ChemWiki - User contributions [en]

Rdm:nmr-publishing

2020-02-07T10:33:12Z

Lp202: /* Publishing the NMR research data (stage 5) */

= Publishing the NMR research data (stage 5) =

#[[Image:Orcid13.jpg|right|300px|step 13]]If you have not already done so, see instructions for [[orcid|registering an ORCID]] (stage 1) and connecting it to the [http://data.hpc.imperial.ac.uk Imperial College Data Repository] (stage 2)
##Log in to the [http://data.hpc.imperial.ac.uk Imperial College Data Repository] and select '''deposit data'''
##You will need to complete the fields indicated with red arrows, Make sure you know the location of the files shown below, as acquired in the previous section.
###[[Image:deposit1.jpg|right|300px|step 14]]The minimum number of files you need is '''two''', a '''Chemdraw .cdxml''' file and a Bruker '''.zip''' archive (or Jeol .jdf file) containing the raw data.
##[[Image:Share-collection.jpg|right|300px|step 14]]With the item '''Member of collection / collaboration''' you should have the authority to make your deposition a member of the '''1st Year undergraduate synthesis laboratory''' (which already has {{DOI|10.14469/hpc/6215}} assigned). If you do not have this authority, contact [mailto:rzepa@ic.ac.uk?subject=Synthesis%20lab%20authority%20and%20help Prof, Rzepa]
##[[Image:deposit2.jpg|right|300px|step 15]]Press the submit button when you should get the response shown. Your publication DOI is shown with the '''red arrow'''. Record this in your notebook.
#[[Image:deposit3.jpg|right|300px|step 16]]Click on the DOI link to show the full record of your data.

== Outcome of the publication process ==
#The Spectrometer data. It contains all the information collected by the instrument such as the FID.
#A licence file specific to the spectrometer data that allows you to use (un)licensed MestreNova to generate and view the spectrum. On college computers you are already using a licensed copy of MestreNova so this file is not actually needed. It allows others without a previously licensed version of MestreNova to view the spectrum. This file is created automatically during the publication process.
#The MestreNova transformation of the spectrometer data, which can contain much additional information about the molecule if added. It is optional.
#The license file for the Mestrenova transformation, corresponding to the spectrometer data in 2. Again, with an already licensed version of Mestrenova you do not need to use this file. This file is created automatically during the publication process.
#A JCAMP-DX version of the spectrum. It contains only the spectrum and no actual spectrometer data. It is included because JCAMP-DX is a widely used format for expressing NMR spectra. It can be viewed by Mestrenova. This file is optional.
#The InChI molecular descriptor for the compound corresponding to the data (as generated from your ChemDraw file). InChI is an international standard for identifying molecules. It is generated automatically by the publication process.
#The InChI Key molecular descriptor for the compound corresponding to the data (as generated from your ChemDraw file) and is a shortened version of the InChI identifier. It can be used for searches of any molecule with the same key on the Web and in most chemical search engines. It is generated automatically by the publication process.

= Summary of what you will have achieved at the end of stage 5=

You will have:

#Registered for an ORCID (Open Researcher and Collaborator Identifier) using your Imperial College affiliation and credentials.
#Authorised the Imperial College Data Repository to associate research data publications with your ORCID account.
#Started to prepare a set of data files for deposition in the Data Repository, including a Chemdraw file describing an associated molecule.
#Retrieved one (or more) NMR data files from the appropriate Spectrometer and checked the spectrum resulting using the Mestrenova program.
#Published the data files on the Repository to be associated with your ORCID and obtained a DOI (Digital object identifier) for your publication.

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Questions, please contact [mailto:rzepa@ic.ac.uk?subject=Synthesis%20lab%20authority%20and%20help Prof, Rzepa]

----

Return to [[Rdm:synthesis-lab|Overview of files for NMR Data publication in synthesis lab ]] (stage 3)

Return to [[Rdm:nmr-bruker|Retrieving an NMR data file from the Bruker Spectrometer]] (used for Synthesis course) (stage 4)

Return to [[Rdm:nmr-jeol|Retrieving an NMR data file from the Jeol Spectrometer]] (not currently used for Synthesis course) (Stage 4)

Return to [[orcid|ORCID]] (stages 1+2)

Questions, please contact [mailto:rzepa@ic.ac.uk?subject=Synthesis%20lab%20authority%20and%20help Prof, Rzepa]

----

Chemtracker Project

2017-05-09T17:33:14Z

Lp202: Added type descriptors from Year 3 labs Proposal document

This page is a collaborative live document concerning the [https://www.imperial.ac.uk/about/leadership-and-strategy/provost/vice-provost-education/the-excellence-fund-for-learning-and-teaching-innovation/ Excellence Fund for Leaning and Teaching Innovation] grant by David Mountford, Laura Patel, João Pedro Malhado and Oscar Ces. This page is to track the evolution of the project, and not likelly to be of use to anyone else.

Most of this coming from on the 17th March, 23rd March {{fontcolor1|green|30th March}}

{{fontcolor1|green|Latest additions in green.}}

==General ideas==

Removal of marks from lab curriculum.

Less chasing of marks, more of a focus on the achievement of specific skills and the ability to demonstrate these skills across a number of contexts.

Tick boxes with student commentary will form the basis of the mark that is allocated for the course.
Academic judgement over marks.

Will students want a mark scheme or will we be required to provide additional details on how the ticks will be converted into marks?

Feedback to students after the experiment could be better, how best to do this in a way that is not too onerous on course leaders?

==Lab Overview==
Each lab course/experiment/question/problem would be broken down into the following constituent parts.
* Consulting literature - Research problem or question.
* Designing experiment.
* Preparing for experiment
** Including risk assessment.
* Doing the experiment
** Keeping records.
** Lab practice
** Synthesis plug-in
*** SOPs
*** Basic/Advanced
* Processing and Analysing. Inferences.
* Concluding with respect to hypothesis.
* Communicating and defending. Integrating transferable skills, professional/soft skills eg teamwork, leadership, presentation skills etc. NB Not everyone will want to be a leader or a presenter…

==Components of the presentation==
# What it is that we want to do in the lab in terms of changing the way that students approach the lab, how they learn in the lab and what they learn.
# Skills passport as a method to allow us to run very different labs in a very different way.
# Demonstrate that the passport is transferable to other departments.
# Q&A
10 minutes for the presentation with 10 minutes for the Q&A.

{{fontcolor1|green|Must place strong emphasis on the problems with the current lab course.}}
{{fontcolor1|green|Build and improve on NSS.}}
{{fontcolor1|green|Independent learning part is missing. Few opportunities for students to think.}}
{{fontcolor1|green|Enabler versus enhancer.}}
{{fontcolor1|green|Make use of clear figures to show what it is that we're proposing.}}

===Notes===
* The Hackspace is specifically transferable to other departments.
* Labs do not need to be tired to the bench.
* There should be a reward for effort and progress from one year to the next, not just absolute achievement in a single year.
* The passport tool should be able to demonstrate a student’s progress during their time here and give an opportunity for a student to reflect on their ability and where appropriate or desirable change how they engage with the labs.
* Remove marks associated with individual labs.
* Provide students with an opportunity for self-assessment.
* Points to get across: Our labs are evolving, this is something that we are already doing (LEGO lab as an example) but to continue with this development, additional changes need to be made in terms of assessment and the broader design of the curriculum.

* {{fontcolor1|green|Assignment of marks is going to be vital, must be seen to be credible and transparent as well as reproducible for 150+ students each year.}}
* {{fontcolor1|green|Limited independence in Year 1 - a safety net, with independence growing over time to the point where they truly are driving the curriculum (Year 2/3?).}}

==Skills Passport v1.0==

[[File:Chemtracker_workflow01.png|frame|none|Possible workflow for the chemtracker tool. ([[:File:Chemtracker_workflow01.svg|Better to edit version.]])]]

