Mod:Second Year Modelling Workshop
From ChemWiki
Forward to coursework or directly to NMR Karplus for expt 1S.
Introduction
This workshop comprises a single 2 hour session which serves as an introduction to a technique known as molecular mechanics modelling. The course consists of the following components
- A short introduction to the molecular modelling program Avogadro.
- An opportunity for you to try this program out on up to a set of mini-projects, each on a slightly different theme (do as many as you can in the workshop time. You should target doing at least the first five).
- At the end of the workshop, you will have produced numerical answers to questions posed in each problem.
- The idea is that you will then use such techniques whenever the opportunity arises during the course of lectures, labs and tutorial problems (but unfortunately not, yet, examinations!).
Follow ups to this Course
The molecular mechanics procedure is quick and simple, but not always accurate. Different molecular mechanics force fields also vary in their accuracy.
A proper molecular model must also take into account electrons, as noted above. But solving the necessary equations takes much more computer time. In the accompanying symmetry course in 2nd year, you will be shown how to use a programs such as Gaussview. This is the front end to a Quantum mechanical modelling program Gaussian, which you will use in earnest in the third and fourth year, along with courses which deal with the theory and practice in much more detail.
Further Documentation, Reading and Viewing
- Ghemical Manual gives more advanced options, but be aware it relates to an earlier version of Ghemical.
- Second year modelling experiment on the thermal expansion of MgO.
- Third year modelling experiment undertaken in the third year organic chemistry laboratory.
- Third year modelling lab on Inorganic Chemistry, including three advanced individual projects on Mo(CO)4L2, boron based acids and Gold interactions with Water.
- A local third year course on organic molecular modelling with a number of more elaborate case studies illustrating the application of molecular modelling.
- Some further local examples of molecular models deriving from first and second year problem classes and tutorials.
- The Wikipedia page on molecular modelling, a short summary which gives some good further leads.
- The Wikipedia page on molecular graphics, a technique that goes hand in hand with molecular modelling.
- A Wikibook on organic chemistry
- The grand Daddy of all molecular models, invented at (what was to become) Imperial College around 1860, and now in the archives of the Royal Institution. These models are the source of the familar colour scheme now used, i.e. Hydrogen=White, Oxygen=Red, Nitrogen=blue, etc.
- Another father of molecular modelling, but only on paper!, also achieved in 1861. Loschmidt constructed these models in the same sense that Watson and Crick did for DNA, as proposals, and not representing structural proof in any way.
- For an interesting way of presenting scientific genealogies of scientists, see J. Andraos, Scientific genealogies of physical and mechanistic organic chemists, Can. J. Chem./Rev. Can. Chim., 2005, 83, 1400-1414. DOI:
- The preception of the 3D character of many molecules can be enhanced by viewing using stereoscopic systems. One such system is available for student use, and lecture theatre C is equipped with stereoscopic projection.
Running Avogadro on your own Computer
- Get Avogadro from here. It is available for Windows, OS X and Linux.
Submitting more accurate calculations to the Departmental HPC Cluster
The Chemistry department runs a HPC (high performance computing) system, which be used to run more time consuming calculations than is possible interactively on a single e.g. laptop or desktop computer whilst sitting in front of it.
One far more reliable and quantitative way of modelling a molecule is to subject it to quantum mechanical modelling using Density Functional theory. In practice, this is implemented here using a program called Gaussian 09. The procedure to submit such a job is as follows:
Creating an Input file
- After you have optimised your sketched molecule using Ghemical, as described above, right click in the black display window. This will produce the floating menu, from which you select file and then Export. Select Gaussian 98/03 Cartesian Input for the type and type a name for the file (make sure that the name of the file ends with .gjf). It will be saved in your H: drive by default.
- The file will have to be edited before it can be submitted. You can do this either with Gaussview as the program, but a much simpler method is to open the file (pentahelicene.gjf in this example) using eg the Windows Wordpad editor. This is invoked simply by double clicking on the file. Remove any existing lines starting with % or # and replace them with one of the following single lines (the second example also results in the vibrational frequences and from these the entropy being computed, and hence the zero-point and free-energy corrected value, ΔG). This latter option will take significantly longer however.
# B3LYP/6-31G(d) opt
or
# B3LYP/6-31G(d) opt freq
to produce a file that looks like the one shown on the right.
- For a molecule the size of e.g. pentahelicene, the calculation will take about 4-5 hours overnite. If for some reason, your molecule is taking longer, you can always reduce the size of the basis set to e.g. B3LYP/3-21G*, or submit the job on a Friday, when it will have the entire weekend available to it. If you want greater accuracy (but for longer computing time), try e.g. # B3LYP/cc-pVTZ opt freq.
Submitting the Input file
- You will have to login as yourself. You can submit as many jobs as you wish through this mechanism, but you must prepare the input (.gjf) file for each first. The SCAN operates during the period 23.00-07.30 overnight. If a job is not completed during this period, it will be scheduled to run again (from the beginning) the next night. For this reason, you should only schedule jobs that can complete in an 8 hour window. In practice this means submitting molecules only a little bit larger than pentahelicene.
- After you are logged in you should organise your jobs by project. Create a suitable new project, then select New job, the Application (currently only Gaussian) the Project, and press continue.
- You now have to find the Gaussian input file, as prepared above. You should Browse to drive H: to find this file. Add a description which will help you identify the job.
- The job will be added to your list of jobs, andyou can view its status (but this depends on there being a vacant machine in the Condor pool).
- When the job has completed, click on the Job List link. This will show all available outputs. Download the program Log file (this will help you chart whether the calculation was successfull) or the Gaussian Formatted Checkpoint file onto the desktop of the computer you are using, and the file should open up Gaussview, where the molecule can be viewed and checked. You can use the latter file to e.g. plot molecular orbitals for the molecule, view vibrational modes, etc. Full details of these procedures are described in the Gaussview manuals.
Archiving the output into a digital repository
A very recent innovation is the Institutional digital repository, a resource for permanently archiving calculations, spectra and crystal structures. You can get a flavour of this by archiving your own calculation in the SPECTRa digital repository. To the right of the Portal display is a link termed Publish. If you click on this, and the calculation is actually in a state to be published (it may for example have failed for some reason) then appropriate metadata for the calculation is collected, and the collection deposited into the repository. From here, it can be retrieved in future.
About this wiki: Opencourseware
This course is presented as a wiki. This differs from conventional hand-outs or web pages in several aspects.
- Anyone (who has a valid Imperial College login and password) can edit it, for the purpose of correcting errors, clarifying ambiguities, and even adding more examples, or references to existing examples. However, this activity is not anonymous; you can see who has done what by inspecting the history of the article. If you are considering making changes, go read these rules first.
- You may notice that some terms appear in red. This is because the original author has enclosed the term thus: [[red]], acting as a suggestion or hint that someone may wish to pick up this term, and expand it into something informative. If you think you can add something helpful to others, please go ahead: click on the red section and starting editing! If the result contains inaccuracies, someone may come along and correct them. If you are dubious that this scheme works, just go visit Wikipedia. The idea behind this is that we produce joined up courses and not just isolated islands of information and knowledge.
- You can also hit the edit button if you want to find out how any particular effect is achieved. You do not have to actually change anything.
- This is an experiment! If you have any comments on the experiment, or suggestions for improvements, go instead to the discussion page and say something there. Do however remember that anyone in the world (!) can see this (it is opencourseware, go read this stimulating and provocative view of how knowledge may be owned and disseminated in the future), so remember not to write anything inappropriate. You cannot do so anonymously!
