
# Learn to use various bibliographic chemistry search systems
# Learn to conduct molecular structure-based search systems
# Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

=Self-Study - Software Familiarity=

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section ''' <u>before you come to the workshop sessions</u>''':

==Before you come to the workshop sessions...==

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.
* Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your [https://exchange.imperial.ac.uk campus email account] through the [https://exchange.imperial.ac.uk web interface].
* Using the '''FireFox''' web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: <tt>http://www.ch.ic.ac.uk/wiki/</tt>). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
* You will be using Firefox to browse the pages of a [http://en.wikipedia.org/wiki/Wiki Wiki]. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will '''replace''' the instruction window. So, get used to clicking on the link with the '''right mouse button''' rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

===Computer, Browser and Wordprocessor familiarity===
*[[Image:login_window.jpg|right|thumb|login window]]Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
*[[Image:home.jpg|left|thumb|Document home]]Perhaps the single most confusing aspect for most people is what the ''Home'' icon (left) means. So let's sort this out immediately. You are working in an ''enterprise'' environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the ''Home'' icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "'''My Documents'''", which the operating system can sometimes display instead of Home.
*[[Image:o2007.jpg|thumb|right|Office 2007]][[Image:subsuper.jpg|right|thumb|Subs and Superscripts]][[Image:o2007b.jpg|thumb|left||EndNote tab]]Start Microsoft '''Office 2007''' (we will assume you still have FireFox running). The basic ('''Home''') Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a '''red''' circle. Copy/paste operations are invoked using the icon encircled in '''purple'''. Other common operations are found to the right of these two in the taskbar, including the chemically useful '''subscript''' and '''superscripts''' (right diagram). Note also the the default document saves invokes the new '''.docx''' format, which is an XML-based type with much interesting ''informatics'' potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older '''.doc''' format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
*[[Image:o2007a.jpg|left|thumb|Insert tab]]There are two other task-bars you will find useful. the '''Insert''' bar inserts a variety of other content, including pictures, tables and the like. The '''EndNote''' tab invokes a citation and reference manager, which you will use as described below ('''Important'''<nowiki>: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).</nowiki>
* Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
*[[Image:FireFox_paste.jpg|thumb|right|Save Firefox image]] '''Images''' are special when it comes to copying. Proceed as follows:
*# Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
*# If one of the options is '''Copy image''', select it. Not all browsers support this, in which case instead invoke ''save this image as'' and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
*# With an Office Word window open, paste the image (if you copied it) or '''Insert/Picture/from file''' (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
*# Do remember how to change between windows (the technical term is that the active window is said to be ''on focus'') by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
{|
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>150</size>
<script>zoom 200; cpk -20;move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|Not everything is always "copyable". Some apparent images are in fact produced by an "applet" [http://wiki.jmol.org:81/index.php/MediaWiki embedded] in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
|}
* Practice naming and saving document files to your ''Home'' (Drive H: on Windows) or a removable medium such as a FlashDrive.
* Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding '''content''' of files may be very slow. Windows Desktop Search is '''NOT''' activated on College systems.
* [http://www.ch.ic.ac.uk/local/email/ Practice setting up E-mail], sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.
=== Configuring storage for your document libraries ===

Programs such as '''EndNote''', '''Mendeley''', '''iTunes''' store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

==== EndNote ====

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => '''userid(\\icfs18.cc.ic.ac.uk) (M:)''' Thereafter you can set it to open this library when the program starts.

==== Mendeley ====

Open the program and invoke '''Tools/Options/File Organiser''' and select drive M: for the library.

==== iTunes ====

Use '''Edit/Preferences/Advanced''' and set the iTunes Media folder location to M: (or other if M: is already full). Also tick '''Copy files to iTunes Media folder when adding to library'''.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

=Start of Demonstration material=
The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are '''positively encouraged to continue working through the material''' at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

== Combined Word/ EndNote Familiarity ==
This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about '''''penicillin''''' and its '''''conversion to cephalosporin'''''.

=== A Web of Knowledge Search ===
#[[Image:Endnote1e.jpg|thumb|left|WoK search]] From the [http://wok.mimas.ac.uk/ Web-of-Knowledge] link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
#'''Connect to the ISI Web of Knowledge Service''' and then select the
#''Web of Science'' tab from along the top and finally from the citation databases, narrow it down to the
# Science Citation Index expanded
#Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the '''Author''' box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the '''advanced''' search such as <tt>au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)</tt>
#When you have some hits, either tick individual citations, or '''All records on page''' or a span of records.
#Next, make sure you have Microsoft Word running, and from the '''EndNote X4''' taskbar of Word, click on '''Go to EndNote'''. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
#[[Image:Endnote1b.jpg|right|saving a list for Endnote]]Return to the Browser window displaying WOS and click on '''Save to EndNote'''. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
#If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name '''uml_view.cgi''' on the desktop) which you can open directly with EndNote (see below).

=== Inserting the citations just found into Word using EndNote===
#[[Image:Endnote1a.jpg|thumb|right|Starting EndNote]]Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
#Via '''Edit/preferences/Libraries''' select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
#[[Image:endnote-style.jpg|thumb|left|Checking the style setting]]From '''Edit/Output style/Open Style Manager''', select the tick-box against a template known as '''Royal Society of Chemistry''' (you may have to use '''Find by/Chemistry''' to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
#If you are importing a citation list rather than relying on the automated procedure, then from '''File/Import''' of EndNote define the Import Option '''ISI-CE''' in the pull down menu, or '''Other Filters/SciFinder (CAS)''' if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
#[[Image:Endnote1c.jpg|thumb|right|]][[Image:Endnote1d.jpg|thumb|left|Word with citations showing|]]Go back to Word , and write some text. At an appropriate point, from the '''Endnote X4 taskbar tab''', press '''Go to EndNote''' when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the '''Insert citation''' tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
#Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

==== Mendeley and other alternatives to EndNote ====
[[image:refworks.jpg|thumb|right]]A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include [https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks] (for which the client software can be downloaded without cost) and an innovative program called [http://www.mendeley.com/ Mendeley] which is available on the computers in the department.

# If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

== Chemdraw Familiarity ==
*[[Image:unknown1.jpg|left|thumb|Click to expand image]] [[Image:taxolhsr.jpg|Taxol|right|300px]] '''Starting and using ChemDraw.''' Start Chemdraw icon from the '''Start/Programs menu'''. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
*Check that you have drawn it correctly by calculating its formula. To do this, Go to '''View/Show analysis''' window and record what you see (it should give you C<sub>47</sub>H<sub>51</sub>NO<sub>14</sub>. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. '''What is the difference in behaviour?'''

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. '''Can you identify what it is called?'''

== Lecture Support: Journal Familiarity ==

You can go visit the databases of some major chemistry publishers, and track down any articles that members of this department (or other departments or your favourite Nobel prize lautreates) may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following:
* [http://pubs.acs.org/search/advanced The American Chemical Society] (where you can subscribe to an RSS feed of the search, which means you will be notified of new items)
* [http://www.rsc.org/Publishing/Journals/cc/index.asp The Royal Society of Chemistry] and their premier journal ''Chemical communications''
* [http://www.nature.com/search/adv_search?sp-a=sp1001702d&sp-x-1=ujournal&sp-q-1=Nature%20Chemistry Nature Chemistry] advanced search.
* [http://www3.interscience.wiley.com/journal/26737/home Wiley Interscience] and their flagship chemistry journal ''Angew. Chemie.''
* [http://www.sciencedirect.com Science Direct]

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

== Lecture Support: Named chemicals ==

# To apply the above skills by using [http://wok.mimas.ac.uk/ WOS] to perform a comprehensive literature search on the '''molecule''' ''Penicillin'', a '''reaction''' (''its conversion to Cephalosporin''), its ''properties'', both physical (spectroscopic) and biological. Thus, type ''penicillin and cephalosporin'' into the '''Topic''' box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the '''Advanced Search''' option.
#* '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (136)
#* '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2629)
##Or, try the drug '''Temozolomide''', currently very much in the [http://news.bbc.co.uk/1/hi/england/west_midlands/7675014.stm news]
##Tasimelteon ([http://news.bbc.co.uk/1/hi/health/7760105.stm time bending drug for jet lag]) or
##[http://news.bbc.co.uk/1/hi/health/8237530.stm Sulforaphane], which occurs in broccoli and cauliflower and protects against heart attacks.
#Compare the results of one of these searches with less specialised search engines such as
#*[http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar],
#*[http://www.scirus.com/srsapp/advanced/index.jsp SciRus],
#*[http://www.bing.com/?scope=web&mkt=en-GB Microsoft Bing],
#*[http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha].

=== Lecture Support: A SciFinder search instead ===
*The [https://scifinder.cas.org/ Scifinder Scholar] system is available for general and student use.
** You cannot use your College login for access, but must request your own login to be created.
*** [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar Go here to register]. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. ''other field''.
** Completing the registration will result in an email being sent to the email address you provide with activation instructions.
*** Once you have obtained an ID, at the [https://origin-scifinder.cas.org SciFinder site], click on '''Explore References''' and in the '''Research topic box''' enter "Conversion of penicillin to cephalosporin".
** You will receive a request to accept an application digital signature at this stage, which you should accept.
You should get ~9 references for an exact match. This interface is supposed to use a more ''natural language'' for its search queries (and it does not employ Booleans).
** Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the '''Export''' link near the top (next to print). From the dialog, set the '''File Type''' to '''Tagged Format'''.
*** You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your '''download''' location. You can then import this into EndNote using the '''SciFinder (CAS)''' import option.
**An alternative search might be the phrase '''arrow pushing formalism''' (can you learn about this topic from the results found for this search?). A synonym might be '''curly arrow formalism'''. Does this find the same references, or a different set?
** You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to '''My connections''' and invite the group, then add comments to relevant references.
** SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

=Laboratory Support=
Here you will find out how to search for safety information about molecules, and then for their properties and reactions. There are two kinds of search for molecules you will have to make during lab courses.
# Where you have an unknown compound whose properties you have measured and you want to know if any known compound matches those properties.
# Where you (think you) know what the structure of your compound is, and you want to know if there are any other reports of this same compound (and whether the properties other have measured match your own).

== A search for known physical properties using Reaxys ==
[[Image:Reaxys1.jpg|right|thumb|]]We will start with two examples of the first category and then move on to the rather more common second category.

*Connect to the [http://www.reaxys.com/ Reaxys] system. You can carry out all the required course work as an ''anonymous user'', but you will not be able to change/save any settings etc in this mode (such as e.g. changing the default structure editor to ChemDraw).
** If you do choose to register at this point, be aware that if you lose/forget your password, you will need to contact Reaxys and not local Imperial College support.
*Select ''substances and Properties''
**In the ''Properties (Advanced)'' box, enter the following, followed by '''Search'''.
**'''MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200'''
This means in effect, show me ANY molecule which melts at a certain temperature range (determined using a melting point apparatus), which has a given molecular formula (determined using mass spectrometry) and an optical rotatory power between certain values (determined using a polarimeter). For this example you should get exactly 1 hit, which should be to a patent. Explore the options at this point, including viewing the original source of the data ( a patent in this case).
* There are about 500 different properties in total which you could specify in this manner. To explore them, click on ''Show Fields and Operators''. This type of technique is useful for identifying an '''unknown''' compound purely from its physical properties (Forensic science, etc).
** Note that some features do not always produce the expected result. For example, the icon labelled with the arrow (right) pulls down various options, one of which is ''copy structure to clipboard''. The clipboard contents however are '''not''' recognised by eg Chemdraw, Word etc.

== A search for known spectroscopic properties ==

[[image:spectra.jpg|240px|right]]It is routine when a compound is first made to record its spectroscopic properties. This would include the characteristic infra-red frequencies, and the <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts. These values are shown for an unknown compound. Your task is to use the [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] to try to identify what the compound is (you could of course also do this entirely logically using just your brain).
#Try first entering only the <sup>13</sup>C NMR chemical shifts (163, 141, 133, 130, 129, 128, 98 ppm, with an anticipated error of around 2ppm). How many matches do you get?
#Add then the <sup>1</sup>H shifts (8.1,7.5,5.1,4.7 and there is an additional broad multiplet across the range 7.3-7.7 which is not entered) and see if the number of possibilities reduces.
#Finally, enter the one characteristic IR vibration (1733 cm<sup>-1</sup>). Do you now get a unique answer? Record any structure(s) you may get at this stage for future reference.
#Try changing the error limits for any of these properties. Thus reduce the NMR limit from 2.0 to 1.5 to 1.0ppm, or the IR limit to 5 or even 1 cm<sup>-1</sup> (in future laboratory courses, you will learn how the way the instrument works determines at least in part the accuracy with which these spectroscopic properties can be measured).

== Reagent/Product searches for laboratory preparations ==

[[image:1-4.jpg|right|250px|Molecules 1-4]]The theme of this section is going to be the following four molecules, which you will in fact encounter in a laboratory course later in the year. You will search for known properties of these molecules, for comparison with those you might measure in the lab, or which may provide useful discussion material for your laboratory reports. Your first task is to generate a so-called SMILES descriptor of the molecule. This is done most simply by drawing the molecule in ChemDraw and using the '''Edit as/Copy''' menu produce the SMILES or InChI-key string onto the clipboard. Here are three SMILES strings and one InCHI-key string. Can you match them up to the structures shown on the right?
# <nowiki>C=CC1=CC=C(C(O[H])=O)C=C1</nowiki>
# <nowiki>S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S</nowiki>
# <nowiki>O[C@H]1[C@H](OCC)CCCC1</nowiki>
# <nowiki>VSIKJPJINIDELZ-UHFFFAOYSA-N</nowiki>
*Search the [http://www.chemspider.com/ ChemSpider] database using a SMILES or InChI-key string as above. What sort of information is revealed about the compound?
*Try reversing the search terms above (instead of SMILEs, try generating an InChI key, or vice versa).
*Try next an advanced search from the same [http://www.chemspider.com/FullSearch.aspx database]. Explore for yourself how to enter the SMILES string and perform the search.
*Search the [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] using a SMILES string. Select the '''substructure/superstructure''' or the '''Identity/Similarity''' option, and then the '''CID, SMILES, InChI''' tab, and past in one of the strings above. Try both '''80% similar''' and '''identical''' if using the Similarity option). Again, explore the properties associated with each hit.
**You might encounter '''artefacts'''. Thus with '''S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S''', something slightly odd happens?
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of Drugs, inorganic and organometallic and natural products which might prove useful to you for laboratories.
* The series [http://www.orgsyn.org/ Organic syntheses] contains tried and tested procedures for the synthesis of many chemicals. However, it is quite limited, and you would be lucky to find more obscure compounds listed here.
=== Sigma-Aldrich Catalogues and MSDS (Safety) information ===

If you know (or suspect you know) what the identity of the molecules are that you will be handling in the laboratory, the first task is to find out any known safety information.
The [http://www.sigmaaldrich.com/catalog/search/AdvancedSearchPage Aldrich] catalogues can be searched for compounds and their associated MSDS safety sheets. This is useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms. If you were able to obtain a name (see previous section), see if you can now find any information on it from the Aldrich catalogue.

=== Reaxys ===
Connect to [http://www.reaxys.com/ Reaxys] as before, but now we are going to do a structure based search, using as examples structures '''1-4''' above. If you click in the frame labelled ''Double click this frame and draw structure query'' you will get a default structure editor called ChemAxon MarvinSketch. It is a little different from Chemdraw, but should not take too much time to master.
# Using the structure editor, draw one of the four molecules 1-4 and invoke '''search'''.
# If you think you know the name of your query, type that instead in the ''Generate structure from name'' box (e.g. '''Taxol''', which as you have seen earlier is a challenge to draw!). You can also paste a SMILES or InChI key into this box (try any of the four above).
# Try hitting '''Synthesize''', but expect to be overwhelmed by the number of hits!

=== Dictionary of organic compounds ===
An alternative database which works in this way is the [http://doc.chemnetbase.com/ Dictionary of organic compounds].


= Extra material for Future Reference - Converting a 2D structure definition to a 3D set of coordinates =

The preceding searches were all effectively conducted on two-dimensional molecules, where we only needed to know how the atoms were connected (in effect the Lewis valence structure). As a prelude to moving into three dimensions, we will illustrate how a 2D search can be used to generate a 3D structure.

* You can use the on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina service to convert a (1D) SMILES string to 3D molecular coordinates].
*# Under options, paste the SMILES string, enter a name, and select 3D structure viewer automatically loaded.
*# Click on Generate 3D structure. A window appears, and after about 20-30 seconds, a structure does as well. At the bottom, click on "Click to download this structure in PDB file format", whereupon a full window diagram appears. Save the molecule as above.

== 3D structure searching of the Cambridge Crystallographic database ==

Our final search type is now of a database which stores '''three-dimensional''' information about molecules. This is where you can infer all sorts of interesting properties about the bonding, the properties and the potential reactivities of molecules. You will be searching the '''Cambridge Crystal Structure Database'''. There are three entry points for this; one local, one via the Web and one via the national '''chemical database service'''.

=== Local invocation of the Cambridge Crystal Structure Database ===
The local based search described below is feature complete and fast. You may also want to try out the [http://webcsd.ccdc.cam.ac.uk/ WebCSD service], which needs only a web-browser.
#[[Image:MgBr2.jpg|right|120px]][[Image:ti1.jpg|right|100px]][[Image:PtCl.jpg|right|100px]][[image:1-4.jpg|right|250px|Molecules 1-4]]Select '''Conquest''' from the '''Start/Programs''' menu. You will have to reply:
##'''yes''' to the question about certificates,
##enter first your username, then
##your password at the two prompts (both of which appear to ask for a password!).
##Next, '''accept''' the license agreement and
##'''accept''' the suggested location for storing the directory.
##Enter the Site No. as '''183''' and the confirm code as '''8FDCE4''' (2013 release)
##Click '''register online'''.
##These prompts are a one-off, and you will not need to do these steps again.
#In the {{Pdf|FoundationTutorialproblems09.pdf|first year tutorial problems}}, question 2 asks you to arrow-push the reaction Et<sub>2</sub>O + MgBr<sub>2</sub> → Et<sub>2</sub>O-MgBr<sub>2</sub>. Here we will pose the question: what is the 3D geometry of the product of this reaction? You will search for it using Conquest. Does the result surprise you? (Hint: TOQKIT)
#Nucleophilic addition to an amide is the prototype of how peptides, proteins and enzymes are broken down in metabolic processes (or using e.g. biological washing powders). The mechanism involves a species known as a '''tetrahedral intermediate''' (right), which is normally considered so unstable that it is rarely detected during the reaction. Nevertheless, can you find any examples of such species in the Cambridge database?
#Cis-Platin is a well known anti-cancer drug. The ''active ingredient'' is the initial hydrolysis product, shown on the right. Can you find any examples of this '''active intermediate''' in the database which contain this sub-structure? What happens if you change the Pt to a '''wild-card''' indicating the central metal could be any of the group known as '''8Z''' (from the '''more''' button of the editor, select '''other elements''' and from there click on the orange box labelled '''8Z''').
#Are there any other '''reactive intermediates''' you might have identified from your arrow-pushing workshop which you might search for?
#When you have finished the above examples, try entering one of the four lab-course molecules shown to the left, exactly as drawn above. For '''3''' specifically, if you draw explicit hydrogens attached to the ''vinyl'' group at the top of the molecule and repeat the search, what difference is there?
#*How many hits do you get?
#*Note the 6-8 letter identifier for the structure you are interested in (for example, for molecule '''3''' above, it should be XAYFEI, XAYFEI01 and XAYFEI02).
#*Save the 3D coordinates in PDB or CIF format via '''File/Export''', decide how you want to select entries, specify one file per entry and '''SAVE'''. Inspect the structure by double clicking the file created, to be found on drive '''L:'''
#You '''may''' now have two versions of any of these four molecules; one a direct experimental structure, and one assembled by the [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] program. How do these differ? Concentrate in particular on compounds '''1''' and '''2''' above right!
#Later on in your course, you may use such coordinates to create an entry in a Wiki page, much like that rotating below.

===An advanced 3D Search. ===
Try the following. The objective will be to find any short interactions between the H of an OH group and the centroid of a phenyl ring as the electron donor (a very unusual type of π-facial hydrogen bond). Proceed as follows:
{|
|
# Open Conquest and invoke the '''Build Queries/Draw''' option
# Deposit a benzene ring from the template which should appear on the left
# Click on '''ADD 3D''', select all the six carbon atoms in turn (they will go green) and define a centroid. A defined object labelled '''CENT1''' now shows. Press Done.
# Back in '''Draw''' mode, select a H and deposit it as an isolated atom. Then select O and draw a bond from it to the H to get an OH. In this system, any undefined valence is '''wild''', ie any group can be attached to the O of the OH.
# In '''ADD 3D''' mode again, click first on the '''H''' of the OH group, then on '''CENT1''' in the list of defined objects. A green line connecting the two appears. When a '''Valid parameter''' entry named '''Distance''' appears, click on '''Define'''.
# Select '''Intramolecular''' from the '''Choose distance type''' menu, OK, then '''Options''', enter 2.0 - 2.4 as the range of distances and '''Separated by 5 - 999''' bonds. Hit '''OK''' and then '''Done'''. Your search query is summarized in a cyan box at the top right of the draw window.
# Select '''Search''', tick the 3D Coordinates determined box and '''Start Search'''. This search should proceed at the rate of about 1% per second. You should get 20 hits.
# View entries via '''3D Visualiser'''. Note the so-called '''REFCODES'''. Note '''[[Coursework#Enantiomers_vs_Diastereomers_Part_1:_Butanes_and__Helicenes.|CIYSIM]]''' in particular!
#A right-mouse click in the blue window of the 3D Visualiser will enable you to set '''spacefill''' mode, and to inspect whether any two atom spheres inter-penetrate each-other indicating an attractive interaction between them.
# Save the coordinates of any selected hits via '''File/Export''', Select PDB or CIF as the format, all selected entries, one file per entry and '''SAVE'''.
# The files will appear on your L: drive. Double click to open up the WebLab Viewer Pro or Mercury program, and resave them if you wish as an MDL Molfile rather than PDB.
# If you want to explore further, define an NH bond rather an OH bond (you might need to increase the distance range to eg 2.0 - 2.5).
# Try this with centroids to other π-electron rich systems, such as an alkyne, alkene, or other rings such as cyclopentadienyl, etc.
#Go to your network drive N: or L: (i.e. username on neon.ch.ic.ac.uk) and double click any .PDB or .CFIF or .MOL files to view the molecule again.
# Or, instead of H-O, just put e.g. Na (metal arene interactions are hugely important biologically). You may need to define a rather longer distance range. Experiment by trying various sets of values.
|<jmol><jmolApplet><title>CIYSIM</title><color>white</color>
<size>300</size><script>zoom 150;spin 3;</script>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents>
</jmolApplet></jmol>
|}

=== The National Chemical Database Service ===

The '''CDS''' is a national service (located as it happens in Daresbury, near Warrington) which offers a range of database services to the UK community. To access this service, follow the [http://cds.dl.ac.uk/cgi-bin/reg/undergrad?sites=Select+Site&SITE=imperial-cds0091 instructions] here (this is necessary to ensure UK usage only and to monitor that usage as part of justifying a national resource). You will be sent a CDS registration account and password by email. You can then use this account in two ways
#Invoke '''ConquestD''' (rather than Conquest) from the Windows start menu and proceed as above, but supply your new CDS account instead of your Imperial account.
#Invoke the CDS portal [https://cds.dl.ac.uk/ here] using your CDS account to log in. It offers many alternative services (including searches for spectral data) as well as a simplified crystal search. Explore in your own time!


=== Further tutorials based on 3D crystal structures ===

These can be viewed [http://www.ccdc.cam.ac.uk/free_services/teaching/modules/teaching_webcsd/toc.html here].

=Continuation of CIT skills=
The skills developed during these workshops will be in almost constant use throughout your course; you are encouraged to keep this up to date and to make use of these skills while writing lab reports and other coursework assignments. As with anything in the digital world, progress is being made all the time with new search engines, new search algorithms, new software. This also means that other searches and software are retired to make way for, newer more efficient tools. This wiki will be a long-term reference which you can refer to and even update, and you are urged to keep it as a bookmark.

== Software for your own computer ==

*The department has a Site License for a program system called [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 ChemBio3D] (which includes ChemDraw for both Windows and Mac), the terms of which allow individual undergraduates to acquire a copy of the program and to install it on their personal computer. The license is an annual one.
*[http://www.straightrunning.com/XmingNotes/ Xming] for accessing the Conquest data base.
*Programs such as Microsoft Office can be licensed via [http://www.microsoft.com/student/discounts/theultimatesteal-uk/default.aspx an academic license for £69.99].
*[https://directory.adeptscience.co.uk/products/search/1/1/474/cat474.html EndNote student edition] retails for £85.00. Alternatively, try RefWorks (usually $100/year but '''free''' for Imperial students through [http://www3.imperial.ac.uk/library/digitallibrary/athensandukfed AthensDA]) It is a slightly simpler web-based program. A comparison between both can be found [http://library.princeton.edu/help/comparison.php here] (Princeton University). You should note that the WOS system supports Endnote directly, but requires a more complicated procedure for using RefWorks or Mendeley.
*A further list of software may be found [[It:software-2011|here]], including other programs you can install on your personal computer which you may find useful.
----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:assignment-2011

2014-10-15T16:16:08Z

Amckinle: /* CIT Assignment 2014 */

It:assignment-2011

2014-10-11T13:35:20Z

Amckinle:

It:assignment-2011

2014-10-11T13:31:29Z

Amckinle: /* CIT Assignment 2012 */

It:coursework-2011

2014-10-11T13:27:50Z

Amckinle: /* Local invocation of the Cambridge Crystal Structure Database */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Overall Objectives of CIT workshops=

The Computer lab (formally booked for your group, A1, A2, B1, B2, C1, C2) is for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library. All "Chemistry Software" should be available also in the Library to your user account. If you find that something is not immediately available, please do get in touch with the ICT Helpdesk. During the lab time allocated for the IT course, you will be expected to achieve the following objectives:

# Accessing course and laboratory notes and using scientific journals to support lectures
# Using '''Word''' in combination with the '''EndNote''' bibliographic database and '''ChemDraw''' to write laboratory reports and essays
# Learn to use various bibliographic chemistry search systems
# Learn to conduct molecular structure-based search systems
# Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

=Self-Study - Software Familiarity=

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section ''' <u>before you come to the workshop sessions</u>''':

==Before you come to the workshop sessions...==

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.
* Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your [https://exchange.imperial.ac.uk campus email account] through the [https://exchange.imperial.ac.uk web interface].
* Using the '''FireFox''' web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: <tt>http://www.ch.ic.ac.uk/wiki/</tt>). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
* You will be using Firefox to browse the pages of a [http://en.wikipedia.org/wiki/Wiki Wiki]. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will '''replace''' the instruction window. So, get used to clicking on the link with the '''right mouse button''' rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

===Computer, Browser and Wordprocessor familiarity===
*[[Image:login_window.jpg|right|thumb|login window]]Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
*[[Image:home.jpg|left|thumb|Document home]]Perhaps the single most confusing aspect for most people is what the ''Home'' icon (left) means. So let's sort this out immediately. You are working in an ''enterprise'' environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the ''Home'' icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "'''My Documents'''", which the operating system can sometimes display instead of Home.
*[[Image:o2007.jpg|thumb|right|Office 2007]][[Image:subsuper.jpg|right|thumb|Subs and Superscripts]][[Image:o2007b.jpg|thumb|left||EndNote tab]]Start Microsoft '''Office 2007''' (we will assume you still have FireFox running). The basic ('''Home''') Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a '''red''' circle. Copy/paste operations are invoked using the icon encircled in '''purple'''. Other common operations are found to the right of these two in the taskbar, including the chemically useful '''subscript''' and '''superscripts''' (right diagram). Note also the the default document saves invokes the new '''.docx''' format, which is an XML-based type with much interesting ''informatics'' potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older '''.doc''' format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
*[[Image:o2007a.jpg|left|thumb|Insert tab]]There are two other task-bars you will find useful. the '''Insert''' bar inserts a variety of other content, including pictures, tables and the like. The '''EndNote''' tab invokes a citation and reference manager, which you will use as described below ('''Important'''<nowiki>: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).</nowiki>
* Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
*[[Image:FireFox_paste.jpg|thumb|right|Save Firefox image]] '''Images''' are special when it comes to copying. Proceed as follows:
*# Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
*# If one of the options is '''Copy image''', select it. Not all browsers support this, in which case instead invoke ''save this image as'' and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
*# With an Office Word window open, paste the image (if you copied it) or '''Insert/Picture/from file''' (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
*# Do remember how to change between windows (the technical term is that the active window is said to be ''on focus'') by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
{|
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>150</size>
<script>zoom 200; cpk -20;move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|Not everything is always "copyable". Some apparent images are in fact produced by an "applet" [http://wiki.jmol.org:81/index.php/MediaWiki embedded] in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
|}
* Practice naming and saving document files to your ''Home'' (Drive H: on Windows) or a removable medium such as a FlashDrive.
* Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding '''content''' of files may be very slow. Windows Desktop Search is '''NOT''' activated on College systems.
* [http://www.ch.ic.ac.uk/local/email/ Practice setting up E-mail], sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.
=== Configuring storage for your document libraries ===

Programs such as '''EndNote''', '''Mendeley''', '''iTunes''' store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

==== EndNote ====

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => '''userid(\\icfs18.cc.ic.ac.uk) (M:)''' Thereafter you can set it to open this library when the program starts.

==== Mendeley ====

Open the program and invoke '''Tools/Options/File Organiser''' and select drive M: for the library.

==== iTunes ====

Use '''Edit/Preferences/Advanced''' and set the iTunes Media folder location to M: (or other if M: is already full). Also tick '''Copy files to iTunes Media folder when adding to library'''.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

=Start of Demonstration material=
The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are '''positively encouraged to continue working through the material''' at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

== Combined Word/ EndNote Familiarity ==
This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about '''''penicillin''''' and its '''''conversion to cephalosporin'''''.

=== A Web of Knowledge Search ===
#[[Image:Endnote1e.jpg|thumb|left|WoK search]] From the [http://wok.mimas.ac.uk/ Web-of-Knowledge] link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
#'''Connect to the ISI Web of Knowledge Service''' and then select the
#''Web of Science'' tab from along the top and finally from the citation databases, narrow it down to the
# Science Citation Index expanded
#Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the '''Author''' box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the '''advanced''' search such as <tt>au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)</tt>
#When you have some hits, either tick individual citations, or '''All records on page''' or a span of records.
#Next, make sure you have Microsoft Word running, and from the '''EndNote X4''' taskbar of Word, click on '''Go to EndNote'''. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
#[[Image:Endnote1b.jpg|right|saving a list for Endnote]]Return to the Browser window displaying WOS and click on '''Save to EndNote'''. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
#If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name '''uml_view.cgi''' on the desktop) which you can open directly with EndNote (see below).

=== Inserting the citations just found into Word using EndNote===
#[[Image:Endnote1a.jpg|thumb|right|Starting EndNote]]Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
#Via '''Edit/preferences/Libraries''' select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
#[[Image:endnote-style.jpg|thumb|left|Checking the style setting]]From '''Edit/Output style/Open Style Mananger''', select the tick-box against a template known as '''Royal Society of Chemistry''' (you may have to use '''Find by/Chemistry''' to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
#If you are importing a citation list rather than relying on the automated procedure, then from '''File/Import''' of EndNote define the Import Option '''ISI-CE''' in the pull down menu, or '''Other Filters/SciFinder (CAS)''' if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
#[[Image:Endnote1c.jpg|thumb|right|]][[Image:Endnote1d.jpg|thumb|left|Word with citations showing|]]Go back to Word 2007, and write some text. At an appropriate point, from the '''Endnote X4 taskbar tab''', press '''Go to EndNote''' when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the '''Insert citation''' tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
#Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

==== Mendeley and other alternatives to EndNote ====
[[image:refworks.jpg|thumb|right]]A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include [https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks] (for which the client software can be downloaded without cost) and an innovative program called [http://www.mendeley.com/ Mendeley] which is available on the computers in the department.

# If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

== Chemdraw Familiarity ==
*[[Image:unknown1.jpg|left|thumb|Click to expand image]] [[Image:taxolhsr.jpg|Taxol|right|300px]] '''Starting and using ChemDraw.''' Start Chemdraw icon from the '''Start/Programs menu'''. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
*Check that you have drawn it correctly by calculating its formula. To do this, Go to '''View/Show analysis''' window and record what you see (it should give you C<sub>47</sub>H<sub>51</sub>NO<sub>14</sub>. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. '''What is the difference in behaviour?'''

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. '''Can you identify what it is called?'''

== Lecture Support: Journal Familiarity ==

You can go visit the databases of some major chemistry publishers, and track down any articles that members of this department (or other departments or your favourite Nobel prize lautreates) may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following:
* [http://pubs.acs.org/search/advanced The American Chemical Society] (where you can subscribe to an RSS feed of the search, which means you will be notified of new items)
* [http://www.rsc.org/Publishing/Journals/cc/index.asp The Royal Society of Chemistry] and their premier journal ''Chemical communications''
* [http://www.nature.com/search/adv_search?sp-a=sp1001702d&sp-x-1=ujournal&sp-q-1=Nature%20Chemistry Nature Chemistry] advanced search.
* [http://www3.interscience.wiley.com/journal/26737/home Wiley Interscience] and their flagship chemistry journal ''Angew. Chemie.''
* [http://www.sciencedirect.com Science Direct]

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

== Lecture Support: Named chemicals ==

# To apply the above skills by using [http://wok.mimas.ac.uk/ WOS] to perform a comprehensive literature search on the '''molecule''' ''Penicillin'', a '''reaction''' (''its conversion to Cephalosporin''), its ''properties'', both physical (spectroscopic) and biological. Thus, type ''penicillin and cephalosporin'' into the '''Topic''' box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the '''Advanced Search''' option.
#* '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (136)
#* '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2629)
##Or, try the drug '''Temozolomide''', currently very much in the [http://news.bbc.co.uk/1/hi/england/west_midlands/7675014.stm news]
##Tasimelteon ([http://news.bbc.co.uk/1/hi/health/7760105.stm time bending drug for jet lag]) or
##[http://news.bbc.co.uk/1/hi/health/8237530.stm Sulforaphane], which occurs in broccoli and cauliflower and protects against heart attacks.
#Compare the results of one of these searches with less specialised search engines such as
#*[http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar],
#*[http://www.scirus.com/srsapp/advanced/index.jsp SciRus],
#*[http://www.bing.com/?scope=web&mkt=en-GB Microsoft Bing],
#*[http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha].

=== Lecture Support: A SciFinder search instead ===
*The [https://scifinder.cas.org/ Scifinder Scholar] system is available for general and student use.
** You cannot use your College login for access, but must request your own login to be created.
*** [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar Go here to register]. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. ''other field''.
** Completing the registration will result in an email being sent to the email address you provide with activation instructions.
*** Once you have obtained an ID, at the [https://origin-scifinder.cas.org SciFinder site], click on '''Explore References''' and in the '''Research topic box''' enter "Conversion of penicillin to cephalosporin".
** You will receive a request to accept an application digital signature at this stage, which you should accept.
You should get ~9 references for an exact match. This interface is supposed to use a more ''natural language'' for its search queries (and it does not employ Booleans).
** Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the '''Export''' link near the top (next to print). From the dialog, set the '''File Type''' to '''Tagged Format'''.
*** You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your '''download''' location. You can then import this into EndNote using the '''SciFinder (CAS)''' import option.
**An alternative search might be the phrase '''arrow pushing formalism''' (can you learn about this topic from the results found for this search?). A synonym might be '''curly arrow formalism'''. Does this find the same references, or a different set?
** You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to '''My connections''' and invite the group, then add comments to relevant references.
** SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

=Laboratory Support=
Here you will find out how to search for safety information about molecules, and then for their properties and reactions. There are two kinds of search for molecules you will have to make during lab courses.
# Where you have an unknown compound whose properties you have measured and you want to know if any known compound matches those properties.
# Where you (think you) know what the structure of your compound is, and you want to know if there are any other reports of this same compound (and whether the properties other have measured match your own).

== A search for known physical properties using Reaxys ==
[[Image:Reaxys1.jpg|right|thumb|]]We will start with two examples of the first category and then move on to the rather more common second category.

*Connect to the [http://www.reaxys.com/ Reaxys] system. You can carry out all the required course work as an ''anonymous user'', but you will not be able to change/save any settings etc in this mode (such as e.g. changing the default structure editor to ChemDraw).
** If you do choose to register at this point, be aware that if you lose/forget your password, you will need to contact Reaxys and not local Imperial College support.
*Select ''substances and Properties''
**In the ''Properties (Advanced)'' box, enter the following, followed by '''Search'''.
**'''MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200'''
This means in effect, show me ANY molecule which melts at a certain temperature range (determined using a melting point apparatus), which has a given molecular formula (determined using mass spectrometry) and an optical rotatory power between certain values (determined using a polarimeter). For this example you should get exactly 1 hit, which should be to a patent. Explore the options at this point, including viewing the original source of the data ( a patent in this case).
* There are about 500 different properties in total which you could specify in this manner. To explore them, click on ''Show Fields and Operators''. This type of technique is useful for identifying an '''unknown''' compound purely from its physical properties (Forensic science, etc).
** Note that some features do not always produce the expected result. For example, the icon labelled with the arrow (right) pulls down various options, one of which is ''copy structure to clipboard''. The clipboard contents however are '''not''' recognised by eg Chemdraw, Word etc.