===Notes===
* Specific criteria for each component of the lab, perhaps 3-4 for each, though there would likely need to be more for specific processes and procedures in the synthetic lab. Pull down menu type.
* “Knows”, “knows how”, “shows how”, “does”, “improves style”.
* Possibly with “familiar”, “competent”, “confident” descriptors to further build on the detail provided in the passport.

{{fontcolor1|green|Include histogram of progress in tracker so that students can track their progress over the year.}}

===OpenBadges===
[https://openbadges.org/get-started/issuing-badges/ OpenBadges] is a technological platform which could be used to implement the passport idea. The badge itself is an openly developed electronic token which is meant to represent some sort of certification (its value depends on the issuer identity). Our use of the badges would correspond to developing a platform for issuing and managing a portfolio of badges. There are several [https://openbadges.org/about/participating-services/ open source implementations] that one could seek to adapt.

Moodle is able to award OpenBadges. Check if Blackboard could do the same (contact Blackboard Inc.). - some potentially useful links: https://help.blackboard.com/Learn/Instructor/Performance/Achievements https://elearn.southampton.ac.uk/blackboard/achievements/ https://sites.google.com/site/openbadgesinhighereducation/blackboard and maybe https://www.coursesites.com/webapps/Bb-sites-course-creation-BBLEARN/pages/getstarted.html

Useful [https://docs.google.com/spreadsheet/ccc?key=0AnUOR-0CBMsTdE1hWnJnYXlNdnktVUlhWWdjVzFVR0E&usp=drive_web#gid=0 spreadsheet] and [http://www.digitalme.co.uk/assets/pdf/DigitalMe-Badge-Design-Canvas.pdf canvas] for helping with the design of the system (useful even if OpenBadges end up not being our chosen solution).

We can explore the idea that our badges live beyond the scope of our labs, and be used by students in approaching future employers.

==Purpose of the experiment==
One of the reasons driving the proposed changes to the lab curriculum is the perception that lab sessions and lab scripts have become over-prescriptive, students end up following the recipe they are given with little learning gain. Most importantly, ''students almost completely miss the crucial steps of setting the goals, and designing and planning the experiment to achieve them''. The emphasis is therefore to give students more responsibility in the development of their lab experience. This increased student responsibility comes mostly in two forms: a more active role in the design of the experiments; more freedom in the choice of experiments and lab curriculum.

We propose to reframe lab experiments into a new classification, more inline with current/research lab practice and less with outdated discipline subdivisions. All experiments should keep a clear relevance for chemistry.

===Make it===
The core of these experiments is the synthesis of molecules or materials. They should be structured such that the student investigates a synthetic route, choosing appropriate apparatus and procedures, as well as purification and characterization methods. The procedure should not be given but rather investigated. Projects could be complemented with further characterization and use of the synthesised compounds, but the emphasis is on the synthesis work.

===Build it===
These experiments consist on the construction of a device, object or computer program to perform a specific task. A very clear and well defined design goal is given to students which need to work towards matching that goal.

(While at an abstract level the synthesis of a molecule is the construction of an object, the specificity of methods and considerations involved in synthesis work, and the 8 orders of magnitude difference in size, grant it to be treated under a different category from build it.)

===Prove it===
The focus of these experiments is in the formulation of an hypothesis in a form that can be tested in the laboratory, and the development of a procedure to test this hypothesis. Students should be able to choose the concept they want to prove (it could be a concept familiar from lectures). There should be an emphasis on the critical analysis of the results and in the discussion of whether the collected data is enough to prove or disprove the hypothesis.

===Hack it===
It consists of addressing a more complex problem, usually involving an interdisciplinary approach.
These could be tackling a practical societal problem or a complex technical problem (for example development or certification of a sensor).
They should develop some sort of project management skills, could be done as a group, and involve a proposal type or presentation component.

==Type of lab space==
* Synthetic
* Hackspace
* PhysChem lab
* Computer room

Lab context should not be defining of an activity, Make it could be in any lab type, a single experiment could, perhaps should provide opportunities for exploration in multiple arenas.

; Year 1 : Skills
; Year 2 : Directed towards lab activities with some integration of areas within a single experiment.
; Year 3 : Students all on their own to decide how they want to investigate and put things into practice.

Experiments should expand beyond just giving a student a script to follow.

Students as scientists

Authentic assessment is key rather than assessment being a mark collecting exercise.

4 types of module/environment – Develop experiments within these types.

Where an experiment exists that is to be retained it would be developed into the new format.

Experiments in Year 3 would be developed into mini-projects.

===Make It! Module===
Mimi – integrated lab and experiment design. Would be good to have on board with design.

Year 3 Proposal document:

•       Make it! projects – In year 3 students plan and carry out syntheses with an investigative purpose and/or employing data-oriented approaches (cf. Dial-a-Molecule). For example: preparing two catalysts and comparing their selectivity; preparing a molecule ''via'' two different multi-step
routes and comparing the outcomes; optimising a reaction protocol or literature procedure. The project is primarily synthetic work, structured such that the student investigates a synthetic route, choosing appropriate apparatus and procedures, as well as purification and characterisation methods, but an element of making comparisons must be incorporated in year 3.

===Prove It! Module===
Year 3 Proposal document:

•       Prove it! projects – In year 3 students design and carry out experimental work attempting to prove, within their selected specific chemical system, their hypothesis derived from concepts encountered in lectures or other study. Students themselves select the concept(s) and propose the project. There should be an
emphasis on the critical analysis of the results and in the discussion of whether the collected data is enough to prove or disprove the hypothesis. For example: Prove the relationship between size and colour of quantum dots. Projects may be primarily physical/analytical, synthetic (eg. prove the selectivity of a given reagent), or computational (eg. prove ''in silico'' the identities of kinetic and thermodynamic products of a reaction type).

===Measure It! Module (<- Build It! Module)===
Year 3 Proposal document:

•       Measure it! projects – Progressing from the LEGO spectrometer labs which instill a ‘know how it works’ mentality in addition to principles of measurement science, in year 3 students may design and build a more complex instrument, plan and carry out a challenging measurement, make measurements to investigate a phenomenon.

===Hack It! Module ===
====Paul Wilde – 20 potential topics to explore (sarin level detector, Pt extraction from cancer patients etc)====
Year 3 lab in 2 parts. Part 1 similar to what was done previously, conceptual and theoretical, part 2 would be the practical application/prototyping. Part 1 needed to do part 2 but no need to do part 2 if you have done part 1.

Flexibility of approach and on the interest of the student.

Group work.

Proposal, presentation, prototype milestones.

Year 3 Proposal document:

•       Hack it! projects – Students carry out research, and potentially practical work based in the Advanced Hack Space, addressing a more complex problem, usually involving an interdisciplinary approach. These could be tackling a practical societal problem or a complex technical problem. For example: can precious metals lost from catalytic converters be recovered from road surfaces?; practical development or certification of a sensor. Projects must be compatible with the deskilled approaches accessible in the hack space.

==Practical concerns==
Academic Workload model should reflect the time needed to develop a new lab.

Number of hours needed to design a course needs to be established to go to AA (70 hours too conservative).

Those contributing need to be amply compensated for their time and have this recognised.

