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Computational Chemistry Exercises #5 Computational Chemistry Exercises #5 21.10.2016 1 Visualization of Molecular Orbitals 1.1 Drawing a Molecule Molecule Imidazole student01 NH3 student02 Formaldehyde student03 Pyridine student04 Thiophene student05 Furan student06 Phenol student07 Oxazole student08 (a) Download and install Avogadro 1 (http://avogadro.cc). (b) Try to draw your molecule ( button). When finished, optimize its geometry in a force field (Auto optimization tool - ). Use the standard configuration for the optimization (Force Field: UFF, Algorithm: Steepest Decent). Once the gradient (dE) reaches zero, stop the optimization. (c) Go to Extensions!Gaussian to automatically generate an input file for Gaussian for a single point calculation at Hartree-Fock/6-31G(d,p) level of theory using 2 processors and 3Gb of memory. Additionally, enable the checkpoint box. 1.2 MOs based on coefficients /home/zech/CompChem TP/ex5/coefficients.spt /home/zech/CompChem TP/submit.job A molecular orbital φi can be represented by a linear combination of a set of atomic orbitals fχg Nbas X φi(~r ) = Cµiχµ(~r ); (1) µ where Cµi are the MO coefficients. In order to plot an orbital, the visualization software needs to know the atomic basis functions and the MO coefficients. In Gaussian the basis set information is not printed by default, which is why you have to include the keywords GFPrint and Pop=Full . (a) Include the necessary keywords in your input file and submit the calculation. (b) Download the log file from the cluster to your local computer and open it with Jmol. (c) Prepare images (see below) of the 5 highest occupied orbitals (HOMO!HOMO-5) and also make note of their energies. Note: Jmol reads more than one \model" from a standard Gaussian output. So you have to make sure that the correct model, which contains the MO data, is active (in my simple case that was model 2, but might depend on the case, e.g. SP or Opt). 1.2.1 How to use Jmol - Part 1 (1) Download the latest version of Jmol (https://sourceforge.net/projects/jmol/). (2) The most powerful aspect of Jmol is its console. Using the buttons and drop-down menus you are a bit limited, but the console offers a lot of possibilities. Table1 shows a couple of commands for the Jmol console: 1 Command Outcome General things background white changes background color to white spacefill 0.25 changes radius of sphere to 0.25A˚ wireframe 0.2 changes diameter of bond to 0.2A˚ model 2 switch to model 2 (if existing) cd ? opens dialogue window to choose default directory write image 1024 786 png \myorb.png" writes PNG image to file (in default directory) molecular orbitals (coeff) mo fill gives MO surface instead of mesh mo cutoff 0.04 draw MO with cutoff value 0.04 mo translucent 0.2 controls transparency of MO mo color purple orange controls colors of MO mo homo plots highes occ. molecular orbital mo 12 plots MO #12 Table 1: Commands in Jmol to control MO plot. 1.3 MOs based on grid information /home/zech/CompChem TP/ex5/grid.spt /home/zech/CompChem TP/do fchk Figure 1: Schematic representation of a grid. Molecular orbitals (and other properties) can be stored in a grid file like Gaussian09's *.cube file format. The grid is defined by three vectors which control the number of grid points. Each grid point P (x; y; z) is assigned a value w. With the Gaussian09 software we have to undergo several steps to produce the *.cube file: (a) The checkpoint file *.chk from the previous calculation needs to be converted to a formatted checkpoint file *.fchk. Just run: ./do fchk <chk filename> The next step is to run the routine cubegen. Copy the two lines (starting with export and source) from the file do fchk one by one into the command line and run them. Then: cubegen 1 MO=n <fchk filename> <cube filename> 0 h This will create the file <cube filename> (a detailed explanation of the parameters can be found in the online manual). Copy it to your local machine and open it with Jmol. (b) Prepare a picture of the LUMO and write down the energy (for your report). 2 1.3.1 How to use Jmol - Part 2 Using *.cube files is a lot different from using just the text output. For starters, you have one *.cube file for each MO. Also, grid files can get very large in size (several hundred of MB), which is why it is usually preferred to use the first visualization method. In Jmol you cannot use the mo command in combination with grid files. Here we have to use isosurface. Table2 shows a few useful commands with isosurface. Command Outcome isosurface moX sign cutoff 0.04 \x.cube" creates isosurfaces for both signs with cutoff values of 0.04 and label moX color $moX translucent controls transparency of isosurface color $moX purple orange controls colors of MO Table 2: Commands in Jmol to control MO plot from grid data. Getting started: • Please install WinSCP, XMING and PuTTY on your harddrive. • Connect to artemis.unige.ch with your student account. Make sure to enable X11 for- warding in order to use graphical interfaces. Submitting a job with Gaussian: 1. Prepare the input file, e.g. example.com. 2. Copy submission script submit.job into the same directory as your input file. 3. Submit job with the following syntax (nothing else has to be specified) sbatch submit.job example.com 4. Gaussian 09 Help: http://gaussian.com/g_tech/g_ur/g09help.htm Report: Please hand in a one page summary including a short description with tables, your name and date. 3.
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