== A search for known spectroscopic properties ==

[[image:spectra.jpg|240px|right]]It is routine when a compound is first made to record its spectroscopic properties. This would include the characteristic infra-red frequencies, and the <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts. These values are shown for an unknown compound. Your task is to use the [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] to try to identify what the compound is (you could of course also do this entirely logically using just your brain).
#Try first entering only the <sup>13</sup>C NMR chemical shifts (163, 141, 133, 130, 129, 128, 98 ppm, with an anticipated error of around 2ppm). How many matches do you get?
#Add then the <sup>1</sup>H shifts (8.1,7.5,5.1,4.7 and there is an additional broad multiplet across the range 7.3-7.7 which is not entered) and see if the number of possibilities reduces.
#Finally, enter the one characteristic IR vibration (1733 cm<sup>-1</sup>). Do you now get a unique answer? Record any structure(s) you may get at this stage for future reference.
#Try changing the error limits for any of these properties. Thus reduce the NMR limit from 2.0 to 1.5 to 1.0ppm, or the IR limit to 5 or even 1 cm<sup>-1</sup> (in future laboratory courses, you will learn how the way the instrument works determines at least in part the accuracy with which these spectroscopic properties can be measured).

== Reagent/Product searches for laboratory preparations ==

[[image:1-4.jpg|right|250px|Molecules 1-4]]The theme of this section is going to be the following four molecules, which you will in fact encounter in a laboratory course later in the year. You will search for known properties of these molecules, for comparison with those you might measure in the lab, or which may provide useful discussion material for your laboratory reports. Your first task is to generate a so-called SMILES descriptor of the molecule. This is done most simply by drawing the molecule in ChemDraw and using the '''Edit as/Copy''' menu produce the SMILES or InChI-key string onto the clipboard. Here are three SMILES strings and one InCHI-key string. Can you match them up to the structures shown on the right?
# <nowiki>C=CC1=CC=C(C(O[H])=O)C=C1</nowiki>
# <nowiki>S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S</nowiki>
# <nowiki>O[C@H]1[C@H](OCC)CCCC1</nowiki>
# <nowiki>VSIKJPJINIDELZ-UHFFFAOYSA-N</nowiki>
*Search the [http://www.chemspider.com/ ChemSpider] database using a SMILES or InChI-key string as above. What sort of information is revealed about the compound?
*Try reversing the search terms above (instead of SMILEs, try generating an InChI key, or vice versa).
*Try next an advanced search from the same [http://www.chemspider.com/FullSearch.aspx database]. Explore for yourself how to enter the SMILES string and perform the search.
*Search the [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] using a SMILES string. Select the '''substructure/superstructure''' or the '''Identity/Similarity''' option, and then the '''CID, SMILES, InChI''' tab, and past in one of the strings above. Try both '''80% similar''' and '''identical''' if using the Similarity option). Again, explore the properties associated with each hit.
**You might encounter '''artefacts'''. Thus with '''S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S''', something slightly odd happens?
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of Drugs, inorganic and organometallic and natural products which might prove useful to you for laboratories.
* The series [http://www.orgsyn.org/ Organic syntheses] contains tried and tested procedures for the synthesis of many chemicals. However, it is quite limited, and you would be lucky to find more obscure compounds listed here.
=== Sigma-Aldrich Catalogues and MSDS (Safety) information ===

If you know (or suspect you know) what the identity of the molecules are that you will be handling in the laboratory, the first task is to find out any known safety information.
The [http://www.sigmaaldrich.com/catalog/search/AdvancedSearchPage Aldrich] catalogues can be searched for compounds and their associated MSDS safety sheets. This is useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms. If you were able to obtain a name (see previous section), see if you can now find any information on it from the Aldrich catalogue.

=== Reaxys ===
Connect to [http://www.reaxys.com/ Reaxys] as before, but now we are going to do a structure based search, using as examples structures '''1-4''' above. If you click in the frame labelled ''Double click this frame and draw structure query'' you will get a default structure editor called ChemAxon MarvinSketch. It is a little different from Chemdraw, but should not take too much time to master.
# Using the structure editor, draw one of the four molecules 1-4 and invoke '''search'''.
# If you think you know the name of your query, type that instead in the ''Generate structure from name'' box (e.g. '''Taxol''', which as you have seen earlier is a challenge to draw!). You can also paste a SMILES or InChI key into this box (try any of the four above).
# Try hitting '''Synthesize''', but expect to be overwhelmed by the number of hits!

=== Dictionary of organic compounds ===
An alternative database which works in this way is the [http://doc.chemnetbase.com/ Dictionary of organic compounds].


= Extra material for Future Reference - Converting a 2D structure definition to a 3D set of coordinates =

The preceding searches were all effectively conducted on two-dimensional molecules, where we only needed to know how the atoms were connected (in effect the Lewis valence structure). As a prelude to moving into three dimensions, we will illustrate how a 2D search can be used to generate a 3D structure.

* You can use the on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina service to convert a (1D) SMILES string to 3D molecular coordinates].
*# Under options, paste the SMILES string, enter a name, and select 3D structure viewer automatically loaded.
*# Click on Generate 3D structure. A window appears, and after about 20-30 seconds, a structure does as well. At the bottom, click on "Click to download this structure in PDB file format", whereupon a full window diagram appears. Save the molecule as above.

== 3D structure searching of the Cambridge Crystallographic database ==

Our final search type is now of a database which stores '''three-dimensional''' information about molecules. This is where you can infer all sorts of interesting properties about the bonding, the properties and the potential reactivities of molecules. You will be searching the '''Cambridge Crystal Structure Database'''. There are three entry points for this; one local, one via the Web and one via the national '''chemical database service'''.

=== Local invocation of the Cambridge Crystal Structure Database ===
The local based search described below is feature complete and fast. You may also want to try out the [http://webcsd.ccdc.cam.ac.uk/ WebCSD service], which needs only a web-browser.
#[[Image:MgBr2.jpg|right|120px]][[Image:ti1.jpg|right|100px]][[Image:PtCl.jpg|right|100px]][[image:1-4.jpg|right|250px|Molecules 1-4]]Select '''Conquest''' from the '''Start/Programs''' menu. You will have to reply:
##'''yes''' to the question about certificates,
##enter first your username, then
##your password at the two prompts (both of which appear to ask for a password!).
##Next, '''accept''' the license agreement and
##'''accept''' the suggested location for storing the directory.
##Enter the Site No. as '''183''' and the confirm code as '''8FDCE4''' (2013 release)
##Click '''register online'''.
##These prompts are a one-off, and you will not need to do these steps again.
#In the {{Pdf|FoundationTutorialproblems09.pdf|first year tutorial problems}}, question 2 asks you to arrow-push the reaction Et<sub>2</sub>O + MgBr<sub>2</sub> → Et<sub>2</sub>O-MgBr<sub>2</sub>. Here we will pose the question: what is the 3D geometry of the product of this reaction? You will search for it using Conquest. Does the result surprise you? (Hint: TOQKIT)
#Nucleophilic addition to an amide is the prototype of how peptides, proteins and enzymes are broken down in metabolic processes (or using e.g. biological washing powders). The mechanism involves a species known as a '''tetrahedral intermediate''' (right), which is normally considered so unstable that it is rarely detected during the reaction. Nevertheless, can you find any examples of such species in the Cambridge database?
#Cis-Platin is a well known anti-cancer drug. The ''active ingredient'' is the initial hydrolysis product, shown on the right. Can you find any examples of this '''active intermediate''' in the database which contain this sub-structure? What happens if you change the Pt to a '''wild-card''' indicating the central metal could be any of the group known as '''8Z''' (from the '''more''' button of the editor, select '''other elements''' and from there click on the orange box labelled '''8Z''').
#Are there any other '''reactive intermediates''' you might have identified from your arrow-pushing workshop which you might search for?
#When you have finished the above examples, try entering one of the four lab-course molecules shown to the left, exactly as drawn above. For '''3''' specifically, if you draw explicit hydrogens attached to the ''vinyl'' group at the top of the molecule and repeat the search, what difference is there?
#*How many hits do you get?
#*Note the 6-8 letter identifier for the structure you are interested in (for example, for molecule '''3''' above, it should be XAYFEI, XAYFEI01 and XAYFEI02).
#*Save the 3D coordinates in PDB or CIF format via '''File/Export''', decide how you want to select entries, specify one file per entry and '''SAVE'''. Inspect the structure by double clicking the file created, to be found on drive '''L:'''
#You '''may''' now have two versions of any of these four molecules; one a direct experimental structure, and one assembled by the [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] program. How do these differ? Concentrate in particular on compounds '''1''' and '''2''' above right!
#Later on in your course, you may use such coordinates to create an entry in a Wiki page, much like that rotating below.

===An advanced 3D Search. ===
Try the following. The objective will be to find any short interactions between the H of an OH group and the centroid of a phenyl ring as the electron donor (a very unusual type of π-facial hydrogen bond). Proceed as follows:
{|
|
# Open Conquest and invoke the '''Build Queries/Draw''' option
# Deposit a benzene ring from the template which should appear on the left
# Click on '''ADD 3D''', select all the six carbon atoms in turn (they will go green) and define a centroid. A defined object labelled '''CENT1''' now shows. Press Done.
# Back in '''Draw''' mode, select a H and deposit it as an isolated atom. Then select O and draw a bond from it to the H to get an OH. In this system, any undefined valence is '''wild''', ie any group can be attached to the O of the OH.
# In '''ADD 3D''' mode again, click first on the '''H''' of the OH group, then on '''CENT1''' in the list of defined objects. A green line connecting the two appears. When a '''Valid parameter''' entry named '''Distance''' appears, click on '''Define'''.
# Select '''Intramolecular''' from the '''Choose distance type''' menu, OK, then '''Options''', enter 2.0 - 2.4 as the range of distances and '''Separated by 5 - 999''' bonds. Hit '''OK''' and then '''Done'''. Your search query is summarized in a cyan box at the top right of the draw window.
# Select '''Search''', tick the 3D Coordinates determined box and '''Start Search'''. This search should proceed at the rate of about 1% per second. You should get 20 hits.
# View entries via '''3D Visualiser'''. Note the so-called '''REFCODES'''. Note '''[[Coursework#Enantiomers_vs_Diastereomers_Part_1:_Butanes_and__Helicenes.|CIYSIM]]''' in particular!
#A right-mouse click in the blue window of the 3D Visualiser will enable you to set '''spacefill''' mode, and to inspect whether any two atom spheres inter-penetrate each-other indicating an attractive interaction between them.
# Save the coordinates of any selected hits via '''File/Export''', Select PDB or CIF as the format, all selected entries, one file per entry and '''SAVE'''.
# The files will appear on your L: drive. Double click to open up the WebLab Viewer Pro or Mercury program, and resave them if you wish as an MDL Molfile rather than PDB.
# If you want to explore further, define an NH bond rather an OH bond (you might need to increase the distance range to eg 2.0 - 2.5).
# Try this with centroids to other π-electron rich systems, such as an alkyne, alkene, or other rings such as cyclopentadienyl, etc.
#Go to your network drive N: or L: (i.e. username on neon.ch.ic.ac.uk) and double click any .PDB or .CFIF or .MOL files to view the molecule again.
# Or, instead of H-O, just put e.g. Na (metal arene interactions are hugely important biologically). You may need to define a rather longer distance range. Experiment by trying various sets of values.
|<jmol><jmolApplet><title>CIYSIM</title><color>white</color>
<size>300</size><script>zoom 150;spin 3;</script>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents>
</jmolApplet></jmol>
|}

=== The National Chemical Database Service ===

The '''CDS''' is a national service (located as it happens in Daresbury, near Warrington) which offers a range of database services to the UK community. To access this service, follow the [http://cds.dl.ac.uk/cgi-bin/reg/undergrad?sites=Select+Site&SITE=imperial-cds0091 instructions] here (this is necessary to ensure UK usage only and to monitor that usage as part of justifying a national resource). You will be sent a CDS registration account and password by email. You can then use this account in two ways
#Invoke '''ConquestD''' (rather than Conquest) from the Windows start menu and proceed as above, but supply your new CDS account instead of your Imperial account.
#Invoke the CDS portal [https://cds.dl.ac.uk/ here] using your CDS account to log in. It offers many alternative services (including searches for spectral data) as well as a simplified crystal search. Explore in your own time!


=== Further tutorials based on 3D crystal structures ===

These can be viewed [http://www.ccdc.cam.ac.uk/free_services/teaching/modules/teaching_webcsd/toc.html here].

=Continuation of CIT skills=
The skills developed during these workshops will be in almost constant use throughout your course; you are encouraged to keep this up to date and to make use of these skills while writing lab reports and other coursework assignments. As with anything in the digital world, progress is being made all the time with new search engines, new search algorithms, new software. This also means that other searches and software are retired to make way for, newer more efficient tools. This wiki will be a long-term reference which you can refer to and even update, and you are urged to keep it as a bookmark.

== Software for your own computer ==

*The department has a Site License for a program system called [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 ChemBio3D] (which includes ChemDraw for both Windows and Mac), the terms of which allow individual undergraduates to acquire a copy of the program and to install it on their personal computer. The license is an annual one.
*[http://www.straightrunning.com/XmingNotes/ Xming] for accessing the Conquest data base.
*Programs such as Microsoft Office can be licensed via [http://www.microsoft.com/student/discounts/theultimatesteal-uk/default.aspx an academic license for £69.99].
*[https://directory.adeptscience.co.uk/products/search/1/1/474/cat474.html EndNote student edition] retails for £85.00. Alternatively, try RefWorks (usually $100/year but '''free''' for Imperial students through [http://www3.imperial.ac.uk/library/digitallibrary/athensandukfed AthensDA]) It is a slightly simpler web-based program. A comparison between both can be found [http://library.princeton.edu/help/comparison.php here] (Princeton University). You should note that the WOS system supports Endnote directly, but requires a more complicated procedure for using RefWorks or Mendeley.
*A further list of software may be found [[It:software-2011|here]], including other programs you can install on your personal computer which you may find useful.
----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:coursework-2011

2014-10-11T13:27:11Z

Amckinle: /* Extra material for Future Reference - Converting a 2D structure definition to a 3D set of coordinates */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Overall Objectives of CIT workshops=

The Computer lab (formally booked for your group, A1, A2, B1, B2, C1, C2) is for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library. All "Chemistry Software" should be available also in the Library to your user account. If you find that something is not immediately available, please do get in touch with the ICT Helpdesk. During the lab time allocated for the IT course, you will be expected to achieve the following objectives:

# Accessing course and laboratory notes and using scientific journals to support lectures
# Using '''Word''' in combination with the '''EndNote''' bibliographic database and '''ChemDraw''' to write laboratory reports and essays
# Learn to use various bibliographic chemistry search systems
# Learn to conduct molecular structure-based search systems
# Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

=Self-Study - Software Familiarity=

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section ''' <u>before you come to the workshop sessions</u>''':

==Before you come to the workshop sessions...==

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.
* Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your [https://exchange.imperial.ac.uk campus email account] through the [https://exchange.imperial.ac.uk web interface].
* Using the '''FireFox''' web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: <tt>http://www.ch.ic.ac.uk/wiki/</tt>). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
* You will be using Firefox to browse the pages of a [http://en.wikipedia.org/wiki/Wiki Wiki]. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will '''replace''' the instruction window. So, get used to clicking on the link with the '''right mouse button''' rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

===Computer, Browser and Wordprocessor familiarity===
*[[Image:login_window.jpg|right|thumb|login window]]Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
*[[Image:home.jpg|left|thumb|Document home]]Perhaps the single most confusing aspect for most people is what the ''Home'' icon (left) means. So let's sort this out immediately. You are working in an ''enterprise'' environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the ''Home'' icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "'''My Documents'''", which the operating system can sometimes display instead of Home.
*[[Image:o2007.jpg|thumb|right|Office 2007]][[Image:subsuper.jpg|right|thumb|Subs and Superscripts]][[Image:o2007b.jpg|thumb|left||EndNote tab]]Start Microsoft '''Office 2007''' (we will assume you still have FireFox running). The basic ('''Home''') Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a '''red''' circle. Copy/paste operations are invoked using the icon encircled in '''purple'''. Other common operations are found to the right of these two in the taskbar, including the chemically useful '''subscript''' and '''superscripts''' (right diagram). Note also the the default document saves invokes the new '''.docx''' format, which is an XML-based type with much interesting ''informatics'' potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older '''.doc''' format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
*[[Image:o2007a.jpg|left|thumb|Insert tab]]There are two other task-bars you will find useful. the '''Insert''' bar inserts a variety of other content, including pictures, tables and the like. The '''EndNote''' tab invokes a citation and reference manager, which you will use as described below ('''Important'''<nowiki>: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).</nowiki>
* Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
*[[Image:FireFox_paste.jpg|thumb|right|Save Firefox image]] '''Images''' are special when it comes to copying. Proceed as follows:
*# Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
*# If one of the options is '''Copy image''', select it. Not all browsers support this, in which case instead invoke ''save this image as'' and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
*# With an Office Word window open, paste the image (if you copied it) or '''Insert/Picture/from file''' (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
*# Do remember how to change between windows (the technical term is that the active window is said to be ''on focus'') by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
{|
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>150</size>
<script>zoom 200; cpk -20;move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|Not everything is always "copyable". Some apparent images are in fact produced by an "applet" [http://wiki.jmol.org:81/index.php/MediaWiki embedded] in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
|}
* Practice naming and saving document files to your ''Home'' (Drive H: on Windows) or a removable medium such as a FlashDrive.
* Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding '''content''' of files may be very slow. Windows Desktop Search is '''NOT''' activated on College systems.
* [http://www.ch.ic.ac.uk/local/email/ Practice setting up E-mail], sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.
=== Configuring storage for your document libraries ===

Programs such as '''EndNote''', '''Mendeley''', '''iTunes''' store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

==== EndNote ====

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => '''userid(\\icfs18.cc.ic.ac.uk) (M:)''' Thereafter you can set it to open this library when the program starts.

==== Mendeley ====

Open the program and invoke '''Tools/Options/File Organiser''' and select drive M: for the library.

==== iTunes ====

Use '''Edit/Preferences/Advanced''' and set the iTunes Media folder location to M: (or other if M: is already full). Also tick '''Copy files to iTunes Media folder when adding to library'''.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

=Start of Demonstration material=
The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are '''positively encouraged to continue working through the material''' at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

== Combined Word/ EndNote Familiarity ==
This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about '''''penicillin''''' and its '''''conversion to cephalosporin'''''.

=== A Web of Knowledge Search ===
#[[Image:Endnote1e.jpg|thumb|left|WoK search]] From the [http://wok.mimas.ac.uk/ Web-of-Knowledge] link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
#'''Connect to the ISI Web of Knowledge Service''' and then select the
#''Web of Science'' tab from along the top and finally from the citation databases, narrow it down to the
# Science Citation Index expanded
#Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the '''Author''' box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the '''advanced''' search such as <tt>au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)</tt>
#When you have some hits, either tick individual citations, or '''All records on page''' or a span of records.
#Next, make sure you have Microsoft Word running, and from the '''EndNote X4''' taskbar of Word, click on '''Go to EndNote'''. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
#[[Image:Endnote1b.jpg|right|saving a list for Endnote]]Return to the Browser window displaying WOS and click on '''Save to EndNote'''. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
#If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name '''uml_view.cgi''' on the desktop) which you can open directly with EndNote (see below).

=== Inserting the citations just found into Word using EndNote===
#[[Image:Endnote1a.jpg|thumb|right|Starting EndNote]]Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
#Via '''Edit/preferences/Libraries''' select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
#[[Image:endnote-style.jpg|thumb|left|Checking the style setting]]From '''Edit/Output style/Open Style Mananger''', select the tick-box against a template known as '''Royal Society of Chemistry''' (you may have to use '''Find by/Chemistry''' to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
#If you are importing a citation list rather than relying on the automated procedure, then from '''File/Import''' of EndNote define the Import Option '''ISI-CE''' in the pull down menu, or '''Other Filters/SciFinder (CAS)''' if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
#[[Image:Endnote1c.jpg|thumb|right|]][[Image:Endnote1d.jpg|thumb|left|Word with citations showing|]]Go back to Word 2007, and write some text. At an appropriate point, from the '''Endnote X4 taskbar tab''', press '''Go to EndNote''' when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the '''Insert citation''' tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
#Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

==== Mendeley and other alternatives to EndNote ====
[[image:refworks.jpg|thumb|right]]A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include [https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks] (for which the client software can be downloaded without cost) and an innovative program called [http://www.mendeley.com/ Mendeley] which is available on the computers in the department.

# If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

== Chemdraw Familiarity ==
*[[Image:unknown1.jpg|left|thumb|Click to expand image]] [[Image:taxolhsr.jpg|Taxol|right|300px]] '''Starting and using ChemDraw.''' Start Chemdraw icon from the '''Start/Programs menu'''. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
*Check that you have drawn it correctly by calculating its formula. To do this, Go to '''View/Show analysis''' window and record what you see (it should give you C<sub>47</sub>H<sub>51</sub>NO<sub>14</sub>. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. '''What is the difference in behaviour?'''

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. '''Can you identify what it is called?'''

== Lecture Support: Journal Familiarity ==

You can go visit the databases of some major chemistry publishers, and track down any articles that members of this department (or other departments or your favourite Nobel prize lautreates) may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following:
* [http://pubs.acs.org/search/advanced The American Chemical Society] (where you can subscribe to an RSS feed of the search, which means you will be notified of new items)
* [http://www.rsc.org/Publishing/Journals/cc/index.asp The Royal Society of Chemistry] and their premier journal ''Chemical communications''
* [http://www.nature.com/search/adv_search?sp-a=sp1001702d&sp-x-1=ujournal&sp-q-1=Nature%20Chemistry Nature Chemistry] advanced search.
* [http://www3.interscience.wiley.com/journal/26737/home Wiley Interscience] and their flagship chemistry journal ''Angew. Chemie.''
* [http://www.sciencedirect.com Science Direct]

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

== Lecture Support: Named chemicals ==

# To apply the above skills by using [http://wok.mimas.ac.uk/ WOS] to perform a comprehensive literature search on the '''molecule''' ''Penicillin'', a '''reaction''' (''its conversion to Cephalosporin''), its ''properties'', both physical (spectroscopic) and biological. Thus, type ''penicillin and cephalosporin'' into the '''Topic''' box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the '''Advanced Search''' option.
#* '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (136)
#* '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2629)
##Or, try the drug '''Temozolomide''', currently very much in the [http://news.bbc.co.uk/1/hi/england/west_midlands/7675014.stm news]
##Tasimelteon ([http://news.bbc.co.uk/1/hi/health/7760105.stm time bending drug for jet lag]) or
##[http://news.bbc.co.uk/1/hi/health/8237530.stm Sulforaphane], which occurs in broccoli and cauliflower and protects against heart attacks.
#Compare the results of one of these searches with less specialised search engines such as
#*[http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar],
#*[http://www.scirus.com/srsapp/advanced/index.jsp SciRus],
#*[http://www.bing.com/?scope=web&mkt=en-GB Microsoft Bing],
#*[http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha].

=== Lecture Support: A SciFinder search instead ===
*The [https://scifinder.cas.org/ Scifinder Scholar] system is available for general and student use.
** You cannot use your College login for access, but must request your own login to be created.
*** [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar Go here to register]. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. ''other field''.
** Completing the registration will result in an email being sent to the email address you provide with activation instructions.
*** Once you have obtained an ID, at the [https://origin-scifinder.cas.org SciFinder site], click on '''Explore References''' and in the '''Research topic box''' enter "Conversion of penicillin to cephalosporin".
** You will receive a request to accept an application digital signature at this stage, which you should accept.
You should get ~9 references for an exact match. This interface is supposed to use a more ''natural language'' for its search queries (and it does not employ Booleans).
** Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the '''Export''' link near the top (next to print). From the dialog, set the '''File Type''' to '''Tagged Format'''.
*** You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your '''download''' location. You can then import this into EndNote using the '''SciFinder (CAS)''' import option.
**An alternative search might be the phrase '''arrow pushing formalism''' (can you learn about this topic from the results found for this search?). A synonym might be '''curly arrow formalism'''. Does this find the same references, or a different set?
** You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to '''My connections''' and invite the group, then add comments to relevant references.
** SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

=Laboratory Support=
Here you will find out how to search for safety information about molecules, and then for their properties and reactions. There are two kinds of search for molecules you will have to make during lab courses.
# Where you have an unknown compound whose properties you have measured and you want to know if any known compound matches those properties.
# Where you (think you) know what the structure of your compound is, and you want to know if there are any other reports of this same compound (and whether the properties other have measured match your own).

== A search for known physical properties using Reaxys ==
[[Image:Reaxys1.jpg|right|thumb|]]We will start with two examples of the first category and then move on to the rather more common second category.

*Connect to the [http://www.reaxys.com/ Reaxys] system. You can carry out all the required course work as an ''anonymous user'', but you will not be able to change/save any settings etc in this mode (such as e.g. changing the default structure editor to ChemDraw).
** If you do choose to register at this point, be aware that if you lose/forget your password, you will need to contact Reaxys and not local Imperial College support.
*Select ''substances and Properties''
**In the ''Properties (Advanced)'' box, enter the following, followed by '''Search'''.
**'''MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200'''
This means in effect, show me ANY molecule which melts at a certain temperature range (determined using a melting point apparatus), which has a given molecular formula (determined using mass spectrometry) and an optical rotatory power between certain values (determined using a polarimeter). For this example you should get exactly 1 hit, which should be to a patent. Explore the options at this point, including viewing the original source of the data ( a patent in this case).
* There are about 500 different properties in total which you could specify in this manner. To explore them, click on ''Show Fields and Operators''. This type of technique is useful for identifying an '''unknown''' compound purely from its physical properties (Forensic science, etc).
** Note that some features do not always produce the expected result. For example, the icon labelled with the arrow (right) pulls down various options, one of which is ''copy structure to clipboard''. The clipboard contents however are '''not''' recognised by eg Chemdraw, Word etc.

== A search for known spectroscopic properties ==

[[image:spectra.jpg|240px|right]]It is routine when a compound is first made to record its spectroscopic properties. This would include the characteristic infra-red frequencies, and the <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts. These values are shown for an unknown compound. Your task is to use the [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] to try to identify what the compound is (you could of course also do this entirely logically using just your brain).
#Try first entering only the <sup>13</sup>C NMR chemical shifts (163, 141, 133, 130, 129, 128, 98 ppm, with an anticipated error of around 2ppm). How many matches do you get?
#Add then the <sup>1</sup>H shifts (8.1,7.5,5.1,4.7 and there is an additional broad multiplet across the range 7.3-7.7 which is not entered) and see if the number of possibilities reduces.
#Finally, enter the one characteristic IR vibration (1733 cm<sup>-1</sup>). Do you now get a unique answer? Record any structure(s) you may get at this stage for future reference.
#Try changing the error limits for any of these properties. Thus reduce the NMR limit from 2.0 to 1.5 to 1.0ppm, or the IR limit to 5 or even 1 cm<sup>-1</sup> (in future laboratory courses, you will learn how the way the instrument works determines at least in part the accuracy with which these spectroscopic properties can be measured).

== Reagent/Product searches for laboratory preparations ==

[[image:1-4.jpg|right|250px|Molecules 1-4]]The theme of this section is going to be the following four molecules, which you will in fact encounter in a laboratory course later in the year. You will search for known properties of these molecules, for comparison with those you might measure in the lab, or which may provide useful discussion material for your laboratory reports. Your first task is to generate a so-called SMILES descriptor of the molecule. This is done most simply by drawing the molecule in ChemDraw and using the '''Edit as/Copy''' menu produce the SMILES or InChI-key string onto the clipboard. Here are three SMILES strings and one InCHI-key string. Can you match them up to the structures shown on the right?
# <nowiki>C=CC1=CC=C(C(O[H])=O)C=C1</nowiki>
# <nowiki>S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S</nowiki>
# <nowiki>O[C@H]1[C@H](OCC)CCCC1</nowiki>
# <nowiki>VSIKJPJINIDELZ-UHFFFAOYSA-N</nowiki>
*Search the [http://www.chemspider.com/ ChemSpider] database using a SMILES or InChI-key string as above. What sort of information is revealed about the compound?
*Try reversing the search terms above (instead of SMILEs, try generating an InChI key, or vice versa).
*Try next an advanced search from the same [http://www.chemspider.com/FullSearch.aspx database]. Explore for yourself how to enter the SMILES string and perform the search.
*Search the [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] using a SMILES string. Select the '''substructure/superstructure''' or the '''Identity/Similarity''' option, and then the '''CID, SMILES, InChI''' tab, and past in one of the strings above. Try both '''80% similar''' and '''identical''' if using the Similarity option). Again, explore the properties associated with each hit.
**You might encounter '''artefacts'''. Thus with '''S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S''', something slightly odd happens?
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of Drugs, inorganic and organometallic and natural products which might prove useful to you for laboratories.
* The series [http://www.orgsyn.org/ Organic syntheses] contains tried and tested procedures for the synthesis of many chemicals. However, it is quite limited, and you would be lucky to find more obscure compounds listed here.
=== Sigma-Aldrich Catalogues and MSDS (Safety) information ===

If you know (or suspect you know) what the identity of the molecules are that you will be handling in the laboratory, the first task is to find out any known safety information.
The [http://www.sigmaaldrich.com/catalog/search/AdvancedSearchPage Aldrich] catalogues can be searched for compounds and their associated MSDS safety sheets. This is useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms. If you were able to obtain a name (see previous section), see if you can now find any information on it from the Aldrich catalogue.

=== Reaxys ===
Connect to [http://www.reaxys.com/ Reaxys] as before, but now we are going to do a structure based search, using as examples structures '''1-4''' above. If you click in the frame labelled ''Double click this frame and draw structure query'' you will get a default structure editor called ChemAxon MarvinSketch. It is a little different from Chemdraw, but should not take too much time to master.
# Using the structure editor, draw one of the four molecules 1-4 and invoke '''search'''.
# If you think you know the name of your query, type that instead in the ''Generate structure from name'' box (e.g. '''Taxol''', which as you have seen earlier is a challenge to draw!). You can also paste a SMILES or InChI key into this box (try any of the four above).
# Try hitting '''Synthesize''', but expect to be overwhelmed by the number of hits!

=== Dictionary of organic compounds ===
An alternative database which works in this way is the [http://doc.chemnetbase.com/ Dictionary of organic compounds].


= Extra material for Future Reference - Converting a 2D structure definition to a 3D set of coordinates =

The preceding searches were all effectively conducted on two-dimensional molecules, where we only needed to know how the atoms were connected (in effect the Lewis valence structure). As a prelude to moving into three dimensions, we will illustrate how a 2D search can be used to generate a 3D structure.

* You can use the on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina service to convert a (1D) SMILES string to 3D molecular coordinates].
*# Under options, paste the SMILES string, enter a name, and select 3D structure viewer automatically loaded.
*# Click on Generate 3D structure. A window appears, and after about 20-30 seconds, a structure does as well. At the bottom, click on "Click to download this structure in PDB file format", whereupon a full window diagram appears. Save the molecule as above.

== 3D structure searching of the Cambridge Crystallographic database ==

Our final search type is now of a database which stores '''three-dimensional''' information about molecules. This is where you can infer all sorts of interesting properties about the bonding, the properties and the potential reactivities of molecules. You will be searching the '''Cambridge Crystal Structure Database'''. There are three entry points for this; one local, one via the Web and one via the national '''chemical database service'''.

=== Local invocation of the Cambridge Crystal Structure Database ===
The local based search described below is feature complete and fast. You may also want to try out the [http://webcsd.ccdc.cam.ac.uk/ WebCSD service], which needs only a web-browser.
#[[Image:MgBr2.jpg|right|120px]][[Image:ti1.jpg|right|100px]][[Image:PtCl.jpg|right|100px]][[image:1-4.jpg|right|250px|Molecules 1-4]]Select '''Conquest''' from the '''Start/Programs''' menu. You will have to reply:
##'''yes''' to the question about certificates,
##enter first your username, then
##your password at the two prompts (both of which appear to ask for a password!).
##Next, '''accept''' the license agreement and
##'''accept''' the suggested location for storing the directory.
##Enter the Site No. as '''183''' and the confirm code as '''8FDCE4''' (2013 release)
##Click '''register online'''.
##These prompts are a one-off, and you will not need to do these steps again.
#In the {{Pdf|FoundationTutorialproblems09.pdf|foundation tutorial problems}}, question 2 asks you to arrow-push the reaction Et<sub>2</sub>O + MgBr<sub>2</sub> → Et<sub>2</sub>O-MgBr<sub>2</sub>. Here we will pose the question: what is the 3D geometry of the product of this reaction? You will search for it using Conquest. Does the result surprise you? (Hint: TOQKIT)
#Nucleophilic addition to an amide is the prototype of how peptides, proteins and enzymes are broken down in metabolic processes (or using e.g. biological washing powders). The mechanism involves a species known as a '''tetrahedral intermediate''' (right), which is normally considered so unstable that it is rarely detected during the reaction. Nevertheless, can you find any examples of such species in the Cambridge database?
#Cis-Platin is a well known anti-cancer drug. The ''active ingredient'' is the initial hydrolysis product, shown on the right. Can you find any examples of this '''active intermediate''' in the database which contain this sub-structure? What happens if you change the Pt to a '''wild-card''' indicating the central metal could be any of the group known as '''8Z''' (from the '''more''' button of the editor, select '''other elements''' and from there click on the orange box labelled '''8Z''').
#Are there any other '''reactive intermediates''' you might have identified from your arrow-pushing workshop which you might search for?
#When you have finished the above examples, try entering one of the four lab-course molecules shown to the left, exactly as drawn above. For '''3''' specifically, if you draw explicit hydrogens attached to the ''vinyl'' group at the top of the molecule and repeat the search, what difference is there?
#*How many hits do you get?
#*Note the 6-8 letter identifier for the structure you are interested in (for example, for molecule '''3''' above, it should be XAYFEI, XAYFEI01 and XAYFEI02).
#*Save the 3D coordinates in PDB or CIF format via '''File/Export''', decide how you want to select entries, specify one file per entry and '''SAVE'''. Inspect the structure by double clicking the file created, to be found on drive '''L:'''
#You '''may''' now have two versions of any of these four molecules; one a direct experimental structure, and one assembled by the [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] program. How do these differ? Concentrate in particular on compounds '''1''' and '''2''' above right!
#Later on in your course, you may use such coordinates to create an entry in a Wiki page, much like that rotating below.

===An advanced 3D Search. ===
Try the following. The objective will be to find any short interactions between the H of an OH group and the centroid of a phenyl ring as the electron donor (a very unusual type of π-facial hydrogen bond). Proceed as follows:
{|
|
# Open Conquest and invoke the '''Build Queries/Draw''' option
# Deposit a benzene ring from the template which should appear on the left
# Click on '''ADD 3D''', select all the six carbon atoms in turn (they will go green) and define a centroid. A defined object labelled '''CENT1''' now shows. Press Done.
# Back in '''Draw''' mode, select a H and deposit it as an isolated atom. Then select O and draw a bond from it to the H to get an OH. In this system, any undefined valence is '''wild''', ie any group can be attached to the O of the OH.
# In '''ADD 3D''' mode again, click first on the '''H''' of the OH group, then on '''CENT1''' in the list of defined objects. A green line connecting the two appears. When a '''Valid parameter''' entry named '''Distance''' appears, click on '''Define'''.
# Select '''Intramolecular''' from the '''Choose distance type''' menu, OK, then '''Options''', enter 2.0 - 2.4 as the range of distances and '''Separated by 5 - 999''' bonds. Hit '''OK''' and then '''Done'''. Your search query is summarized in a cyan box at the top right of the draw window.
# Select '''Search''', tick the 3D Coordinates determined box and '''Start Search'''. This search should proceed at the rate of about 1% per second. You should get 20 hits.
# View entries via '''3D Visualiser'''. Note the so-called '''REFCODES'''. Note '''[[Coursework#Enantiomers_vs_Diastereomers_Part_1:_Butanes_and__Helicenes.|CIYSIM]]''' in particular!
#A right-mouse click in the blue window of the 3D Visualiser will enable you to set '''spacefill''' mode, and to inspect whether any two atom spheres inter-penetrate each-other indicating an attractive interaction between them.
# Save the coordinates of any selected hits via '''File/Export''', Select PDB or CIF as the format, all selected entries, one file per entry and '''SAVE'''.
# The files will appear on your L: drive. Double click to open up the WebLab Viewer Pro or Mercury program, and resave them if you wish as an MDL Molfile rather than PDB.
# If you want to explore further, define an NH bond rather an OH bond (you might need to increase the distance range to eg 2.0 - 2.5).
# Try this with centroids to other π-electron rich systems, such as an alkyne, alkene, or other rings such as cyclopentadienyl, etc.
#Go to your network drive N: or L: (i.e. username on neon.ch.ic.ac.uk) and double click any .PDB or .CFIF or .MOL files to view the molecule again.
# Or, instead of H-O, just put e.g. Na (metal arene interactions are hugely important biologically). You may need to define a rather longer distance range. Experiment by trying various sets of values.
|<jmol><jmolApplet><title>CIYSIM</title><color>white</color>
<size>300</size><script>zoom 150;spin 3;</script>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents>
</jmolApplet></jmol>
|}

=== The National Chemical Database Service ===

The '''CDS''' is a national service (located as it happens in Daresbury, near Warrington) which offers a range of database services to the UK community. To access this service, follow the [http://cds.dl.ac.uk/cgi-bin/reg/undergrad?sites=Select+Site&SITE=imperial-cds0091 instructions] here (this is necessary to ensure UK usage only and to monitor that usage as part of justifying a national resource). You will be sent a CDS registration account and password by email. You can then use this account in two ways
#Invoke '''ConquestD''' (rather than Conquest) from the Windows start menu and proceed as above, but supply your new CDS account instead of your Imperial account.
#Invoke the CDS portal [https://cds.dl.ac.uk/ here] using your CDS account to log in. It offers many alternative services (including searches for spectral data) as well as a simplified crystal search. Explore in your own time!