{{fontcolor1|green|Year 3 project options - How will these fit with the curriculum? What will the scope of the project be? A project in each of the environments or an opportunity to specialise?}}

==RSC Collaboration==

{{fontcolor1|green|Discussions with RSC early on is going to be essential.}}
* {{fontcolor1|green|Accreditation concerns.}}
* {{fontcolor1|green|Possible technical support or input into the passport.}}
* {{fontcolor1|green|Publicity and potential wider roll out of the scheme.}}
* {{fontcolor1|green|RSC funding opportunities?}}

{{fontcolor1|green|Advisory board/ steering group which includes industry input.}}
* {{fontcolor1|green|P&G, GSK someone from biodiagnostics.}}

==To do:==
; David : Outline for presentation based on discussions. {{fontcolor1|green|Approach RSC over partnering.}}
; Laura : Year 3 plan of action. {{fontcolor1|green|Begin thinking about pictorial representations of approach.}}
; Joao : Look into “badges” as an alternative to passport. Talk to PW about ideas for new labs.

Chemtracker Project

2017-04-07T13:08:44Z

Lp202: /* OpenBadges */

Chemtracker Project

2017-04-07T12:55:45Z

Lp202: /* OpenBadges */

Chemtracker Project

2017-04-03T16:27:05Z

Lp202: /* Lab Overview */

Mod:writeup

2014-10-04T08:35:18Z

Lp202:

See also: [[mod:organic|Module 1C]],[[Mod:inorganic|Inorganic Computational lab]], [[Mod:phys3|Physical computational lab]],[[File:Wiki-writeup.png|right|250px]][[Mod:phys3|Module 3]],[[Mod:writeup|Writing up]],[[Mod:Cheatsheet|cheatsheet]]
== The expected length of the report ==
A Wiki does not have pages as such. But as a very rough guide, expect to produce something the equivalent of about six printed pages (although you can invoke ''pop-ups'' and the like which make a page count only very approximate). Use graphics reasonably sparingly, and to the point.

= Why Wiki? =
Since everyone is used to using [http://www.wordonwiki.com Microsoft Word], why do we [[talks:rzepa2011|use a Wiki]] for this course? Well, the Wiki format has several advantages.
#A full revision and fully dated history across sessions is kept (Word only keeps this during a session). This is more suited for laboratory work, where you indeed might need to go back to a particular day and experiment to check your notes.
#The (chemistry) Wiki allows you to include molecule coordinates, vibrations and MO surfaces which can be rotated and inspected, along with other chemical extensions. Word does not offer this.
#The Wiki allows you to include "zoomable" graphics in the form of SVG (which Gaussview generates), and access to the 17-million large [http://commons.wikimedia.org/wiki/Main_Page WikiCommons] image library, as well as access to the Wikipedia InterWiki.
#The [[w::Help:Template|template]] concept allows pre-formated entry. There are lots of powerful [[w:Category:Chemical_element_symbol_templates|chemical templates]] available.
#Autonumbered referencing, and particularly cross-referencing, is actually easier than using Word.
#You (and the graders) can access your report anywhere online, it is not held on a local hard drive which you may not have immediate access to.
#It has automatic date and identity stamps for ALL components, which means we can assess that part of the report handed in by any deadline, and deal separately with anything which has a date-stamp past a given deadline. A Word document has only a single date-and-time stamp and so deadlines must apply to the whole document.
#And we have been using Wikis for course work since '''2006''', so there is lots of expertise around!
#And finally, Wiki is an example of a [http://en.wikipedia.org/wiki/Markdown MarkDown] language, one designed to facilitate writing using an easy-to-read, easy-to-write plain text format (with the option of converting it to structurally valid XHTML).

=Report Preparation =

== Before you start writing ==
Before you start writing, you might wish to read this article<ref name="adma.200400767">G.M. Whitesides, "Whitesides' Group: Writing a Paper", ''Advanced Materials'', '''2004''', ''16'', 1375–137 {{DOI|10.1002/adma.200400767}}</ref> (or perchance this advice<ref name="ac2000169">R. Murray, "Skillful writing of an awful research paper", ''Anal. Chem.'', '''2011''', ''83'', 633. {{DOI|10.1021/ac2000169}}</ref>). In your report you should discuss your evaluation of each of the techniques you use here. You should include at least '''three literature references in addition to the ones given here'''. You might also want to check the [[Mod:latebreak|late breaking news]] to see if there are any helpful hints about the project you might want to refer to. You will be writing your report in Wiki format, and it is best to do this continually as you do the experiment. In effect, your Wiki report is also your laboratory manual.

#[[File:Wiked.jpg|right|400px|WikED editor]]Open Firefox as a Web browser.
#There should be a tab for the course Wiki, but if not, use the URL '''www.ch.ic.ac.uk'''
#*[[Image:exception1.jpg|right|thumb|Security exception]]If the browser asks you to add a security exception, do so and proceed to '''view/confirm''' the certificate.
#You can view the Wiki without logging in, but to create a report, you will have to login as yourself. Check '''Remember my login on this computer'''
#Before you start, you might want to visit the [[Special:Preferences|preferences]] page to customise the Wiki for yourself.
#Follow the procedures below. Check that the WikED icon is present at the top, just to the right of the log out text (ringed in red). If you want a minimalist editing interface, click this icon to switch it off. A [http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet cheatsheet] summarises the commands with a [[It:projects|playpen]] for playing. You can write your report by simply typing the appropriate text as shown in the cheatsheet, or by using the WikEd buttons in Word-style composition.

=== Assigning your report an identifier ===
#*[[Image:New_report.jpg|right|400px|Creating a report page]] In the address box, type something like
#**'''wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:{{fontcolor1|yellow|black|XYZ1234}}'''
#*The characters '''Mod''' indicate a report associated with the modelling course, and '''{{fontcolor1|yellow|black|XYZ1234}}''' is your secret password for the report. It can be any length, but do not make it too long! It should then tell you there is no text in this page. If not, try another more unique password. You should now click on the '''edit this page''' link to start. Use a different address for each module of the course you are submitting.
#*It is a {{fontcolor1|yellow|black|good idea}} to add a bookmark to this page, so that you can go back to it quickly.
==== Assigning your report a persistent (DOI-style) identifier.====
Use [http://spectradspace.lib.imperial.ac.uk/url2handle/ this tool] to assign a shorter identifier for your report (one that can be invoked using eg <nowiki>{{DOI|shortidentifier]]</nowiki>.

=== Converters to the Wiki format ===
#Convert a Word document. Open it in '''OpenOffice''' (rather than the Microsoft version) and '''export''' as Mediawiki. Open the resulting .txt file in eg WordPad, select all the text, copy, and then paste this into the Wiki editing page. You will still have to upload the graphical images from the original Word document separately.
#There is also a [http://labs.seapine.com/htmltowiki.cgi HTML to Wiki] converter which you can use to import HTML code from an existing Web page into a (Media)Wiki.

