University College Cork Lecture Series on Computational Chemistry - Lecture 3

1. Quantum Mechanics Calculations III Noel M. O’Boyle Apr 2010 Postgrad course on Comp Chem

2. Overview of QM methods Molecular mechanics Quantum mechanics (wavefunction) Quantum mechanics (electron density) Including correlation HF (“ab initio”) Semi-empirical DFT Speed/Accuracy Forcefields

3. Carrying out calculations http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid_state_physics_software Gaussian (commercial) The most widely used package Can do most everything, and is pretty robust. Presumably not the fastest (the only software whose license prohibits published comparisons). Gaussian09 available through ICHEC, also faster (8-CPU machines) ORCA (free for academics) General purpose http://www.thch.uni-bonn.de/tc/orca/ Lots of other commercial packages: ADF (for DFT), Jaguar MOPAC2009 (commercial but free for academics) Semi-empirical calculations, Stewart NWChem (free for academics) General purpose http://www.emsl.pnl.gov/capabilities/computing/nwchem/ GAMESS (available for free) General purpose calculations. (See next page) Firefly Fork of GAMESS, formerly “PC GAMESS” Faster than GAMESS (especially on Windows) PSI3 (Open Source) HF and higher level http://www.psicode.org/, no Windows support

4. Once you have the QM software... Set up calculations Avogadro (OS, http://avogadro.sf.net) GaussView (commercial, available when buying Gaussian) Analyse results Avogadro Molekel (OS, http://molekel.cscs.ch) GaussSum (OS, http://gausssum.sf.net, by me) MacMolPlt (free, http://www.scl.ameslab.gov/MacMolPlt/) ...and many others

5. Get GAMESS GAMESS is free (but not open-source) software developed by the Gordon Group and collaborators To get it... Go to http://www.msg.ameslab.gov/GAMESS/ Click on “How to get GAMESS” Click “Obtaining GAMESS” Click “I agree” Enter email address, and tick box for “GAMESS version January 12, 2009 R3 for Microsoft Windows” (also a ChemOffice version – haven’t tried it) Click “Submit request” You will receive an email with a link, and a username and password Follow the link to download the installer and enter the username and password when requested To install it... Run the installer Click Next a few times It installs to C:inGAMESS To use it... Documentation is in C:inGAMESSanuals Following C:inGAMESSanualsinGAMESS.pdf we can... Create a shortcut to C:inGAMESSG_DDE.bat on the desktop Drag-and-drop GAMESS input files onto this shortcut How do we create an input file? Install Avogadro and MacMolPlt

6. Input for a calculation What type of calculation to do Location and atomic number of atoms Charge on molecule Multiplicity of molecule No need for bond orders No need to say where the charge is The charge is simply used to calculate the total number of electrons Typical calculations are in vacuo i.e. not in solid or liquid state, or in solvent If required, there is software for handling bulk solids, and there are methods to include solvent effects

7. Jan Jensen’s GAMESS Screencasts http://molecularmodelingbasics.blogspot.com/ Look at all of Jan’s screencasts and posts starting from the oldest On the right-hand side, see under Blog Archive Tools of the trade (all free, some open source) http://molecularmodelingbasics.blogspot.com/2009/06/tools-of-trade.html Building a molecule http://molecularmodelingbasics.blogspot.com/2009/07/building-complicated-molecule-2d-to-3d.html Finding the lowest energy conformer http://molecularmodelingbasics.blogspot.com/2009/07/building-complicated-molecule-and.html Look at the GAMESS input file http://molecularmodelingbasics.blogspot.com/2009/07/some-gamess-input-basics_24.html Set up a calculation using Avogadro http://molecularmodelingbasics.blogspot.com/2009/07/typical-set-of-gamess-calculations.html Finding a transition state http://molecularmodelingbasics.blogspot.com/2009/08/finding-transition-state-sn2-reaction.html Finding the path connecting reactant to product (intrinsic reaction coordinate) http://molecularmodelingbasics.blogspot.com/2009/10/get-reaction-intrinsic-reaction.html

8. Practical tips To speed up a geometry optimization, you can optimise first with a smaller basis set and then continue from there If you have trouble with SCF convergence, it can be a good idea to try converging it with a smaller basis set first and then projecting from that as the initial guess Molecules with geometrical symmetry will be corresponding faster (on the other hand, if you require symmetry to be broken during the calculation, you should turn off symmetry perception)