=== Further tutorials based on 3D crystal structures ===

These can be viewed [http://www.ccdc.cam.ac.uk/free_services/teaching/modules/teaching_webcsd/toc.html here].

=Continuation of CIT skills=
The skills developed during these workshops will be in almost constant use throughout your course; you are encouraged to keep this up to date and to make use of these skills while writing lab reports and other coursework assignments. As with anything in the digital world, progress is being made all the time with new search engines, new search algorithms, new software. This also means that other searches and software are retired to make way for, newer more efficient tools. This wiki will be a long-term reference which you can refer to and even update, and you are urged to keep it as a bookmark.

== Software for your own computer ==

*The department has a Site License for a program system called [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 ChemBio3D] (which includes ChemDraw for both Windows and Mac), the terms of which allow individual undergraduates to acquire a copy of the program and to install it on their personal computer. The license is an annual one.
*[http://www.straightrunning.com/XmingNotes/ Xming] for accessing the Conquest data base.
*Programs such as Microsoft Office can be licensed via [http://www.microsoft.com/student/discounts/theultimatesteal-uk/default.aspx an academic license for £69.99].
*[https://directory.adeptscience.co.uk/products/search/1/1/474/cat474.html EndNote student edition] retails for £85.00. Alternatively, try RefWorks (usually $100/year but '''free''' for Imperial students through [http://www3.imperial.ac.uk/library/digitallibrary/athensandukfed AthensDA]) It is a slightly simpler web-based program. A comparison between both can be found [http://library.princeton.edu/help/comparison.php here] (Princeton University). You should note that the WOS system supports Endnote directly, but requires a more complicated procedure for using RefWorks or Mendeley.
*A further list of software may be found [[It:software-2011|here]], including other programs you can install on your personal computer which you may find useful.
----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:coursework-2011

2014-10-11T13:26:58Z

Amckinle: /* 3D structure searching of the Cambridge Crystallographic database */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Overall Objectives of CIT workshops=

The Computer lab (formally booked for your group, A1, A2, B1, B2, C1, C2) is for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library. All "Chemistry Software" should be available also in the Library to your user account. If you find that something is not immediately available, please do get in touch with the ICT Helpdesk. During the lab time allocated for the IT course, you will be expected to achieve the following objectives:

# Accessing course and laboratory notes and using scientific journals to support lectures
# Using '''Word''' in combination with the '''EndNote''' bibliographic database and '''ChemDraw''' to write laboratory reports and essays
# Learn to use various bibliographic chemistry search systems
# Learn to conduct molecular structure-based search systems
# Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

=Self-Study - Software Familiarity=

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section ''' <u>before you come to the workshop sessions</u>''':

==Before you come to the workshop sessions...==

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.
* Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your [https://exchange.imperial.ac.uk campus email account] through the [https://exchange.imperial.ac.uk web interface].
* Using the '''FireFox''' web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: <tt>http://www.ch.ic.ac.uk/wiki/</tt>). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
* You will be using Firefox to browse the pages of a [http://en.wikipedia.org/wiki/Wiki Wiki]. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will '''replace''' the instruction window. So, get used to clicking on the link with the '''right mouse button''' rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

===Computer, Browser and Wordprocessor familiarity===
*[[Image:login_window.jpg|right|thumb|login window]]Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
*[[Image:home.jpg|left|thumb|Document home]]Perhaps the single most confusing aspect for most people is what the ''Home'' icon (left) means. So let's sort this out immediately. You are working in an ''enterprise'' environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the ''Home'' icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "'''My Documents'''", which the operating system can sometimes display instead of Home.
*[[Image:o2007.jpg|thumb|right|Office 2007]][[Image:subsuper.jpg|right|thumb|Subs and Superscripts]][[Image:o2007b.jpg|thumb|left||EndNote tab]]Start Microsoft '''Office 2007''' (we will assume you still have FireFox running). The basic ('''Home''') Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a '''red''' circle. Copy/paste operations are invoked using the icon encircled in '''purple'''. Other common operations are found to the right of these two in the taskbar, including the chemically useful '''subscript''' and '''superscripts''' (right diagram). Note also the the default document saves invokes the new '''.docx''' format, which is an XML-based type with much interesting ''informatics'' potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older '''.doc''' format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
*[[Image:o2007a.jpg|left|thumb|Insert tab]]There are two other task-bars you will find useful. the '''Insert''' bar inserts a variety of other content, including pictures, tables and the like. The '''EndNote''' tab invokes a citation and reference manager, which you will use as described below ('''Important'''<nowiki>: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).</nowiki>
* Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
*[[Image:FireFox_paste.jpg|thumb|right|Save Firefox image]] '''Images''' are special when it comes to copying. Proceed as follows:
*# Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
*# If one of the options is '''Copy image''', select it. Not all browsers support this, in which case instead invoke ''save this image as'' and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
*# With an Office Word window open, paste the image (if you copied it) or '''Insert/Picture/from file''' (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
*# Do remember how to change between windows (the technical term is that the active window is said to be ''on focus'') by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
{|
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>150</size>
<script>zoom 200; cpk -20;move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|Not everything is always "copyable". Some apparent images are in fact produced by an "applet" [http://wiki.jmol.org:81/index.php/MediaWiki embedded] in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
|}
* Practice naming and saving document files to your ''Home'' (Drive H: on Windows) or a removable medium such as a FlashDrive.
* Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding '''content''' of files may be very slow. Windows Desktop Search is '''NOT''' activated on College systems.
* [http://www.ch.ic.ac.uk/local/email/ Practice setting up E-mail], sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.
=== Configuring storage for your document libraries ===

Programs such as '''EndNote''', '''Mendeley''', '''iTunes''' store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

==== EndNote ====

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => '''userid(\\icfs18.cc.ic.ac.uk) (M:)''' Thereafter you can set it to open this library when the program starts.

==== Mendeley ====

Open the program and invoke '''Tools/Options/File Organiser''' and select drive M: for the library.

==== iTunes ====

Use '''Edit/Preferences/Advanced''' and set the iTunes Media folder location to M: (or other if M: is already full). Also tick '''Copy files to iTunes Media folder when adding to library'''.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

=Start of Demonstration material=
The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are '''positively encouraged to continue working through the material''' at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

== Combined Word/ EndNote Familiarity ==
This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about '''''penicillin''''' and its '''''conversion to cephalosporin'''''.

=== A Web of Knowledge Search ===
#[[Image:Endnote1e.jpg|thumb|left|WoK search]] From the [http://wok.mimas.ac.uk/ Web-of-Knowledge] link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
#'''Connect to the ISI Web of Knowledge Service''' and then select the
#''Web of Science'' tab from along the top and finally from the citation databases, narrow it down to the
# Science Citation Index expanded
#Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the '''Author''' box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the '''advanced''' search such as <tt>au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)</tt>
#When you have some hits, either tick individual citations, or '''All records on page''' or a span of records.
#Next, make sure you have Microsoft Word running, and from the '''EndNote X4''' taskbar of Word, click on '''Go to EndNote'''. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
#[[Image:Endnote1b.jpg|right|saving a list for Endnote]]Return to the Browser window displaying WOS and click on '''Save to EndNote'''. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
#If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name '''uml_view.cgi''' on the desktop) which you can open directly with EndNote (see below).

=== Inserting the citations just found into Word using EndNote===
#[[Image:Endnote1a.jpg|thumb|right|Starting EndNote]]Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
#Via '''Edit/preferences/Libraries''' select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
#[[Image:endnote-style.jpg|thumb|left|Checking the style setting]]From '''Edit/Output style/Open Style Mananger''', select the tick-box against a template known as '''Royal Society of Chemistry''' (you may have to use '''Find by/Chemistry''' to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
#If you are importing a citation list rather than relying on the automated procedure, then from '''File/Import''' of EndNote define the Import Option '''ISI-CE''' in the pull down menu, or '''Other Filters/SciFinder (CAS)''' if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
#[[Image:Endnote1c.jpg|thumb|right|]][[Image:Endnote1d.jpg|thumb|left|Word with citations showing|]]Go back to Word 2007, and write some text. At an appropriate point, from the '''Endnote X4 taskbar tab''', press '''Go to EndNote''' when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the '''Insert citation''' tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
#Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

==== Mendeley and other alternatives to EndNote ====
[[image:refworks.jpg|thumb|right]]A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include [https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks] (for which the client software can be downloaded without cost) and an innovative program called [http://www.mendeley.com/ Mendeley] which is available on the computers in the department.

# If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

== Chemdraw Familiarity ==
*[[Image:unknown1.jpg|left|thumb|Click to expand image]] [[Image:taxolhsr.jpg|Taxol|right|300px]] '''Starting and using ChemDraw.''' Start Chemdraw icon from the '''Start/Programs menu'''. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
*Check that you have drawn it correctly by calculating its formula. To do this, Go to '''View/Show analysis''' window and record what you see (it should give you C<sub>47</sub>H<sub>51</sub>NO<sub>14</sub>. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. '''What is the difference in behaviour?'''

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. '''Can you identify what it is called?'''

== Lecture Support: Journal Familiarity ==

You can go visit the databases of some major chemistry publishers, and track down any articles that members of this department (or other departments or your favourite Nobel prize lautreates) may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following:
* [http://pubs.acs.org/search/advanced The American Chemical Society] (where you can subscribe to an RSS feed of the search, which means you will be notified of new items)
* [http://www.rsc.org/Publishing/Journals/cc/index.asp The Royal Society of Chemistry] and their premier journal ''Chemical communications''
* [http://www.nature.com/search/adv_search?sp-a=sp1001702d&sp-x-1=ujournal&sp-q-1=Nature%20Chemistry Nature Chemistry] advanced search.
* [http://www3.interscience.wiley.com/journal/26737/home Wiley Interscience] and their flagship chemistry journal ''Angew. Chemie.''
* [http://www.sciencedirect.com Science Direct]

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

== Lecture Support: Named chemicals ==

# To apply the above skills by using [http://wok.mimas.ac.uk/ WOS] to perform a comprehensive literature search on the '''molecule''' ''Penicillin'', a '''reaction''' (''its conversion to Cephalosporin''), its ''properties'', both physical (spectroscopic) and biological. Thus, type ''penicillin and cephalosporin'' into the '''Topic''' box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the '''Advanced Search''' option.
#* '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (136)
#* '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2629)
##Or, try the drug '''Temozolomide''', currently very much in the [http://news.bbc.co.uk/1/hi/england/west_midlands/7675014.stm news]
##Tasimelteon ([http://news.bbc.co.uk/1/hi/health/7760105.stm time bending drug for jet lag]) or
##[http://news.bbc.co.uk/1/hi/health/8237530.stm Sulforaphane], which occurs in broccoli and cauliflower and protects against heart attacks.
#Compare the results of one of these searches with less specialised search engines such as
#*[http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar],
#*[http://www.scirus.com/srsapp/advanced/index.jsp SciRus],
#*[http://www.bing.com/?scope=web&mkt=en-GB Microsoft Bing],
#*[http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha].

=== Lecture Support: A SciFinder search instead ===
*The [https://scifinder.cas.org/ Scifinder Scholar] system is available for general and student use.
** You cannot use your College login for access, but must request your own login to be created.
*** [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar Go here to register]. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. ''other field''.
** Completing the registration will result in an email being sent to the email address you provide with activation instructions.
*** Once you have obtained an ID, at the [https://origin-scifinder.cas.org SciFinder site], click on '''Explore References''' and in the '''Research topic box''' enter "Conversion of penicillin to cephalosporin".
** You will receive a request to accept an application digital signature at this stage, which you should accept.
You should get ~9 references for an exact match. This interface is supposed to use a more ''natural language'' for its search queries (and it does not employ Booleans).
** Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the '''Export''' link near the top (next to print). From the dialog, set the '''File Type''' to '''Tagged Format'''.
*** You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your '''download''' location. You can then import this into EndNote using the '''SciFinder (CAS)''' import option.
**An alternative search might be the phrase '''arrow pushing formalism''' (can you learn about this topic from the results found for this search?). A synonym might be '''curly arrow formalism'''. Does this find the same references, or a different set?
** You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to '''My connections''' and invite the group, then add comments to relevant references.
** SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

=Laboratory Support=
Here you will find out how to search for safety information about molecules, and then for their properties and reactions. There are two kinds of search for molecules you will have to make during lab courses.
# Where you have an unknown compound whose properties you have measured and you want to know if any known compound matches those properties.
# Where you (think you) know what the structure of your compound is, and you want to know if there are any other reports of this same compound (and whether the properties other have measured match your own).

== A search for known physical properties using Reaxys ==
[[Image:Reaxys1.jpg|right|thumb|]]We will start with two examples of the first category and then move on to the rather more common second category.

*Connect to the [http://www.reaxys.com/ Reaxys] system. You can carry out all the required course work as an ''anonymous user'', but you will not be able to change/save any settings etc in this mode (such as e.g. changing the default structure editor to ChemDraw).
** If you do choose to register at this point, be aware that if you lose/forget your password, you will need to contact Reaxys and not local Imperial College support.
*Select ''substances and Properties''
**In the ''Properties (Advanced)'' box, enter the following, followed by '''Search'''.
**'''MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200'''
This means in effect, show me ANY molecule which melts at a certain temperature range (determined using a melting point apparatus), which has a given molecular formula (determined using mass spectrometry) and an optical rotatory power between certain values (determined using a polarimeter). For this example you should get exactly 1 hit, which should be to a patent. Explore the options at this point, including viewing the original source of the data ( a patent in this case).
* There are about 500 different properties in total which you could specify in this manner. To explore them, click on ''Show Fields and Operators''. This type of technique is useful for identifying an '''unknown''' compound purely from its physical properties (Forensic science, etc).
** Note that some features do not always produce the expected result. For example, the icon labelled with the arrow (right) pulls down various options, one of which is ''copy structure to clipboard''. The clipboard contents however are '''not''' recognised by eg Chemdraw, Word etc.

== A search for known spectroscopic properties ==

[[image:spectra.jpg|240px|right]]It is routine when a compound is first made to record its spectroscopic properties. This would include the characteristic infra-red frequencies, and the <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts. These values are shown for an unknown compound. Your task is to use the [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] to try to identify what the compound is (you could of course also do this entirely logically using just your brain).
#Try first entering only the <sup>13</sup>C NMR chemical shifts (163, 141, 133, 130, 129, 128, 98 ppm, with an anticipated error of around 2ppm). How many matches do you get?
#Add then the <sup>1</sup>H shifts (8.1,7.5,5.1,4.7 and there is an additional broad multiplet across the range 7.3-7.7 which is not entered) and see if the number of possibilities reduces.
#Finally, enter the one characteristic IR vibration (1733 cm<sup>-1</sup>). Do you now get a unique answer? Record any structure(s) you may get at this stage for future reference.
#Try changing the error limits for any of these properties. Thus reduce the NMR limit from 2.0 to 1.5 to 1.0ppm, or the IR limit to 5 or even 1 cm<sup>-1</sup> (in future laboratory courses, you will learn how the way the instrument works determines at least in part the accuracy with which these spectroscopic properties can be measured).

== Reagent/Product searches for laboratory preparations ==

[[image:1-4.jpg|right|250px|Molecules 1-4]]The theme of this section is going to be the following four molecules, which you will in fact encounter in a laboratory course later in the year. You will search for known properties of these molecules, for comparison with those you might measure in the lab, or which may provide useful discussion material for your laboratory reports. Your first task is to generate a so-called SMILES descriptor of the molecule. This is done most simply by drawing the molecule in ChemDraw and using the '''Edit as/Copy''' menu produce the SMILES or InChI-key string onto the clipboard. Here are three SMILES strings and one InCHI-key string. Can you match them up to the structures shown on the right?
# <nowiki>C=CC1=CC=C(C(O[H])=O)C=C1</nowiki>
# <nowiki>S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S</nowiki>
# <nowiki>O[C@H]1[C@H](OCC)CCCC1</nowiki>
# <nowiki>VSIKJPJINIDELZ-UHFFFAOYSA-N</nowiki>
*Search the [http://www.chemspider.com/ ChemSpider] database using a SMILES or InChI-key string as above. What sort of information is revealed about the compound?
*Try reversing the search terms above (instead of SMILEs, try generating an InChI key, or vice versa).
*Try next an advanced search from the same [http://www.chemspider.com/FullSearch.aspx database]. Explore for yourself how to enter the SMILES string and perform the search.
*Search the [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] using a SMILES string. Select the '''substructure/superstructure''' or the '''Identity/Similarity''' option, and then the '''CID, SMILES, InChI''' tab, and past in one of the strings above. Try both '''80% similar''' and '''identical''' if using the Similarity option). Again, explore the properties associated with each hit.
**You might encounter '''artefacts'''. Thus with '''S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S''', something slightly odd happens?
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of Drugs, inorganic and organometallic and natural products which might prove useful to you for laboratories.
* The series [http://www.orgsyn.org/ Organic syntheses] contains tried and tested procedures for the synthesis of many chemicals. However, it is quite limited, and you would be lucky to find more obscure compounds listed here.
=== Sigma-Aldrich Catalogues and MSDS (Safety) information ===

If you know (or suspect you know) what the identity of the molecules are that you will be handling in the laboratory, the first task is to find out any known safety information.
The [http://www.sigmaaldrich.com/catalog/search/AdvancedSearchPage Aldrich] catalogues can be searched for compounds and their associated MSDS safety sheets. This is useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms. If you were able to obtain a name (see previous section), see if you can now find any information on it from the Aldrich catalogue.

=== Reaxys ===
Connect to [http://www.reaxys.com/ Reaxys] as before, but now we are going to do a structure based search, using as examples structures '''1-4''' above. If you click in the frame labelled ''Double click this frame and draw structure query'' you will get a default structure editor called ChemAxon MarvinSketch. It is a little different from Chemdraw, but should not take too much time to master.
# Using the structure editor, draw one of the four molecules 1-4 and invoke '''search'''.
# If you think you know the name of your query, type that instead in the ''Generate structure from name'' box (e.g. '''Taxol''', which as you have seen earlier is a challenge to draw!). You can also paste a SMILES or InChI key into this box (try any of the four above).
# Try hitting '''Synthesize''', but expect to be overwhelmed by the number of hits!

=== Dictionary of organic compounds ===
An alternative database which works in this way is the [http://doc.chemnetbase.com/ Dictionary of organic compounds].


== Extra material for Future Reference - Converting a 2D structure definition to a 3D set of coordinates ==

The preceding searches were all effectively conducted on two-dimensional molecules, where we only needed to know how the atoms were connected (in effect the Lewis valence structure). As a prelude to moving into three dimensions, we will illustrate how a 2D search can be used to generate a 3D structure.

* You can use the on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina service to convert a (1D) SMILES string to 3D molecular coordinates].
*# Under options, paste the SMILES string, enter a name, and select 3D structure viewer automatically loaded.
*# Click on Generate 3D structure. A window appears, and after about 20-30 seconds, a structure does as well. At the bottom, click on "Click to download this structure in PDB file format", whereupon a full window diagram appears. Save the molecule as above.

== 3D structure searching of the Cambridge Crystallographic database ==

Our final search type is now of a database which stores '''three-dimensional''' information about molecules. This is where you can infer all sorts of interesting properties about the bonding, the properties and the potential reactivities of molecules. You will be searching the '''Cambridge Crystal Structure Database'''. There are three entry points for this; one local, one via the Web and one via the national '''chemical database service'''.

=== Local invocation of the Cambridge Crystal Structure Database ===
The local based search described below is feature complete and fast. You may also want to try out the [http://webcsd.ccdc.cam.ac.uk/ WebCSD service], which needs only a web-browser.
#[[Image:MgBr2.jpg|right|120px]][[Image:ti1.jpg|right|100px]][[Image:PtCl.jpg|right|100px]][[image:1-4.jpg|right|250px|Molecules 1-4]]Select '''Conquest''' from the '''Start/Programs''' menu. You will have to reply:
##'''yes''' to the question about certificates,
##enter first your username, then
##your password at the two prompts (both of which appear to ask for a password!).
##Next, '''accept''' the license agreement and
##'''accept''' the suggested location for storing the directory.
##Enter the Site No. as '''183''' and the confirm code as '''8FDCE4''' (2013 release)
##Click '''register online'''.
##These prompts are a one-off, and you will not need to do these steps again.
#In the {{Pdf|FoundationTutorialproblems09.pdf|foundation tutorial problems}}, question 2 asks you to arrow-push the reaction Et<sub>2</sub>O + MgBr<sub>2</sub> → Et<sub>2</sub>O-MgBr<sub>2</sub>. Here we will pose the question: what is the 3D geometry of the product of this reaction? You will search for it using Conquest. Does the result surprise you? (Hint: TOQKIT)
#Nucleophilic addition to an amide is the prototype of how peptides, proteins and enzymes are broken down in metabolic processes (or using e.g. biological washing powders). The mechanism involves a species known as a '''tetrahedral intermediate''' (right), which is normally considered so unstable that it is rarely detected during the reaction. Nevertheless, can you find any examples of such species in the Cambridge database?
#Cis-Platin is a well known anti-cancer drug. The ''active ingredient'' is the initial hydrolysis product, shown on the right. Can you find any examples of this '''active intermediate''' in the database which contain this sub-structure? What happens if you change the Pt to a '''wild-card''' indicating the central metal could be any of the group known as '''8Z''' (from the '''more''' button of the editor, select '''other elements''' and from there click on the orange box labelled '''8Z''').
#Are there any other '''reactive intermediates''' you might have identified from your arrow-pushing workshop which you might search for?
#When you have finished the above examples, try entering one of the four lab-course molecules shown to the left, exactly as drawn above. For '''3''' specifically, if you draw explicit hydrogens attached to the ''vinyl'' group at the top of the molecule and repeat the search, what difference is there?
#*How many hits do you get?
#*Note the 6-8 letter identifier for the structure you are interested in (for example, for molecule '''3''' above, it should be XAYFEI, XAYFEI01 and XAYFEI02).
#*Save the 3D coordinates in PDB or CIF format via '''File/Export''', decide how you want to select entries, specify one file per entry and '''SAVE'''. Inspect the structure by double clicking the file created, to be found on drive '''L:'''
#You '''may''' now have two versions of any of these four molecules; one a direct experimental structure, and one assembled by the [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] program. How do these differ? Concentrate in particular on compounds '''1''' and '''2''' above right!
#Later on in your course, you may use such coordinates to create an entry in a Wiki page, much like that rotating below.

===An advanced 3D Search. ===
Try the following. The objective will be to find any short interactions between the H of an OH group and the centroid of a phenyl ring as the electron donor (a very unusual type of π-facial hydrogen bond). Proceed as follows:
{|
|
# Open Conquest and invoke the '''Build Queries/Draw''' option
# Deposit a benzene ring from the template which should appear on the left
# Click on '''ADD 3D''', select all the six carbon atoms in turn (they will go green) and define a centroid. A defined object labelled '''CENT1''' now shows. Press Done.
# Back in '''Draw''' mode, select a H and deposit it as an isolated atom. Then select O and draw a bond from it to the H to get an OH. In this system, any undefined valence is '''wild''', ie any group can be attached to the O of the OH.
# In '''ADD 3D''' mode again, click first on the '''H''' of the OH group, then on '''CENT1''' in the list of defined objects. A green line connecting the two appears. When a '''Valid parameter''' entry named '''Distance''' appears, click on '''Define'''.
# Select '''Intramolecular''' from the '''Choose distance type''' menu, OK, then '''Options''', enter 2.0 - 2.4 as the range of distances and '''Separated by 5 - 999''' bonds. Hit '''OK''' and then '''Done'''. Your search query is summarized in a cyan box at the top right of the draw window.
# Select '''Search''', tick the 3D Coordinates determined box and '''Start Search'''. This search should proceed at the rate of about 1% per second. You should get 20 hits.
# View entries via '''3D Visualiser'''. Note the so-called '''REFCODES'''. Note '''[[Coursework#Enantiomers_vs_Diastereomers_Part_1:_Butanes_and__Helicenes.|CIYSIM]]''' in particular!
#A right-mouse click in the blue window of the 3D Visualiser will enable you to set '''spacefill''' mode, and to inspect whether any two atom spheres inter-penetrate each-other indicating an attractive interaction between them.
# Save the coordinates of any selected hits via '''File/Export''', Select PDB or CIF as the format, all selected entries, one file per entry and '''SAVE'''.
# The files will appear on your L: drive. Double click to open up the WebLab Viewer Pro or Mercury program, and resave them if you wish as an MDL Molfile rather than PDB.
# If you want to explore further, define an NH bond rather an OH bond (you might need to increase the distance range to eg 2.0 - 2.5).
# Try this with centroids to other π-electron rich systems, such as an alkyne, alkene, or other rings such as cyclopentadienyl, etc.
#Go to your network drive N: or L: (i.e. username on neon.ch.ic.ac.uk) and double click any .PDB or .CFIF or .MOL files to view the molecule again.
# Or, instead of H-O, just put e.g. Na (metal arene interactions are hugely important biologically). You may need to define a rather longer distance range. Experiment by trying various sets of values.
|<jmol><jmolApplet><title>CIYSIM</title><color>white</color>
<size>300</size><script>zoom 150;spin 3;</script>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents>
</jmolApplet></jmol>
|}

=== The National Chemical Database Service ===

The '''CDS''' is a national service (located as it happens in Daresbury, near Warrington) which offers a range of database services to the UK community. To access this service, follow the [http://cds.dl.ac.uk/cgi-bin/reg/undergrad?sites=Select+Site&SITE=imperial-cds0091 instructions] here (this is necessary to ensure UK usage only and to monitor that usage as part of justifying a national resource). You will be sent a CDS registration account and password by email. You can then use this account in two ways
#Invoke '''ConquestD''' (rather than Conquest) from the Windows start menu and proceed as above, but supply your new CDS account instead of your Imperial account.
#Invoke the CDS portal [https://cds.dl.ac.uk/ here] using your CDS account to log in. It offers many alternative services (including searches for spectral data) as well as a simplified crystal search. Explore in your own time!


=== Further tutorials based on 3D crystal structures ===

These can be viewed [http://www.ccdc.cam.ac.uk/free_services/teaching/modules/teaching_webcsd/toc.html here].

=Continuation of CIT skills=
The skills developed during these workshops will be in almost constant use throughout your course; you are encouraged to keep this up to date and to make use of these skills while writing lab reports and other coursework assignments. As with anything in the digital world, progress is being made all the time with new search engines, new search algorithms, new software. This also means that other searches and software are retired to make way for, newer more efficient tools. This wiki will be a long-term reference which you can refer to and even update, and you are urged to keep it as a bookmark.

== Software for your own computer ==

*The department has a Site License for a program system called [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 ChemBio3D] (which includes ChemDraw for both Windows and Mac), the terms of which allow individual undergraduates to acquire a copy of the program and to install it on their personal computer. The license is an annual one.
*[http://www.straightrunning.com/XmingNotes/ Xming] for accessing the Conquest data base.
*Programs such as Microsoft Office can be licensed via [http://www.microsoft.com/student/discounts/theultimatesteal-uk/default.aspx an academic license for £69.99].
*[https://directory.adeptscience.co.uk/products/search/1/1/474/cat474.html EndNote student edition] retails for £85.00. Alternatively, try RefWorks (usually $100/year but '''free''' for Imperial students through [http://www3.imperial.ac.uk/library/digitallibrary/athensandukfed AthensDA]) It is a slightly simpler web-based program. A comparison between both can be found [http://library.princeton.edu/help/comparison.php here] (Princeton University). You should note that the WOS system supports Endnote directly, but requires a more complicated procedure for using RefWorks or Mendeley.
*A further list of software may be found [[It:software-2011|here]], including other programs you can install on your personal computer which you may find useful.
----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:coursework-2011

2014-10-11T13:26:39Z

Amckinle: /* 3D structure searching of the Cambridge Crystallographic database */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Overall Objectives of CIT workshops=

The Computer lab (formally booked for your group, A1, A2, B1, B2, C1, C2) is for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library. All "Chemistry Software" should be available also in the Library to your user account. If you find that something is not immediately available, please do get in touch with the ICT Helpdesk. During the lab time allocated for the IT course, you will be expected to achieve the following objectives:

# Accessing course and laboratory notes and using scientific journals to support lectures
# Using '''Word''' in combination with the '''EndNote''' bibliographic database and '''ChemDraw''' to write laboratory reports and essays
# Learn to use various bibliographic chemistry search systems
# Learn to conduct molecular structure-based search systems
# Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

=Self-Study - Software Familiarity=

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section ''' <u>before you come to the workshop sessions</u>''':

==Before you come to the workshop sessions...==

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.
* Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your [https://exchange.imperial.ac.uk campus email account] through the [https://exchange.imperial.ac.uk web interface].
* Using the '''FireFox''' web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: <tt>http://www.ch.ic.ac.uk/wiki/</tt>). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
* You will be using Firefox to browse the pages of a [http://en.wikipedia.org/wiki/Wiki Wiki]. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will '''replace''' the instruction window. So, get used to clicking on the link with the '''right mouse button''' rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

===Computer, Browser and Wordprocessor familiarity===
*[[Image:login_window.jpg|right|thumb|login window]]Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
*[[Image:home.jpg|left|thumb|Document home]]Perhaps the single most confusing aspect for most people is what the ''Home'' icon (left) means. So let's sort this out immediately. You are working in an ''enterprise'' environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the ''Home'' icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "'''My Documents'''", which the operating system can sometimes display instead of Home.
*[[Image:o2007.jpg|thumb|right|Office 2007]][[Image:subsuper.jpg|right|thumb|Subs and Superscripts]][[Image:o2007b.jpg|thumb|left||EndNote tab]]Start Microsoft '''Office 2007''' (we will assume you still have FireFox running). The basic ('''Home''') Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a '''red''' circle. Copy/paste operations are invoked using the icon encircled in '''purple'''. Other common operations are found to the right of these two in the taskbar, including the chemically useful '''subscript''' and '''superscripts''' (right diagram). Note also the the default document saves invokes the new '''.docx''' format, which is an XML-based type with much interesting ''informatics'' potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older '''.doc''' format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
*[[Image:o2007a.jpg|left|thumb|Insert tab]]There are two other task-bars you will find useful. the '''Insert''' bar inserts a variety of other content, including pictures, tables and the like. The '''EndNote''' tab invokes a citation and reference manager, which you will use as described below ('''Important'''<nowiki>: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).</nowiki>
* Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
*[[Image:FireFox_paste.jpg|thumb|right|Save Firefox image]] '''Images''' are special when it comes to copying. Proceed as follows:
*# Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
*# If one of the options is '''Copy image''', select it. Not all browsers support this, in which case instead invoke ''save this image as'' and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
*# With an Office Word window open, paste the image (if you copied it) or '''Insert/Picture/from file''' (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
*# Do remember how to change between windows (the technical term is that the active window is said to be ''on focus'') by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
{|
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>150</size>
<script>zoom 200; cpk -20;move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|Not everything is always "copyable". Some apparent images are in fact produced by an "applet" [http://wiki.jmol.org:81/index.php/MediaWiki embedded] in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
|}
* Practice naming and saving document files to your ''Home'' (Drive H: on Windows) or a removable medium such as a FlashDrive.
* Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding '''content''' of files may be very slow. Windows Desktop Search is '''NOT''' activated on College systems.
* [http://www.ch.ic.ac.uk/local/email/ Practice setting up E-mail], sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.
=== Configuring storage for your document libraries ===

Programs such as '''EndNote''', '''Mendeley''', '''iTunes''' store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

==== EndNote ====

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => '''userid(\\icfs18.cc.ic.ac.uk) (M:)''' Thereafter you can set it to open this library when the program starts.

==== Mendeley ====

Open the program and invoke '''Tools/Options/File Organiser''' and select drive M: for the library.

==== iTunes ====

Use '''Edit/Preferences/Advanced''' and set the iTunes Media folder location to M: (or other if M: is already full). Also tick '''Copy files to iTunes Media folder when adding to library'''.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

=Start of Demonstration material=
The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are '''positively encouraged to continue working through the material''' at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

== Combined Word/ EndNote Familiarity ==
This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about '''''penicillin''''' and its '''''conversion to cephalosporin'''''.

=== A Web of Knowledge Search ===
#[[Image:Endnote1e.jpg|thumb|left|WoK search]] From the [http://wok.mimas.ac.uk/ Web-of-Knowledge] link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
#'''Connect to the ISI Web of Knowledge Service''' and then select the
#''Web of Science'' tab from along the top and finally from the citation databases, narrow it down to the
# Science Citation Index expanded
#Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the '''Author''' box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the '''advanced''' search such as <tt>au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)</tt>
#When you have some hits, either tick individual citations, or '''All records on page''' or a span of records.
#Next, make sure you have Microsoft Word running, and from the '''EndNote X4''' taskbar of Word, click on '''Go to EndNote'''. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
#[[Image:Endnote1b.jpg|right|saving a list for Endnote]]Return to the Browser window displaying WOS and click on '''Save to EndNote'''. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
#If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name '''uml_view.cgi''' on the desktop) which you can open directly with EndNote (see below).

=== Inserting the citations just found into Word using EndNote===
#[[Image:Endnote1a.jpg|thumb|right|Starting EndNote]]Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
#Via '''Edit/preferences/Libraries''' select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
#[[Image:endnote-style.jpg|thumb|left|Checking the style setting]]From '''Edit/Output style/Open Style Mananger''', select the tick-box against a template known as '''Royal Society of Chemistry''' (you may have to use '''Find by/Chemistry''' to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
#If you are importing a citation list rather than relying on the automated procedure, then from '''File/Import''' of EndNote define the Import Option '''ISI-CE''' in the pull down menu, or '''Other Filters/SciFinder (CAS)''' if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
#[[Image:Endnote1c.jpg|thumb|right|]][[Image:Endnote1d.jpg|thumb|left|Word with citations showing|]]Go back to Word 2007, and write some text. At an appropriate point, from the '''Endnote X4 taskbar tab''', press '''Go to EndNote''' when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the '''Insert citation''' tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
#Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

==== Mendeley and other alternatives to EndNote ====
[[image:refworks.jpg|thumb|right]]A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include [https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks] (for which the client software can be downloaded without cost) and an innovative program called [http://www.mendeley.com/ Mendeley] which is available on the computers in the department.

# If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

== Chemdraw Familiarity ==
*[[Image:unknown1.jpg|left|thumb|Click to expand image]] [[Image:taxolhsr.jpg|Taxol|right|300px]] '''Starting and using ChemDraw.''' Start Chemdraw icon from the '''Start/Programs menu'''. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
*Check that you have drawn it correctly by calculating its formula. To do this, Go to '''View/Show analysis''' window and record what you see (it should give you C<sub>47</sub>H<sub>51</sub>NO<sub>14</sub>. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. '''What is the difference in behaviour?'''

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. '''Can you identify what it is called?'''

== Lecture Support: Journal Familiarity ==

You can go visit the databases of some major chemistry publishers, and track down any articles that members of this department (or other departments or your favourite Nobel prize lautreates) may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following:
* [http://pubs.acs.org/search/advanced The American Chemical Society] (where you can subscribe to an RSS feed of the search, which means you will be notified of new items)
* [http://www.rsc.org/Publishing/Journals/cc/index.asp The Royal Society of Chemistry] and their premier journal ''Chemical communications''
* [http://www.nature.com/search/adv_search?sp-a=sp1001702d&sp-x-1=ujournal&sp-q-1=Nature%20Chemistry Nature Chemistry] advanced search.
* [http://www3.interscience.wiley.com/journal/26737/home Wiley Interscience] and their flagship chemistry journal ''Angew. Chemie.''
* [http://www.sciencedirect.com Science Direct]

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

== Lecture Support: Named chemicals ==

# To apply the above skills by using [http://wok.mimas.ac.uk/ WOS] to perform a comprehensive literature search on the '''molecule''' ''Penicillin'', a '''reaction''' (''its conversion to Cephalosporin''), its ''properties'', both physical (spectroscopic) and biological. Thus, type ''penicillin and cephalosporin'' into the '''Topic''' box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the '''Advanced Search''' option.
#* '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (136)
#* '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2629)
##Or, try the drug '''Temozolomide''', currently very much in the [http://news.bbc.co.uk/1/hi/england/west_midlands/7675014.stm news]
##Tasimelteon ([http://news.bbc.co.uk/1/hi/health/7760105.stm time bending drug for jet lag]) or
##[http://news.bbc.co.uk/1/hi/health/8237530.stm Sulforaphane], which occurs in broccoli and cauliflower and protects against heart attacks.
#Compare the results of one of these searches with less specialised search engines such as
#*[http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar],
#*[http://www.scirus.com/srsapp/advanced/index.jsp SciRus],
#*[http://www.bing.com/?scope=web&mkt=en-GB Microsoft Bing],
#*[http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha].