== Basic editing ==
An [[Mod:inorganic_wiki_page_instructions|introductory tutorial]] is available which complements the information here.
*A [http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet cheatsheet] summarises the commands with a [[It:projects|playpen]] for playing. You can write your report by simply typing the appropriate text as shown in the cheatsheet, or by using the WikEd buttons in Word-style composition.
*[[Image:report12345.jpg|right|thumb|The editing environment]]You will need to create a separate report page on this Wiki for each module of the course. Keep its location private (i.e. do not share the URL with others).
*The WikED toolbar along the top of the page has a number of tools for:
**adding citation references,
**superscript and subscripting (the H<sub>2</sub>O WikEd symbol will automatically do this for a formula),
**creating tables
**adding links (Wiki links are internal, External links do what they say on the tin)
**# local to the wiki, as <nowiki>[[mod:writeup|text of link]]</nowiki>
**# remote, as <nowiki>[http://www.webelements.com/ text of link]</nowiki>
**# Interwiki, as <nowiki>[[w:Mauveine|Mauveine]]</nowiki>
**# DOI links are invoked using the DOI template <nowiki>{{DOI|..the doi string ..}}</nowiki> or the more modern form <nowiki>[[doi:..the dpi string..]]</nowiki>
**# Links to an Acrobat file you have previously uploaded to the Wiki can be invoked using this template: <nowiki>{{Pdf|tables_for_group_theory.pdf|...description of link ...}}</nowiki>
**# There are lots of other [[Special:UncategorizedTemplates|templates]] to make your life easier such as the [[w:Template:Chembox|ChemBox]]
**If you need some help, invoke it from the left hand side of this page.
*Upload all graphics files also with unique names (so that they do not conflict with other people's names). If you are asked to replace an image, '''REFUSE''' since you are likely to be over-writing someone else's image!
** Invoke such an uploaded file as <nowiki>[[image:nameoffile.jpg|right|200px|Caption]] </nowiki>
**We support WikiComons, whereby images from the [http://commons.wikimedia.org/wiki/Main_Page content (of ~10 million files)] from [http://meta.wikimedia.org/wiki/Wikimedia_Commons Wikimedia Commons Library] can be referenced for your own document. If there is a name conflict, then the local version will be used before the Wiki Commons one.
***To find a file, go to [http://commons.wikimedia.org/wiki/Main_Page Commons]
***Find the file you want using the search facility
***Invoke the top menu, '''use this file in a Wiki''', and copy the string it gives you into your Wiki page
*** <nowiki>[[File:Armstrong Edward centric benzene.jpg|thumb|Armstrong Edward centric benzene]]</nowiki>
*Colour can be added (sparingly) using this {{fontcolor1|yellow|black|text fontcolor}} template. (invoked as <nowiki>{{fontcolor1|yellow|black|text fontcolor}}</nowiki> )
*Save and preview constantly (this makes a new version, which you can always revert to). It goes without saying that you should not reference this page from any other page, or indeed tell anyone else its name.
*'''Important:''' Every 1-2 hours, you might also want to make a [[Mod:writeup#Backing_up_your_report|backup of your report]]. This is particularly important when adding Jmol material, since any error in the pasted code can result in XML errors. The current Wiki version does not flag these errors properly, but instead just hangs the page. Whilst you can try to [[Mod:writeup#Fixing_broken__Pages|repair the page]] as described below, it is much safer to also have a backup!
*You should get into the habit of recording results, and appropriate discussion, soon after they are available, in the manner of a laboratory note book.

== More Editing features ==
=== Handling References/citations with a DOI ===
This section shows how literature citations<ref name="jp027596s">W. T. Klooster , T. F. Koetzle , P. E. M. Siegbahn , T. B. Richardson , and R. H. Crabtree, "Study of the N-H···H-B Dihydrogen Bond Including the Crystal Structure of BH<sub>3</sub>NH<sub>3</sub> by Neutron Diffraction", ''J. Am. Chem. Soc.'', '''1999''', ''121'', 6337–6343. {{DOI|10.1021/ja9825332}}</ref> can be added to text<ref name="dataset1"> Henry S. Rzepa, "Gaussian Job Archive for C4H6NO3S(1-)", 2013. {{DOI|10.6084/m9.figshare.679974}}</ref> using the '''<nowiki>{{DOI|value}}</nowiki>''' (digital object identifier) template to produce a nice effect. Citations can be easily added from the WikED toolbar.
*The following text is added to the wiki, exactly as shown here: '''<nowiki><ref name="ja9825332">W. T. Klooster , T. F. Koetzle , P. E. M. Siegbahn , T. B. Richardson , and R. H. Crabtree, "Study of the N-H···H-B Dihydrogen Bond Including the Crystal Structure of BH<sub>3</sub>NH<sub>3</sub> by Neutron Diffraction", ''J. Am. Chem. Soc.'', '''1999''', ''121'', 6337–6343.{{DOI|10.1021/ja9825332}}</ref></nowiki>'''
*Giving a reference a unique identifier, such as '''<nowiki><ref name="ja9825332"></nowiki>''' allows you to refer to the same footnote again by using a ref tag with the same name. The text inside the second tag doesn't matter, because the text already exists in the first reference. You can either copy the whole footnote, or you can use a terminated empty ref tag that looks like this: '''<nowiki><ref name="ja9825332" /></nowiki>'''.
*Collected citations will appear below wherever you place the '''<nowiki><references /></nowiki>''' tag, as here. If you forget to include this tag, the references will not appear!
==== Including the DOI for your experiment data ====
The datasets associated with your experiment can be given a DOI by '''publishing''' any entry in the [https://scanweb.cc.imperial.ac.uk/uportal2/ SCAN Portal]. You can include this DOI as a normal citation.<ref name="dataset1"> Henry S. Rzepa, "Gaussian Job Archive for C4H6NO3S(1-)", 2013. {{DOI|10.6084/m9.figshare.679974}}</ref>

==== Additional citation handling ====
* A macro-based reference formatting program has been developed in Microsoft Excel to not only produce the wiki code for direct pasting into your report, but that '''''also''''' formats text for placing in documents, such as synthesis lab reports. This program is available [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Reference_Formatting_Program here].
* A '''[[Template:Cite_journal|Cite journal]] template''' is installed for anyone who wants to experiment
----

References and citations
<references />

----

=== Using an iPad ===

[https://itunes.apple.com/gb/app/wiki-edit/id391012741?mt=8 Wiki Edit] for IOS allows a Wiki to be edited using an iPad. You can dictate your text using '''Siri''' if your speed at '''thumb-typing''' is not what it should be.

= Bringing your report to life =
== Basic JSmol ==
You can use coordinate files created as part of your work (in CML or Molfile format) to insert rotating molecules for your page.
#Using your graphical program (ChemBio3D or Gaussview), '''save''' your molecule as an '''MDL File''', which has the extension '''.mol''', or as '''chemical markup language''', which has the extension '''.cml'''.
#Or, if your calculation ran on the SCAN batch system, '''publish''' the calculation, and in the resulting deposited space, download the .cml or the '''logfile.out''' file to be found there (the latter should be used for vibrations only).
#On the Wiki, '''Upload File''' (from the left hand panel) and select the molecule file you have just placed on your hard drive as above.
#On your Wiki page, insert <nowiki><jmolFile text="Explanatory text for link">BCl3-09.log</jmolFile></nowiki> where in this example, BCl3-09.log is the just uploaded file.
##The should produce <jmolFile text="this link">BCl3-09.log</jmolFile>. When clicked, it will open up a separate floating window for your molecule.
##Further actions upon the loaded molecule (such as selecting a vibrational mode and animating the vibration) are done by right-mouse clicking in the Jmol window.

