RUNNING SIMPLE CALCS IN GAUSSIAN (part 1) Right-click Gaussian (or GaussView) > Run as Administrator (otherwise... "link d ied") --.gjf is a Gaussian Input File with the instructions for calculation to be run .chk is a checkpoint file with intermediate results of our calculation we can run further calculations on the same system using the .chk file WAVEFUNCTION IS STORED IN THE CHK FILE! (unformatted, written in machine language) .out is Gaussian output file. You will see at the end "Normal termination of Gau ssian 09" .log is GaussView output file --Explanation of .gjf file format % #
set up checkpoint file method for solving Schrodinger equation "blank card" Title section (as many lines as you want) "blank card" [charge] [spin multiplicity] [atom] "blank card"
The final "blank card" or blank line at the end is required and must not be omit ted. --Manually create a .gjf file by typing this and saving as [Ar.gjf] %chk=C:\Users\TempUser1\Desktop\Ar.chk # HF/STO-3G Ar test calculation 0 1 Ar --Start the job in Gaussian or GaussView (no difference as GaussView will call Gau ssian anyway) But if running from GaussView, make sure to close any other instances of Gaussia n first. Gaussian File > Open [Ar.gjf] > Check-Route > RUN >> [Ar.out] will be output GaussView File > Open [Ar.gjf] > Calculate > Gaussian Calculation Setup > Submit >> [Ar.lo g] output
-----VIEWING CALCULATION RESULTS IN GAUSSVIEW ENERGY Open the [Ar.out] or [Ar.log] file in GaussView to see the energy Results > Summary > E(RHF) in a.u. (a.u. = Hartrees; 1 Hartree = 27.2 eV = 2625. 5 kJ/mol) Close the [Ar.out] or [Ar.log] file --ELECTROSTATIC POTENTIAL and ELECTRON DENSITY Open the [Ar.chk] file in GaussView Results > Surfaces/Contours Cube Actions > New Cube > "ESP" (Medium) Cube Actions > New Cube > "Total Density" (Medium) (Under Cubes Available, select "Electron density from Total SCF ..." before cont inuing!) Surface Actions > New Surface (electron density will appear) > Hide Surface Surface Actions > New Mapped Surface ("Electrostatic potential ...") View > Display Format > Surface > Mesh or Transparent --MOLECULAR ORBITALS Edit > MOs > Visualize > Cube Grid (Medium), Isovalue (0.02-0.04), Add List (1a7a) > Update -----CREATING INPUT FILES IN GAUSSVIEW Manually creating a .gjf file is impractical for larger molecules. Instead, we use GaussView to generate .gjf files automatically. In the (purple) New Molecule window... Click ONCE to add (by default) tetrahedral carbon with hydrogens attache d, i.e. CH4 Click&drag in the window to rotate the molecule. CTRL+Click&drag [left and right] to rotate the molecule differently. CTRL+Click&drag [up and down] to zoom in and out. SHIFT+Click&drag in the window to move the molecule around. CTRL+Z to undo molecule creation / Click the big red X icon in Main Pane l to delete
or close New Molecule window and open a new one (File > New > Create Mol ecule Group) In the (grey) Main Panel... Click the [6C] icon to choose an element from the periodic table display Select oxygen, and below, select the fragment with two single bonds Because hydrogens are automatically attached to the dangling bonds, this gives H2O Now H2O is displayed in the Main Panel but there's nothing in the New Mo lecule Window In the (purple) New Molecule window... Click ONCE to add single-bonded oxygen with hydrogens attached, i.e. H2O Click on Bond Length tool, then click on O and click on H > can change b ond length Click on Bond Angle tool, then click on H,O,H in turn > can change bond angle too (Don't worry about messing up the lengths and angles because we can easi ly clean up!) In the (grey) Main Panel... Clean [brush icon] Symmetrize [mirror plane icon]
(the symmetry C2v / C1 now shows at the
bottom) Clean corrects all bond lengths and angles to "typical" values. However, note that this is not necessarily the true molecular ge ometry! Symmetrize chooses a coordinate system that gives highest molecu lar symmetry. This can help to speed up calculations as some integrals can be re-used. Calculate > Gaussian Calculation Setup Job Type Method tral singlet Title Link 0 cify > 2
Energy Ground State Hartree-Fock Default Spin, STO-3G ! check that the charge and spin are correct. H2O is neu water STO-3G energy Memory Limit > Specify > 1 GB;
Shared Processors > Spe
Submit... Save [H2O.gjf] >> [H2O.chk] and [H2O.log] output Now repeat the earlier steps to find the energy, visualize electrostatic potenti al and MOs! **Tip - Don't forget to increase the Memory Limit to at least 1 GB or some calcs may fail. Use as many shared processors as your CPU has to speed up calculation s, & always Symmetrize! ---
SOLVATION The calculations we have performed so far are in the gas phase (the molecules ar e isolated). We can introduce explicit solvation by adding in more molecules but this is comp utationally expensive. Instead, more commonly used is *implicit* solvation wherein the solve nt is treated as a continuous medium or continuum, rather than individual molecules. We can set up a calculation using the Onsager solvation model (spherical dipole molecule). Run an energy calculation with additional keyword "volume" >> output will contai n the line: "Recommended a0 for SCRF calculation = X angstrom ( Y bohr)" Here, a0 is the solute radius estimated by a Monte Carlo procedure. Now remove the keyword "volume" and add in keyword "scrf=dipole" (to call the On sager model). Save this input file as .gjf but do not run the calculation yet. Edit the file in a word-processing software and add in two lines after the final blank card: [solute radius a0 in Angstrom] [solvent dielectric constant] [blank card] At this point the Onsager solvation calculation is ready to be run. The energy calculated for the solvated molecule can be compared with its gas pha se energy to determine the solvation energy. Of course, the same level of theory should be us ed for both. ! Note that the geometry of the molecule should be *optimized* in the gas phase, and again in the solvent, for the result to be more accurate. Optimization will be discussed in part 2. **Tip - Onsager solvation model really sucks! Choose something more decent from the drop-down menu in Gaussian Calculation Setup > Solvation > Model. The default model is PCM , and other even better models such as CPCM and SMD can be selected. The default solvent is water (but H-bonding is not taken into account as these are all implicit solvation models).