=== Lecture Support: A SciFinder search instead ===
*The [https://scifinder.cas.org/ Scifinder Scholar] system is available for general and student use.
** You cannot use your College login for access, but must request your own login to be created.
*** [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar Go here to register]. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. ''other field''.
** Completing the registration will result in an email being sent to the email address you provide with activation instructions.
*** Once you have obtained an ID, at the [https://origin-scifinder.cas.org SciFinder site], click on '''Explore References''' and in the '''Research topic box''' enter "Conversion of penicillin to cephalosporin".
** You will receive a request to accept an application digital signature at this stage, which you should accept.
You should get ~9 references for an exact match. This interface is supposed to use a more ''natural language'' for its search queries (and it does not employ Booleans).
** Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the '''Export''' link near the top (next to print). From the dialog, set the '''File Type''' to '''Tagged Format'''.
*** You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your '''download''' location. You can then import this into EndNote using the '''SciFinder (CAS)''' import option.
**An alternative search might be the phrase '''arrow pushing formalism''' (can you learn about this topic from the results found for this search?). A synonym might be '''curly arrow formalism'''. Does this find the same references, or a different set?
** You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to '''My connections''' and invite the group, then add comments to relevant references.
** SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

=Laboratory Support=
Here you will find out how to search for safety information about molecules, and then for their properties and reactions. There are two kinds of search for molecules you will have to make during lab courses.
# Where you have an unknown compound whose properties you have measured and you want to know if any known compound matches those properties.
# Where you (think you) know what the structure of your compound is, and you want to know if there are any other reports of this same compound (and whether the properties other have measured match your own).

== A search for known physical properties using Reaxys ==
[[Image:Reaxys1.jpg|right|thumb|]]We will start with two examples of the first category and then move on to the rather more common second category.

*Connect to the [http://www.reaxys.com/ Reaxys] system. You can carry out all the required course work as an ''anonymous user'', but you will not be able to change/save any settings etc in this mode (such as e.g. changing the default structure editor to ChemDraw).
** If you do choose to register at this point, be aware that if you lose/forget your password, you will need to contact Reaxys and not local Imperial College support.
*Select ''substances and Properties''
**In the ''Properties (Advanced)'' box, enter the following, followed by '''Search'''.
**'''MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200'''
This means in effect, show me ANY molecule which melts at a certain temperature range (determined using a melting point apparatus), which has a given molecular formula (determined using mass spectrometry) and an optical rotatory power between certain values (determined using a polarimeter). For this example you should get exactly 1 hit, which should be to a patent. Explore the options at this point, including viewing the original source of the data ( a patent in this case).
* There are about 500 different properties in total which you could specify in this manner. To explore them, click on ''Show Fields and Operators''. This type of technique is useful for identifying an '''unknown''' compound purely from its physical properties (Forensic science, etc).
** Note that some features do not always produce the expected result. For example, the icon labelled with the arrow (right) pulls down various options, one of which is ''copy structure to clipboard''. The clipboard contents however are '''not''' recognised by eg Chemdraw, Word etc.

== A search for known spectroscopic properties ==

[[image:spectra.jpg|240px|right]]It is routine when a compound is first made to record its spectroscopic properties. This would include the characteristic infra-red frequencies, and the <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts. These values are shown for an unknown compound. Your task is to use the [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] to try to identify what the compound is (you could of course also do this entirely logically using just your brain).
#Try first entering only the <sup>13</sup>C NMR chemical shifts (163, 141, 133, 130, 129, 128, 98 ppm, with an anticipated error of around 2ppm). How many matches do you get?
#Add then the <sup>1</sup>H shifts (8.1,7.5,5.1,4.7 and there is an additional broad multiplet across the range 7.3-7.7 which is not entered) and see if the number of possibilities reduces.
#Finally, enter the one characteristic IR vibration (1733 cm<sup>-1</sup>). Do you now get a unique answer? Record any structure(s) you may get at this stage for future reference.
#Try changing the error limits for any of these properties. Thus reduce the NMR limit from 2.0 to 1.5 to 1.0ppm, or the IR limit to 5 or even 1 cm<sup>-1</sup> (in future laboratory courses, you will learn how the way the instrument works determines at least in part the accuracy with which these spectroscopic properties can be measured).

== Reagent/Product searches for laboratory preparations ==

[[image:1-4.jpg|right|250px|Molecules 1-4]]The theme of this section is going to be the following four molecules, which you will in fact encounter in a laboratory course later in the year. You will search for known properties of these molecules, for comparison with those you might measure in the lab, or which may provide useful discussion material for your laboratory reports. Your first task is to generate a so-called SMILES descriptor of the molecule. This is done most simply by drawing the molecule in ChemDraw and using the '''Edit as/Copy''' menu produce the SMILES or InChI-key string onto the clipboard. Here are three SMILES strings and one InCHI-key string. Can you match them up to the structures shown on the right?
# <nowiki>C=CC1=CC=C(C(O[H])=O)C=C1</nowiki>
# <nowiki>S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S</nowiki>
# <nowiki>O[C@H]1[C@H](OCC)CCCC1</nowiki>
# <nowiki>VSIKJPJINIDELZ-UHFFFAOYSA-N</nowiki>
*Search the [http://www.chemspider.com/ ChemSpider] database using a SMILES or InChI-key string as above. What sort of information is revealed about the compound?
*Try reversing the search terms above (instead of SMILEs, try generating an InChI key, or vice versa).
*Try next an advanced search from the same [http://www.chemspider.com/FullSearch.aspx database]. Explore for yourself how to enter the SMILES string and perform the search.
*Search the [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] using a SMILES string. Select the '''substructure/superstructure''' or the '''Identity/Similarity''' option, and then the '''CID, SMILES, InChI''' tab, and past in one of the strings above. Try both '''80% similar''' and '''identical''' if using the Similarity option). Again, explore the properties associated with each hit.
**You might encounter '''artefacts'''. Thus with '''S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S''', something slightly odd happens?
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of Drugs, inorganic and organometallic and natural products which might prove useful to you for laboratories.
* The series [http://www.orgsyn.org/ Organic syntheses] contains tried and tested procedures for the synthesis of many chemicals. However, it is quite limited, and you would be lucky to find more obscure compounds listed here.
=== Sigma-Aldrich Catalogues and MSDS (Safety) information ===

If you know (or suspect you know) what the identity of the molecules are that you will be handling in the laboratory, the first task is to find out any known safety information.
The [http://www.sigmaaldrich.com/catalog/search/AdvancedSearchPage Aldrich] catalogues can be searched for compounds and their associated MSDS safety sheets. This is useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms. If you were able to obtain a name (see previous section), see if you can now find any information on it from the Aldrich catalogue.

=== Reaxys ===
Connect to [http://www.reaxys.com/ Reaxys] as before, but now we are going to do a structure based search, using as examples structures '''1-4''' above. If you click in the frame labelled ''Double click this frame and draw structure query'' you will get a default structure editor called ChemAxon MarvinSketch. It is a little different from Chemdraw, but should not take too much time to master.
# Using the structure editor, draw one of the four molecules 1-4 and invoke '''search'''.
# If you think you know the name of your query, type that instead in the ''Generate structure from name'' box (e.g. '''Taxol''', which as you have seen earlier is a challenge to draw!). You can also paste a SMILES or InChI key into this box (try any of the four above).
# Try hitting '''Synthesize''', but expect to be overwhelmed by the number of hits!

=== Dictionary of organic compounds ===
An alternative database which works in this way is the [http://doc.chemnetbase.com/ Dictionary of organic compounds].


== Extra material for Future Reference - Converting a 2D structure definition to a 3D set of coordinates ==

The preceding searches were all effectively conducted on two-dimensional molecules, where we only needed to know how the atoms were connected (in effect the Lewis valence structure). As a prelude to moving into three dimensions, we will illustrate how a 2D search can be used to generate a 3D structure.

* You can use the on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina service to convert a (1D) SMILES string to 3D molecular coordinates].
*# Under options, paste the SMILES string, enter a name, and select 3D structure viewer automatically loaded.
*# Click on Generate 3D structure. A window appears, and after about 20-30 seconds, a structure does as well. At the bottom, click on "Click to download this structure in PDB file format", whereupon a full window diagram appears. Save the molecule as above.

= 3D structure searching of the Cambridge Crystallographic database =

Our final search type is now of a database which stores '''three-dimensional''' information about molecules. This is where you can infer all sorts of interesting properties about the bonding, the properties and the potential reactivities of molecules. You will be searching the '''Cambridge Crystal Structure Database'''. There are three entry points for this; one local, one via the Web and one via the national '''chemical database service'''.

=== Local invocation of the Cambridge Crystal Structure Database ===
The local based search described below is feature complete and fast. You may also want to try out the [http://webcsd.ccdc.cam.ac.uk/ WebCSD service], which needs only a web-browser.
#[[Image:MgBr2.jpg|right|120px]][[Image:ti1.jpg|right|100px]][[Image:PtCl.jpg|right|100px]][[image:1-4.jpg|right|250px|Molecules 1-4]]Select '''Conquest''' from the '''Start/Programs''' menu. You will have to reply:
##'''yes''' to the question about certificates,
##enter first your username, then
##your password at the two prompts (both of which appear to ask for a password!).
##Next, '''accept''' the license agreement and
##'''accept''' the suggested location for storing the directory.
##Enter the Site No. as '''183''' and the confirm code as '''8FDCE4''' (2013 release)
##Click '''register online'''.
##These prompts are a one-off, and you will not need to do these steps again.
#In the {{Pdf|FoundationTutorialproblems09.pdf|foundation tutorial problems}}, question 2 asks you to arrow-push the reaction Et<sub>2</sub>O + MgBr<sub>2</sub> → Et<sub>2</sub>O-MgBr<sub>2</sub>. Here we will pose the question: what is the 3D geometry of the product of this reaction? You will search for it using Conquest. Does the result surprise you? (Hint: TOQKIT)
#Nucleophilic addition to an amide is the prototype of how peptides, proteins and enzymes are broken down in metabolic processes (or using e.g. biological washing powders). The mechanism involves a species known as a '''tetrahedral intermediate''' (right), which is normally considered so unstable that it is rarely detected during the reaction. Nevertheless, can you find any examples of such species in the Cambridge database?
#Cis-Platin is a well known anti-cancer drug. The ''active ingredient'' is the initial hydrolysis product, shown on the right. Can you find any examples of this '''active intermediate''' in the database which contain this sub-structure? What happens if you change the Pt to a '''wild-card''' indicating the central metal could be any of the group known as '''8Z''' (from the '''more''' button of the editor, select '''other elements''' and from there click on the orange box labelled '''8Z''').
#Are there any other '''reactive intermediates''' you might have identified from your arrow-pushing workshop which you might search for?
#When you have finished the above examples, try entering one of the four lab-course molecules shown to the left, exactly as drawn above. For '''3''' specifically, if you draw explicit hydrogens attached to the ''vinyl'' group at the top of the molecule and repeat the search, what difference is there?
#*How many hits do you get?
#*Note the 6-8 letter identifier for the structure you are interested in (for example, for molecule '''3''' above, it should be XAYFEI, XAYFEI01 and XAYFEI02).
#*Save the 3D coordinates in PDB or CIF format via '''File/Export''', decide how you want to select entries, specify one file per entry and '''SAVE'''. Inspect the structure by double clicking the file created, to be found on drive '''L:'''
#You '''may''' now have two versions of any of these four molecules; one a direct experimental structure, and one assembled by the [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] program. How do these differ? Concentrate in particular on compounds '''1''' and '''2''' above right!
#Later on in your course, you may use such coordinates to create an entry in a Wiki page, much like that rotating below.

===An advanced 3D Search. ===
Try the following. The objective will be to find any short interactions between the H of an OH group and the centroid of a phenyl ring as the electron donor (a very unusual type of π-facial hydrogen bond). Proceed as follows:
{|
|
# Open Conquest and invoke the '''Build Queries/Draw''' option
# Deposit a benzene ring from the template which should appear on the left
# Click on '''ADD 3D''', select all the six carbon atoms in turn (they will go green) and define a centroid. A defined object labelled '''CENT1''' now shows. Press Done.
# Back in '''Draw''' mode, select a H and deposit it as an isolated atom. Then select O and draw a bond from it to the H to get an OH. In this system, any undefined valence is '''wild''', ie any group can be attached to the O of the OH.
# In '''ADD 3D''' mode again, click first on the '''H''' of the OH group, then on '''CENT1''' in the list of defined objects. A green line connecting the two appears. When a '''Valid parameter''' entry named '''Distance''' appears, click on '''Define'''.
# Select '''Intramolecular''' from the '''Choose distance type''' menu, OK, then '''Options''', enter 2.0 - 2.4 as the range of distances and '''Separated by 5 - 999''' bonds. Hit '''OK''' and then '''Done'''. Your search query is summarized in a cyan box at the top right of the draw window.
# Select '''Search''', tick the 3D Coordinates determined box and '''Start Search'''. This search should proceed at the rate of about 1% per second. You should get 20 hits.
# View entries via '''3D Visualiser'''. Note the so-called '''REFCODES'''. Note '''[[Coursework#Enantiomers_vs_Diastereomers_Part_1:_Butanes_and__Helicenes.|CIYSIM]]''' in particular!
#A right-mouse click in the blue window of the 3D Visualiser will enable you to set '''spacefill''' mode, and to inspect whether any two atom spheres inter-penetrate each-other indicating an attractive interaction between them.
# Save the coordinates of any selected hits via '''File/Export''', Select PDB or CIF as the format, all selected entries, one file per entry and '''SAVE'''.
# The files will appear on your L: drive. Double click to open up the WebLab Viewer Pro or Mercury program, and resave them if you wish as an MDL Molfile rather than PDB.
# If you want to explore further, define an NH bond rather an OH bond (you might need to increase the distance range to eg 2.0 - 2.5).
# Try this with centroids to other π-electron rich systems, such as an alkyne, alkene, or other rings such as cyclopentadienyl, etc.
#Go to your network drive N: or L: (i.e. username on neon.ch.ic.ac.uk) and double click any .PDB or .CFIF or .MOL files to view the molecule again.
# Or, instead of H-O, just put e.g. Na (metal arene interactions are hugely important biologically). You may need to define a rather longer distance range. Experiment by trying various sets of values.
|<jmol><jmolApplet><title>CIYSIM</title><color>white</color>
<size>300</size><script>zoom 150;spin 3;</script>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents>
</jmolApplet></jmol>
|}

=== The National Chemical Database Service ===

The '''CDS''' is a national service (located as it happens in Daresbury, near Warrington) which offers a range of database services to the UK community. To access this service, follow the [http://cds.dl.ac.uk/cgi-bin/reg/undergrad?sites=Select+Site&SITE=imperial-cds0091 instructions] here (this is necessary to ensure UK usage only and to monitor that usage as part of justifying a national resource). You will be sent a CDS registration account and password by email. You can then use this account in two ways
#Invoke '''ConquestD''' (rather than Conquest) from the Windows start menu and proceed as above, but supply your new CDS account instead of your Imperial account.
#Invoke the CDS portal [https://cds.dl.ac.uk/ here] using your CDS account to log in. It offers many alternative services (including searches for spectral data) as well as a simplified crystal search. Explore in your own time!


=== Further tutorials based on 3D crystal structures ===

These can be viewed [http://www.ccdc.cam.ac.uk/free_services/teaching/modules/teaching_webcsd/toc.html here].

=Continuation of CIT skills=
The skills developed during these workshops will be in almost constant use throughout your course; you are encouraged to keep this up to date and to make use of these skills while writing lab reports and other coursework assignments. As with anything in the digital world, progress is being made all the time with new search engines, new search algorithms, new software. This also means that other searches and software are retired to make way for, newer more efficient tools. This wiki will be a long-term reference which you can refer to and even update, and you are urged to keep it as a bookmark.

== Software for your own computer ==

*The department has a Site License for a program system called [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 ChemBio3D] (which includes ChemDraw for both Windows and Mac), the terms of which allow individual undergraduates to acquire a copy of the program and to install it on their personal computer. The license is an annual one.
*[http://www.straightrunning.com/XmingNotes/ Xming] for accessing the Conquest data base.
*Programs such as Microsoft Office can be licensed via [http://www.microsoft.com/student/discounts/theultimatesteal-uk/default.aspx an academic license for £69.99].
*[https://directory.adeptscience.co.uk/products/search/1/1/474/cat474.html EndNote student edition] retails for £85.00. Alternatively, try RefWorks (usually $100/year but '''free''' for Imperial students through [http://www3.imperial.ac.uk/library/digitallibrary/athensandukfed AthensDA]) It is a slightly simpler web-based program. A comparison between both can be found [http://library.princeton.edu/help/comparison.php here] (Princeton University). You should note that the WOS system supports Endnote directly, but requires a more complicated procedure for using RefWorks or Mendeley.
*A further list of software may be found [[It:software-2011|here]], including other programs you can install on your personal computer which you may find useful.
----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:coursework-2011

2014-10-11T13:26:26Z

Amckinle: /* Converting a 2D structure definition to a 3D set of coordinates */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Overall Objectives of CIT workshops=

The Computer lab (formally booked for your group, A1, A2, B1, B2, C1, C2) is for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library. All "Chemistry Software" should be available also in the Library to your user account. If you find that something is not immediately available, please do get in touch with the ICT Helpdesk. During the lab time allocated for the IT course, you will be expected to achieve the following objectives:

# Accessing course and laboratory notes and using scientific journals to support lectures
# Using '''Word''' in combination with the '''EndNote''' bibliographic database and '''ChemDraw''' to write laboratory reports and essays
# Learn to use various bibliographic chemistry search systems
# Learn to conduct molecular structure-based search systems
# Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

=Self-Study - Software Familiarity=

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section ''' <u>before you come to the workshop sessions</u>''':

==Before you come to the workshop sessions...==

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.
* Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your [https://exchange.imperial.ac.uk campus email account] through the [https://exchange.imperial.ac.uk web interface].
* Using the '''FireFox''' web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: <tt>http://www.ch.ic.ac.uk/wiki/</tt>). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
* You will be using Firefox to browse the pages of a [http://en.wikipedia.org/wiki/Wiki Wiki]. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will '''replace''' the instruction window. So, get used to clicking on the link with the '''right mouse button''' rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

===Computer, Browser and Wordprocessor familiarity===
*[[Image:login_window.jpg|right|thumb|login window]]Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
*[[Image:home.jpg|left|thumb|Document home]]Perhaps the single most confusing aspect for most people is what the ''Home'' icon (left) means. So let's sort this out immediately. You are working in an ''enterprise'' environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the ''Home'' icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "'''My Documents'''", which the operating system can sometimes display instead of Home.
*[[Image:o2007.jpg|thumb|right|Office 2007]][[Image:subsuper.jpg|right|thumb|Subs and Superscripts]][[Image:o2007b.jpg|thumb|left||EndNote tab]]Start Microsoft '''Office 2007''' (we will assume you still have FireFox running). The basic ('''Home''') Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a '''red''' circle. Copy/paste operations are invoked using the icon encircled in '''purple'''. Other common operations are found to the right of these two in the taskbar, including the chemically useful '''subscript''' and '''superscripts''' (right diagram). Note also the the default document saves invokes the new '''.docx''' format, which is an XML-based type with much interesting ''informatics'' potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older '''.doc''' format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
*[[Image:o2007a.jpg|left|thumb|Insert tab]]There are two other task-bars you will find useful. the '''Insert''' bar inserts a variety of other content, including pictures, tables and the like. The '''EndNote''' tab invokes a citation and reference manager, which you will use as described below ('''Important'''<nowiki>: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).</nowiki>
* Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
*[[Image:FireFox_paste.jpg|thumb|right|Save Firefox image]] '''Images''' are special when it comes to copying. Proceed as follows:
*# Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
*# If one of the options is '''Copy image''', select it. Not all browsers support this, in which case instead invoke ''save this image as'' and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
*# With an Office Word window open, paste the image (if you copied it) or '''Insert/Picture/from file''' (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
*# Do remember how to change between windows (the technical term is that the active window is said to be ''on focus'') by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
{|
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>150</size>
<script>zoom 200; cpk -20;move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|Not everything is always "copyable". Some apparent images are in fact produced by an "applet" [http://wiki.jmol.org:81/index.php/MediaWiki embedded] in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
|}
* Practice naming and saving document files to your ''Home'' (Drive H: on Windows) or a removable medium such as a FlashDrive.
* Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding '''content''' of files may be very slow. Windows Desktop Search is '''NOT''' activated on College systems.
* [http://www.ch.ic.ac.uk/local/email/ Practice setting up E-mail], sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.
=== Configuring storage for your document libraries ===

Programs such as '''EndNote''', '''Mendeley''', '''iTunes''' store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

==== EndNote ====

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => '''userid(\\icfs18.cc.ic.ac.uk) (M:)''' Thereafter you can set it to open this library when the program starts.

==== Mendeley ====

Open the program and invoke '''Tools/Options/File Organiser''' and select drive M: for the library.

==== iTunes ====

Use '''Edit/Preferences/Advanced''' and set the iTunes Media folder location to M: (or other if M: is already full). Also tick '''Copy files to iTunes Media folder when adding to library'''.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

=Start of Demonstration material=
The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are '''positively encouraged to continue working through the material''' at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

== Combined Word/ EndNote Familiarity ==
This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about '''''penicillin''''' and its '''''conversion to cephalosporin'''''.

=== A Web of Knowledge Search ===
#[[Image:Endnote1e.jpg|thumb|left|WoK search]] From the [http://wok.mimas.ac.uk/ Web-of-Knowledge] link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
#'''Connect to the ISI Web of Knowledge Service''' and then select the
#''Web of Science'' tab from along the top and finally from the citation databases, narrow it down to the
# Science Citation Index expanded
#Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the '''Author''' box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the '''advanced''' search such as <tt>au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)</tt>
#When you have some hits, either tick individual citations, or '''All records on page''' or a span of records.
#Next, make sure you have Microsoft Word running, and from the '''EndNote X4''' taskbar of Word, click on '''Go to EndNote'''. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
#[[Image:Endnote1b.jpg|right|saving a list for Endnote]]Return to the Browser window displaying WOS and click on '''Save to EndNote'''. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
#If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name '''uml_view.cgi''' on the desktop) which you can open directly with EndNote (see below).

=== Inserting the citations just found into Word using EndNote===
#[[Image:Endnote1a.jpg|thumb|right|Starting EndNote]]Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
#Via '''Edit/preferences/Libraries''' select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
#[[Image:endnote-style.jpg|thumb|left|Checking the style setting]]From '''Edit/Output style/Open Style Mananger''', select the tick-box against a template known as '''Royal Society of Chemistry''' (you may have to use '''Find by/Chemistry''' to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
#If you are importing a citation list rather than relying on the automated procedure, then from '''File/Import''' of EndNote define the Import Option '''ISI-CE''' in the pull down menu, or '''Other Filters/SciFinder (CAS)''' if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
#[[Image:Endnote1c.jpg|thumb|right|]][[Image:Endnote1d.jpg|thumb|left|Word with citations showing|]]Go back to Word 2007, and write some text. At an appropriate point, from the '''Endnote X4 taskbar tab''', press '''Go to EndNote''' when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the '''Insert citation''' tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
#Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

==== Mendeley and other alternatives to EndNote ====
[[image:refworks.jpg|thumb|right]]A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include [https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks] (for which the client software can be downloaded without cost) and an innovative program called [http://www.mendeley.com/ Mendeley] which is available on the computers in the department.

# If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

== Chemdraw Familiarity ==
*[[Image:unknown1.jpg|left|thumb|Click to expand image]] [[Image:taxolhsr.jpg|Taxol|right|300px]] '''Starting and using ChemDraw.''' Start Chemdraw icon from the '''Start/Programs menu'''. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
*Check that you have drawn it correctly by calculating its formula. To do this, Go to '''View/Show analysis''' window and record what you see (it should give you C<sub>47</sub>H<sub>51</sub>NO<sub>14</sub>. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. '''What is the difference in behaviour?'''

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. '''Can you identify what it is called?'''

== Lecture Support: Journal Familiarity ==

You can go visit the databases of some major chemistry publishers, and track down any articles that members of this department (or other departments or your favourite Nobel prize lautreates) may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following:
* [http://pubs.acs.org/search/advanced The American Chemical Society] (where you can subscribe to an RSS feed of the search, which means you will be notified of new items)
* [http://www.rsc.org/Publishing/Journals/cc/index.asp The Royal Society of Chemistry] and their premier journal ''Chemical communications''
* [http://www.nature.com/search/adv_search?sp-a=sp1001702d&sp-x-1=ujournal&sp-q-1=Nature%20Chemistry Nature Chemistry] advanced search.
* [http://www3.interscience.wiley.com/journal/26737/home Wiley Interscience] and their flagship chemistry journal ''Angew. Chemie.''
* [http://www.sciencedirect.com Science Direct]

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

== Lecture Support: Named chemicals ==

# To apply the above skills by using [http://wok.mimas.ac.uk/ WOS] to perform a comprehensive literature search on the '''molecule''' ''Penicillin'', a '''reaction''' (''its conversion to Cephalosporin''), its ''properties'', both physical (spectroscopic) and biological. Thus, type ''penicillin and cephalosporin'' into the '''Topic''' box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the '''Advanced Search''' option.
#* '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (136)
#* '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2629)
##Or, try the drug '''Temozolomide''', currently very much in the [http://news.bbc.co.uk/1/hi/england/west_midlands/7675014.stm news]
##Tasimelteon ([http://news.bbc.co.uk/1/hi/health/7760105.stm time bending drug for jet lag]) or
##[http://news.bbc.co.uk/1/hi/health/8237530.stm Sulforaphane], which occurs in broccoli and cauliflower and protects against heart attacks.
#Compare the results of one of these searches with less specialised search engines such as
#*[http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar],
#*[http://www.scirus.com/srsapp/advanced/index.jsp SciRus],
#*[http://www.bing.com/?scope=web&mkt=en-GB Microsoft Bing],
#*[http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha].

=== Lecture Support: A SciFinder search instead ===
*The [https://scifinder.cas.org/ Scifinder Scholar] system is available for general and student use.
** You cannot use your College login for access, but must request your own login to be created.
*** [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar Go here to register]. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. ''other field''.
** Completing the registration will result in an email being sent to the email address you provide with activation instructions.
*** Once you have obtained an ID, at the [https://origin-scifinder.cas.org SciFinder site], click on '''Explore References''' and in the '''Research topic box''' enter "Conversion of penicillin to cephalosporin".
** You will receive a request to accept an application digital signature at this stage, which you should accept.
You should get ~9 references for an exact match. This interface is supposed to use a more ''natural language'' for its search queries (and it does not employ Booleans).
** Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the '''Export''' link near the top (next to print). From the dialog, set the '''File Type''' to '''Tagged Format'''.
*** You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your '''download''' location. You can then import this into EndNote using the '''SciFinder (CAS)''' import option.
**An alternative search might be the phrase '''arrow pushing formalism''' (can you learn about this topic from the results found for this search?). A synonym might be '''curly arrow formalism'''. Does this find the same references, or a different set?
** You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to '''My connections''' and invite the group, then add comments to relevant references.
** SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

=Laboratory Support=
Here you will find out how to search for safety information about molecules, and then for their properties and reactions. There are two kinds of search for molecules you will have to make during lab courses.
# Where you have an unknown compound whose properties you have measured and you want to know if any known compound matches those properties.
# Where you (think you) know what the structure of your compound is, and you want to know if there are any other reports of this same compound (and whether the properties other have measured match your own).

== A search for known physical properties using Reaxys ==
[[Image:Reaxys1.jpg|right|thumb|]]We will start with two examples of the first category and then move on to the rather more common second category.

*Connect to the [http://www.reaxys.com/ Reaxys] system. You can carry out all the required course work as an ''anonymous user'', but you will not be able to change/save any settings etc in this mode (such as e.g. changing the default structure editor to ChemDraw).
** If you do choose to register at this point, be aware that if you lose/forget your password, you will need to contact Reaxys and not local Imperial College support.
*Select ''substances and Properties''
**In the ''Properties (Advanced)'' box, enter the following, followed by '''Search'''.
**'''MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200'''
This means in effect, show me ANY molecule which melts at a certain temperature range (determined using a melting point apparatus), which has a given molecular formula (determined using mass spectrometry) and an optical rotatory power between certain values (determined using a polarimeter). For this example you should get exactly 1 hit, which should be to a patent. Explore the options at this point, including viewing the original source of the data ( a patent in this case).
* There are about 500 different properties in total which you could specify in this manner. To explore them, click on ''Show Fields and Operators''. This type of technique is useful for identifying an '''unknown''' compound purely from its physical properties (Forensic science, etc).
** Note that some features do not always produce the expected result. For example, the icon labelled with the arrow (right) pulls down various options, one of which is ''copy structure to clipboard''. The clipboard contents however are '''not''' recognised by eg Chemdraw, Word etc.

== A search for known spectroscopic properties ==

[[image:spectra.jpg|240px|right]]It is routine when a compound is first made to record its spectroscopic properties. This would include the characteristic infra-red frequencies, and the <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts. These values are shown for an unknown compound. Your task is to use the [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] to try to identify what the compound is (you could of course also do this entirely logically using just your brain).
#Try first entering only the <sup>13</sup>C NMR chemical shifts (163, 141, 133, 130, 129, 128, 98 ppm, with an anticipated error of around 2ppm). How many matches do you get?
#Add then the <sup>1</sup>H shifts (8.1,7.5,5.1,4.7 and there is an additional broad multiplet across the range 7.3-7.7 which is not entered) and see if the number of possibilities reduces.
#Finally, enter the one characteristic IR vibration (1733 cm<sup>-1</sup>). Do you now get a unique answer? Record any structure(s) you may get at this stage for future reference.
#Try changing the error limits for any of these properties. Thus reduce the NMR limit from 2.0 to 1.5 to 1.0ppm, or the IR limit to 5 or even 1 cm<sup>-1</sup> (in future laboratory courses, you will learn how the way the instrument works determines at least in part the accuracy with which these spectroscopic properties can be measured).

== Reagent/Product searches for laboratory preparations ==

[[image:1-4.jpg|right|250px|Molecules 1-4]]The theme of this section is going to be the following four molecules, which you will in fact encounter in a laboratory course later in the year. You will search for known properties of these molecules, for comparison with those you might measure in the lab, or which may provide useful discussion material for your laboratory reports. Your first task is to generate a so-called SMILES descriptor of the molecule. This is done most simply by drawing the molecule in ChemDraw and using the '''Edit as/Copy''' menu produce the SMILES or InChI-key string onto the clipboard. Here are three SMILES strings and one InCHI-key string. Can you match them up to the structures shown on the right?
# <nowiki>C=CC1=CC=C(C(O[H])=O)C=C1</nowiki>
# <nowiki>S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S</nowiki>
# <nowiki>O[C@H]1[C@H](OCC)CCCC1</nowiki>
# <nowiki>VSIKJPJINIDELZ-UHFFFAOYSA-N</nowiki>
*Search the [http://www.chemspider.com/ ChemSpider] database using a SMILES or InChI-key string as above. What sort of information is revealed about the compound?
*Try reversing the search terms above (instead of SMILEs, try generating an InChI key, or vice versa).
*Try next an advanced search from the same [http://www.chemspider.com/FullSearch.aspx database]. Explore for yourself how to enter the SMILES string and perform the search.
*Search the [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] using a SMILES string. Select the '''substructure/superstructure''' or the '''Identity/Similarity''' option, and then the '''CID, SMILES, InChI''' tab, and past in one of the strings above. Try both '''80% similar''' and '''identical''' if using the Similarity option). Again, explore the properties associated with each hit.
**You might encounter '''artefacts'''. Thus with '''S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S''', something slightly odd happens?
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of Drugs, inorganic and organometallic and natural products which might prove useful to you for laboratories.
* The series [http://www.orgsyn.org/ Organic syntheses] contains tried and tested procedures for the synthesis of many chemicals. However, it is quite limited, and you would be lucky to find more obscure compounds listed here.
=== Sigma-Aldrich Catalogues and MSDS (Safety) information ===

If you know (or suspect you know) what the identity of the molecules are that you will be handling in the laboratory, the first task is to find out any known safety information.
The [http://www.sigmaaldrich.com/catalog/search/AdvancedSearchPage Aldrich] catalogues can be searched for compounds and their associated MSDS safety sheets. This is useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms. If you were able to obtain a name (see previous section), see if you can now find any information on it from the Aldrich catalogue.

=== Reaxys ===
Connect to [http://www.reaxys.com/ Reaxys] as before, but now we are going to do a structure based search, using as examples structures '''1-4''' above. If you click in the frame labelled ''Double click this frame and draw structure query'' you will get a default structure editor called ChemAxon MarvinSketch. It is a little different from Chemdraw, but should not take too much time to master.
# Using the structure editor, draw one of the four molecules 1-4 and invoke '''search'''.
# If you think you know the name of your query, type that instead in the ''Generate structure from name'' box (e.g. '''Taxol''', which as you have seen earlier is a challenge to draw!). You can also paste a SMILES or InChI key into this box (try any of the four above).
# Try hitting '''Synthesize''', but expect to be overwhelmed by the number of hits!

=== Dictionary of organic compounds ===
An alternative database which works in this way is the [http://doc.chemnetbase.com/ Dictionary of organic compounds].


== Extra material for Future Reference - Converting a 2D structure definition to a 3D set of coordinates ==

The preceding searches were all effectively conducted on two-dimensional molecules, where we only needed to know how the atoms were connected (in effect the Lewis valence structure). As a prelude to moving into three dimensions, we will illustrate how a 2D search can be used to generate a 3D structure.

* You can use the on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina service to convert a (1D) SMILES string to 3D molecular coordinates].
*# Under options, paste the SMILES string, enter a name, and select 3D structure viewer automatically loaded.
*# Click on Generate 3D structure. A window appears, and after about 20-30 seconds, a structure does as well. At the bottom, click on "Click to download this structure in PDB file format", whereupon a full window diagram appears. Save the molecule as above.

== 3D structure searching of the Cambridge Crystallographic database ==

Our final search type is now of a database which stores '''three-dimensional''' information about molecules. This is where you can infer all sorts of interesting properties about the bonding, the properties and the potential reactivities of molecules. You will be searching the '''Cambridge Crystal Structure Database'''. There are three entry points for this; one local, one via the Web and one via the national '''chemical database service'''.

=== Local invocation of the Cambridge Crystal Structure Database ===
The local based search described below is feature complete and fast. You may also want to try out the [http://webcsd.ccdc.cam.ac.uk/ WebCSD service], which needs only a web-browser.
#[[Image:MgBr2.jpg|right|120px]][[Image:ti1.jpg|right|100px]][[Image:PtCl.jpg|right|100px]][[image:1-4.jpg|right|250px|Molecules 1-4]]Select '''Conquest''' from the '''Start/Programs''' menu. You will have to reply:
##'''yes''' to the question about certificates,
##enter first your username, then
##your password at the two prompts (both of which appear to ask for a password!).
##Next, '''accept''' the license agreement and
##'''accept''' the suggested location for storing the directory.
##Enter the Site No. as '''183''' and the confirm code as '''8FDCE4''' (2013 release)
##Click '''register online'''.
##These prompts are a one-off, and you will not need to do these steps again.
#In the {{Pdf|FoundationTutorialproblems09.pdf|foundation tutorial problems}}, question 2 asks you to arrow-push the reaction Et<sub>2</sub>O + MgBr<sub>2</sub> → Et<sub>2</sub>O-MgBr<sub>2</sub>. Here we will pose the question: what is the 3D geometry of the product of this reaction? You will search for it using Conquest. Does the result surprise you? (Hint: TOQKIT)
#Nucleophilic addition to an amide is the prototype of how peptides, proteins and enzymes are broken down in metabolic processes (or using e.g. biological washing powders). The mechanism involves a species known as a '''tetrahedral intermediate''' (right), which is normally considered so unstable that it is rarely detected during the reaction. Nevertheless, can you find any examples of such species in the Cambridge database?
#Cis-Platin is a well known anti-cancer drug. The ''active ingredient'' is the initial hydrolysis product, shown on the right. Can you find any examples of this '''active intermediate''' in the database which contain this sub-structure? What happens if you change the Pt to a '''wild-card''' indicating the central metal could be any of the group known as '''8Z''' (from the '''more''' button of the editor, select '''other elements''' and from there click on the orange box labelled '''8Z''').
#Are there any other '''reactive intermediates''' you might have identified from your arrow-pushing workshop which you might search for?
#When you have finished the above examples, try entering one of the four lab-course molecules shown to the left, exactly as drawn above. For '''3''' specifically, if you draw explicit hydrogens attached to the ''vinyl'' group at the top of the molecule and repeat the search, what difference is there?
#*How many hits do you get?
#*Note the 6-8 letter identifier for the structure you are interested in (for example, for molecule '''3''' above, it should be XAYFEI, XAYFEI01 and XAYFEI02).
#*Save the 3D coordinates in PDB or CIF format via '''File/Export''', decide how you want to select entries, specify one file per entry and '''SAVE'''. Inspect the structure by double clicking the file created, to be found on drive '''L:'''
#You '''may''' now have two versions of any of these four molecules; one a direct experimental structure, and one assembled by the [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] program. How do these differ? Concentrate in particular on compounds '''1''' and '''2''' above right!
#Later on in your course, you may use such coordinates to create an entry in a Wiki page, much like that rotating below.