#When using animations, please let them pop up in a separate window using the <jmolAppletButton> function. Your browser won't slow down and you will make your life so much simpler. =)
##Read more on how to do that [http://wiki.jmol.org/index.php/MediaWiki#Jmol_applet_in_a_popup_window here ]. --[[User:Rea12|Rea12]] 20:58, 8 September 2014 (BST)

== Advanced JSmol ==

A much more powerful invocation is as follows. The following allows a molecule to be directly embedded into the report, and it also shows how to put a script in to control the final display.
{| class="wikitable" border="2"
|-
! copy/paste either of the two sections below into your own Wiki
|-
|<pre><jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>yourmolecule.cml</uploadedFileContents>
</jmolApplet>
</jmol>


<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>200</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script><uploadedFileContents>BCl3-09.log</uploadedFileContents>
</jmolApplet>
</jmol></pre>
|-
! First molecule (if you see yellow below, then check the [[Mod:latebreak#Firefox.2C_Java_and_the_Wiki|late breaking news]])
|-
|<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color><size>300</size>
<script>select atomno=3,atomno=4,atomno=5; color purple;measure 3 5;measure 5 4;</script>
<uploadedFileContents>pentahelicene.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|-
! Second molecule (if you see yellow below, then check the [[Mod:latebreak#Firefox.2C_Java_and_the_Wiki|late breaking news]])

|-
|<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>300</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script>
<uploadedFileContents>BCl3-09.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}
Every time you embed a molecule in a Wiki page in the above manner, the Web browser must set aside memory. Too many molecules, and the memory starts to run out, and the browser may slow down significantly. So use the feature sparingly, only including key examples where some structural feature would benefit from the rotational capabilities.
It is [http://chemapps.stolaf.edu/jmol/docs/ possible] to add many other commands to the JSmol container above. For example, '''<nowiki><script>select atomno=3,atomno=4,atomno=5; color purple;measure 3 5;measure 5 4;</script></nowiki>''' will colour atoms 3 4 and 5 (obtained by mouse-overs) purple, and then measure the length of the 3-5 bond. Further examples of how to invoke Jmol are [http://www.mediawiki.org/wiki/Extension:Jmol#Installing_Jmol_Extension found here], and a comprehensive list [http://chemapps.stolaf.edu/jmol/docs/ given here].

== Incorporating orbital/electrostatic potential isosurfaces ==
The procedure is as follows
# Run a Gaussian calculation on the SCAN
# When complete, select ''Formatted checkpoint file'' from the output files and download
# Double click on the file to load into Gaussview
##To generate a molecule orbital, '''Edit/MOs''' and select (= yellow) your required orbitals.
##* '''Visualise''' and '''Update''' to generate them
## To generate an electrostatic potential, '''Results/Surfaces and Contours''', then '''Cube Actions/New Cube/Type=ESP'''. This will take 2-3 minutes to generate
##* In '''Surfaces available''' pre-set the Density to '''0.02''' and then '''Surface Actions/New Surface'''. Try experimenting with the value of Density for the best result. Save the cube as per below.
# In '''Results/Surfaces and contours''' from the '''cubes available''' list, select one and '''Cube actions/save cube'''
# Invoke [http://www.ch.ic.ac.uk/rzepa/cub2jvxl/ this page] and you will be asked to select your cube file,
# followed by three file save dialogs, one for the coordinates (.xyz), one for the MO surface (.jvxl) and a shrink-wrapped bundle (.pngj).
# Insert the following code into your Wiki, replacing the file name with your own choice from the preceding file save dialogs.
<pre><nowiki><jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/1/1b/AHB_mo22-2.cub.jvxl" translucent;</script>
<uploadedFileContents>AHB_mo22.xyz</uploadedFileContents>
</jmolApplet>
</jmol></nowiki>
</pre>
# [[image:absolute_path.jpg|right|350px]]Next, upload these two files into the Wiki (one file at a time, the multiple file uploader does not seem to work for this task)
## Now for the tough bit. You will need to find the absolute path for the .jvxl file. Above, this appears as images/1/1b/AHB_mo22-2.cub.jvxl
## Just after uploading a .jvxl file, you will see a response as shown on the right.
## Right click on '''Edit this file using an external application'''. You can used any text editor (Wordpad etc).
## This text file will contain something like: <br /><tt>; or go to the URL <nowiki>https://wiki.ch.ic.ac.uk/wiki/images/1/1b/AHB_mo22-2.cub.jvxl</nowiki></tt>
#Select just the string '''images/1/1b/AHB_mo22-2.cub.jvxl''' and paste it in as shown above:
#You should get something akin to:
<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/1/1b/AHB_mo22-2.cub.jvxl" translucent;
</script>
<uploadedFileContents>AHB_mo22.xyz</uploadedFileContents>
</jmolApplet>
</jmol>
* You can superimpose two surfaces. Change the script contents above to append a second surface to the first: <pre><script>isosurface color orange purple "images/4/42/AHB_mo22.jvxl" translucent;isosurface append color red blue "images/1/1b/AHB_mo22-2.cub.jvxl" translucent;</script></pre>
* The four colours used in this line can be changed to whatever you consider appropriate.
=== An alternative way of loading surfaces ===
This method avoids the need to specify paths to files as seen above. Instead uses the '''.pngj''' bundle which contains all necessary information and can be invoked by
<pre><nowiki><jmolFile text="just a link">CF3_mo30.cub.pngj</jmolFile></nowiki></pre> which produces <jmolFile text="just a link">CF3_mo30.cub.pngj</jmolFile>.
# It only supports one surface (you cannot superimpose two orbitals)
# You can also load other surfaces, such as <jmolFile text="molecular electrostatic potentials">Checkpoint_60018_esp.cub.pngj‎</jmolFile> generated from a cube of electrostatic potential (ESP) values created using Gaussview as follows:
## Download .fchk file from SCAN
## Open using Gaussview
## '''Results/Surfaces & contours/Cube actions/New Cube/ESP''' and then '''cube actions/save cube''' which is how the above was generated. You may have to play around with the value of the density (~0.02).

=== MOPAC orbitals ===
# Run MOPAC from ChemBio3D, selecting '''Compute Properties/Molecular Surface''' from the '''properties''' pane, and in the '''General pane''' specify a location for the output and deselect '''Kill temporary files''' if not already so.
# Upload the '''.mgf''' file so produced to the Wiki
# Invoke as follows ('''MO 35;''' means the 35th most stable orbital for that molecule).
<pre><nowiki><jmol>
<jmolApplet>
<title>MOPAC Orbital</title><color>white</color><size>300</size>
<script>MO 35;mo fill nomesh translucent;</script>
<uploadedFileContents>test.mgf</uploadedFileContents>
</jmolApplet>
</jmol></nowiki></pre>
<jmol>
<jmolApplet>
<title>MOPAC Orbital</title><color>white</color><size>200</size>
<script>MO 35;mo fill nomesh translucent;</script>
<uploadedFileContents>test.mgf</uploadedFileContents>
</jmolApplet>
</jmol>

== Enhancing your report with Equations ==
*You may have need to express some [http://meta.wikimedia.org/wiki/Help:Formula equations] on the Wiki. This is currently supported only using a notation derived from '''LaTeX''', and as with the Jmol insertion above, is enabled within a '''<nowiki><math>\frac{-b\pm \sqrt{b^{2}-4ac}}{2a}</math></nowiki>''' field inserted using the default editor (the SQRT(n) button), and producing the following effect:
<math>\frac{-b\pm \sqrt{b^{2}-4ac}}{2a}</math>

The requisite syntax can be produced by using
*MathType as an equation editor (used standalone or in Word). It places the required LaTeX onto the clipboard for pasting into the Wiki).
*[http://www.lyx.org/ Lyx] which is a free stand-alone editor.
*A more general solution to this problem is simply to create a graphical image of your equation, and insert that instead as a picture.

== Inserting Tables ==
Instead of inserting screenshots of Excel, tables can be produced using MediaWiki markup (see [http://www.mediawiki.org/wiki/Help:Tables this page]), where you can also find lots of examples of different styles of table. However, this can be quite time consuming when you have a lot of tabulated data and need to copy it from somewhere like Excel into ChemWiki. Instead of typing it by hand, you can save your Excel worksheet as a comma separated file (.csv) and then use this [[http://area23.brightbyte.de/csv2wp.php CSV to MediaWiki markup]] convertor. Note that cells starting with "-", e.g. for negative numbers, need a space inserted between the - and | in the output otherwise MediaWiki interprets it as a new row.

Another web-based utility is available called [http://excel2wiki.net/ Excel2Wiki] which can be used to generate MediaWiki code from an Excel table.