===An advanced 3D Search. ===
Try the following. The objective will be to find any short interactions between the H of an OH group and the centroid of a phenyl ring as the electron donor (a very unusual type of π-facial hydrogen bond). Proceed as follows:
{|
|
# Open Conquest and invoke the '''Build Queries/Draw''' option
# Deposit a benzene ring from the template which should appear on the left
# Click on '''ADD 3D''', select all the six carbon atoms in turn (they will go green) and define a centroid. A defined object labelled '''CENT1''' now shows. Press Done.
# Back in '''Draw''' mode, select a H and deposit it as an isolated atom. Then select O and draw a bond from it to the H to get an OH. In this system, any undefined valence is '''wild''', ie any group can be attached to the O of the OH.
# In '''ADD 3D''' mode again, click first on the '''H''' of the OH group, then on '''CENT1''' in the list of defined objects. A green line connecting the two appears. When a '''Valid parameter''' entry named '''Distance''' appears, click on '''Define'''.
# Select '''Intramolecular''' from the '''Choose distance type''' menu, OK, then '''Options''', enter 2.0 - 2.4 as the range of distances and '''Separated by 5 - 999''' bonds. Hit '''OK''' and then '''Done'''. Your search query is summarized in a cyan box at the top right of the draw window.
# Select '''Search''', tick the 3D Coordinates determined box and '''Start Search'''. This search should proceed at the rate of about 1% per second. You should get 20 hits.
# View entries via '''3D Visualiser'''. Note the so-called '''REFCODES'''. Note '''[[Coursework#Enantiomers_vs_Diastereomers_Part_1:_Butanes_and__Helicenes.|CIYSIM]]''' in particular!
#A right-mouse click in the blue window of the 3D Visualiser will enable you to set '''spacefill''' mode, and to inspect whether any two atom spheres inter-penetrate each-other indicating an attractive interaction between them.
# Save the coordinates of any selected hits via '''File/Export''', Select PDB or CIF as the format, all selected entries, one file per entry and '''SAVE'''.
# The files will appear on your L: drive. Double click to open up the WebLab Viewer Pro or Mercury program, and resave them if you wish as an MDL Molfile rather than PDB.
# If you want to explore further, define an NH bond rather an OH bond (you might need to increase the distance range to eg 2.0 - 2.5).
# Try this with centroids to other π-electron rich systems, such as an alkyne, alkene, or other rings such as cyclopentadienyl, etc.
#Go to your network drive N: or L: (i.e. username on neon.ch.ic.ac.uk) and double click any .PDB or .CFIF or .MOL files to view the molecule again.
# Or, instead of H-O, just put e.g. Na (metal arene interactions are hugely important biologically). You may need to define a rather longer distance range. Experiment by trying various sets of values.
|<jmol><jmolApplet><title>CIYSIM</title><color>white</color>
<size>300</size><script>zoom 150;spin 3;</script>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents>
</jmolApplet></jmol>
|}

=== The National Chemical Database Service ===

The '''CDS''' is a national service (located as it happens in Daresbury, near Warrington) which offers a range of database services to the UK community. To access this service, follow the [http://cds.dl.ac.uk/cgi-bin/reg/undergrad?sites=Select+Site&SITE=imperial-cds0091 instructions] here (this is necessary to ensure UK usage only and to monitor that usage as part of justifying a national resource). You will be sent a CDS registration account and password by email. You can then use this account in two ways
#Invoke '''ConquestD''' (rather than Conquest) from the Windows start menu and proceed as above, but supply your new CDS account instead of your Imperial account.
#Invoke the CDS portal [https://cds.dl.ac.uk/ here] using your CDS account to log in. It offers many alternative services (including searches for spectral data) as well as a simplified crystal search. Explore in your own time!


=== Further tutorials based on 3D crystal structures ===

These can be viewed [http://www.ccdc.cam.ac.uk/free_services/teaching/modules/teaching_webcsd/toc.html here].

=Continuation of CIT skills=
The skills developed during these workshops will be in almost constant use throughout your course; you are encouraged to keep this up to date and to make use of these skills while writing lab reports and other coursework assignments. As with anything in the digital world, progress is being made all the time with new search engines, new search algorithms, new software. This also means that other searches and software are retired to make way for, newer more efficient tools. This wiki will be a long-term reference which you can refer to and even update, and you are urged to keep it as a bookmark.

== Software for your own computer ==

*The department has a Site License for a program system called [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 ChemBio3D] (which includes ChemDraw for both Windows and Mac), the terms of which allow individual undergraduates to acquire a copy of the program and to install it on their personal computer. The license is an annual one.
*[http://www.straightrunning.com/XmingNotes/ Xming] for accessing the Conquest data base.
*Programs such as Microsoft Office can be licensed via [http://www.microsoft.com/student/discounts/theultimatesteal-uk/default.aspx an academic license for £69.99].
*[https://directory.adeptscience.co.uk/products/search/1/1/474/cat474.html EndNote student edition] retails for £85.00. Alternatively, try RefWorks (usually $100/year but '''free''' for Imperial students through [http://www3.imperial.ac.uk/library/digitallibrary/athensandukfed AthensDA]) It is a slightly simpler web-based program. A comparison between both can be found [http://library.princeton.edu/help/comparison.php here] (Princeton University). You should note that the WOS system supports Endnote directly, but requires a more complicated procedure for using RefWorks or Mendeley.
*A further list of software may be found [[It:software-2011|here]], including other programs you can install on your personal computer which you may find useful.
----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:coursework-2011

2014-10-11T13:25:10Z

Amckinle: /* Start of Workshop material */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Overall Objectives of CIT workshops=

The Computer lab (formally booked for your group, A1, A2, B1, B2, C1, C2) is for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library. All "Chemistry Software" should be available also in the Library to your user account. If you find that something is not immediately available, please do get in touch with the ICT Helpdesk. During the lab time allocated for the IT course, you will be expected to achieve the following objectives:

# Accessing course and laboratory notes and using scientific journals to support lectures
# Using '''Word''' in combination with the '''EndNote''' bibliographic database and '''ChemDraw''' to write laboratory reports and essays
# Learn to use various bibliographic chemistry search systems
# Learn to conduct molecular structure-based search systems
# Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

=Self-Study - Software Familiarity=

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section ''' <u>before you come to the workshop sessions</u>''':

==Before you come to the workshop sessions...==

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.
* Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your [https://exchange.imperial.ac.uk campus email account] through the [https://exchange.imperial.ac.uk web interface].
* Using the '''FireFox''' web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: <tt>http://www.ch.ic.ac.uk/wiki/</tt>). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
* You will be using Firefox to browse the pages of a [http://en.wikipedia.org/wiki/Wiki Wiki]. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will '''replace''' the instruction window. So, get used to clicking on the link with the '''right mouse button''' rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

===Computer, Browser and Wordprocessor familiarity===
*[[Image:login_window.jpg|right|thumb|login window]]Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
*[[Image:home.jpg|left|thumb|Document home]]Perhaps the single most confusing aspect for most people is what the ''Home'' icon (left) means. So let's sort this out immediately. You are working in an ''enterprise'' environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the ''Home'' icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "'''My Documents'''", which the operating system can sometimes display instead of Home.
*[[Image:o2007.jpg|thumb|right|Office 2007]][[Image:subsuper.jpg|right|thumb|Subs and Superscripts]][[Image:o2007b.jpg|thumb|left||EndNote tab]]Start Microsoft '''Office 2007''' (we will assume you still have FireFox running). The basic ('''Home''') Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a '''red''' circle. Copy/paste operations are invoked using the icon encircled in '''purple'''. Other common operations are found to the right of these two in the taskbar, including the chemically useful '''subscript''' and '''superscripts''' (right diagram). Note also the the default document saves invokes the new '''.docx''' format, which is an XML-based type with much interesting ''informatics'' potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older '''.doc''' format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
*[[Image:o2007a.jpg|left|thumb|Insert tab]]There are two other task-bars you will find useful. the '''Insert''' bar inserts a variety of other content, including pictures, tables and the like. The '''EndNote''' tab invokes a citation and reference manager, which you will use as described below ('''Important'''<nowiki>: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).</nowiki>
* Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
*[[Image:FireFox_paste.jpg|thumb|right|Save Firefox image]] '''Images''' are special when it comes to copying. Proceed as follows:
*# Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
*# If one of the options is '''Copy image''', select it. Not all browsers support this, in which case instead invoke ''save this image as'' and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
*# With an Office Word window open, paste the image (if you copied it) or '''Insert/Picture/from file''' (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
*# Do remember how to change between windows (the technical term is that the active window is said to be ''on focus'') by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
{|
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>150</size>
<script>zoom 200; cpk -20;move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|Not everything is always "copyable". Some apparent images are in fact produced by an "applet" [http://wiki.jmol.org:81/index.php/MediaWiki embedded] in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
|}
* Practice naming and saving document files to your ''Home'' (Drive H: on Windows) or a removable medium such as a FlashDrive.
* Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding '''content''' of files may be very slow. Windows Desktop Search is '''NOT''' activated on College systems.
* [http://www.ch.ic.ac.uk/local/email/ Practice setting up E-mail], sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.
=== Configuring storage for your document libraries ===

Programs such as '''EndNote''', '''Mendeley''', '''iTunes''' store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

==== EndNote ====

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => '''userid(\\icfs18.cc.ic.ac.uk) (M:)''' Thereafter you can set it to open this library when the program starts.

==== Mendeley ====

Open the program and invoke '''Tools/Options/File Organiser''' and select drive M: for the library.

==== iTunes ====

Use '''Edit/Preferences/Advanced''' and set the iTunes Media folder location to M: (or other if M: is already full). Also tick '''Copy files to iTunes Media folder when adding to library'''.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

=Start of Demonstration material=
The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are '''positively encouraged to continue working through the material''' at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

== Combined Word/ EndNote Familiarity ==
This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about '''''penicillin''''' and its '''''conversion to cephalosporin'''''.

=== A Web of Knowledge Search ===
#[[Image:Endnote1e.jpg|thumb|left|WoK search]] From the [http://wok.mimas.ac.uk/ Web-of-Knowledge] link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
#'''Connect to the ISI Web of Knowledge Service''' and then select the
#''Web of Science'' tab from along the top and finally from the citation databases, narrow it down to the
# Science Citation Index expanded
#Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the '''Author''' box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the '''advanced''' search such as <tt>au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)</tt>
#When you have some hits, either tick individual citations, or '''All records on page''' or a span of records.
#Next, make sure you have Microsoft Word running, and from the '''EndNote X4''' taskbar of Word, click on '''Go to EndNote'''. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
#[[Image:Endnote1b.jpg|right|saving a list for Endnote]]Return to the Browser window displaying WOS and click on '''Save to EndNote'''. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
#If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name '''uml_view.cgi''' on the desktop) which you can open directly with EndNote (see below).

=== Inserting the citations just found into Word using EndNote===
#[[Image:Endnote1a.jpg|thumb|right|Starting EndNote]]Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
#Via '''Edit/preferences/Libraries''' select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
#[[Image:endnote-style.jpg|thumb|left|Checking the style setting]]From '''Edit/Output style/Open Style Mananger''', select the tick-box against a template known as '''Royal Society of Chemistry''' (you may have to use '''Find by/Chemistry''' to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
#If you are importing a citation list rather than relying on the automated procedure, then from '''File/Import''' of EndNote define the Import Option '''ISI-CE''' in the pull down menu, or '''Other Filters/SciFinder (CAS)''' if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
#[[Image:Endnote1c.jpg|thumb|right|]][[Image:Endnote1d.jpg|thumb|left|Word with citations showing|]]Go back to Word 2007, and write some text. At an appropriate point, from the '''Endnote X4 taskbar tab''', press '''Go to EndNote''' when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the '''Insert citation''' tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
#Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

==== Mendeley and other alternatives to EndNote ====
[[image:refworks.jpg|thumb|right]]A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include [https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks] (for which the client software can be downloaded without cost) and an innovative program called [http://www.mendeley.com/ Mendeley] which is available on the computers in the department.

# If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

== Chemdraw Familiarity ==
*[[Image:unknown1.jpg|left|thumb|Click to expand image]] [[Image:taxolhsr.jpg|Taxol|right|300px]] '''Starting and using ChemDraw.''' Start Chemdraw icon from the '''Start/Programs menu'''. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
*Check that you have drawn it correctly by calculating its formula. To do this, Go to '''View/Show analysis''' window and record what you see (it should give you C<sub>47</sub>H<sub>51</sub>NO<sub>14</sub>. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. '''What is the difference in behaviour?'''

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. '''Can you identify what it is called?'''

== Lecture Support: Journal Familiarity ==

You can go visit the databases of some major chemistry publishers, and track down any articles that members of this department (or other departments or your favourite Nobel prize lautreates) may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following:
* [http://pubs.acs.org/search/advanced The American Chemical Society] (where you can subscribe to an RSS feed of the search, which means you will be notified of new items)
* [http://www.rsc.org/Publishing/Journals/cc/index.asp The Royal Society of Chemistry] and their premier journal ''Chemical communications''
* [http://www.nature.com/search/adv_search?sp-a=sp1001702d&sp-x-1=ujournal&sp-q-1=Nature%20Chemistry Nature Chemistry] advanced search.
* [http://www3.interscience.wiley.com/journal/26737/home Wiley Interscience] and their flagship chemistry journal ''Angew. Chemie.''
* [http://www.sciencedirect.com Science Direct]

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

== Lecture Support: Named chemicals ==

# To apply the above skills by using [http://wok.mimas.ac.uk/ WOS] to perform a comprehensive literature search on the '''molecule''' ''Penicillin'', a '''reaction''' (''its conversion to Cephalosporin''), its ''properties'', both physical (spectroscopic) and biological. Thus, type ''penicillin and cephalosporin'' into the '''Topic''' box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the '''Advanced Search''' option.
#* '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (136)
#* '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2629)
##Or, try the drug '''Temozolomide''', currently very much in the [http://news.bbc.co.uk/1/hi/england/west_midlands/7675014.stm news]
##Tasimelteon ([http://news.bbc.co.uk/1/hi/health/7760105.stm time bending drug for jet lag]) or
##[http://news.bbc.co.uk/1/hi/health/8237530.stm Sulforaphane], which occurs in broccoli and cauliflower and protects against heart attacks.
#Compare the results of one of these searches with less specialised search engines such as
#*[http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar],
#*[http://www.scirus.com/srsapp/advanced/index.jsp SciRus],
#*[http://www.bing.com/?scope=web&mkt=en-GB Microsoft Bing],
#*[http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha].

=== Lecture Support: A SciFinder search instead ===
*The [https://scifinder.cas.org/ Scifinder Scholar] system is available for general and student use.
** You cannot use your College login for access, but must request your own login to be created.
*** [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar Go here to register]. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. ''other field''.
** Completing the registration will result in an email being sent to the email address you provide with activation instructions.
*** Once you have obtained an ID, at the [https://origin-scifinder.cas.org SciFinder site], click on '''Explore References''' and in the '''Research topic box''' enter "Conversion of penicillin to cephalosporin".
** You will receive a request to accept an application digital signature at this stage, which you should accept.
You should get ~9 references for an exact match. This interface is supposed to use a more ''natural language'' for its search queries (and it does not employ Booleans).
** Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the '''Export''' link near the top (next to print). From the dialog, set the '''File Type''' to '''Tagged Format'''.
*** You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your '''download''' location. You can then import this into EndNote using the '''SciFinder (CAS)''' import option.
**An alternative search might be the phrase '''arrow pushing formalism''' (can you learn about this topic from the results found for this search?). A synonym might be '''curly arrow formalism'''. Does this find the same references, or a different set?
** You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to '''My connections''' and invite the group, then add comments to relevant references.
** SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

=Laboratory Support=
Here you will find out how to search for safety information about molecules, and then for their properties and reactions. There are two kinds of search for molecules you will have to make during lab courses.
# Where you have an unknown compound whose properties you have measured and you want to know if any known compound matches those properties.
# Where you (think you) know what the structure of your compound is, and you want to know if there are any other reports of this same compound (and whether the properties other have measured match your own).

== A search for known physical properties using Reaxys ==
[[Image:Reaxys1.jpg|right|thumb|]]We will start with two examples of the first category and then move on to the rather more common second category.

*Connect to the [http://www.reaxys.com/ Reaxys] system. You can carry out all the required course work as an ''anonymous user'', but you will not be able to change/save any settings etc in this mode (such as e.g. changing the default structure editor to ChemDraw).
** If you do choose to register at this point, be aware that if you lose/forget your password, you will need to contact Reaxys and not local Imperial College support.
*Select ''substances and Properties''
**In the ''Properties (Advanced)'' box, enter the following, followed by '''Search'''.
**'''MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200'''
This means in effect, show me ANY molecule which melts at a certain temperature range (determined using a melting point apparatus), which has a given molecular formula (determined using mass spectrometry) and an optical rotatory power between certain values (determined using a polarimeter). For this example you should get exactly 1 hit, which should be to a patent. Explore the options at this point, including viewing the original source of the data ( a patent in this case).
* There are about 500 different properties in total which you could specify in this manner. To explore them, click on ''Show Fields and Operators''. This type of technique is useful for identifying an '''unknown''' compound purely from its physical properties (Forensic science, etc).
** Note that some features do not always produce the expected result. For example, the icon labelled with the arrow (right) pulls down various options, one of which is ''copy structure to clipboard''. The clipboard contents however are '''not''' recognised by eg Chemdraw, Word etc.

== A search for known spectroscopic properties ==

[[image:spectra.jpg|240px|right]]It is routine when a compound is first made to record its spectroscopic properties. This would include the characteristic infra-red frequencies, and the <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts. These values are shown for an unknown compound. Your task is to use the [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] to try to identify what the compound is (you could of course also do this entirely logically using just your brain).
#Try first entering only the <sup>13</sup>C NMR chemical shifts (163, 141, 133, 130, 129, 128, 98 ppm, with an anticipated error of around 2ppm). How many matches do you get?
#Add then the <sup>1</sup>H shifts (8.1,7.5,5.1,4.7 and there is an additional broad multiplet across the range 7.3-7.7 which is not entered) and see if the number of possibilities reduces.
#Finally, enter the one characteristic IR vibration (1733 cm<sup>-1</sup>). Do you now get a unique answer? Record any structure(s) you may get at this stage for future reference.
#Try changing the error limits for any of these properties. Thus reduce the NMR limit from 2.0 to 1.5 to 1.0ppm, or the IR limit to 5 or even 1 cm<sup>-1</sup> (in future laboratory courses, you will learn how the way the instrument works determines at least in part the accuracy with which these spectroscopic properties can be measured).

== Reagent/Product searches for laboratory preparations ==

[[image:1-4.jpg|right|250px|Molecules 1-4]]The theme of this section is going to be the following four molecules, which you will in fact encounter in a laboratory course later in the year. You will search for known properties of these molecules, for comparison with those you might measure in the lab, or which may provide useful discussion material for your laboratory reports. Your first task is to generate a so-called SMILES descriptor of the molecule. This is done most simply by drawing the molecule in ChemDraw and using the '''Edit as/Copy''' menu produce the SMILES or InChI-key string onto the clipboard. Here are three SMILES strings and one InCHI-key string. Can you match them up to the structures shown on the right?
# <nowiki>C=CC1=CC=C(C(O[H])=O)C=C1</nowiki>
# <nowiki>S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S</nowiki>
# <nowiki>O[C@H]1[C@H](OCC)CCCC1</nowiki>
# <nowiki>VSIKJPJINIDELZ-UHFFFAOYSA-N</nowiki>
*Search the [http://www.chemspider.com/ ChemSpider] database using a SMILES or InChI-key string as above. What sort of information is revealed about the compound?
*Try reversing the search terms above (instead of SMILEs, try generating an InChI key, or vice versa).
*Try next an advanced search from the same [http://www.chemspider.com/FullSearch.aspx database]. Explore for yourself how to enter the SMILES string and perform the search.
*Search the [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] using a SMILES string. Select the '''substructure/superstructure''' or the '''Identity/Similarity''' option, and then the '''CID, SMILES, InChI''' tab, and past in one of the strings above. Try both '''80% similar''' and '''identical''' if using the Similarity option). Again, explore the properties associated with each hit.
**You might encounter '''artefacts'''. Thus with '''S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S''', something slightly odd happens?
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of Drugs, inorganic and organometallic and natural products which might prove useful to you for laboratories.
* The series [http://www.orgsyn.org/ Organic syntheses] contains tried and tested procedures for the synthesis of many chemicals. However, it is quite limited, and you would be lucky to find more obscure compounds listed here.
=== Sigma-Aldrich Catalogues and MSDS (Safety) information ===

If you know (or suspect you know) what the identity of the molecules are that you will be handling in the laboratory, the first task is to find out any known safety information.
The [http://www.sigmaaldrich.com/catalog/search/AdvancedSearchPage Aldrich] catalogues can be searched for compounds and their associated MSDS safety sheets. This is useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms. If you were able to obtain a name (see previous section), see if you can now find any information on it from the Aldrich catalogue.

=== Reaxys ===
Connect to [http://www.reaxys.com/ Reaxys] as before, but now we are going to do a structure based search, using as examples structures '''1-4''' above. If you click in the frame labelled ''Double click this frame and draw structure query'' you will get a default structure editor called ChemAxon MarvinSketch. It is a little different from Chemdraw, but should not take too much time to master.
# Using the structure editor, draw one of the four molecules 1-4 and invoke '''search'''.
# If you think you know the name of your query, type that instead in the ''Generate structure from name'' box (e.g. '''Taxol''', which as you have seen earlier is a challenge to draw!). You can also paste a SMILES or InChI key into this box (try any of the four above).
# Try hitting '''Synthesize''', but expect to be overwhelmed by the number of hits!

=== Dictionary of organic compounds ===
An alternative database which works in this way is the [http://doc.chemnetbase.com/ Dictionary of organic compounds].


== Converting a 2D structure definition to a 3D set of coordinates ==

The preceding searches were all effectively conducted on two-dimensional molecules, where we only needed to know how the atoms were connected (in effect the Lewis valence structure). As a prelude to moving into three dimensions, we will illustrate how a 2D search can be used to generate a 3D structure.

* You can use the on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina service to convert a (1D) SMILES string to 3D molecular coordinates].
*# Under options, paste the SMILES string, enter a name, and select 3D structure viewer automatically loaded.
*# Click on Generate 3D structure. A window appears, and after about 20-30 seconds, a structure does as well. At the bottom, click on "Click to download this structure in PDB file format", whereupon a full window diagram appears. Save the molecule as above.

== 3D structure searching of the Cambridge Crystallographic database ==

Our final search type is now of a database which stores '''three-dimensional''' information about molecules. This is where you can infer all sorts of interesting properties about the bonding, the properties and the potential reactivities of molecules. You will be searching the '''Cambridge Crystal Structure Database'''. There are three entry points for this; one local, one via the Web and one via the national '''chemical database service'''.

=== Local invocation of the Cambridge Crystal Structure Database ===
The local based search described below is feature complete and fast. You may also want to try out the [http://webcsd.ccdc.cam.ac.uk/ WebCSD service], which needs only a web-browser.
#[[Image:MgBr2.jpg|right|120px]][[Image:ti1.jpg|right|100px]][[Image:PtCl.jpg|right|100px]][[image:1-4.jpg|right|250px|Molecules 1-4]]Select '''Conquest''' from the '''Start/Programs''' menu. You will have to reply:
##'''yes''' to the question about certificates,
##enter first your username, then
##your password at the two prompts (both of which appear to ask for a password!).
##Next, '''accept''' the license agreement and
##'''accept''' the suggested location for storing the directory.
##Enter the Site No. as '''183''' and the confirm code as '''8FDCE4''' (2013 release)
##Click '''register online'''.
##These prompts are a one-off, and you will not need to do these steps again.
#In the {{Pdf|FoundationTutorialproblems09.pdf|foundation tutorial problems}}, question 2 asks you to arrow-push the reaction Et<sub>2</sub>O + MgBr<sub>2</sub> → Et<sub>2</sub>O-MgBr<sub>2</sub>. Here we will pose the question: what is the 3D geometry of the product of this reaction? You will search for it using Conquest. Does the result surprise you? (Hint: TOQKIT)
#Nucleophilic addition to an amide is the prototype of how peptides, proteins and enzymes are broken down in metabolic processes (or using e.g. biological washing powders). The mechanism involves a species known as a '''tetrahedral intermediate''' (right), which is normally considered so unstable that it is rarely detected during the reaction. Nevertheless, can you find any examples of such species in the Cambridge database?
#Cis-Platin is a well known anti-cancer drug. The ''active ingredient'' is the initial hydrolysis product, shown on the right. Can you find any examples of this '''active intermediate''' in the database which contain this sub-structure? What happens if you change the Pt to a '''wild-card''' indicating the central metal could be any of the group known as '''8Z''' (from the '''more''' button of the editor, select '''other elements''' and from there click on the orange box labelled '''8Z''').
#Are there any other '''reactive intermediates''' you might have identified from your arrow-pushing workshop which you might search for?
#When you have finished the above examples, try entering one of the four lab-course molecules shown to the left, exactly as drawn above. For '''3''' specifically, if you draw explicit hydrogens attached to the ''vinyl'' group at the top of the molecule and repeat the search, what difference is there?
#*How many hits do you get?
#*Note the 6-8 letter identifier for the structure you are interested in (for example, for molecule '''3''' above, it should be XAYFEI, XAYFEI01 and XAYFEI02).
#*Save the 3D coordinates in PDB or CIF format via '''File/Export''', decide how you want to select entries, specify one file per entry and '''SAVE'''. Inspect the structure by double clicking the file created, to be found on drive '''L:'''
#You '''may''' now have two versions of any of these four molecules; one a direct experimental structure, and one assembled by the [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] program. How do these differ? Concentrate in particular on compounds '''1''' and '''2''' above right!
#Later on in your course, you may use such coordinates to create an entry in a Wiki page, much like that rotating below.

===An advanced 3D Search. ===
Try the following. The objective will be to find any short interactions between the H of an OH group and the centroid of a phenyl ring as the electron donor (a very unusual type of π-facial hydrogen bond). Proceed as follows:
{|
|
# Open Conquest and invoke the '''Build Queries/Draw''' option
# Deposit a benzene ring from the template which should appear on the left
# Click on '''ADD 3D''', select all the six carbon atoms in turn (they will go green) and define a centroid. A defined object labelled '''CENT1''' now shows. Press Done.
# Back in '''Draw''' mode, select a H and deposit it as an isolated atom. Then select O and draw a bond from it to the H to get an OH. In this system, any undefined valence is '''wild''', ie any group can be attached to the O of the OH.
# In '''ADD 3D''' mode again, click first on the '''H''' of the OH group, then on '''CENT1''' in the list of defined objects. A green line connecting the two appears. When a '''Valid parameter''' entry named '''Distance''' appears, click on '''Define'''.
# Select '''Intramolecular''' from the '''Choose distance type''' menu, OK, then '''Options''', enter 2.0 - 2.4 as the range of distances and '''Separated by 5 - 999''' bonds. Hit '''OK''' and then '''Done'''. Your search query is summarized in a cyan box at the top right of the draw window.
# Select '''Search''', tick the 3D Coordinates determined box and '''Start Search'''. This search should proceed at the rate of about 1% per second. You should get 20 hits.
# View entries via '''3D Visualiser'''. Note the so-called '''REFCODES'''. Note '''[[Coursework#Enantiomers_vs_Diastereomers_Part_1:_Butanes_and__Helicenes.|CIYSIM]]''' in particular!
#A right-mouse click in the blue window of the 3D Visualiser will enable you to set '''spacefill''' mode, and to inspect whether any two atom spheres inter-penetrate each-other indicating an attractive interaction between them.
# Save the coordinates of any selected hits via '''File/Export''', Select PDB or CIF as the format, all selected entries, one file per entry and '''SAVE'''.
# The files will appear on your L: drive. Double click to open up the WebLab Viewer Pro or Mercury program, and resave them if you wish as an MDL Molfile rather than PDB.
# If you want to explore further, define an NH bond rather an OH bond (you might need to increase the distance range to eg 2.0 - 2.5).
# Try this with centroids to other π-electron rich systems, such as an alkyne, alkene, or other rings such as cyclopentadienyl, etc.
#Go to your network drive N: or L: (i.e. username on neon.ch.ic.ac.uk) and double click any .PDB or .CFIF or .MOL files to view the molecule again.
# Or, instead of H-O, just put e.g. Na (metal arene interactions are hugely important biologically). You may need to define a rather longer distance range. Experiment by trying various sets of values.
|<jmol><jmolApplet><title>CIYSIM</title><color>white</color>
<size>300</size><script>zoom 150;spin 3;</script>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents>
</jmolApplet></jmol>
|}

=== The National Chemical Database Service ===

The '''CDS''' is a national service (located as it happens in Daresbury, near Warrington) which offers a range of database services to the UK community. To access this service, follow the [http://cds.dl.ac.uk/cgi-bin/reg/undergrad?sites=Select+Site&SITE=imperial-cds0091 instructions] here (this is necessary to ensure UK usage only and to monitor that usage as part of justifying a national resource). You will be sent a CDS registration account and password by email. You can then use this account in two ways
#Invoke '''ConquestD''' (rather than Conquest) from the Windows start menu and proceed as above, but supply your new CDS account instead of your Imperial account.
#Invoke the CDS portal [https://cds.dl.ac.uk/ here] using your CDS account to log in. It offers many alternative services (including searches for spectral data) as well as a simplified crystal search. Explore in your own time!


=== Further tutorials based on 3D crystal structures ===

These can be viewed [http://www.ccdc.cam.ac.uk/free_services/teaching/modules/teaching_webcsd/toc.html here].

=Continuation of CIT skills=
The skills developed during these workshops will be in almost constant use throughout your course; you are encouraged to keep this up to date and to make use of these skills while writing lab reports and other coursework assignments. As with anything in the digital world, progress is being made all the time with new search engines, new search algorithms, new software. This also means that other searches and software are retired to make way for, newer more efficient tools. This wiki will be a long-term reference which you can refer to and even update, and you are urged to keep it as a bookmark.

== Software for your own computer ==

*The department has a Site License for a program system called [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 ChemBio3D] (which includes ChemDraw for both Windows and Mac), the terms of which allow individual undergraduates to acquire a copy of the program and to install it on their personal computer. The license is an annual one.
*[http://www.straightrunning.com/XmingNotes/ Xming] for accessing the Conquest data base.
*Programs such as Microsoft Office can be licensed via [http://www.microsoft.com/student/discounts/theultimatesteal-uk/default.aspx an academic license for £69.99].
*[https://directory.adeptscience.co.uk/products/search/1/1/474/cat474.html EndNote student edition] retails for £85.00. Alternatively, try RefWorks (usually $100/year but '''free''' for Imperial students through [http://www3.imperial.ac.uk/library/digitallibrary/athensandukfed AthensDA]) It is a slightly simpler web-based program. A comparison between both can be found [http://library.princeton.edu/help/comparison.php here] (Princeton University). You should note that the WOS system supports Endnote directly, but requires a more complicated procedure for using RefWorks or Mendeley.
*A further list of software may be found [[It:software-2011|here]], including other programs you can install on your personal computer which you may find useful.
----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:coursework-2011

2014-10-11T13:24:20Z

Amckinle: /* Software Familiarity */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Overall Objectives of CIT workshops=

The Computer lab (formally booked for your group, A1, A2, B1, B2, C1, C2) is for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library. All "Chemistry Software" should be available also in the Library to your user account. If you find that something is not immediately available, please do get in touch with the ICT Helpdesk. During the lab time allocated for the IT course, you will be expected to achieve the following objectives:

# Accessing course and laboratory notes and using scientific journals to support lectures
# Using '''Word''' in combination with the '''EndNote''' bibliographic database and '''ChemDraw''' to write laboratory reports and essays
# Learn to use various bibliographic chemistry search systems
# Learn to conduct molecular structure-based search systems
# Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

=Self-Study - Software Familiarity=

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section ''' <u>before you come to the workshop sessions</u>''':

==Before you come to the workshop sessions...==

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.
* Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your [https://exchange.imperial.ac.uk campus email account] through the [https://exchange.imperial.ac.uk web interface].
* Using the '''FireFox''' web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: <tt>http://www.ch.ic.ac.uk/wiki/</tt>). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
* You will be using Firefox to browse the pages of a [http://en.wikipedia.org/wiki/Wiki Wiki]. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will '''replace''' the instruction window. So, get used to clicking on the link with the '''right mouse button''' rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

===Computer, Browser and Wordprocessor familiarity===
*[[Image:login_window.jpg|right|thumb|login window]]Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
*[[Image:home.jpg|left|thumb|Document home]]Perhaps the single most confusing aspect for most people is what the ''Home'' icon (left) means. So let's sort this out immediately. You are working in an ''enterprise'' environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the ''Home'' icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "'''My Documents'''", which the operating system can sometimes display instead of Home.
*[[Image:o2007.jpg|thumb|right|Office 2007]][[Image:subsuper.jpg|right|thumb|Subs and Superscripts]][[Image:o2007b.jpg|thumb|left||EndNote tab]]Start Microsoft '''Office 2007''' (we will assume you still have FireFox running). The basic ('''Home''') Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a '''red''' circle. Copy/paste operations are invoked using the icon encircled in '''purple'''. Other common operations are found to the right of these two in the taskbar, including the chemically useful '''subscript''' and '''superscripts''' (right diagram). Note also the the default document saves invokes the new '''.docx''' format, which is an XML-based type with much interesting ''informatics'' potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older '''.doc''' format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
*[[Image:o2007a.jpg|left|thumb|Insert tab]]There are two other task-bars you will find useful. the '''Insert''' bar inserts a variety of other content, including pictures, tables and the like. The '''EndNote''' tab invokes a citation and reference manager, which you will use as described below ('''Important'''<nowiki>: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).</nowiki>
* Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
*[[Image:FireFox_paste.jpg|thumb|right|Save Firefox image]] '''Images''' are special when it comes to copying. Proceed as follows:
*# Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
*# If one of the options is '''Copy image''', select it. Not all browsers support this, in which case instead invoke ''save this image as'' and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
*# With an Office Word window open, paste the image (if you copied it) or '''Insert/Picture/from file''' (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
*# Do remember how to change between windows (the technical term is that the active window is said to be ''on focus'') by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
{|
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>150</size>
<script>zoom 200; cpk -20;move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|Not everything is always "copyable". Some apparent images are in fact produced by an "applet" [http://wiki.jmol.org:81/index.php/MediaWiki embedded] in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
|}
* Practice naming and saving document files to your ''Home'' (Drive H: on Windows) or a removable medium such as a FlashDrive.
* Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding '''content''' of files may be very slow. Windows Desktop Search is '''NOT''' activated on College systems.
* [http://www.ch.ic.ac.uk/local/email/ Practice setting up E-mail], sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.
=== Configuring storage for your document libraries ===

Programs such as '''EndNote''', '''Mendeley''', '''iTunes''' store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

==== EndNote ====

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => '''userid(\\icfs18.cc.ic.ac.uk) (M:)''' Thereafter you can set it to open this library when the program starts.

==== Mendeley ====

Open the program and invoke '''Tools/Options/File Organiser''' and select drive M: for the library.

==== iTunes ====

Use '''Edit/Preferences/Advanced''' and set the iTunes Media folder location to M: (or other if M: is already full). Also tick '''Copy files to iTunes Media folder when adding to library'''.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

==Start of Workshop material==
The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are '''positively encouraged to continue working through the material''' at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

== Combined Word/ EndNote Familiarity ==
This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about '''''penicillin''''' and its '''''conversion to cephalosporin'''''.

=== A Web of Knowledge Search ===
#[[Image:Endnote1e.jpg|thumb|left|WoK search]] From the [http://wok.mimas.ac.uk/ Web-of-Knowledge] link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
#'''Connect to the ISI Web of Knowledge Service''' and then select the
#''Web of Science'' tab from along the top and finally from the citation databases, narrow it down to the
# Science Citation Index expanded
#Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the '''Author''' box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the '''advanced''' search such as <tt>au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)</tt>
#When you have some hits, either tick individual citations, or '''All records on page''' or a span of records.
#Next, make sure you have Microsoft Word running, and from the '''EndNote X4''' taskbar of Word, click on '''Go to EndNote'''. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
#[[Image:Endnote1b.jpg|right|saving a list for Endnote]]Return to the Browser window displaying WOS and click on '''Save to EndNote'''. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
#If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name '''uml_view.cgi''' on the desktop) which you can open directly with EndNote (see below).

=== Inserting the citations just found into Word using EndNote===
#[[Image:Endnote1a.jpg|thumb|right|Starting EndNote]]Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
#Via '''Edit/preferences/Libraries''' select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
#[[Image:endnote-style.jpg|thumb|left|Checking the style setting]]From '''Edit/Output style/Open Style Mananger''', select the tick-box against a template known as '''Royal Society of Chemistry''' (you may have to use '''Find by/Chemistry''' to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
#If you are importing a citation list rather than relying on the automated procedure, then from '''File/Import''' of EndNote define the Import Option '''ISI-CE''' in the pull down menu, or '''Other Filters/SciFinder (CAS)''' if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
#[[Image:Endnote1c.jpg|thumb|right|]][[Image:Endnote1d.jpg|thumb|left|Word with citations showing|]]Go back to Word 2007, and write some text. At an appropriate point, from the '''Endnote X4 taskbar tab''', press '''Go to EndNote''' when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the '''Insert citation''' tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
#Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

==== Mendeley and other alternatives to EndNote ====
[[image:refworks.jpg|thumb|right]]A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include [https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks] (for which the client software can be downloaded without cost) and an innovative program called [http://www.mendeley.com/ Mendeley] which is available on the computers in the department.

# If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

== Chemdraw Familiarity ==
*[[Image:unknown1.jpg|left|thumb|Click to expand image]] [[Image:taxolhsr.jpg|Taxol|right|300px]] '''Starting and using ChemDraw.''' Start Chemdraw icon from the '''Start/Programs menu'''. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
*Check that you have drawn it correctly by calculating its formula. To do this, Go to '''View/Show analysis''' window and record what you see (it should give you C<sub>47</sub>H<sub>51</sub>NO<sub>14</sub>. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. '''What is the difference in behaviour?'''

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. '''Can you identify what it is called?'''

== Lecture Support: Journal Familiarity ==

You can go visit the databases of some major chemistry publishers, and track down any articles that members of this department (or other departments or your favourite Nobel prize lautreates) may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following:
* [http://pubs.acs.org/search/advanced The American Chemical Society] (where you can subscribe to an RSS feed of the search, which means you will be notified of new items)
* [http://www.rsc.org/Publishing/Journals/cc/index.asp The Royal Society of Chemistry] and their premier journal ''Chemical communications''
* [http://www.nature.com/search/adv_search?sp-a=sp1001702d&sp-x-1=ujournal&sp-q-1=Nature%20Chemistry Nature Chemistry] advanced search.
* [http://www3.interscience.wiley.com/journal/26737/home Wiley Interscience] and their flagship chemistry journal ''Angew. Chemie.''
* [http://www.sciencedirect.com Science Direct]

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

== Lecture Support: Named chemicals ==

# To apply the above skills by using [http://wok.mimas.ac.uk/ WOS] to perform a comprehensive literature search on the '''molecule''' ''Penicillin'', a '''reaction''' (''its conversion to Cephalosporin''), its ''properties'', both physical (spectroscopic) and biological. Thus, type ''penicillin and cephalosporin'' into the '''Topic''' box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the '''Advanced Search''' option.
#* '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (136)
#* '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2629)
##Or, try the drug '''Temozolomide''', currently very much in the [http://news.bbc.co.uk/1/hi/england/west_midlands/7675014.stm news]
##Tasimelteon ([http://news.bbc.co.uk/1/hi/health/7760105.stm time bending drug for jet lag]) or
##[http://news.bbc.co.uk/1/hi/health/8237530.stm Sulforaphane], which occurs in broccoli and cauliflower and protects against heart attacks.
#Compare the results of one of these searches with less specialised search engines such as
#*[http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar],
#*[http://www.scirus.com/srsapp/advanced/index.jsp SciRus],
#*[http://www.bing.com/?scope=web&mkt=en-GB Microsoft Bing],
#*[http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha].

=== Lecture Support: A SciFinder search instead ===
*The [https://scifinder.cas.org/ Scifinder Scholar] system is available for general and student use.
** You cannot use your College login for access, but must request your own login to be created.
*** [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar Go here to register]. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. ''other field''.
** Completing the registration will result in an email being sent to the email address you provide with activation instructions.
*** Once you have obtained an ID, at the [https://origin-scifinder.cas.org SciFinder site], click on '''Explore References''' and in the '''Research topic box''' enter "Conversion of penicillin to cephalosporin".
** You will receive a request to accept an application digital signature at this stage, which you should accept.
You should get ~9 references for an exact match. This interface is supposed to use a more ''natural language'' for its search queries (and it does not employ Booleans).
** Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the '''Export''' link near the top (next to print). From the dialog, set the '''File Type''' to '''Tagged Format'''.
*** You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your '''download''' location. You can then import this into EndNote using the '''SciFinder (CAS)''' import option.
**An alternative search might be the phrase '''arrow pushing formalism''' (can you learn about this topic from the results found for this search?). A synonym might be '''curly arrow formalism'''. Does this find the same references, or a different set?
** You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to '''My connections''' and invite the group, then add comments to relevant references.
** SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

=Laboratory Support=
Here you will find out how to search for safety information about molecules, and then for their properties and reactions. There are two kinds of search for molecules you will have to make during lab courses.
# Where you have an unknown compound whose properties you have measured and you want to know if any known compound matches those properties.
# Where you (think you) know what the structure of your compound is, and you want to know if there are any other reports of this same compound (and whether the properties other have measured match your own).

== A search for known physical properties using Reaxys ==
[[Image:Reaxys1.jpg|right|thumb|]]We will start with two examples of the first category and then move on to the rather more common second category.

*Connect to the [http://www.reaxys.com/ Reaxys] system. You can carry out all the required course work as an ''anonymous user'', but you will not be able to change/save any settings etc in this mode (such as e.g. changing the default structure editor to ChemDraw).
** If you do choose to register at this point, be aware that if you lose/forget your password, you will need to contact Reaxys and not local Imperial College support.
*Select ''substances and Properties''
**In the ''Properties (Advanced)'' box, enter the following, followed by '''Search'''.
**'''MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200'''
This means in effect, show me ANY molecule which melts at a certain temperature range (determined using a melting point apparatus), which has a given molecular formula (determined using mass spectrometry) and an optical rotatory power between certain values (determined using a polarimeter). For this example you should get exactly 1 hit, which should be to a patent. Explore the options at this point, including viewing the original source of the data ( a patent in this case).
* There are about 500 different properties in total which you could specify in this manner. To explore them, click on ''Show Fields and Operators''. This type of technique is useful for identifying an '''unknown''' compound purely from its physical properties (Forensic science, etc).
** Note that some features do not always produce the expected result. For example, the icon labelled with the arrow (right) pulls down various options, one of which is ''copy structure to clipboard''. The clipboard contents however are '''not''' recognised by eg Chemdraw, Word etc.

== A search for known spectroscopic properties ==

[[image:spectra.jpg|240px|right]]It is routine when a compound is first made to record its spectroscopic properties. This would include the characteristic infra-red frequencies, and the <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts. These values are shown for an unknown compound. Your task is to use the [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] to try to identify what the compound is (you could of course also do this entirely logically using just your brain).
#Try first entering only the <sup>13</sup>C NMR chemical shifts (163, 141, 133, 130, 129, 128, 98 ppm, with an anticipated error of around 2ppm). How many matches do you get?
#Add then the <sup>1</sup>H shifts (8.1,7.5,5.1,4.7 and there is an additional broad multiplet across the range 7.3-7.7 which is not entered) and see if the number of possibilities reduces.
#Finally, enter the one characteristic IR vibration (1733 cm<sup>-1</sup>). Do you now get a unique answer? Record any structure(s) you may get at this stage for future reference.
#Try changing the error limits for any of these properties. Thus reduce the NMR limit from 2.0 to 1.5 to 1.0ppm, or the IR limit to 5 or even 1 cm<sup>-1</sup> (in future laboratory courses, you will learn how the way the instrument works determines at least in part the accuracy with which these spectroscopic properties can be measured).

== Reagent/Product searches for laboratory preparations ==

[[image:1-4.jpg|right|250px|Molecules 1-4]]The theme of this section is going to be the following four molecules, which you will in fact encounter in a laboratory course later in the year. You will search for known properties of these molecules, for comparison with those you might measure in the lab, or which may provide useful discussion material for your laboratory reports. Your first task is to generate a so-called SMILES descriptor of the molecule. This is done most simply by drawing the molecule in ChemDraw and using the '''Edit as/Copy''' menu produce the SMILES or InChI-key string onto the clipboard. Here are three SMILES strings and one InCHI-key string. Can you match them up to the structures shown on the right?
# <nowiki>C=CC1=CC=C(C(O[H])=O)C=C1</nowiki>
# <nowiki>S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S</nowiki>
# <nowiki>O[C@H]1[C@H](OCC)CCCC1</nowiki>
# <nowiki>VSIKJPJINIDELZ-UHFFFAOYSA-N</nowiki>
*Search the [http://www.chemspider.com/ ChemSpider] database using a SMILES or InChI-key string as above. What sort of information is revealed about the compound?
*Try reversing the search terms above (instead of SMILEs, try generating an InChI key, or vice versa).
*Try next an advanced search from the same [http://www.chemspider.com/FullSearch.aspx database]. Explore for yourself how to enter the SMILES string and perform the search.
*Search the [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] using a SMILES string. Select the '''substructure/superstructure''' or the '''Identity/Similarity''' option, and then the '''CID, SMILES, InChI''' tab, and past in one of the strings above. Try both '''80% similar''' and '''identical''' if using the Similarity option). Again, explore the properties associated with each hit.
**You might encounter '''artefacts'''. Thus with '''S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S''', something slightly odd happens?
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of Drugs, inorganic and organometallic and natural products which might prove useful to you for laboratories.
* The series [http://www.orgsyn.org/ Organic syntheses] contains tried and tested procedures for the synthesis of many chemicals. However, it is quite limited, and you would be lucky to find more obscure compounds listed here.
=== Sigma-Aldrich Catalogues and MSDS (Safety) information ===

If you know (or suspect you know) what the identity of the molecules are that you will be handling in the laboratory, the first task is to find out any known safety information.
The [http://www.sigmaaldrich.com/catalog/search/AdvancedSearchPage Aldrich] catalogues can be searched for compounds and their associated MSDS safety sheets. This is useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms. If you were able to obtain a name (see previous section), see if you can now find any information on it from the Aldrich catalogue.

=== Reaxys ===
Connect to [http://www.reaxys.com/ Reaxys] as before, but now we are going to do a structure based search, using as examples structures '''1-4''' above. If you click in the frame labelled ''Double click this frame and draw structure query'' you will get a default structure editor called ChemAxon MarvinSketch. It is a little different from Chemdraw, but should not take too much time to master.
# Using the structure editor, draw one of the four molecules 1-4 and invoke '''search'''.
# If you think you know the name of your query, type that instead in the ''Generate structure from name'' box (e.g. '''Taxol''', which as you have seen earlier is a challenge to draw!). You can also paste a SMILES or InChI key into this box (try any of the four above).
# Try hitting '''Synthesize''', but expect to be overwhelmed by the number of hits!

=== Dictionary of organic compounds ===
An alternative database which works in this way is the [http://doc.chemnetbase.com/ Dictionary of organic compounds].


== Converting a 2D structure definition to a 3D set of coordinates ==

The preceding searches were all effectively conducted on two-dimensional molecules, where we only needed to know how the atoms were connected (in effect the Lewis valence structure). As a prelude to moving into three dimensions, we will illustrate how a 2D search can be used to generate a 3D structure.

* You can use the on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina service to convert a (1D) SMILES string to 3D molecular coordinates].
*# Under options, paste the SMILES string, enter a name, and select 3D structure viewer automatically loaded.
*# Click on Generate 3D structure. A window appears, and after about 20-30 seconds, a structure does as well. At the bottom, click on "Click to download this structure in PDB file format", whereupon a full window diagram appears. Save the molecule as above.

== 3D structure searching of the Cambridge Crystallographic database ==

Our final search type is now of a database which stores '''three-dimensional''' information about molecules. This is where you can infer all sorts of interesting properties about the bonding, the properties and the potential reactivities of molecules. You will be searching the '''Cambridge Crystal Structure Database'''. There are three entry points for this; one local, one via the Web and one via the national '''chemical database service'''.

=== Local invocation of the Cambridge Crystal Structure Database ===
The local based search described below is feature complete and fast. You may also want to try out the [http://webcsd.ccdc.cam.ac.uk/ WebCSD service], which needs only a web-browser.
#[[Image:MgBr2.jpg|right|120px]][[Image:ti1.jpg|right|100px]][[Image:PtCl.jpg|right|100px]][[image:1-4.jpg|right|250px|Molecules 1-4]]Select '''Conquest''' from the '''Start/Programs''' menu. You will have to reply:
##'''yes''' to the question about certificates,
##enter first your username, then
##your password at the two prompts (both of which appear to ask for a password!).
##Next, '''accept''' the license agreement and
##'''accept''' the suggested location for storing the directory.
##Enter the Site No. as '''183''' and the confirm code as '''8FDCE4''' (2013 release)
##Click '''register online'''.
##These prompts are a one-off, and you will not need to do these steps again.
#In the {{Pdf|FoundationTutorialproblems09.pdf|foundation tutorial problems}}, question 2 asks you to arrow-push the reaction Et<sub>2</sub>O + MgBr<sub>2</sub> → Et<sub>2</sub>O-MgBr<sub>2</sub>. Here we will pose the question: what is the 3D geometry of the product of this reaction? You will search for it using Conquest. Does the result surprise you? (Hint: TOQKIT)
#Nucleophilic addition to an amide is the prototype of how peptides, proteins and enzymes are broken down in metabolic processes (or using e.g. biological washing powders). The mechanism involves a species known as a '''tetrahedral intermediate''' (right), which is normally considered so unstable that it is rarely detected during the reaction. Nevertheless, can you find any examples of such species in the Cambridge database?
#Cis-Platin is a well known anti-cancer drug. The ''active ingredient'' is the initial hydrolysis product, shown on the right. Can you find any examples of this '''active intermediate''' in the database which contain this sub-structure? What happens if you change the Pt to a '''wild-card''' indicating the central metal could be any of the group known as '''8Z''' (from the '''more''' button of the editor, select '''other elements''' and from there click on the orange box labelled '''8Z''').
#Are there any other '''reactive intermediates''' you might have identified from your arrow-pushing workshop which you might search for?
#When you have finished the above examples, try entering one of the four lab-course molecules shown to the left, exactly as drawn above. For '''3''' specifically, if you draw explicit hydrogens attached to the ''vinyl'' group at the top of the molecule and repeat the search, what difference is there?
#*How many hits do you get?
#*Note the 6-8 letter identifier for the structure you are interested in (for example, for molecule '''3''' above, it should be XAYFEI, XAYFEI01 and XAYFEI02).
#*Save the 3D coordinates in PDB or CIF format via '''File/Export''', decide how you want to select entries, specify one file per entry and '''SAVE'''. Inspect the structure by double clicking the file created, to be found on drive '''L:'''
#You '''may''' now have two versions of any of these four molecules; one a direct experimental structure, and one assembled by the [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] program. How do these differ? Concentrate in particular on compounds '''1''' and '''2''' above right!
#Later on in your course, you may use such coordinates to create an entry in a Wiki page, much like that rotating below.

===An advanced 3D Search. ===
Try the following. The objective will be to find any short interactions between the H of an OH group and the centroid of a phenyl ring as the electron donor (a very unusual type of π-facial hydrogen bond). Proceed as follows:
{|
|
# Open Conquest and invoke the '''Build Queries/Draw''' option
# Deposit a benzene ring from the template which should appear on the left
# Click on '''ADD 3D''', select all the six carbon atoms in turn (they will go green) and define a centroid. A defined object labelled '''CENT1''' now shows. Press Done.
# Back in '''Draw''' mode, select a H and deposit it as an isolated atom. Then select O and draw a bond from it to the H to get an OH. In this system, any undefined valence is '''wild''', ie any group can be attached to the O of the OH.
# In '''ADD 3D''' mode again, click first on the '''H''' of the OH group, then on '''CENT1''' in the list of defined objects. A green line connecting the two appears. When a '''Valid parameter''' entry named '''Distance''' appears, click on '''Define'''.
# Select '''Intramolecular''' from the '''Choose distance type''' menu, OK, then '''Options''', enter 2.0 - 2.4 as the range of distances and '''Separated by 5 - 999''' bonds. Hit '''OK''' and then '''Done'''. Your search query is summarized in a cyan box at the top right of the draw window.
# Select '''Search''', tick the 3D Coordinates determined box and '''Start Search'''. This search should proceed at the rate of about 1% per second. You should get 20 hits.
# View entries via '''3D Visualiser'''. Note the so-called '''REFCODES'''. Note '''[[Coursework#Enantiomers_vs_Diastereomers_Part_1:_Butanes_and__Helicenes.|CIYSIM]]''' in particular!
#A right-mouse click in the blue window of the 3D Visualiser will enable you to set '''spacefill''' mode, and to inspect whether any two atom spheres inter-penetrate each-other indicating an attractive interaction between them.
# Save the coordinates of any selected hits via '''File/Export''', Select PDB or CIF as the format, all selected entries, one file per entry and '''SAVE'''.
# The files will appear on your L: drive. Double click to open up the WebLab Viewer Pro or Mercury program, and resave them if you wish as an MDL Molfile rather than PDB.
# If you want to explore further, define an NH bond rather an OH bond (you might need to increase the distance range to eg 2.0 - 2.5).
# Try this with centroids to other π-electron rich systems, such as an alkyne, alkene, or other rings such as cyclopentadienyl, etc.
#Go to your network drive N: or L: (i.e. username on neon.ch.ic.ac.uk) and double click any .PDB or .CFIF or .MOL files to view the molecule again.
# Or, instead of H-O, just put e.g. Na (metal arene interactions are hugely important biologically). You may need to define a rather longer distance range. Experiment by trying various sets of values.
|<jmol><jmolApplet><title>CIYSIM</title><color>white</color>
<size>300</size><script>zoom 150;spin 3;</script>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents>
</jmolApplet></jmol>
|}

=== The National Chemical Database Service ===

The '''CDS''' is a national service (located as it happens in Daresbury, near Warrington) which offers a range of database services to the UK community. To access this service, follow the [http://cds.dl.ac.uk/cgi-bin/reg/undergrad?sites=Select+Site&SITE=imperial-cds0091 instructions] here (this is necessary to ensure UK usage only and to monitor that usage as part of justifying a national resource). You will be sent a CDS registration account and password by email. You can then use this account in two ways
#Invoke '''ConquestD''' (rather than Conquest) from the Windows start menu and proceed as above, but supply your new CDS account instead of your Imperial account.
#Invoke the CDS portal [https://cds.dl.ac.uk/ here] using your CDS account to log in. It offers many alternative services (including searches for spectral data) as well as a simplified crystal search. Explore in your own time!


=== Further tutorials based on 3D crystal structures ===

These can be viewed [http://www.ccdc.cam.ac.uk/free_services/teaching/modules/teaching_webcsd/toc.html here].

=Continuation of CIT skills=
The skills developed during these workshops will be in almost constant use throughout your course; you are encouraged to keep this up to date and to make use of these skills while writing lab reports and other coursework assignments. As with anything in the digital world, progress is being made all the time with new search engines, new search algorithms, new software. This also means that other searches and software are retired to make way for, newer more efficient tools. This wiki will be a long-term reference which you can refer to and even update, and you are urged to keep it as a bookmark.

== Software for your own computer ==

*The department has a Site License for a program system called [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 ChemBio3D] (which includes ChemDraw for both Windows and Mac), the terms of which allow individual undergraduates to acquire a copy of the program and to install it on their personal computer. The license is an annual one.
*[http://www.straightrunning.com/XmingNotes/ Xming] for accessing the Conquest data base.
*Programs such as Microsoft Office can be licensed via [http://www.microsoft.com/student/discounts/theultimatesteal-uk/default.aspx an academic license for £69.99].
*[https://directory.adeptscience.co.uk/products/search/1/1/474/cat474.html EndNote student edition] retails for £85.00. Alternatively, try RefWorks (usually $100/year but '''free''' for Imperial students through [http://www3.imperial.ac.uk/library/digitallibrary/athensandukfed AthensDA]) It is a slightly simpler web-based program. A comparison between both can be found [http://library.princeton.edu/help/comparison.php here] (Princeton University). You should note that the WOS system supports Endnote directly, but requires a more complicated procedure for using RefWorks or Mendeley.
*A further list of software may be found [[It:software-2011|here]], including other programs you can install on your personal computer which you may find useful.
----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:coursework-2011

2014-10-11T13:23:55Z

Amckinle: /* Overall Objectives of CIT workshops */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Overall Objectives of CIT workshops=

The Computer lab (formally booked for your group, A1, A2, B1, B2, C1, C2) is for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library. All "Chemistry Software" should be available also in the Library to your user account. If you find that something is not immediately available, please do get in touch with the ICT Helpdesk. During the lab time allocated for the IT course, you will be expected to achieve the following objectives:

# Accessing course and laboratory notes and using scientific journals to support lectures
# Using '''Word''' in combination with the '''EndNote''' bibliographic database and '''ChemDraw''' to write laboratory reports and essays
# Learn to use various bibliographic chemistry search systems
# Learn to conduct molecular structure-based search systems
# Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

=Software Familiarity=

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section ''' <u>before you come to the workshop sessions</u>''':

==Before you come to the workshop sessions...==

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.
* Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your [https://exchange.imperial.ac.uk campus email account] through the [https://exchange.imperial.ac.uk web interface].
* Using the '''FireFox''' web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: <tt>http://www.ch.ic.ac.uk/wiki/</tt>). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
* You will be using Firefox to browse the pages of a [http://en.wikipedia.org/wiki/Wiki Wiki]. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will '''replace''' the instruction window. So, get used to clicking on the link with the '''right mouse button''' rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

===Computer, Browser and Wordprocessor familiarity===
*[[Image:login_window.jpg|right|thumb|login window]]Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
*[[Image:home.jpg|left|thumb|Document home]]Perhaps the single most confusing aspect for most people is what the ''Home'' icon (left) means. So let's sort this out immediately. You are working in an ''enterprise'' environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the ''Home'' icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "'''My Documents'''", which the operating system can sometimes display instead of Home.
*[[Image:o2007.jpg|thumb|right|Office 2007]][[Image:subsuper.jpg|right|thumb|Subs and Superscripts]][[Image:o2007b.jpg|thumb|left||EndNote tab]]Start Microsoft '''Office 2007''' (we will assume you still have FireFox running). The basic ('''Home''') Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a '''red''' circle. Copy/paste operations are invoked using the icon encircled in '''purple'''. Other common operations are found to the right of these two in the taskbar, including the chemically useful '''subscript''' and '''superscripts''' (right diagram). Note also the the default document saves invokes the new '''.docx''' format, which is an XML-based type with much interesting ''informatics'' potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older '''.doc''' format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
*[[Image:o2007a.jpg|left|thumb|Insert tab]]There are two other task-bars you will find useful. the '''Insert''' bar inserts a variety of other content, including pictures, tables and the like. The '''EndNote''' tab invokes a citation and reference manager, which you will use as described below ('''Important'''<nowiki>: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).</nowiki>
* Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
*[[Image:FireFox_paste.jpg|thumb|right|Save Firefox image]] '''Images''' are special when it comes to copying. Proceed as follows:
*# Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
*# If one of the options is '''Copy image''', select it. Not all browsers support this, in which case instead invoke ''save this image as'' and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
*# With an Office Word window open, paste the image (if you copied it) or '''Insert/Picture/from file''' (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
*# Do remember how to change between windows (the technical term is that the active window is said to be ''on focus'') by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
{|
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>150</size>
<script>zoom 200; cpk -20;move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|Not everything is always "copyable". Some apparent images are in fact produced by an "applet" [http://wiki.jmol.org:81/index.php/MediaWiki embedded] in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
|}
* Practice naming and saving document files to your ''Home'' (Drive H: on Windows) or a removable medium such as a FlashDrive.
* Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding '''content''' of files may be very slow. Windows Desktop Search is '''NOT''' activated on College systems.
* [http://www.ch.ic.ac.uk/local/email/ Practice setting up E-mail], sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.
=== Configuring storage for your document libraries ===

Programs such as '''EndNote''', '''Mendeley''', '''iTunes''' store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

==== EndNote ====

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => '''userid(\\icfs18.cc.ic.ac.uk) (M:)''' Thereafter you can set it to open this library when the program starts.

==== Mendeley ====

Open the program and invoke '''Tools/Options/File Organiser''' and select drive M: for the library.

==== iTunes ====

Use '''Edit/Preferences/Advanced''' and set the iTunes Media folder location to M: (or other if M: is already full). Also tick '''Copy files to iTunes Media folder when adding to library'''.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

==Start of Workshop material==
The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are '''positively encouraged to continue working through the material''' at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

== Combined Word/ EndNote Familiarity ==
This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about '''''penicillin''''' and its '''''conversion to cephalosporin'''''.

=== A Web of Knowledge Search ===
#[[Image:Endnote1e.jpg|thumb|left|WoK search]] From the [http://wok.mimas.ac.uk/ Web-of-Knowledge] link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
#'''Connect to the ISI Web of Knowledge Service''' and then select the
#''Web of Science'' tab from along the top and finally from the citation databases, narrow it down to the
# Science Citation Index expanded
#Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the '''Author''' box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the '''advanced''' search such as <tt>au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)</tt>
#When you have some hits, either tick individual citations, or '''All records on page''' or a span of records.
#Next, make sure you have Microsoft Word running, and from the '''EndNote X4''' taskbar of Word, click on '''Go to EndNote'''. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
#[[Image:Endnote1b.jpg|right|saving a list for Endnote]]Return to the Browser window displaying WOS and click on '''Save to EndNote'''. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
#If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name '''uml_view.cgi''' on the desktop) which you can open directly with EndNote (see below).

=== Inserting the citations just found into Word using EndNote===
#[[Image:Endnote1a.jpg|thumb|right|Starting EndNote]]Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
#Via '''Edit/preferences/Libraries''' select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
#[[Image:endnote-style.jpg|thumb|left|Checking the style setting]]From '''Edit/Output style/Open Style Mananger''', select the tick-box against a template known as '''Royal Society of Chemistry''' (you may have to use '''Find by/Chemistry''' to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
#If you are importing a citation list rather than relying on the automated procedure, then from '''File/Import''' of EndNote define the Import Option '''ISI-CE''' in the pull down menu, or '''Other Filters/SciFinder (CAS)''' if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
#[[Image:Endnote1c.jpg|thumb|right|]][[Image:Endnote1d.jpg|thumb|left|Word with citations showing|]]Go back to Word 2007, and write some text. At an appropriate point, from the '''Endnote X4 taskbar tab''', press '''Go to EndNote''' when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the '''Insert citation''' tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
#Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

==== Mendeley and other alternatives to EndNote ====
[[image:refworks.jpg|thumb|right]]A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include [https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks] (for which the client software can be downloaded without cost) and an innovative program called [http://www.mendeley.com/ Mendeley] which is available on the computers in the department.

# If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

== Chemdraw Familiarity ==
*[[Image:unknown1.jpg|left|thumb|Click to expand image]] [[Image:taxolhsr.jpg|Taxol|right|300px]] '''Starting and using ChemDraw.''' Start Chemdraw icon from the '''Start/Programs menu'''. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
*Check that you have drawn it correctly by calculating its formula. To do this, Go to '''View/Show analysis''' window and record what you see (it should give you C<sub>47</sub>H<sub>51</sub>NO<sub>14</sub>. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. '''What is the difference in behaviour?'''

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. '''Can you identify what it is called?'''

== Lecture Support: Journal Familiarity ==

You can go visit the databases of some major chemistry publishers, and track down any articles that members of this department (or other departments or your favourite Nobel prize lautreates) may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following:
* [http://pubs.acs.org/search/advanced The American Chemical Society] (where you can subscribe to an RSS feed of the search, which means you will be notified of new items)
* [http://www.rsc.org/Publishing/Journals/cc/index.asp The Royal Society of Chemistry] and their premier journal ''Chemical communications''
* [http://www.nature.com/search/adv_search?sp-a=sp1001702d&sp-x-1=ujournal&sp-q-1=Nature%20Chemistry Nature Chemistry] advanced search.
* [http://www3.interscience.wiley.com/journal/26737/home Wiley Interscience] and their flagship chemistry journal ''Angew. Chemie.''
* [http://www.sciencedirect.com Science Direct]

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

== Lecture Support: Named chemicals ==

# To apply the above skills by using [http://wok.mimas.ac.uk/ WOS] to perform a comprehensive literature search on the '''molecule''' ''Penicillin'', a '''reaction''' (''its conversion to Cephalosporin''), its ''properties'', both physical (spectroscopic) and biological. Thus, type ''penicillin and cephalosporin'' into the '''Topic''' box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the '''Advanced Search''' option.
#* '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (136)
#* '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2629)
##Or, try the drug '''Temozolomide''', currently very much in the [http://news.bbc.co.uk/1/hi/england/west_midlands/7675014.stm news]
##Tasimelteon ([http://news.bbc.co.uk/1/hi/health/7760105.stm time bending drug for jet lag]) or
##[http://news.bbc.co.uk/1/hi/health/8237530.stm Sulforaphane], which occurs in broccoli and cauliflower and protects against heart attacks.
#Compare the results of one of these searches with less specialised search engines such as
#*[http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar],
#*[http://www.scirus.com/srsapp/advanced/index.jsp SciRus],
#*[http://www.bing.com/?scope=web&mkt=en-GB Microsoft Bing],
#*[http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha].

=== Lecture Support: A SciFinder search instead ===
*The [https://scifinder.cas.org/ Scifinder Scholar] system is available for general and student use.
** You cannot use your College login for access, but must request your own login to be created.
*** [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar Go here to register]. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. ''other field''.
** Completing the registration will result in an email being sent to the email address you provide with activation instructions.
*** Once you have obtained an ID, at the [https://origin-scifinder.cas.org SciFinder site], click on '''Explore References''' and in the '''Research topic box''' enter "Conversion of penicillin to cephalosporin".
** You will receive a request to accept an application digital signature at this stage, which you should accept.
You should get ~9 references for an exact match. This interface is supposed to use a more ''natural language'' for its search queries (and it does not employ Booleans).
** Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the '''Export''' link near the top (next to print). From the dialog, set the '''File Type''' to '''Tagged Format'''.
*** You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your '''download''' location. You can then import this into EndNote using the '''SciFinder (CAS)''' import option.
**An alternative search might be the phrase '''arrow pushing formalism''' (can you learn about this topic from the results found for this search?). A synonym might be '''curly arrow formalism'''. Does this find the same references, or a different set?
** You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to '''My connections''' and invite the group, then add comments to relevant references.
** SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

=Laboratory Support=
Here you will find out how to search for safety information about molecules, and then for their properties and reactions. There are two kinds of search for molecules you will have to make during lab courses.
# Where you have an unknown compound whose properties you have measured and you want to know if any known compound matches those properties.
# Where you (think you) know what the structure of your compound is, and you want to know if there are any other reports of this same compound (and whether the properties other have measured match your own).

== A search for known physical properties using Reaxys ==
[[Image:Reaxys1.jpg|right|thumb|]]We will start with two examples of the first category and then move on to the rather more common second category.

*Connect to the [http://www.reaxys.com/ Reaxys] system. You can carry out all the required course work as an ''anonymous user'', but you will not be able to change/save any settings etc in this mode (such as e.g. changing the default structure editor to ChemDraw).
** If you do choose to register at this point, be aware that if you lose/forget your password, you will need to contact Reaxys and not local Imperial College support.
*Select ''substances and Properties''
**In the ''Properties (Advanced)'' box, enter the following, followed by '''Search'''.
**'''MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200'''
This means in effect, show me ANY molecule which melts at a certain temperature range (determined using a melting point apparatus), which has a given molecular formula (determined using mass spectrometry) and an optical rotatory power between certain values (determined using a polarimeter). For this example you should get exactly 1 hit, which should be to a patent. Explore the options at this point, including viewing the original source of the data ( a patent in this case).
* There are about 500 different properties in total which you could specify in this manner. To explore them, click on ''Show Fields and Operators''. This type of technique is useful for identifying an '''unknown''' compound purely from its physical properties (Forensic science, etc).
** Note that some features do not always produce the expected result. For example, the icon labelled with the arrow (right) pulls down various options, one of which is ''copy structure to clipboard''. The clipboard contents however are '''not''' recognised by eg Chemdraw, Word etc.

== A search for known spectroscopic properties ==

[[image:spectra.jpg|240px|right]]It is routine when a compound is first made to record its spectroscopic properties. This would include the characteristic infra-red frequencies, and the <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts. These values are shown for an unknown compound. Your task is to use the [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] to try to identify what the compound is (you could of course also do this entirely logically using just your brain).
#Try first entering only the <sup>13</sup>C NMR chemical shifts (163, 141, 133, 130, 129, 128, 98 ppm, with an anticipated error of around 2ppm). How many matches do you get?
#Add then the <sup>1</sup>H shifts (8.1,7.5,5.1,4.7 and there is an additional broad multiplet across the range 7.3-7.7 which is not entered) and see if the number of possibilities reduces.
#Finally, enter the one characteristic IR vibration (1733 cm<sup>-1</sup>). Do you now get a unique answer? Record any structure(s) you may get at this stage for future reference.
#Try changing the error limits for any of these properties. Thus reduce the NMR limit from 2.0 to 1.5 to 1.0ppm, or the IR limit to 5 or even 1 cm<sup>-1</sup> (in future laboratory courses, you will learn how the way the instrument works determines at least in part the accuracy with which these spectroscopic properties can be measured).

== Reagent/Product searches for laboratory preparations ==

[[image:1-4.jpg|right|250px|Molecules 1-4]]The theme of this section is going to be the following four molecules, which you will in fact encounter in a laboratory course later in the year. You will search for known properties of these molecules, for comparison with those you might measure in the lab, or which may provide useful discussion material for your laboratory reports. Your first task is to generate a so-called SMILES descriptor of the molecule. This is done most simply by drawing the molecule in ChemDraw and using the '''Edit as/Copy''' menu produce the SMILES or InChI-key string onto the clipboard. Here are three SMILES strings and one InCHI-key string. Can you match them up to the structures shown on the right?
# <nowiki>C=CC1=CC=C(C(O[H])=O)C=C1</nowiki>
# <nowiki>S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S</nowiki>
# <nowiki>O[C@H]1[C@H](OCC)CCCC1</nowiki>
# <nowiki>VSIKJPJINIDELZ-UHFFFAOYSA-N</nowiki>
*Search the [http://www.chemspider.com/ ChemSpider] database using a SMILES or InChI-key string as above. What sort of information is revealed about the compound?
*Try reversing the search terms above (instead of SMILEs, try generating an InChI key, or vice versa).
*Try next an advanced search from the same [http://www.chemspider.com/FullSearch.aspx database]. Explore for yourself how to enter the SMILES string and perform the search.
*Search the [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] using a SMILES string. Select the '''substructure/superstructure''' or the '''Identity/Similarity''' option, and then the '''CID, SMILES, InChI''' tab, and past in one of the strings above. Try both '''80% similar''' and '''identical''' if using the Similarity option). Again, explore the properties associated with each hit.
**You might encounter '''artefacts'''. Thus with '''S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S''', something slightly odd happens?
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of Drugs, inorganic and organometallic and natural products which might prove useful to you for laboratories.
* The series [http://www.orgsyn.org/ Organic syntheses] contains tried and tested procedures for the synthesis of many chemicals. However, it is quite limited, and you would be lucky to find more obscure compounds listed here.
=== Sigma-Aldrich Catalogues and MSDS (Safety) information ===

If you know (or suspect you know) what the identity of the molecules are that you will be handling in the laboratory, the first task is to find out any known safety information.
The [http://www.sigmaaldrich.com/catalog/search/AdvancedSearchPage Aldrich] catalogues can be searched for compounds and their associated MSDS safety sheets. This is useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms. If you were able to obtain a name (see previous section), see if you can now find any information on it from the Aldrich catalogue.

=== Reaxys ===
Connect to [http://www.reaxys.com/ Reaxys] as before, but now we are going to do a structure based search, using as examples structures '''1-4''' above. If you click in the frame labelled ''Double click this frame and draw structure query'' you will get a default structure editor called ChemAxon MarvinSketch. It is a little different from Chemdraw, but should not take too much time to master.
# Using the structure editor, draw one of the four molecules 1-4 and invoke '''search'''.
# If you think you know the name of your query, type that instead in the ''Generate structure from name'' box (e.g. '''Taxol''', which as you have seen earlier is a challenge to draw!). You can also paste a SMILES or InChI key into this box (try any of the four above).
# Try hitting '''Synthesize''', but expect to be overwhelmed by the number of hits!

=== Dictionary of organic compounds ===
An alternative database which works in this way is the [http://doc.chemnetbase.com/ Dictionary of organic compounds].


== Converting a 2D structure definition to a 3D set of coordinates ==

The preceding searches were all effectively conducted on two-dimensional molecules, where we only needed to know how the atoms were connected (in effect the Lewis valence structure). As a prelude to moving into three dimensions, we will illustrate how a 2D search can be used to generate a 3D structure.

* You can use the on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina service to convert a (1D) SMILES string to 3D molecular coordinates].
*# Under options, paste the SMILES string, enter a name, and select 3D structure viewer automatically loaded.
*# Click on Generate 3D structure. A window appears, and after about 20-30 seconds, a structure does as well. At the bottom, click on "Click to download this structure in PDB file format", whereupon a full window diagram appears. Save the molecule as above.

== 3D structure searching of the Cambridge Crystallographic database ==

Our final search type is now of a database which stores '''three-dimensional''' information about molecules. This is where you can infer all sorts of interesting properties about the bonding, the properties and the potential reactivities of molecules. You will be searching the '''Cambridge Crystal Structure Database'''. There are three entry points for this; one local, one via the Web and one via the national '''chemical database service'''.