== SVG (for display of IR/NMR/Chiroptical Spectra) ==
[[File:IR.svg|300px|right|SVG]]SVG stands for '''scaleable-vector-graphics'''. Its advantage is well, that it scales properly (but it has many others, including the ability to make simple edit to captions etc using Wordpad or similar). From your point of view, it is readily generated using Gaussview. If you view an '''IR/NMR/UV-vis/IRC/Scan/''' spectrum in this program, it allows you to export the spectrum as SVG (right-mouse-click on the spectrum to pull down the required menu). Upload this file, and invoke it as <nowiki>[[File:IR.svg|200px|right|SVG]]</nowiki> If you open eg IR.svg in Wordpad (or other text editor), you can edit the captions, font sizes etc (its fairly obvious). Oh, you will need to use a web browser that actually displays SVG. Internet Explorer 8 does not (9 is supposed to). Use Firefox/Chrome/Safari etc.

== Chemical Templates ==
An example is the [[w:Template:Chembox|ChemBox]]. Volunteers needed to test/extend these!

= Submitting your report =
For the '''combined synthetic and organic''' experiment submit your Wiki personal URL as obtained above to [mailto:Org-8@imperial.ac.uk?subject=Computational_lab_1C Org-8@ic.ac.uk] with a deadline of the Friday of the second week of any 2-week experiment at '''12noon'''.

For the '''Computational Chemistry Lab''': inorganic and physical submit your wiki URL address on Blackboard by 5pm on the friday of the 2-week experiment.

= Backing up your report =
[[Image:export1.jpg|left|250px]][[Image:Export2.jpg|right|200px]]Invoke [[Special:Export|this utility]] to back your project up. In the box provided, enter e.g. '''Mod:wzyz1234''' being the password for your report. This will generate a page (right) which can be saved using the Firefox '''File/Save_Page_as''' menu. Specify '''Web Page, XML only''' as the format, and add .xml to the file suffix. You might want to do this eg on a daily basis to secure against corruption. This is in addition to the notes for how to repair broken pages.

The same file can now be reloaded using [[Special:Import|Import]].

= Fixing broken Pages =
There are several ways in which a page can break.

*We have had instances of people inserting a corrupted version of the Jmol lines into their project, resulting in a '''XML error''' or '''Database error'''. Recovering from such an error is not simple. So we do ask that you carefully check what you are pasting into the Wiki, and that its form is exactly as shown above. For example, below is a real example of inducing such an error. Can you see where the fault lies? (Answer: the <nowiki><jmol></nowiki> tag is not matched by <nowiki></jmol></nowiki>. If tags are not balanced, XML errors will occur).
<pre><jmol><jmolApplet><title>equatorial</title><color>white</color>
<size>200</size><script>zoom 200; cpk -20;</script>
<uploadedFileContents>Pl506_14_equatorial.mol</uploadedFileContents></pre>
*Another example might be wish to indicate a citation using <nowiki><ref>...details </ref></nowiki> but in fact end up entering <nowiki><ref> ...</nowiki> (i.e. missing out the <nowiki></ref></nowiki>)
*If you do encounter such an error, try invoking your project as '''<nowiki>https://www.ch.ic.ac.uk/wiki/index.php?title=Mod:wzyz1234&action=history</nowiki>''' and edit and then save an uncorrupted version. You will need to be already logged in before you attempt to view the history in this way, since logging in '''after''' you invoke the above will return you not to the history, but to the corrupted page (Hint: it sometimes helps to check '''Remember my login on this computer''' as you log in). For example, the history for this page can be seen [https://www.ch.imperial.ac.uk/wiki/index.php?title=Mod:writeup&action=history here]. You can eg load this preceeding page, and then use it to replace '''writeup''' with your own project address.
*If the preceeding does not work try the instructions shown [[mod:fix|here]].

= Feedback =
Each Wiki page has a discussion section, including your submitted report page. This latter will be populated with comments about your report within a week of submission.

See also: [[mod:organic|Module 1C]],[[Mod:inorganic|Inorganic Computational lab]], [[Mod:phys3|Physical computational lab]],[[File:Wiki-writeup.png|right|250px]][[Mod:phys3|Module 3]],[[Mod:writeup|Writing up]],[[Mod:Cheatsheet|cheatsheet]]

Mod:intro

2013-09-26T19:11:16Z

Lp202:

See also: [[http://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page#Third_Year_Computational_Chemistry_Lab|Comp Chem Lab]], [[Mod:latebreak|Breaking news]], [[mod:laptop|Laptop use]], [[Mod:lectures|Intro lecture]], [[mod:programs|Programs]], [[Mod:inorganic|Inorganic]], [[Mod:physical|Physical]], [[Mod:writeup|Writing up]]

== Objectives ==
This four week course rotates with two other laboratory-based courses during the third year of the Imperial College chemistry degree. Its aim is to enhance and relate to not just to the ''wet'' experiments in the other labs, but also to the lecture courses you have had during the first three years, using appropriate theory and quantitative evaluation applied to real problems.

== Experiment Timetable ==

*EXP1: Inorganic, Dr. Hunt
*EXP2: Physical, Dr. Bearpark
*EXP3: Inorganic, Dr. Hunt
*EXP4: Physical, Dr. Bearpark

== Specific times ==
*Week 1 (Monday): Laptop sign-out ('''12.00-1.00''') from Room 237A
Before you go to collect the laptop, you must sign the [https://vle.imperial.ac.uk/webct/logon/5047144695021 Y3C Laptop issue agreement] which can be found at the '''3rd Year Chemistry Laboratories (2013-2014)''' folder in Blackboard.
*Week 2 (Friday): Laptop return ('''12.00-1.00''') from Room 237A or B
*Week 2 (Friday): '''submit your wiki address on Blackboard by 5pm'''

Laptops are limited, and will be issued on a first come basis. If for a very good reason you are unable to collect a laptop at this assigned time please contact [mailto:laura.patel@imperial.ac.uk Dr Patel] with your explanation to see if there is one available.

== Locations ==
You can work in either of the computer labs Level 1 or Level 2 or in the library. In addition to the laptops the desk-top computers in these locations can be used to undertake the lab (they have more processing power and will be faster than the laptops)

The three tables along the north edge of the study area on level two have been prioritised at 12:00-17:00 on Mondays, Tuesdays, Thursdays and Fridays for students carrying out the computational lab. There are docking stations available if you want to work using a larger screen (22").

== Expected hours in the Lab ==

The official lab times are 12am-5pm and Mon, Tue, Thur and Fri 12am-5pm. However, the advantage of having a dedicated laptop at your disposal is that you not restricted to these times. An important part of this course is learning how to manage your time and resources in a flexible and sensible way. It is up to you to manage your time, not to do too much and not to do too little. Ask a staff member if you are at all unsure.

You have the advantage of having a laptop computer enabling you to work on the lab at anytime, however you should manage your time so that you put in the '''equivalent of 4hrs per lab day'''.

Even though you have a laptop this does not mean that the lab demonstrators are available all day, manage your time so that if you need help you have an opportunity to get the help you need in time for it to be useful. Address your questions to the demonstrators during the lab hours they are available. If you are struggling with the suggested times allocated for each part of the experiment seek help from a demonstrator.

== Demonstrator and Staff help and feedback times ==
'''Demonstrators are available from 12-1 and 2-4 Mon,Tues,Thur,Fri.''' This works as a drop in surgery in the Level2 computer room. If you have a question talk with a demonstrator FIRST. Demonstrators are not just there to help they can offer '''feedback''' on completed work before it is marked.

'''Dr Bearpark and Dr Hunt have different ways of providing support'''
*Please find Dr Bearpark in his office or contact him via email to arrange an appointment at a mutually convient time. [mailto:m.bearpark@imperial.ac.uk Dr Bearpark]
*Dr Hunt will be available 2-3 Mon, Tue, Thur and Fri in the Level 1 or 2 computer rooms.

== Report submission ==

Submit the URL for your Wiki report from [https://vle.imperial.ac.uk/webct/logon/5047144695021 this address] by the appropriate deadline. These deadlines are on the Friday of the end of the second week of each course.

If we do not receive the URL of your report (submitted via the Blackboard system, and '''NOT''' emailed to the individual members of the course team), Raj will attempt to contact you by email within one working day (Mon-Fri) of the deadline to check it has not gone missing. You should expect to get a grade on blackboard within 10 working days. If you have heard nothing and have not received a grade in blackboard, please contact [mailto:r.sandhu@imperial.ac.uk Raj Sandhu] immediately.

'''Please note an new College policy: work submitted late will receive zero marks.''' Any sections completed by the hand-in date will be assessed for full marks, additional material added after this will not be marked. If you are having problems, are ill or have extenuating circumstances please see [mailto:laura.patel@imperial.ac.uk Dr Patel] as early as possible, extensions may be granted and will be determined on a case-by-case basis.

== Lab overview: ==
=== The modules on offer: ===
Each of the lab modules introduces new types of computational chemistry techniques and their applications. Some of these computational methods involve only a few seconds of actual computing, and are easily accomplished on a laptop computer interactively. Others may run for many hours, and are best done in''batch'' mode on a computing cluster. You will learn how to handle your laptop computer as "a laboratory instrument", delivering a variety of information about molecular systems.
=====Module 1: Bonding analyses using ''Ab initio'' and Density functional techniques. =====
=====Module 2: Reaction mechanisms and transition states.=====

The nature of the topic requires a different mode of presentation to the usual word-processed document. You will instead present your results in the form of a '''Wiki page''' unique to yourself. The course documentation also takes the form of a Wiki, and '''''YOU''''' as well as the course organisers can contribute to the instructions. If you feel you can improve on aspects of the documentation, or ''e.g.'' add further key literature references etc (very much in the spirit of the Wikipedia itself), do please go ahead and take the plunge!

#Access the course
## The link in the [https://vle.imperial.ac.uk/webct/logon/5047144695021 BlackBoard VLE folder for 3rd year labs].
##The link '''''http://www.ch.imperial.ac.uk/''''' and follow the links down to the Computational Chemistry Course
##or go directly here '''''http://www.ch.imperial.ac.uk/wiki/index.php/Mod:intro'''''

----

See also:[[http://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page#Third_Year_Computational_Chemistry_Lab|Comp Chem Lab]] [[Mod:latebreak|Breaking news]], [[mod:laptop|Laptop use]], [[Mod:lectures|Intro lecture]],[[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Inorganic]], [[Mod:physical|Physical]], [[Mod:writeup|Writing up]]

Mod:intro

2013-09-26T19:05:34Z

Lp202:

See also: [[http://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page#Third_Year_Computational_Chemistry_Lab|Comp Chem Lab]], [[Mod:latebreak|Breaking news]], [[mod:laptop|Laptop use]], [[Mod:lectures|Intro lecture]], [[mod:programs|Programs]], [[Mod:inorganic|Inorganic]], [[Mod:physical|Physical]], [[Mod:writeup|Writing up]]

== Objectives ==
This four week course rotates with three other laboratory-based courses during the third year of the Imperial College chemistry degree. Its aim is to enhance and relate to not just to the ''wet'' experiments in the other labs, but also to the lecture courses you have had during the first three years, using appropriate theory and quantitative evaluation applied to real problems.

== Experiment Timetable ==

*EXP1: Inorganic, Dr. Hunt
*EXP2: Physical, Dr. Bearpark
*EXP3: Inorganic, Dr. Hunt
*EXP4: Physical, Dr. Bearpark

== Specific times ==
*Week 1 (Monday): Laptop sign-out ('''12.00-1.00''') from Room 237A
Before you go to collect the laptop, you must sign the [https://vle.imperial.ac.uk/webct/logon/5047144695021 Y3C Laptop issue agreement] which can be found at the '''3rd Year Chemistry Laboratories (2012-2013)''' folder in Blackboard.
*Week 2 (Friday): Laptop return ('''3.00-4.00''') from Room 237A
*Week 2 (Friday): '''submit your wiki address on Blackboard by 5pm'''

Laptops are limited, and will be issued on a first come basis. If for a very good reason you are unable to collect a laptop at this assigned time please contact [mailto:laura.patel@imperial.ac.uk Dr Patel] with your explanation to see if there is one available.

== Locations ==
You can work in either of the computer labs Level 1 or Level 2 or in the library. In addition to the laptops the desk-top computers in these locations can be used to undertake the lab (they have more processing power and will be faster than the laptops)

The three tables along the north edge of the study area on level two have been prioritised at 12:00-17:00 on Mondays, Tuesdays, Thursdays and Fridays for students carrying out the computational lab. There are docking stations available if you want to work using a larger screen (22").

== Expected hours in the Lab ==

The official lab times are 12am-5pm and Mon, Tue, Thur and Fri 12am-5pm. However, the advantage of having a dedicated laptop at your disposal is that you not restricted to these times. An important part of this course is learning how to manage your time and resources in a flexible and sensible way. It is up to you to manage your time, not to do too much and not to do too little. Ask a staff member if you are at all unsure.

You have the advantage of having a laptop computer enabling you to work on the lab at anytime, however you should manage your time so that you put in the '''equivalent of 4hrs per lab day'''.

Even though you have a laptop this does not mean that the lab demonstrators are available all day, manage your time so that if you need help you have an opportunity to get the help you need in time for it to be useful. Address your questions to the demonstrators during the lab hours they are available. If you are struggling with the suggested times allocated for each part of the experiment seek help from a demonstrator.

== Demonstrator and Staff help and feedback times ==
'''Demonstrators are available from 12-1 and 2-4 Mon,Tues,Thur,Fri.''' This works as a drop in surgery in the Level2 computer room. If you have a question talk with a demonstrator FIRST. Demonstrators are not just there to help they can offer '''feedback''' on completed work before it is marked.

'''Dr Bearpark and Dr Hunt have different ways of providing support'''
*Please find Dr Bearpark in his office or contact him via email to arrange an appointment at a mutually convient time. [mailto:m.bearpark@imperial.ac.uk Dr Bearpark]
*Dr Hunt will be available 2-3 Mon, Tue, Thur and Fri in the Level 1 or 2 computer rooms.

== Report submission ==

Submit the URL for your Wiki report from [https://vle.imperial.ac.uk/webct/logon/5047144695021 this address] by the appropriate deadline. These deadlines are on the Friday of the end of the second week of each course.

If we do not receive the URL of your report (submitted via the Blackboard system, and '''NOT''' emailed to the individual members of the course team), Raj will attempt to contact you by email within one working day (Mon-Fri) of the deadline to check it has not gone missing. You should expect to get a grade on blackboard within 10 working days. If you have heard nothing and have not received a grade in blackboard, please contact [mailto:r.sandhu@imperial.ac.uk Raj Sandhu] immediately.

'''Please note an new College policy: work submitted late will receive zero marks.''' Any sections completed by the hand-in date will be assessed for full marks, additional material added after this will not be marked. If you are having problems, are ill or have extenuating circumstances please see [mailto:laura.patel@imperial.ac.uk Dr Patel] as early as possible, extensions may be granted and will be determined on a case-by-case basis.