=== Local invocation of the Cambridge Crystal Structure Database ===
The local based search described below is feature complete and fast. You may also want to try out the [http://webcsd.ccdc.cam.ac.uk/ WebCSD service], which needs only a web-browser.
#[[Image:MgBr2.jpg|right|120px]][[Image:ti1.jpg|right|100px]][[Image:PtCl.jpg|right|100px]][[image:1-4.jpg|right|250px|Molecules 1-4]]Select '''Conquest''' from the '''Start/Programs''' menu. You will have to reply:
##'''yes''' to the question about certificates,
##enter first your username, then
##your password at the two prompts (both of which appear to ask for a password!).
##Next, '''accept''' the license agreement and
##'''accept''' the suggested location for storing the directory.
##Enter the Site No. as '''183''' and the confirm code as '''8FDCE4''' (2013 release)
##Click '''register online'''.
##These prompts are a one-off, and you will not need to do these steps again.
#In the {{Pdf|FoundationTutorialproblems09.pdf|foundation tutorial problems}}, question 2 asks you to arrow-push the reaction Et<sub>2</sub>O + MgBr<sub>2</sub> → Et<sub>2</sub>O-MgBr<sub>2</sub>. Here we will pose the question: what is the 3D geometry of the product of this reaction? You will search for it using Conquest. Does the result surprise you? (Hint: TOQKIT)
#Nucleophilic addition to an amide is the prototype of how peptides, proteins and enzymes are broken down in metabolic processes (or using e.g. biological washing powders). The mechanism involves a species known as a '''tetrahedral intermediate''' (right), which is normally considered so unstable that it is rarely detected during the reaction. Nevertheless, can you find any examples of such species in the Cambridge database?
#Cis-Platin is a well known anti-cancer drug. The ''active ingredient'' is the initial hydrolysis product, shown on the right. Can you find any examples of this '''active intermediate''' in the database which contain this sub-structure? What happens if you change the Pt to a '''wild-card''' indicating the central metal could be any of the group known as '''8Z''' (from the '''more''' button of the editor, select '''other elements''' and from there click on the orange box labelled '''8Z''').
#Are there any other '''reactive intermediates''' you might have identified from your arrow-pushing workshop which you might search for?
#When you have finished the above examples, try entering one of the four lab-course molecules shown to the left, exactly as drawn above. For '''3''' specifically, if you draw explicit hydrogens attached to the ''vinyl'' group at the top of the molecule and repeat the search, what difference is there?
#*How many hits do you get?
#*Note the 6-8 letter identifier for the structure you are interested in (for example, for molecule '''3''' above, it should be XAYFEI, XAYFEI01 and XAYFEI02).
#*Save the 3D coordinates in PDB or CIF format via '''File/Export''', decide how you want to select entries, specify one file per entry and '''SAVE'''. Inspect the structure by double clicking the file created, to be found on drive '''L:'''
#You '''may''' now have two versions of any of these four molecules; one a direct experimental structure, and one assembled by the [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] program. How do these differ? Concentrate in particular on compounds '''1''' and '''2''' above right!
#Later on in your course, you may use such coordinates to create an entry in a Wiki page, much like that rotating below.

===An advanced 3D Search. ===
Try the following. The objective will be to find any short interactions between the H of an OH group and the centroid of a phenyl ring as the electron donor (a very unusual type of π-facial hydrogen bond). Proceed as follows:
{|
|
# Open Conquest and invoke the '''Build Queries/Draw''' option
# Deposit a benzene ring from the template which should appear on the left
# Click on '''ADD 3D''', select all the six carbon atoms in turn (they will go green) and define a centroid. A defined object labelled '''CENT1''' now shows. Press Done.
# Back in '''Draw''' mode, select a H and deposit it as an isolated atom. Then select O and draw a bond from it to the H to get an OH. In this system, any undefined valence is '''wild''', ie any group can be attached to the O of the OH.
# In '''ADD 3D''' mode again, click first on the '''H''' of the OH group, then on '''CENT1''' in the list of defined objects. A green line connecting the two appears. When a '''Valid parameter''' entry named '''Distance''' appears, click on '''Define'''.
# Select '''Intramolecular''' from the '''Choose distance type''' menu, OK, then '''Options''', enter 2.0 - 2.4 as the range of distances and '''Separated by 5 - 999''' bonds. Hit '''OK''' and then '''Done'''. Your search query is summarized in a cyan box at the top right of the draw window.
# Select '''Search''', tick the 3D Coordinates determined box and '''Start Search'''. This search should proceed at the rate of about 1% per second. You should get 20 hits.
# View entries via '''3D Visualiser'''. Note the so-called '''REFCODES'''. Note '''[[Coursework#Enantiomers_vs_Diastereomers_Part_1:_Butanes_and__Helicenes.|CIYSIM]]''' in particular!
#A right-mouse click in the blue window of the 3D Visualiser will enable you to set '''spacefill''' mode, and to inspect whether any two atom spheres inter-penetrate each-other indicating an attractive interaction between them.
# Save the coordinates of any selected hits via '''File/Export''', Select PDB or CIF as the format, all selected entries, one file per entry and '''SAVE'''.
# The files will appear on your L: drive. Double click to open up the WebLab Viewer Pro or Mercury program, and resave them if you wish as an MDL Molfile rather than PDB.
# If you want to explore further, define an NH bond rather an OH bond (you might need to increase the distance range to eg 2.0 - 2.5).
# Try this with centroids to other π-electron rich systems, such as an alkyne, alkene, or other rings such as cyclopentadienyl, etc.
#Go to your network drive N: or L: (i.e. username on neon.ch.ic.ac.uk) and double click any .PDB or .CFIF or .MOL files to view the molecule again.
# Or, instead of H-O, just put e.g. Na (metal arene interactions are hugely important biologically). You may need to define a rather longer distance range. Experiment by trying various sets of values.
|<jmol><jmolApplet><title>CIYSIM</title><color>white</color>
<size>300</size><script>zoom 150;spin 3;</script>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents>
</jmolApplet></jmol>
|}

=== The National Chemical Database Service ===

The '''CDS''' is a national service (located as it happens in Daresbury, near Warrington) which offers a range of database services to the UK community. To access this service, follow the [http://cds.dl.ac.uk/cgi-bin/reg/undergrad?sites=Select+Site&SITE=imperial-cds0091 instructions] here (this is necessary to ensure UK usage only and to monitor that usage as part of justifying a national resource). You will be sent a CDS registration account and password by email. You can then use this account in two ways
#Invoke '''ConquestD''' (rather than Conquest) from the Windows start menu and proceed as above, but supply your new CDS account instead of your Imperial account.
#Invoke the CDS portal [https://cds.dl.ac.uk/ here] using your CDS account to log in. It offers many alternative services (including searches for spectral data) as well as a simplified crystal search. Explore in your own time!


=== Further tutorials based on 3D crystal structures ===

These can be viewed [http://www.ccdc.cam.ac.uk/free_services/teaching/modules/teaching_webcsd/toc.html here].

=Continuation of CIT skills=
The skills developed during these workshops will be in almost constant use throughout your course; you are encouraged to keep this up to date and to make use of these skills while writing lab reports and other coursework assignments. As with anything in the digital world, progress is being made all the time with new search engines, new search algorithms, new software. This also means that other searches and software are retired to make way for, newer more efficient tools. This wiki will be a long-term reference which you can refer to and even update, and you are urged to keep it as a bookmark.

== Software for your own computer ==

*The department has a Site License for a program system called [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 ChemBio3D] (which includes ChemDraw for both Windows and Mac), the terms of which allow individual undergraduates to acquire a copy of the program and to install it on their personal computer. The license is an annual one.
*[http://www.straightrunning.com/XmingNotes/ Xming] for accessing the Conquest data base.
*Programs such as Microsoft Office can be licensed via [http://www.microsoft.com/student/discounts/theultimatesteal-uk/default.aspx an academic license for £69.99].
*[https://directory.adeptscience.co.uk/products/search/1/1/474/cat474.html EndNote student edition] retails for £85.00. Alternatively, try RefWorks (usually $100/year but '''free''' for Imperial students through [http://www3.imperial.ac.uk/library/digitallibrary/athensandukfed AthensDA]) It is a slightly simpler web-based program. A comparison between both can be found [http://library.princeton.edu/help/comparison.php here] (Princeton University). You should note that the WOS system supports Endnote directly, but requires a more complicated procedure for using RefWorks or Mendeley.
*A further list of software may be found [[It:software-2011|here]], including other programs you can install on your personal computer which you may find useful.
----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

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[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Overall Objectives of CIT workshops=
The workshop will take place in the Computer Lab at the following times:
* Group A1: Thursday 11th October and Friday 26th October 2012, 14:00-17:00
* Group A2: Thursday 18th October and Friday 2nd November 2012, 14:00-17:00
* Group B1: Monday 8th October and Monday 22nd October 2012, 13:00-16:00
* Group B2: Monday 15th October and Monday 29th October 2012, 13:00-16:00

The Computer lab (formally booked for your group, [[Media:Y1-labgroups-2011.pdf|A1, A2, B1, B2]]) is for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library, although you may find not all of the chemistry-related programs will be available there. During the lab time allocated for the IT course (two 3 hour sessions per group), you will be expected to achieve the following objectives:
# Accessing course and laboratory notes and using scientific journals to support lectures
# Using '''Word''' in combination with the '''EndNote''' bibliographic database and '''ChemDraw''' to write laboratory reports and essays
# Learn to use various bibliographic chemistry search systems
# Learn to conduct molecular structure-based search systems
# Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

=Software Familiarity=

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section ''' <u>before you come to the workshop sessions</u>''':

==Before you come to the workshop sessions...==

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.
* Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your [https://exchange.imperial.ac.uk campus email account] through the [https://exchange.imperial.ac.uk web interface].
* Using the '''FireFox''' web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: <tt>http://www.ch.ic.ac.uk/wiki/</tt>). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
* You will be using Firefox to browse the pages of a [http://en.wikipedia.org/wiki/Wiki Wiki]. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will '''replace''' the instruction window. So, get used to clicking on the link with the '''right mouse button''' rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

===Computer, Browser and Wordprocessor familiarity===
*[[Image:login_window.jpg|right|thumb|login window]]Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
*[[Image:home.jpg|left|thumb|Document home]]Perhaps the single most confusing aspect for most people is what the ''Home'' icon (left) means. So let's sort this out immediately. You are working in an ''enterprise'' environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the ''Home'' icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "'''My Documents'''", which the operating system can sometimes display instead of Home.
*[[Image:o2007.jpg|thumb|right|Office 2007]][[Image:subsuper.jpg|right|thumb|Subs and Superscripts]][[Image:o2007b.jpg|thumb|left||EndNote tab]]Start Microsoft '''Office 2007''' (we will assume you still have FireFox running). The basic ('''Home''') Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a '''red''' circle. Copy/paste operations are invoked using the icon encircled in '''purple'''. Other common operations are found to the right of these two in the taskbar, including the chemically useful '''subscript''' and '''superscripts''' (right diagram). Note also the the default document saves invokes the new '''.docx''' format, which is an XML-based type with much interesting ''informatics'' potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older '''.doc''' format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
*[[Image:o2007a.jpg|left|thumb|Insert tab]]There are two other task-bars you will find useful. the '''Insert''' bar inserts a variety of other content, including pictures, tables and the like. The '''EndNote''' tab invokes a citation and reference manager, which you will use as described below ('''Important'''<nowiki>: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).</nowiki>
* Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
*[[Image:FireFox_paste.jpg|thumb|right|Save Firefox image]] '''Images''' are special when it comes to copying. Proceed as follows:
*# Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
*# If one of the options is '''Copy image''', select it. Not all browsers support this, in which case instead invoke ''save this image as'' and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
*# With an Office Word window open, paste the image (if you copied it) or '''Insert/Picture/from file''' (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
*# Do remember how to change between windows (the technical term is that the active window is said to be ''on focus'') by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
{|
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>150</size>
<script>zoom 200; cpk -20;move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|Not everything is always "copyable". Some apparent images are in fact produced by an "applet" [http://wiki.jmol.org:81/index.php/MediaWiki embedded] in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
|}
* Practice naming and saving document files to your ''Home'' (Drive H: on Windows) or a removable medium such as a FlashDrive.
* Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding '''content''' of files may be very slow. Windows Desktop Search is '''NOT''' activated on College systems.
* [http://www.ch.ic.ac.uk/local/email/ Practice setting up E-mail], sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.
=== Configuring storage for your document libraries ===

Programs such as '''EndNote''', '''Mendeley''', '''iTunes''' store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

==== EndNote ====

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => '''userid(\\icfs18.cc.ic.ac.uk) (M:)''' Thereafter you can set it to open this library when the program starts.

==== Mendeley ====

Open the program and invoke '''Tools/Options/File Organiser''' and select drive M: for the library.

==== iTunes ====

Use '''Edit/Preferences/Advanced''' and set the iTunes Media folder location to M: (or other if M: is already full). Also tick '''Copy files to iTunes Media folder when adding to library'''.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

==Start of Workshop material==
The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are '''positively encouraged to continue working through the material''' at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

== Combined Word/ EndNote Familiarity ==
This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about '''''penicillin''''' and its '''''conversion to cephalosporin'''''.

=== A Web of Knowledge Search ===
#[[Image:Endnote1e.jpg|thumb|left|WoK search]] From the [http://wok.mimas.ac.uk/ Web-of-Knowledge] link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
#'''Connect to the ISI Web of Knowledge Service''' and then select the
#''Web of Science'' tab from along the top and finally from the citation databases, narrow it down to the
# Science Citation Index expanded
#Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the '''Author''' box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the '''advanced''' search such as <tt>au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)</tt>
#When you have some hits, either tick individual citations, or '''All records on page''' or a span of records.
#Next, make sure you have Microsoft Word running, and from the '''EndNote X4''' taskbar of Word, click on '''Go to EndNote'''. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
#[[Image:Endnote1b.jpg|right|saving a list for Endnote]]Return to the Browser window displaying WOS and click on '''Save to EndNote'''. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
#If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name '''uml_view.cgi''' on the desktop) which you can open directly with EndNote (see below).

=== Inserting the citations just found into Word using EndNote===
#[[Image:Endnote1a.jpg|thumb|right|Starting EndNote]]Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
#Via '''Edit/preferences/Libraries''' select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
#[[Image:endnote-style.jpg|thumb|left|Checking the style setting]]From '''Edit/Output style/Open Style Mananger''', select the tick-box against a template known as '''Royal Society of Chemistry''' (you may have to use '''Find by/Chemistry''' to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
#If you are importing a citation list rather than relying on the automated procedure, then from '''File/Import''' of EndNote define the Import Option '''ISI-CE''' in the pull down menu, or '''Other Filters/SciFinder (CAS)''' if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
#[[Image:Endnote1c.jpg|thumb|right|]][[Image:Endnote1d.jpg|thumb|left|Word with citations showing|]]Go back to Word 2007, and write some text. At an appropriate point, from the '''Endnote X4 taskbar tab''', press '''Go to EndNote''' when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the '''Insert citation''' tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
#Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

==== Mendeley and other alternatives to EndNote ====
[[image:refworks.jpg|thumb|right]]A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include [https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks] (for which the client software can be downloaded without cost) and an innovative program called [http://www.mendeley.com/ Mendeley] which is available on the computers in the department.

# If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

== Chemdraw Familiarity ==
*[[Image:unknown1.jpg|left|thumb|Click to expand image]] [[Image:taxolhsr.jpg|Taxol|right|300px]] '''Starting and using ChemDraw.''' Start Chemdraw icon from the '''Start/Programs menu'''. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
*Check that you have drawn it correctly by calculating its formula. To do this, Go to '''View/Show analysis''' window and record what you see (it should give you C<sub>47</sub>H<sub>51</sub>NO<sub>14</sub>. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. '''What is the difference in behaviour?'''

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. '''Can you identify what it is called?'''

== Lecture Support: Journal Familiarity ==

You can go visit the databases of some major chemistry publishers, and track down any articles that members of this department (or other departments or your favourite Nobel prize lautreates) may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following:
* [http://pubs.acs.org/search/advanced The American Chemical Society] (where you can subscribe to an RSS feed of the search, which means you will be notified of new items)
* [http://www.rsc.org/Publishing/Journals/cc/index.asp The Royal Society of Chemistry] and their premier journal ''Chemical communications''
* [http://www.nature.com/search/adv_search?sp-a=sp1001702d&sp-x-1=ujournal&sp-q-1=Nature%20Chemistry Nature Chemistry] advanced search.
* [http://www3.interscience.wiley.com/journal/26737/home Wiley Interscience] and their flagship chemistry journal ''Angew. Chemie.''
* [http://www.sciencedirect.com Science Direct]

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

== Lecture Support: Named chemicals ==

# To apply the above skills by using [http://wok.mimas.ac.uk/ WOS] to perform a comprehensive literature search on the '''molecule''' ''Penicillin'', a '''reaction''' (''its conversion to Cephalosporin''), its ''properties'', both physical (spectroscopic) and biological. Thus, type ''penicillin and cephalosporin'' into the '''Topic''' box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the '''Advanced Search''' option.
#* '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (136)
#* '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2629)
##Or, try the drug '''Temozolomide''', currently very much in the [http://news.bbc.co.uk/1/hi/england/west_midlands/7675014.stm news]
##Tasimelteon ([http://news.bbc.co.uk/1/hi/health/7760105.stm time bending drug for jet lag]) or
##[http://news.bbc.co.uk/1/hi/health/8237530.stm Sulforaphane], which occurs in broccoli and cauliflower and protects against heart attacks.
#Compare the results of one of these searches with less specialised search engines such as
#*[http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar],
#*[http://www.scirus.com/srsapp/advanced/index.jsp SciRus],
#*[http://www.bing.com/?scope=web&mkt=en-GB Microsoft Bing],
#*[http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha].

=== Lecture Support: A SciFinder search instead ===
*The [https://scifinder.cas.org/ Scifinder Scholar] system is available for general and student use.
** You cannot use your College login for access, but must request your own login to be created.
*** [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar Go here to register]. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. ''other field''.
** Completing the registration will result in an email being sent to the email address you provide with activation instructions.
*** Once you have obtained an ID, at the [https://origin-scifinder.cas.org SciFinder site], click on '''Explore References''' and in the '''Research topic box''' enter "Conversion of penicillin to cephalosporin".
** You will receive a request to accept an application digital signature at this stage, which you should accept.
You should get ~9 references for an exact match. This interface is supposed to use a more ''natural language'' for its search queries (and it does not employ Booleans).
** Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the '''Export''' link near the top (next to print). From the dialog, set the '''File Type''' to '''Tagged Format'''.
*** You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your '''download''' location. You can then import this into EndNote using the '''SciFinder (CAS)''' import option.
**An alternative search might be the phrase '''arrow pushing formalism''' (can you learn about this topic from the results found for this search?). A synonym might be '''curly arrow formalism'''. Does this find the same references, or a different set?
** You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to '''My connections''' and invite the group, then add comments to relevant references.
** SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

=Laboratory Support=
Here you will find out how to search for safety information about molecules, and then for their properties and reactions. There are two kinds of search for molecules you will have to make during lab courses.
# Where you have an unknown compound whose properties you have measured and you want to know if any known compound matches those properties.
# Where you (think you) know what the structure of your compound is, and you want to know if there are any other reports of this same compound (and whether the properties other have measured match your own).

== A search for known physical properties using Reaxys ==
[[Image:Reaxys1.jpg|right|thumb|]]We will start with two examples of the first category and then move on to the rather more common second category.

*Connect to the [http://www.reaxys.com/ Reaxys] system. You can carry out all the required course work as an ''anonymous user'', but you will not be able to change/save any settings etc in this mode (such as e.g. changing the default structure editor to ChemDraw).
** If you do choose to register at this point, be aware that if you lose/forget your password, you will need to contact Reaxys and not local Imperial College support.
*Select ''substances and Properties''
**In the ''Properties (Advanced)'' box, enter the following, followed by '''Search'''.
**'''MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200'''
This means in effect, show me ANY molecule which melts at a certain temperature range (determined using a melting point apparatus), which has a given molecular formula (determined using mass spectrometry) and an optical rotatory power between certain values (determined using a polarimeter). For this example you should get exactly 1 hit, which should be to a patent. Explore the options at this point, including viewing the original source of the data ( a patent in this case).
* There are about 500 different properties in total which you could specify in this manner. To explore them, click on ''Show Fields and Operators''. This type of technique is useful for identifying an '''unknown''' compound purely from its physical properties (Forensic science, etc).
** Note that some features do not always produce the expected result. For example, the icon labelled with the arrow (right) pulls down various options, one of which is ''copy structure to clipboard''. The clipboard contents however are '''not''' recognised by eg Chemdraw, Word etc.

== A search for known spectroscopic properties ==

[[image:spectra.jpg|240px|right]]It is routine when a compound is first made to record its spectroscopic properties. This would include the characteristic infra-red frequencies, and the <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts. These values are shown for an unknown compound. Your task is to use the [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] to try to identify what the compound is (you could of course also do this entirely logically using just your brain).
#Try first entering only the <sup>13</sup>C NMR chemical shifts (163, 141, 133, 130, 129, 128, 98 ppm, with an anticipated error of around 2ppm). How many matches do you get?
#Add then the <sup>1</sup>H shifts (8.1,7.5,5.1,4.7 and there is an additional broad multiplet across the range 7.3-7.7 which is not entered) and see if the number of possibilities reduces.
#Finally, enter the one characteristic IR vibration (1733 cm<sup>-1</sup>). Do you now get a unique answer? Record any structure(s) you may get at this stage for future reference.
#Try changing the error limits for any of these properties. Thus reduce the NMR limit from 2.0 to 1.5 to 1.0ppm, or the IR limit to 5 or even 1 cm<sup>-1</sup> (in future laboratory courses, you will learn how the way the instrument works determines at least in part the accuracy with which these spectroscopic properties can be measured).

== Reagent/Product searches for laboratory preparations ==

[[image:1-4.jpg|right|250px|Molecules 1-4]]The theme of this section is going to be the following four molecules, which you will in fact encounter in a laboratory course later in the year. You will search for known properties of these molecules, for comparison with those you might measure in the lab, or which may provide useful discussion material for your laboratory reports. Your first task is to generate a so-called SMILES descriptor of the molecule. This is done most simply by drawing the molecule in ChemDraw and using the '''Edit as/Copy''' menu produce the SMILES or InChI-key string onto the clipboard. Here are three SMILES strings and one InCHI-key string. Can you match them up to the structures shown on the right?
# <nowiki>C=CC1=CC=C(C(O[H])=O)C=C1</nowiki>
# <nowiki>S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S</nowiki>
# <nowiki>O[C@H]1[C@H](OCC)CCCC1</nowiki>
# <nowiki>VSIKJPJINIDELZ-UHFFFAOYSA-N</nowiki>
*Search the [http://www.chemspider.com/ ChemSpider] database using a SMILES or InChI-key string as above. What sort of information is revealed about the compound?
*Try reversing the search terms above (instead of SMILEs, try generating an InChI key, or vice versa).
*Try next an advanced search from the same [http://www.chemspider.com/FullSearch.aspx database]. Explore for yourself how to enter the SMILES string and perform the search.
*Search the [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] using a SMILES string. Select the '''substructure/superstructure''' or the '''Identity/Similarity''' option, and then the '''CID, SMILES, InChI''' tab, and past in one of the strings above. Try both '''80% similar''' and '''identical''' if using the Similarity option). Again, explore the properties associated with each hit.
**You might encounter '''artefacts'''. Thus with '''S=C=N[Ni]([P](C)(C)C)([P](C)(C)C)N=C=S''', something slightly odd happens?
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of Drugs, inorganic and organometallic and natural products which might prove useful to you for laboratories.
* The series [http://www.orgsyn.org/ Organic syntheses] contains tried and tested procedures for the synthesis of many chemicals. However, it is quite limited, and you would be lucky to find more obscure compounds listed here.
=== Sigma-Aldrich Catalogues and MSDS (Safety) information ===

If you know (or suspect you know) what the identity of the molecules are that you will be handling in the laboratory, the first task is to find out any known safety information.
The [http://www.sigmaaldrich.com/catalog/search/AdvancedSearchPage Aldrich] catalogues can be searched for compounds and their associated MSDS safety sheets. This is useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms. If you were able to obtain a name (see previous section), see if you can now find any information on it from the Aldrich catalogue.

=== Reaxys ===
Connect to [http://www.reaxys.com/ Reaxys] as before, but now we are going to do a structure based search, using as examples structures '''1-4''' above. If you click in the frame labelled ''Double click this frame and draw structure query'' you will get a default structure editor called ChemAxon MarvinSketch. It is a little different from Chemdraw, but should not take too much time to master.
# Using the structure editor, draw one of the four molecules 1-4 and invoke '''search'''.
# If you think you know the name of your query, type that instead in the ''Generate structure from name'' box (e.g. '''Taxol''', which as you have seen earlier is a challenge to draw!). You can also paste a SMILES or InChI key into this box (try any of the four above).
# Try hitting '''Synthesize''', but expect to be overwhelmed by the number of hits!

=== Dictionary of organic compounds ===
An alternative database which works in this way is the [http://doc.chemnetbase.com/ Dictionary of organic compounds].


== Converting a 2D structure definition to a 3D set of coordinates ==

The preceding searches were all effectively conducted on two-dimensional molecules, where we only needed to know how the atoms were connected (in effect the Lewis valence structure). As a prelude to moving into three dimensions, we will illustrate how a 2D search can be used to generate a 3D structure.

* You can use the on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina service to convert a (1D) SMILES string to 3D molecular coordinates].
*# Under options, paste the SMILES string, enter a name, and select 3D structure viewer automatically loaded.
*# Click on Generate 3D structure. A window appears, and after about 20-30 seconds, a structure does as well. At the bottom, click on "Click to download this structure in PDB file format", whereupon a full window diagram appears. Save the molecule as above.

== 3D structure searching of the Cambridge Crystallographic database ==

Our final search type is now of a database which stores '''three-dimensional''' information about molecules. This is where you can infer all sorts of interesting properties about the bonding, the properties and the potential reactivities of molecules. You will be searching the '''Cambridge Crystal Structure Database'''. There are three entry points for this; one local, one via the Web and one via the national '''chemical database service'''.

=== Local invocation of the Cambridge Crystal Structure Database ===
The local based search described below is feature complete and fast. You may also want to try out the [http://webcsd.ccdc.cam.ac.uk/ WebCSD service], which needs only a web-browser.
#[[Image:MgBr2.jpg|right|120px]][[Image:ti1.jpg|right|100px]][[Image:PtCl.jpg|right|100px]][[image:1-4.jpg|right|250px|Molecules 1-4]]Select '''Conquest''' from the '''Start/Programs''' menu. You will have to reply:
##'''yes''' to the question about certificates,
##enter first your username, then
##your password at the two prompts (both of which appear to ask for a password!).
##Next, '''accept''' the license agreement and
##'''accept''' the suggested location for storing the directory.
##Enter the Site No. as '''183''' and the confirm code as '''8FDCE4''' (2013 release)
##Click '''register online'''.
##These prompts are a one-off, and you will not need to do these steps again.
#In the {{Pdf|FoundationTutorialproblems09.pdf|foundation tutorial problems}}, question 2 asks you to arrow-push the reaction Et<sub>2</sub>O + MgBr<sub>2</sub> → Et<sub>2</sub>O-MgBr<sub>2</sub>. Here we will pose the question: what is the 3D geometry of the product of this reaction? You will search for it using Conquest. Does the result surprise you? (Hint: TOQKIT)
#Nucleophilic addition to an amide is the prototype of how peptides, proteins and enzymes are broken down in metabolic processes (or using e.g. biological washing powders). The mechanism involves a species known as a '''tetrahedral intermediate''' (right), which is normally considered so unstable that it is rarely detected during the reaction. Nevertheless, can you find any examples of such species in the Cambridge database?
#Cis-Platin is a well known anti-cancer drug. The ''active ingredient'' is the initial hydrolysis product, shown on the right. Can you find any examples of this '''active intermediate''' in the database which contain this sub-structure? What happens if you change the Pt to a '''wild-card''' indicating the central metal could be any of the group known as '''8Z''' (from the '''more''' button of the editor, select '''other elements''' and from there click on the orange box labelled '''8Z''').
#Are there any other '''reactive intermediates''' you might have identified from your arrow-pushing workshop which you might search for?
#When you have finished the above examples, try entering one of the four lab-course molecules shown to the left, exactly as drawn above. For '''3''' specifically, if you draw explicit hydrogens attached to the ''vinyl'' group at the top of the molecule and repeat the search, what difference is there?
#*How many hits do you get?
#*Note the 6-8 letter identifier for the structure you are interested in (for example, for molecule '''3''' above, it should be XAYFEI, XAYFEI01 and XAYFEI02).
#*Save the 3D coordinates in PDB or CIF format via '''File/Export''', decide how you want to select entries, specify one file per entry and '''SAVE'''. Inspect the structure by double clicking the file created, to be found on drive '''L:'''
#You '''may''' now have two versions of any of these four molecules; one a direct experimental structure, and one assembled by the [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] program. How do these differ? Concentrate in particular on compounds '''1''' and '''2''' above right!
#Later on in your course, you may use such coordinates to create an entry in a Wiki page, much like that rotating below.

===An advanced 3D Search. ===
Try the following. The objective will be to find any short interactions between the H of an OH group and the centroid of a phenyl ring as the electron donor (a very unusual type of π-facial hydrogen bond). Proceed as follows:
{|
|
# Open Conquest and invoke the '''Build Queries/Draw''' option
# Deposit a benzene ring from the template which should appear on the left
# Click on '''ADD 3D''', select all the six carbon atoms in turn (they will go green) and define a centroid. A defined object labelled '''CENT1''' now shows. Press Done.
# Back in '''Draw''' mode, select a H and deposit it as an isolated atom. Then select O and draw a bond from it to the H to get an OH. In this system, any undefined valence is '''wild''', ie any group can be attached to the O of the OH.
# In '''ADD 3D''' mode again, click first on the '''H''' of the OH group, then on '''CENT1''' in the list of defined objects. A green line connecting the two appears. When a '''Valid parameter''' entry named '''Distance''' appears, click on '''Define'''.
# Select '''Intramolecular''' from the '''Choose distance type''' menu, OK, then '''Options''', enter 2.0 - 2.4 as the range of distances and '''Separated by 5 - 999''' bonds. Hit '''OK''' and then '''Done'''. Your search query is summarized in a cyan box at the top right of the draw window.
# Select '''Search''', tick the 3D Coordinates determined box and '''Start Search'''. This search should proceed at the rate of about 1% per second. You should get 20 hits.
# View entries via '''3D Visualiser'''. Note the so-called '''REFCODES'''. Note '''[[Coursework#Enantiomers_vs_Diastereomers_Part_1:_Butanes_and__Helicenes.|CIYSIM]]''' in particular!
#A right-mouse click in the blue window of the 3D Visualiser will enable you to set '''spacefill''' mode, and to inspect whether any two atom spheres inter-penetrate each-other indicating an attractive interaction between them.
# Save the coordinates of any selected hits via '''File/Export''', Select PDB or CIF as the format, all selected entries, one file per entry and '''SAVE'''.
# The files will appear on your L: drive. Double click to open up the WebLab Viewer Pro or Mercury program, and resave them if you wish as an MDL Molfile rather than PDB.
# If you want to explore further, define an NH bond rather an OH bond (you might need to increase the distance range to eg 2.0 - 2.5).
# Try this with centroids to other π-electron rich systems, such as an alkyne, alkene, or other rings such as cyclopentadienyl, etc.
#Go to your network drive N: or L: (i.e. username on neon.ch.ic.ac.uk) and double click any .PDB or .CFIF or .MOL files to view the molecule again.
# Or, instead of H-O, just put e.g. Na (metal arene interactions are hugely important biologically). You may need to define a rather longer distance range. Experiment by trying various sets of values.
|<jmol><jmolApplet><title>CIYSIM</title><color>white</color>
<size>300</size><script>zoom 150;spin 3;</script>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents>
</jmolApplet></jmol>
|}

=== The National Chemical Database Service ===

The '''CDS''' is a national service (located as it happens in Daresbury, near Warrington) which offers a range of database services to the UK community. To access this service, follow the [http://cds.dl.ac.uk/cgi-bin/reg/undergrad?sites=Select+Site&SITE=imperial-cds0091 instructions] here (this is necessary to ensure UK usage only and to monitor that usage as part of justifying a national resource). You will be sent a CDS registration account and password by email. You can then use this account in two ways
#Invoke '''ConquestD''' (rather than Conquest) from the Windows start menu and proceed as above, but supply your new CDS account instead of your Imperial account.
#Invoke the CDS portal [https://cds.dl.ac.uk/ here] using your CDS account to log in. It offers many alternative services (including searches for spectral data) as well as a simplified crystal search. Explore in your own time!


=== Further tutorials based on 3D crystal structures ===

These can be viewed [http://www.ccdc.cam.ac.uk/free_services/teaching/modules/teaching_webcsd/toc.html here].

=Continuation of CIT skills=
The skills developed during these workshops will be in almost constant use throughout your course; you are encouraged to keep this up to date and to make use of these skills while writing lab reports and other coursework assignments. As with anything in the digital world, progress is being made all the time with new search engines, new search algorithms, new software. This also means that other searches and software are retired to make way for, newer more efficient tools. This wiki will be a long-term reference which you can refer to and even update, and you are urged to keep it as a bookmark.

== Software for your own computer ==

*The department has a Site License for a program system called [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 ChemBio3D] (which includes ChemDraw for both Windows and Mac), the terms of which allow individual undergraduates to acquire a copy of the program and to install it on their personal computer. The license is an annual one.
*[http://www.straightrunning.com/XmingNotes/ Xming] for accessing the Conquest data base.
*Programs such as Microsoft Office can be licensed via [http://www.microsoft.com/student/discounts/theultimatesteal-uk/default.aspx an academic license for £69.99].
*[https://directory.adeptscience.co.uk/products/search/1/1/474/cat474.html EndNote student edition] retails for £85.00. Alternatively, try RefWorks (usually $100/year but '''free''' for Imperial students through [http://www3.imperial.ac.uk/library/digitallibrary/athensandukfed AthensDA]) It is a slightly simpler web-based program. A comparison between both can be found [http://library.princeton.edu/help/comparison.php here] (Princeton University). You should note that the WOS system supports Endnote directly, but requires a more complicated procedure for using RefWorks or Mendeley.
*A further list of software may be found [[It:software-2011|here]], including other programs you can install on your personal computer which you may find useful.
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[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Workshops]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-10-11T13:19:54Z

Amckinle:

[[It:intro-2011|Go to Introduction]] | '''Go to Workshops''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
----

==Workshop material - Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

----
<references />
----

===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wos.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the '''only''' formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=Workshop Exercises - IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

=Extra Material for Future Reference - 3D Structure based searches=
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

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[[It:intro-2011|Go to Introduction]] | '''Go to Workshops''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:intro-2011

2014-10-11T13:19:29Z

Amckinle:

It:lectures-2011

2014-10-11T13:18:55Z

Amckinle: /* Workshop Exercises - IT for Laboratories and Reports */

[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
----

==Workshop material - Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

----
<references />
----

===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wos.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the '''only''' formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=Workshop Exercises - IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

=Extra Material for Future Reference - 3D Structure based searches=
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

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[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-10-11T13:18:16Z

Amckinle: /* 3D Structure based searches */

[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
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==Workshop material - Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

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<references />
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===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wos.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the '''only''' formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=Workshop Exercises - IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

==Extra Material for Future Reference - 3D Structure based searches==
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

----
[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-10-11T13:17:45Z

Amckinle: /* Workshop demonstrations - IT for Laboratories and Reports */

[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
----

==Workshop material - Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

----
<references />
----

===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wos.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the '''only''' formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=Workshop Exercises - IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

==3D Structure based searches==
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

----
[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-10-11T13:16:25Z

Amckinle: /* IT for Laboratories and Reports */

[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
----

==Workshop material - Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

----
<references />
----

===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wos.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the '''only''' formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=Workshop demonstrations - IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

==3D Structure based searches==
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

----
[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-10-11T13:15:07Z

Amckinle: /* Using software for preparation of reports and assignments */

[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
----

==Workshop material - Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

----
<references />
----

===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wos.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the '''only''' formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

==3D Structure based searches==
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

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[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-10-11T13:12:25Z

Amckinle: /* Accessing scientific journals and Bibliographic Searches */

[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

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<references />
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==Workshop material - Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

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<references />
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===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wos.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the only formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

==3D Structure based searches==
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

----
[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-10-11T13:11:56Z

Amckinle: /* Accessing lecture notes and submission of assignments */

[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Self Study - Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
----

==Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

----
<references />
----

===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wos.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the only formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

==3D Structure based searches==
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

----
[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-10-11T13:11:39Z

Amckinle: /* Managing your location */

[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Self Study - Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
----

==Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

----
<references />
----

===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wos.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the only formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

==3D Structure based searches==
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

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[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:lectures-2011

2014-10-11T13:10:50Z

Amckinle: /* Chemical Information Technology 2012-2013 */

[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=

=IT for lecture courses, tutorials and set projects=

Two pages available for general IT skills; not fully part of this course, but important for reference
* General [[It:it_facillities|IT facilities]]
* General [[It:it_files|file management]]

==Managing your location==
It is important to manage your location while accessing scientific journals as access to almost every electronic resource is controlled by your internet (IP) address. You will not need to worry about this when you are connecting to your resources on campus (which by definition also includes South Kensington Halls of residence). If you are outside this catchment area however, some IT services will not work unless you enter the campus ''virtually'' by switching on something called a [http://www3.imperial.ac.uk/ict/services/personalcomputersupportandmobileservices/mobileaccessservices VPN], or ''Virtual Private Network''. It allows you to access resources through the campus network from your own internet connection.

==Accessing lecture notes and submission of assignments==

===Lecture materials online===
[[Image:blackboard1.png|thumb|107px|[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard VLE] ]]Course notes may be found either using the College ''Virtual Learning Environment'', called '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]''' or using the Chemistry Wiki (which you are using now). Most lecture notes will be available as a Portable Document Format (a '''PDF''' document) or, less commonly, a Powerpoint slide show. These may be downloaded to your computer and stored in a document library (e.g., '''EndNote''' or '''Mendeley'''), printed or viewed on the computer. You are encouraged to annotate lecture notes during the lecture and to review them afterwards, rather than simply filing them away until to Revision Week!

<big>'''Lecture notes are <u>not intended to be exhaustive in their content</u> and you are encouraged to support them with further information from textbooks and other sources as appropriate.'''</big>

Lecture notes will be placed on Blackboard by the lecturers for your convenience, however the PDF document alone will not necessarily contain all the content required for understanding; in the event of missing a lecture you should go over the content with the aid of textbooks to ensure you understand the concepts.

===Online submission of assignments===
Almost all assignments are now submitted electronically through '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard].''' Submissions will be then be checked by Turn-It-In, a software package designed to 'read' assignments and, through comparison with a huge number of resources, will assign it an "''originality score''". This is also known as "''Plagiarism Detection Software''". Instructions for the submission of assignments can be found within each module on '''[http://www3.imperial.ac.uk/ict/services/e-learning/vle Blackboard]'''. '''Always ask in advance''' if you are unsure how any course submission works, or if you are having problems.

'''If you know you will not be able to submit work on time, <u>contact your tutor or course leader</u> as soon as possible''' - the sooner we know if you are having problems the more we can do to help you find a solution. If you miss a deadline for whatever reason, you '''must''' contact the course leader as soon as possible or you will not receive a mark for that assignment.

===Plagiarism===
The College has a simple attitude towards plagiarism; ''' "Do not plagiarise" '''.

The College's official statement on plagiarism is thus:<br>
<blockquote>"Plagiarism is interpreted by the College as '''the act of presenting the work of others as one's own work, without acknowledgement'''. Plagiarism is considered as academically fraudulent, and an offence against College discipline. '''The College considers plagiarism to be a major offence''', and subject to the disciplinary procedures of the College. <br>
"Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence lies '''not in the attitude or intention''' of the perpetrator, but '''in the action and in its consequences'''."<ref name=humhandbook1> ''Humanities Student Handbook'', Imperial College London, 2010</ref></blockquote>

The Library has extensive information on plagiarism and how to avoid it [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here]: you are encouraged to read and learn about plagiarism [http://www3.imperial.ac.uk/library/subjectsandsupport/plagiarism here].

----
<references />
----

==Accessing scientific journals and Bibliographic Searches==
The world's scientific and chemical data, information and knowledge resides in the following types of [http://en.wikipedia.org/wiki/Wikipedia:Reliable_source_examples reliable resources]:
# [https://vle.imperial.ac.uk/ '''Course Notes'''], written by experts in their field, which will often themselves cite:
# Primary '''[http://en.wikipedia.org/wiki/Peer_review Peer-reviewed]''' scientific journals ([http://rstl.royalsocietypublishing.org/content/6/69-80/3075.full.pdf+html 1665] - onwards), as ''articles'' with identified authors and hence provenance;
# Secondary '''Peer-reviewed''' scientific journals, as ''review articles/books'' with identified authors
# Tertiary sources such as ''abstracts'' gleaned from the above two sources, collaboratively authored (peer review by a different name) ''wikipedia''-like entries, some blogs and curated/edited database collections.
'''Golden rule:''' Always cite your sources, and if possible always cite a '''primary''' source.

''Silver rule:'' If you cite something, it means you have read it - do not cite something you haven't read first hand. (If "Smith et al" tell you that "Jones et al. tell us that oranges actually smell of peas", do not cite Jones yourself unless you have read that paper. If you cite Smith, you should say "Smith et al. report Jones' findings that oranges smell of peas")

''Bronze rule:'' Don't cite Wikipedia. It is far too transient to be a reliable resource.

===Scientific Journals (Primary and Secondary sources)===
Journals and books are identified using a formal citation within the article (or course notes). The style of this citation varies according to publication, but within chemistry it traditionally takes the form of a numeric superscript<ref name="scott">S. D. Rychnovsky, ''Org. Lett.,'' '''2006''', ''13'', 2895-2898. {{DOI|10.1021/ol0611346}}</ref>. Most journals are available online and, as long as the institution has paid for access, are readily available for viewing and searching. It has become almost universal to add the citation to a ''digital object identifier'', or '''DOI''' link which allows you to visit the journal directly<ref>N. Paski, Digital Object Identifiers for scientific data, ''Data Science Journal'', '''2005''', 12-20. {{DOI|10.2481/dsj.4.12 }}</ref>. Clicking the DOI link will take you directly to the journal page, presenting you with an abstract. Such links can be embedded in HTML or in PDF files. If only the DOI is given, it can be linked to by typing http://dx.doi.org/the-DOI-itself into the browser window (or it can be found [http://www.crossref.org/SimpleTextQuery/ here] if you know the author and title). The article can then be viewed in either HTML or PDF format.

# HTML (Hypertext markup language) ''vs'' PDF (Portable document format)
#* PDF is the format preferred for producing printed copies, and is just starting to be deployed in new Bibliographic database systems such as [http://www.mendeley.com Mendeley] and in 3D forms<ref>P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler and A. Ziegler, ''Trend. Biochem. Sci.'', '''2008''', ''33'', 408-412. {{DOI|10.1016/j.tibs.2008.06.004}}</ref>.
#* HTML is nowadays viewed by an increasing number of publishers as the medium best suited for '''enhancing''' the journal article beyond the printable form. Many articles nowadays include rotatable molecules, and other interactive media.
#Journals themselves divide into those published by '''learned societies''' and by purely commercial organisations. Between them, the four below should cover perhaps 90% of the journals that you will need to access.
#*The [http://pubs.acs.org/journals/jacsat/index.html American Chemical Society (ACS)] hosts many of the most useful articles quoted in lectures, and it also has some of the best examples of [http://pubs.acs.org/doi/media/10.1021/jp902176a/index.html enhanced] articles<ref>C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, ''J. Phys. Chem.'', '''2009''', {{DOI|10.1021/jp902176a}}</ref>.
#*The [http://www.rsc.org/Publishing/Journals/Index.asp Royal Society of Chemistry (RSC)] and its innovative [http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp Project Prospect] are another useful source.
#*[http://www.sciencedirect.com/ Science Direct] and [http://info.onlinelibrary.wiley.com/view/0/index.html Wiley online library] represent two major commercial publishers, each offering an aggregation of journals (a shopping mall if you like).
#*Most publishers now offer e.g. iPhone and iPad '''[[it:apps|apps]]''' to facilitate reading journals in this manner.
#The above represent the primary literature, and the articles there designed primarily for researchers. An excellent journal which addresses the more [http://en.wikipedia.org/wiki/Pedagogy pedagogic] aspects of chemistry is the [http://pubs.acs.org/journal/jceda8 Journal of Chemical Education] (abbreviated to ''J. Chem. Ed.'') which not only covers aspects of lectures, but also describes new and interesting laboratory experiments (some of which materialise in our own labs!).
#The central library has a chemistry librarian ('''Katharine Thompson''') and many chemistry [http://www3.imperial.ac.uk/library/subjectsandsupport/chemistry collections] and a complete alphabetic list of [http://www3.imperial.ac.uk/library/find/ejournals Journals], together with an [http://www3.imperial.ac.uk/library/find/documentdelivery Inter-library] loan (ILL) system for requesting reprints of journal and [http://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/0/0/0/57/64/BOOKILL books] not held on campus. A [http://www3.imperial.ac.uk/library/find/documentdelivery/secureelectronicdelivery fully digital version of the ILL] has recently been introduced ([https://unicorn.lib.ic.ac.uk/uhtbin/cgisirsi/oVGWvTH7co/0/0/57/64/JOURILL try this direct link here]), although (unlike most digital music) this has DRM (digital rights management). 

When writing a laboratory report (and in later years literature reports, essays and perhaps even your own published article), you will be expected to cite your sources, in the manner shown below.

===Tertiary sources (Wikipedia and others)===
Wikipedia and scientific blogs are very good sources of information, however be aware that these may be skewed by opinion, and facts may be distorted (though Wikipedia tries very hard to balance its articles for neutrality). Most chemistry sources tend to be fairly good as a first point of reference, but do not always assume it is correct; aim to back up the information with primary sources such as textbooks (particularly for equations), and cite the primary source.

''' Do not think that Wikipedia is bad ''' - on the contrary, Wikipedia is a marvelous resource, and its culture of knowledge philanthropy is something of which it should be rightfully proud. It is an excellent place to ''start'' your reading on a given subject, but when it comes to your authoritative writing '''you should cite a permanent''', peer-reviewed primary or secondary source, '''not''' Wikipedia.

----
<references />
----

===Bibliographic Searches===
[[Image:penicillin1.png|thumb|250px| Conversion of a penicillin core to a cephalosporin core ]]This part of the course deals with how to find information using ''search strings'' To illustrate this, we will define the following search:

'''The conversion of penicillin to cephalosporin.'''

In order to locate information, we need to introduce a few concepts:

* Boolean logical operators: '''AND''', '''SAME''', '''OR''', '''NOT''', '''XOR'''
* Wildcard (Stemming) characters: '''?''' vs '''*''' vs '''$''', '''*SULPHUR''' vs '''SUL*UR'''
* Grouping: '''A AND (B OR C)''' vs '''(A AND B) OR C'''
* Metadata-driven searches (fielded searches): '''author''', '''year-of-publication''' with the syntax '''author:Bloggs''' or '''au=Bloggs'''

A summary of these features for hte four main search engines can be found [http://www.websearchguide.ca/research/guifram.htm here]

====Web of Science, WOS====
[http://wos.mimas.ac.uk WOS] (Web of Science) uses:
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/h_advanced_fieldtags.html field tags] (such as title, author, publication name or organization)
* [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html Booleans]: AND, OR, NOT, SAME = Proximity operator,
* ? = [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_wildcd.html 1 wild character], SUL*UR and BIOLOG* (but not *NATAL, ie middle and right) = 1 or more wild character,
* (...) for [http://images.isiknowledge.com/WOKRS410B4/help/WOS/ht_operators.html grouped expressions], i.e. A NOT (B OR C). Examples:
** '''au=Welton t* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)'''
** '''TI=Reaction AND (TI=penicillin OR TI=cephalosporin)''' (141)
** '''(TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin''' (2683)
** '''TI=Carbapenem AND TI=Penicillin and ti=synthesis''' (8)

====Other Search Engines====

[http://en.wikipedia.org/wiki/Web_search_engine '''Robot Based Internet Indices''']
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google Scholar] with [http://scholar.google.com/intl/en/scholar/refinesearch.html advanced search tips]
* [http://www.scirus.com/srsapp/advanced/index.jsp SciRus] with [http://www.scirus.com/html/help/advanced.html advanced search tips]
* [http://academic.research.microsoft.com/ Microsoft Academic] with [http://academic.research.microsoft.com/About/Help.htm advanced search tips]
* [http://www.wolframalpha.com/examples/Chemistry.html Wolfram Alpha] accessed via their ''' ''advanced search'' ''' option
* [https://scifinder.cas.org/ SciFinder] natural language search (You will need to '''register for use''' [http://www3.imperial.ac.uk/library/find/databases/scifinderscholar here])

==Using software for preparation of reports and assignments==

There are a great deal of software combinations out there for preparing reports, however we shall only deal here with the most common combination.

===Using Microsoft Office with Endnote: Bibliographic Citation Software===
Many source of bibliographic information allow the export of the '''hit list''' to citation management software. Here the use of just one combination: WOS and Word+EndNote will be demonstrated, and you will have a chance to try it for yourselves in the lab sessions.

===Using Mendeley as an organiser===
Mendeley is a document organiser and knowledge mining system. The inputs to the program are citation lists obtained from bibliographic searches, and the associated Acrobat files for the documents themselves. Mendeley will index these, and allow you to search a collection of documents in a very similar manner to the '''iTunes''' music tracks. It also has a feature similar in concept to the iTunes '''Genius bar''', whereby articles in your collection can be compared with related articles found by others. For example, you could add a reprint associated with a lab course, and find similar articles which may provide you with additional information.

===Document submission through Blackboard and Turn-It-In===
When submitting a document through the online system, the only formats available are to submit as a PDF or as a Microsoft word document (.doc or .docx). Windows does not have the ability to produce a PDF without dedicated software, but [http://www.primopdf.com/ PrimoPDF] is a package that is available free of charge and behaves as a '''virtual printer''', delivering any document to a PDF format through the "print document" dialog box.

"Print to PDF" is readily available in Mac OS-X through the "print document" dialog box without installing additional software.

Submissions in Microsoft Word format are preferable as documents can be annotated by markers for delivering feedback, however conversion to PDF means that a wider range of softwares can be used, e.g., LaTeX, OpenOffice, Microsoft Works, Apple's Pages etc...

=IT for Laboratories and Reports=
Within the laboratory, many of the same skills are used as for lecture support with regard to bibliographic searches, however in a laboratory we are more interested in locating physical properties, synthetic routes and safety data.

==MSDS Safety Sheets==
The [http://www.sigmaaldrich.com Aldrich] catalogues can be searched for compounds and their MSDS safety sheets. These are useful for completing [http://www.hse.gov.uk/coshh/ COSHH] forms (Control of Substances Hazardous to Health). It is also useful for searching to find an Aldrich catalogue number (e.g. '''254738''') to acquire an MSDS data sheet which can then be stored in your Mendeley library for future access (e.g. using a mobile device).

==Property based searches==

A number of search tools can be used to find properties of compounds:

# Reaxys
#* "penicillin '''AND''' cephalosporin" as a '''text authors and more''' search. [https://www.reaxys.com/reaxys/WebHelp/All_Files/Text_Searching.htm Available Booleans]: '''AND''', '''NOT''', '''OR''', '''PROXIMITY''', '''NEAR''' and '''NEXT''' with * as a wildcard anywhere in the query (unlike WOS). Grouping not supported.
#* MP.MP=155-156 and IDE.MF=C29H28N2O6S1 and ORP.ORP=190-200 as a '''field search''' using '''Properties (Advanced)''' from the ''' Substances and Properties''' option and illustrating '''property ranges''' (which implies you have to be aware of the typical errors in many of the experimental measurements made on chemical instrumentation, such as melting points, optical rotations or as below NMR chemical shifts).
# The [http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Spectral Database for Organic Compounds SDBS] can be searched for matching observed spectral peaks (with estimated errors).
#* <sup>13</sup>C peaks: 163, 141, 133, 130, 129, 128, 98 (how big is the error?)
#* <sup>H</sup> peaks: 8.1,7.5,5.1,4.7 (how big is the error?
#* IR peak: 1733 (how big is the error?)
# The [http://webbook.nist.gov/chemistry/ NIST Chemistry WebBook] can be searched for thermodynamic and spectral properties
# Use of "added-value" properties such as [http://www.chemcalc.org/ ChemCalc] for molecular mass calculations as either '''C47H51NO14''' (Taxol), which predicts how the mass spectrum (MS) may look given a formula, or as input of a (MS-derived) '''accurate mass''' (say 148.052±0.0005) which is converted to the most likely formula.

==Using ChemDraw for 2D searches==
Using ChemDraw we can produce simple, tidy chemical structures for use in reports; it also has the very powerful tool that it can produce a '''SMILES''' string. This string is a way of 'encoding' chemical structure information e.g. '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2'''.

'''To output a SMILES string, select a structure in ChemDraw, and go to "Edit"->"Copy as"->SMILES.'''

Another type of string which encodes structural information is an '''InChI''' string; this can be copied out of ChemDraw in a very similar manner.

These strings can then be used to search structural databases:

* [http://www.chemspider.com/FullSearch.aspx ChemSpider] from the RSC can take a SMILES string and deliver information on that compound.
* The [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem database] can be searched using a '''SMILES''' or '''InChI''' string from ChemDraw; '''O=C1C(N)C2N1C(C(O)=O)C(C)(C)S2''' or '''InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)''' for "95% similar" (XX Hits)
* [http://www.chemnetbase.com/ ChemNetBase] has compilations of drugs, inorganic and organometallic and natural products which might prove useful for laboratories
* [http://www.orgsyn.org/ Organic syntheses] for specific molecule queries.
* Application of [http://www.reaxys.com Reaxys] for specific molecule queries: search for the melting point of aspirin.

==3D Structure based searches==
Smiles strings are a 1D way of encoding 2D information; when we start to consider larger molecules, and particularly biological molecules, consideration of the three dimensional properties becomes important, particularly within medicinal chemistry.

* The on-line [http://www.molecular-networks.com/online_demos/corina_demo.html Corina] service will take and convert a 1D SMILES string into 3D molecular coordinates - a 1D to 3D conversion!
*Substructure searching of the [http://www.portlandpress.com/pp/books/online/tiepac/session6/ch2.htm Cambridge Crystal Database] of organic and organometallic molecules for specific molecules and intermolecular interactions (e.g. unusual π-H-O hydrogen bonds). Using the ConQuest program:
** Name based search: '''penicillin''', 34.
** 2D structure based search: '''penicillin''', 54 (SMILES string is NOT accepted by this program)
** 2D structure based search for one of the four molecules shown above
** 3D structure based search for hydrogen bonds is shown in the lab course pages.
* Use of JMol to [http://www.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1w0e display complex protein structures]; there is also a demo page and Nanotech model for use.
* The [http://www.rcsb.org/pdb/advSearch.do Protein Databank] ([http://dx.doi.org/10.1107/S0108767307035623 DOI:10.1107/S0108767307035623]) can be used to locate many protein structures - keywords penicillin and tetrahedral should reveal any enzyme inhibited with an analogue of a transition state and relating to penicillin
* Also [http://www.proteinexplorer.org/ Protein Explorer] ([http://molvis.sdsc.edu/fgij/index.htm direct entry] and trying entering 1blh).
* Finally, there are [http://ndbserver.rutgers.edu/NDB/structure-finder/index.html alternate searches of biomolecules, including DNA] availble.

'''The materials presented here are by no means exhaustive, and there are many more search engines out there - if you find any good ones, feel free to add to this Wiki!'''

----
[[It:intro-2011|Go to Introduction]] | '''Go to Lectures''' | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:intro-2011

2014-10-11T13:09:56Z

Amckinle: /* Structure of the course */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Lectures]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=
[[Image:Logo.gif|thumb|154| ]]
''A series of lecture demonstrations and workshops by Dr. Andrew McKinley and Dr. Paul Wilde'' [email a.mckinley, p.wilde]<br>

==Course Overview==
The CIT course is designed to give you an introduction to using information services in your pursuit of your studies and to give you grounding in the tools used by the chemistry sector at large.

New services are being implemented all the time, and new features added to existing services; these pages are to serve as a guide to services, and the Wiki format allows anyone (with an IC login) to edit and update - this allows you to update the pages if you spot a mistake or become aware of a useful resource to share with others. Please do feel free to log in and annotate the pages if you see areas for improvement (though be aware that this cannot be done anonymously!)

As of October 2014 [http://www.cas.org/index there were]:
* 90,094,287 organic and inorganic molecules and substances (and increasing by the minute!)
* 65,925,835 biological sequences
* undertaking 57,830,398 described reactions
* for which there are >2 billion reported experimental properties
* described in >1 million scientific articles, 250,000 patents and 4,500 books published each year across 10,000 chemistry journals and databases.

Finding information is less like finding a "''needle in a haystack''"; more like finding a *'''specific piece of hay'''* across '''100 haystacks'''!

==Intended Learning Outcomes==
By the end of the course, students should:

# '''Recognise''' the wide availability of chemistry search tools.
# '''Understand''' the importance of correctly citing information sources.
# '''Identify''' appropriate search tools for a given task.
# '''Implement''' searches of the scientific literature to find information.
# '''Employ''' bibliographic tools to store information.
# '''Demonstrate''' appropriate citation of information sources.
# '''Generate''' enthusiasm for chemistry in a wider context through related reading.

Use these learning outcomes as a framework to measure your progress through the course - as you write your report, reflect upon these outcomes and ask yourself if you have achieved them!

==Structure of the course==

# [[It:lectures-2011|Self Study]] - Resources for you to use for your self study and exploration
#* [[It:lectures-2011#IT_for_lecture_courses.2C_tutorials_and_set_projects|'''IT for lecture courses, tutorials and set projects''']]
#** [[It:lectures-2011#Managing_your_location |Managing your computer desktop and location]]
#** [[It:lectures-2011#Accessing_lecture_notes_and_submission_of_assignments |Accessing lecture notes and submission of assignments]]
#** [[It:lectures-2011#Accessing_scientific_journals_and_Bibliographic_Searches |Bibliographic searches and accessing scientific journals]]
#** [[It:lectures-2011#Using_software_for_preparation_of_reports_and_assignments |Using software for preparation of reports and assignments]]
# [[It:coursework-2011|Coursework classes]] Run in Week 2 of Term 1.
# [[It:assignment-2011|Assignment]]

Your CIT skills will also be employed all throughout your course, and you will be able to use skills in the following areas.
# [[It:lectures-2011#IT_for_Laboratories_and_Reports |'''IT for laboratories and reports''']]
#* [[It:lectures-2011#MSDS_Safety_Sheets|MSDS Safety sheets]]
#* [[It:lectures-2011#Property_based_searches |Property based searches]]
#* [[It:lectures-2011#Using_ChemDraw_for_2D_searches |Using ChemDraw (and others) for 2D structure based searches]]
#* [[It:lectures-2011#3D_Structure_based_searches |3D Structure-based searches and Molecular Biology]]

===Workshop slots===
You will undertake your work in the allocated workshop slots on Thursday 16th October (A1, A2, B1) and Friday 17th October (B2, C1, C2)

During these hours the computer suites (Room 232 and Room 135) are reserved for your group and we will be available to answer your questions in the class. Please do feel free to work on this course outside of these hours - students doing course and study work always have priority over students using the computers for non-chemistry related uses.

===Lab Coursework===

You are encouraged to work through the examples in this course at your own pace, and you should not feel that everything must be completed in the scheduled sessions.<br>
There is one assignment provided for this course, and details may be found [[It:assignment-2011|here]]. There is no 'start time' for this, but all projects must be submitted online using the TurnItIn gateway by 5pm Friday of Week 6 (5pm, Friday 14th November). You will obtain feedback on your report, and you will also be able to see the TurnItIn "Originality report" for your submission.
The coursework is entirely formative; this means that it is used solely for feedback and does not contribute to your degree total. However, as discussed during Induction Week, such coursework is vital for developing skills that you will use in the future, and this is your opportunity for gaining feedback.

===Course History===
This course is heavily based on that delivered by Professor Henry Rzepa from 1995 to 2010; the notes presented for this course are derived from those written by Prof. Rzepa, and much of the content is directly taken from his notes which are still available for reference on this wiki.

----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Lectures]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:intro-2011

2014-10-11T13:09:22Z

Amckinle: /* Structure of the course */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Lectures]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=
[[Image:Logo.gif|thumb|154| ]]
''A series of lecture demonstrations and workshops by Dr. Andrew McKinley and Dr. Paul Wilde'' [email a.mckinley, p.wilde]<br>

==Course Overview==
The CIT course is designed to give you an introduction to using information services in your pursuit of your studies and to give you grounding in the tools used by the chemistry sector at large.

New services are being implemented all the time, and new features added to existing services; these pages are to serve as a guide to services, and the Wiki format allows anyone (with an IC login) to edit and update - this allows you to update the pages if you spot a mistake or become aware of a useful resource to share with others. Please do feel free to log in and annotate the pages if you see areas for improvement (though be aware that this cannot be done anonymously!)

As of October 2014 [http://www.cas.org/index there were]:
* 90,094,287 organic and inorganic molecules and substances (and increasing by the minute!)
* 65,925,835 biological sequences
* undertaking 57,830,398 described reactions
* for which there are >2 billion reported experimental properties
* described in >1 million scientific articles, 250,000 patents and 4,500 books published each year across 10,000 chemistry journals and databases.

Finding information is less like finding a "''needle in a haystack''"; more like finding a *'''specific piece of hay'''* across '''100 haystacks'''!

==Intended Learning Outcomes==
By the end of the course, students should:

# '''Recognise''' the wide availability of chemistry search tools.
# '''Understand''' the importance of correctly citing information sources.
# '''Identify''' appropriate search tools for a given task.
# '''Implement''' searches of the scientific literature to find information.
# '''Employ''' bibliographic tools to store information.
# '''Demonstrate''' appropriate citation of information sources.
# '''Generate''' enthusiasm for chemistry in a wider context through related reading.

Use these learning outcomes as a framework to measure your progress through the course - as you write your report, reflect upon these outcomes and ask yourself if you have achieved them!

==Structure of the course==

# [[It:lectures-2011|Self Study]] - Resources for you to use for your self study and exploration
#* [[It:lectures-2011#IT_for_lecture_courses.2C_tutorials_and_set_projects|'''IT for lecture courses, tutorials and set projects''']]
#** [[It:lectures-2011#Managing_your_location |Managing your computer desktop and location]]
#** [[It:lectures-2011#Accessing_lecture_notes_and_submission_of_assignments |Accessing lecture notes and submission of assignments]]
#** [[It:lectures-2011#Accessing_scientific_journals_and_Bibliographic_Searches |Bibliographic searches and accessing scientific journals]]
#** [[It:lectures-2011#Using_software_for_preparation_of_reports_and_assignments |Using software for preparation of reports and assignments]]

# [[It:coursework-2011|Coursework classes]] Run in Week 2 of Term 1.
# [[It:assignment-2011|Assignment]]

Your CIT skills will also be employed all throughout your course, and you will be able to use skills in the following areas.
# [[It:lectures-2011#IT_for_Laboratories_and_Reports |'''IT for laboratories and reports''']]
#* [[It:lectures-2011#MSDS_Safety_Sheets|MSDS Safety sheets]]
#* [[It:lectures-2011#Property_based_searches |Property based searches]]
#* [[It:lectures-2011#Using_ChemDraw_for_2D_searches |Using ChemDraw (and others) for 2D structure based searches]]
#* [[It:lectures-2011#3D_Structure_based_searches |3D Structure-based searches and Molecular Biology]]

===Workshop slots===
You will undertake your work in the allocated workshop slots on Thursday 16th October (A1, A2, B1) and Friday 17th October (B2, C1, C2)

During these hours the computer suites (Room 232 and Room 135) are reserved for your group and we will be available to answer your questions in the class. Please do feel free to work on this course outside of these hours - students doing course and study work always have priority over students using the computers for non-chemistry related uses.

===Lab Coursework===

You are encouraged to work through the examples in this course at your own pace, and you should not feel that everything must be completed in the scheduled sessions.<br>
There is one assignment provided for this course, and details may be found [[It:assignment-2011|here]]. There is no 'start time' for this, but all projects must be submitted online using the TurnItIn gateway by 5pm Friday of Week 6 (5pm, Friday 14th November). You will obtain feedback on your report, and you will also be able to see the TurnItIn "Originality report" for your submission.
The coursework is entirely formative; this means that it is used solely for feedback and does not contribute to your degree total. However, as discussed during Induction Week, such coursework is vital for developing skills that you will use in the future, and this is your opportunity for gaining feedback.

===Course History===
This course is heavily based on that delivered by Professor Henry Rzepa from 1995 to 2010; the notes presented for this course are derived from those written by Prof. Rzepa, and much of the content is directly taken from his notes which are still available for reference on this wiki.

----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Lectures]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:intro-2011

2014-10-11T12:59:34Z

Amckinle: /* Course Overview */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Lectures]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=
[[Image:Logo.gif|thumb|154| ]]
''A series of lecture demonstrations and workshops by Dr. Andrew McKinley and Dr. Paul Wilde'' [email a.mckinley, p.wilde]<br>

==Course Overview==
The CIT course is designed to give you an introduction to using information services in your pursuit of your studies and to give you grounding in the tools used by the chemistry sector at large.

New services are being implemented all the time, and new features added to existing services; these pages are to serve as a guide to services, and the Wiki format allows anyone (with an IC login) to edit and update - this allows you to update the pages if you spot a mistake or become aware of a useful resource to share with others. Please do feel free to log in and annotate the pages if you see areas for improvement (though be aware that this cannot be done anonymously!)

As of October 2014 [http://www.cas.org/index there were]:
* 90,094,287 organic and inorganic molecules and substances (and increasing by the minute!)
* 65,925,835 biological sequences
* undertaking 57,830,398 described reactions
* for which there are >2 billion reported experimental properties
* described in >1 million scientific articles, 250,000 patents and 4,500 books published each year across 10,000 chemistry journals and databases.

Finding information is less like finding a "''needle in a haystack''"; more like finding a *'''specific piece of hay'''* across '''100 haystacks'''!

==Intended Learning Outcomes==
By the end of the course, students should:

# '''Recognise''' the wide availability of chemistry search tools.
# '''Understand''' the importance of correctly citing information sources.
# '''Identify''' appropriate search tools for a given task.
# '''Implement''' searches of the scientific literature to find information.
# '''Employ''' bibliographic tools to store information.
# '''Demonstrate''' appropriate citation of information sources.
# '''Generate''' enthusiasm for chemistry in a wider context through related reading.

Use these learning outcomes as a framework to measure your progress through the course - as you write your report, reflect upon these outcomes and ask yourself if you have achieved them!

==Structure of the course==

# [[It:lectures-2011|Lecture classes]] (Pippard LT, Level 5, Sherfield Building)
#* [[It:lectures-2011#IT_for_lecture_courses.2C_tutorials_and_set_projects|'''IT for lecture courses, tutorials and set projects''']]
#** [[It:lectures-2011#Managing_your_location |Managing your computer desktop and location]]
#** [[It:lectures-2011#Accessing_lecture_notes_and_submission_of_assignments |Accessing lecture notes and submission of assignments]]
#** [[It:lectures-2011#Accessing_scientific_journals_and_Bibliographic_Searches |Bibliographic searches and accessing scientific journals]]
#** [[It:lectures-2011#Using_software_for_preparation_of_reports_and_assignments |Using software for preparation of reports and assignments]]
#* [[It:lectures-2011#IT_for_Laboratories_and_Reports |'''IT for laboratories and reports''']]
#** [[It:lectures-2011#MSDS_Safety_Sheets|MSDS Safety sheets]]
#** [[It:lectures-2011#Property_based_searches |Property based searches]]
#** [[It:lectures-2011#Using_ChemDraw_for_2D_searches |Using ChemDraw (and others) for 2D structure based searches]]
#** [[It:lectures-2011#3D_Structure_based_searches |3D Structure-based searches and Molecular Biology]]
# [[It:coursework-2011|Coursework classes]]
# [[It:assignment-2011|Assignment]]

===Workshop slots===
You will be allocated one of four groups (A1, A2, B1 and B2, '''listings can be found [[Media:Y1-labgroups-2011.pdf|here]]'''). Workshops take place in the '''Computing Room''' on the First floor of '''Chemistry C1, room 135''' in your usual lab groups with two 3hr sessions per student.

* Group A1: Thursday 11th October and Friday 26th October 2012, 14:00-17:00
* Group A2: Thursday 18th October and Friday 2nd November 2012, 14:00-17:00
* Group B1: Monday 8th October and Monday 22nd October 2012, 13:00-16:00
* Group B2: Monday 15th October and Monday 29th October 2012, 13:00-16:00

During these hours the computer suite is reserved for your group and demonstrators will be available to answer your questions in the class. Please do feel free to work on this course outside of these hours - students doing course and study work always have priority over students using the computers for non-chemistry related uses.

===Lab Coursework===

You are encouraged to work through the examples in this course at your own pace, and you should not feel that everything must be completed in the scheduled sessions.<br>
There is one assignment provided for this course, and details may be found [[It:assignment-2011|here]]. There is no 'start time' for this, but all projects must be ready for presentation by the 9th November:

* '''Presentations will be made at 14:00, Friday 9th November'''

Everyone will be encouraged to participate and you will be presenting not only to staff, but also to your peers!

===Course History===
This course is heavily based on that delivered by Professor Henry Rzepa from 1995 to 2010; the notes presented for this course are derived from those written by Prof. Rzepa, and much of the content is directly taken from his notes which are still available for reference on this wiki.

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[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Lectures]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

It:intro-2011

2014-10-11T12:56:21Z

Amckinle: /* Chemical Information Technology 2014-2015 */

[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Lectures]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]

=Chemical Information Technology 2014-2015=
[[Image:Logo.gif|thumb|154| ]]
''A series of lecture demonstrations and workshops by Dr. Andrew McKinley and Dr. Paul Wilde'' [email a.mckinley, p.wilde]<br>

==Course Overview==
The CIT course is designed to give you an introduction to using information services in your pursuit of your studies and to give you grounding in the tools used by the chemistry sector at large.

New services are being implemented all the time, and new features added to existing services; these pages are to serve as a guide to services, and the Wiki format allows anyone (with an IC login) to edit and update - this allows you to update the pages if you spot a mistake or become aware of a useful resource to share with others. Please do feel free to log in and annotate the pages if you see areas for improvement (though be aware that this cannot be done anonymously!)

As of August 2012 [http://www.cas.org/cgi-bin/cas/regreport.pl there were]:
* 69,068,881 organic and inorganic molecules and substances
* 63,925,835 biological sequences
* undertaking 57,830,398 described reactions
* for which there are >2 billion reported experimental properties
* described in >1 million scientific articles, 250,000 patents and 4,500 books published each year across 10,000 chemistry journals and databases.

Finding information is less like finding a "''needle in a haystack''"; more like finding a *'''specific piece of hay'''* across '''100 haystacks'''!

==Intended Learning Outcomes==
By the end of the course, students should:

# '''Recognise''' the wide availability of chemistry search tools.
# '''Understand''' the importance of correctly citing information sources.
# '''Identify''' appropriate search tools for a given task.
# '''Implement''' searches of the scientific literature to find information.
# '''Employ''' bibliographic tools to store information.
# '''Demonstrate''' appropriate citation of information sources.
# '''Generate''' enthusiasm for chemistry in a wider context through related reading.

Use these learning outcomes as a framework to measure your progress through the course - as you write your report, reflect upon these outcomes and ask yourself if you have achieved them!

==Structure of the course==

# [[It:lectures-2011|Lecture classes]] (Pippard LT, Level 5, Sherfield Building)
#* [[It:lectures-2011#IT_for_lecture_courses.2C_tutorials_and_set_projects|'''IT for lecture courses, tutorials and set projects''']]
#** [[It:lectures-2011#Managing_your_location |Managing your computer desktop and location]]
#** [[It:lectures-2011#Accessing_lecture_notes_and_submission_of_assignments |Accessing lecture notes and submission of assignments]]
#** [[It:lectures-2011#Accessing_scientific_journals_and_Bibliographic_Searches |Bibliographic searches and accessing scientific journals]]
#** [[It:lectures-2011#Using_software_for_preparation_of_reports_and_assignments |Using software for preparation of reports and assignments]]
#* [[It:lectures-2011#IT_for_Laboratories_and_Reports |'''IT for laboratories and reports''']]
#** [[It:lectures-2011#MSDS_Safety_Sheets|MSDS Safety sheets]]
#** [[It:lectures-2011#Property_based_searches |Property based searches]]
#** [[It:lectures-2011#Using_ChemDraw_for_2D_searches |Using ChemDraw (and others) for 2D structure based searches]]
#** [[It:lectures-2011#3D_Structure_based_searches |3D Structure-based searches and Molecular Biology]]
# [[It:coursework-2011|Coursework classes]]
# [[It:assignment-2011|Assignment]]

===Workshop slots===
You will be allocated one of four groups (A1, A2, B1 and B2, '''listings can be found [[Media:Y1-labgroups-2011.pdf|here]]'''). Workshops take place in the '''Computing Room''' on the First floor of '''Chemistry C1, room 135''' in your usual lab groups with two 3hr sessions per student.

* Group A1: Thursday 11th October and Friday 26th October 2012, 14:00-17:00
* Group A2: Thursday 18th October and Friday 2nd November 2012, 14:00-17:00
* Group B1: Monday 8th October and Monday 22nd October 2012, 13:00-16:00
* Group B2: Monday 15th October and Monday 29th October 2012, 13:00-16:00

During these hours the computer suite is reserved for your group and demonstrators will be available to answer your questions in the class. Please do feel free to work on this course outside of these hours - students doing course and study work always have priority over students using the computers for non-chemistry related uses.

===Lab Coursework===

You are encouraged to work through the examples in this course at your own pace, and you should not feel that everything must be completed in the scheduled sessions.<br>
There is one assignment provided for this course, and details may be found [[It:assignment-2011|here]]. There is no 'start time' for this, but all projects must be ready for presentation by the 9th November:

* '''Presentations will be made at 14:00, Friday 9th November'''

Everyone will be encouraged to participate and you will be presenting not only to staff, but also to your peers!

===Course History===
This course is heavily based on that delivered by Professor Henry Rzepa from 1995 to 2010; the notes presented for this course are derived from those written by Prof. Rzepa, and much of the content is directly taken from his notes which are still available for reference on this wiki.

----
[[It:intro-2011|Go to Introduction]] | [[It:lectures-2011|Go to Lectures]] | [[It:coursework-2011|Go to Coursework]] | [[It:assignment-2011|Go to Assignment]] | [[It:software-2011|List of Software]] | [[It:searches-2011|List of Searches]]