== Lab overview: ==
=== The modules on offer: ===
Each of the lab modules introduces new types of computational chemistry techniques and their applications. Some of these computational methods involve only a few seconds of actual computing, and are easily accomplished on a laptop computer interactively. Others may run for many hours, and are best done in''batch'' mode on a computing cluster. You will learn how to handle your laptop computer as "a laboratory instrument", delivering a variety of information about molecular systems.
=====Module 1: Bonding analyses using ''Ab initio'' and Density functional techniques. =====
=====Module 2: Reaction mechanisms and transition states.=====

The nature of the topic requires a different mode of presentation to the usual word-processed document. You will instead present your results in the form of a '''Wiki page''' unique to yourself. The course documentation also takes the form of a Wiki, and '''''YOU''''' as well as the course organisers can contribute to the instructions. If you feel you can improve on aspects of the documentation, or ''e.g.'' add further key literature references etc (very much in the spirit of the Wikipedia itself), do please go ahead and take the plunge!

#Access the course
## The link in the [https://vle.imperial.ac.uk/webct/logon/5047144695021 BlackBoard VLE folder for 3rd year labs].
##The link '''''http://www.ch.imperial.ac.uk/''''' and follow the links down to the Computational Chemistry Course
##or go directly here '''''http://www.ch.imperial.ac.uk/wiki/index.php/Mod:intro'''''

----

See also:[[http://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page#Third_Year_Computational_Chemistry_Lab|Comp Chem Lab]] [[Mod:latebreak|Breaking news]], [[mod:laptop|Laptop use]], [[Mod:lectures|Intro lecture]],[[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Inorganic]], [[Mod:physical|Physical]], [[Mod:writeup|Writing up]]

Mod:intro

2013-09-26T19:04:14Z

Lp202:

See also: [[http://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page#Third_Year_Computational_Chemistry_Lab|Comp Chem Lab]], [[Mod:latebreak|Breaking news]], [[mod:laptop|Laptop use]], [[Mod:lectures|Intro lecture]], [[mod:programs|Programs]], [[Mod:inorganic|Inorganic]], [[Mod:physical|Physical]], [[Mod:writeup|Writing up]]

== Objectives ==
This four week course rotates with three other laboratory-based courses during the third year of the Imperial College chemistry degree. Its aim is to enhance and relate to not just to the ''wet'' experiments in the other labs, but also to the lecture courses you have had during the first three years, using appropriate theory and quantitative evaluation applied to real problems.

== Experiment Timetable ==

*EXP1: Inorganic, Dr. Hunt
*EXP2: Physical, Dr. Bearpark
*EXP3: Inorganic, Dr. Hunt
*EXP4: Physical, Dr. Bearpark

== Specific times ==
*Week 1 (Monday): Laptop sign-out ('''12.00-1.00''') from Room 237A
Before you go to collect the laptop, you must sign the [https://vle.imperial.ac.uk/webct/logon/5047144695021 Y3C Laptop issue agreement] which can be found at the '''3rd Year Chemistry Laboratories (2012-2013)''' folder in Blackboard.
*Week 2 (Friday): Laptop return ('''3.00-4.00''') from Room 237A
*Week 2 (Friday): '''submit your wiki address on Blackboard by 5pm'''

Laptops are limited, and will be issued on a first come basis. If for a very good reason you are unable to collect a laptop at this assigned time please contact [mailto:laura.patel@imperial.ac.uk Dr Patel] with your explanation to see if there is one available.

== Locations ==
You can work in either of the computer labs Level 1 or Level 2 or in the library. In addition to the laptops the desk-top computers in these locations can be used to undertake the lab (they have more processing power and will be faster than the laptops)

The three tables along the north edge of the study area on level two have been prioritised at 12:00-17:00 on Mondays, Tuesdays, Thursdays and Fridays for students carrying out the computational lab. There are docking stations available if you want to work using a larger screen (22").

== Expected hours in the Lab ==

The official lab times are 12am-5pm and Mon, Tue, Thur and Fri 12am-5pm. However, the advantage of having a dedicated laptop at your disposal is that you not restricted to these times. An important part of this course is learning how to manage your time and resources in a flexible and sensible way. It is up to you to manage your time, not to do too much and not to do too little. Ask a staff member if you are at all unsure.

You have the advantage of having a laptop computer enabling you to work on the lab at anytime, however you should manage your time so that you put in the '''equivalent of 4hrs per lab day'''.

Even though you have a laptop this does not mean that the lab demonstrators are available all day, manage your time so that if you need help you have an opportunity to get the help you need in time for it to be useful. Address your questions to the demonstrators during the lab hours they are available. If you are struggling with the suggested times allocated for each part of the experiment seek help from a demonstrator.

== Demonstrator and Staff help and feedback times ==
'''Demonstrators are available from 12-1 and 2-4 Mon,Tues,Thur,Fri.''' This works as a drop in surgery in the Level2 computer room. If you have a question talk with a demonstrator FIRST. Demonstrators are not just there to help they can offer '''feedback''' on completed work before it is marked.

'''Dr Bearpark and Dr Hunt have different ways of providing support'''
*Please find Dr Bearpark in his office or contact him via email to arrange an appointment at a mutually convient time. [mailto:m.bearpark@imperial.ac.uk Dr Bearpark]
*Dr Hunt will be available 2-3 Mon, Tue, Thur and Fri in the Level 1 or 2 computer rooms.

== Report submission ==

Submit the URL for your Wiki report from [https://vle.imperial.ac.uk/webct/logon/5047144695021 this address] by the appropriate deadline. These deadlines are on the Friday of the end of the second week of each course.

If we do not receive the URL of your report (submitted via the Blackboard system, and '''NOT''' emailed to the individual members of the course team), Raj will attempt to contact you by email within one working day (Mon-Fri) of the deadline to check it has not gone missing. You should expect to get a grade on blackboard within 10 working days. If you have heard nothing and have not received a grade in blackboard, please contact [mailto:r.sandhu@imperial.ac.uk Raj Sandhu] immediately.

'''Please note an new College policy: work submitted late will receive zero marks''' Any sections completed by the hand-in date will be assessed for full marks, additional material added after this will not be marked. If you are having problems, are ill or have extenuating circumstances please see [mailto:laura.patel@imperial.ac.uk Dr Patel] as early as possible, extensions may be granted and will be determined on a case-by-case basis.

== Lab overview: ==
=== The modules on offer: ===
Each of the lab modules introduces new types of computational chemistry techniques and their applications. Some of these computational methods involve only a few seconds of actual computing, and are easily accomplished on a laptop computer interactively. Others may run for many hours, and are best done in''batch'' mode on a computing cluster. You will learn how to handle your laptop computer as "a laboratory instrument", delivering a variety of information about molecular systems.
=====Module 1: Bonding analyses using ''Ab initio'' and Density functional techniques. =====
=====Module 2: Reaction mechanisms and transition states.=====

The nature of the topic requires a different mode of presentation to the usual word-processed document. You will instead present your results in the form of a '''Wiki page''' unique to yourself. The course documentation also takes the form of a Wiki, and '''''YOU''''' as well as the course organisers can contribute to the instructions. If you feel you can improve on aspects of the documentation, or ''e.g.'' add further key literature references etc (very much in the spirit of the Wikipedia itself), do please go ahead and take the plunge!

#Access the course
## The link in the [https://vle.imperial.ac.uk/webct/logon/5047144695021 BlackBoard VLE folder for 3rd year labs].
##The link '''''http://www.ch.imperial.ac.uk/''''' and follow the links down to the Computational Chemistry Course
##or go directly here '''''http://www.ch.imperial.ac.uk/wiki/index.php/Mod:intro'''''

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See also:[[http://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page#Third_Year_Computational_Chemistry_Lab|Comp Chem Lab]] [[Mod:latebreak|Breaking news]], [[mod:laptop|Laptop use]], [[Mod:lectures|Intro lecture]],[[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Inorganic]], [[Mod:physical|Physical]], [[Mod:writeup|Writing up]]