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Molecular Quantum Chemistry
Gaussian and all that…
Herbert Früchtl
Overview
Using Gaussian on the clusterComputational methods overviewBasis setsCalculation of different propertiesGaussview on cluster and PC
A typical calculation
1. Get initial geometry
2. Edit input
3. Run calculation
4. Analyse results
Geometry in Gaussian Input Format
Convert known geometry from different formatbabel –i<fmt> <inputfile> -og03 <input>.gjfbabel –H
Build molecule with builder softwareMolden, Maestro, Gaussview
Don’t run long calculations from Gaussview oncluster!
Notation: replace <something> with actual argument
Elements of G09 Input
Checkpoint file (for restart or orbital analysis)
Memory requirement (too much may slowcalculation down)
Number of processors (12 on wardlaw node)
Keywords
Title (must be present, but has no effect)
Charge and multiplicity
Geometry (Cartesian or Z-matrix)
Empty lines (required)
There could be additional information for
some methods
Running SLURM Batch Jobs
Submit script to batch queuefor execution when acompute node is available
Job script with SLURMdirectives at the start:
Name of job
Request one nodeUse 12 coresRun for 48h maxUse complete nodesScript to run Gaussian
SLURM directives
Commands toexecute when jobstarts
Analysis of Results
Text output: <input>.logEnergy, final geometry, …
Checkpoint file (name specified in input)Additional information (orbitals, …)
formchk <file>.chkCreates “formatted checkpoint” for transfer to differentcomputer
cubegen <file>.fchkCreates density map to be displayed with various otherprograms
.log, .chk, .fchk can be viewed with Gaussview
Gaussview / File Transfer Caveats
Text files (.log, .fchk) may need conversion to Windows format(dos2unix, unix2dos)
Only formatted checkpoint files (.fchk) are transferablebetween machines. Create them with formchk.
Gaussview 4 can not read frequencies from Gaussian 09 logfiles. Translate to G03 format with g09tog03.
Modelling Methods for Molecules
1 10 100 1000 10000 100000 1000000
Number of Atoms
Accu
racy
FCI
CCSD(T)
DFT
Hartree-Fock
Molecular Mechanics
QM/MM
Semiempirical Methods
MP2
Molecular Mechanics
Parametrised forces betweenatoms or groups
No description of electronicstructure
Cheap large systems and/orlong dynamics simulations
Not good for change in bondstructure
Often problems associating atomtypes
Force fields optimised for certainclass of molecule
Force Fields:UFFAMBERCHARMMOPLSDreiding
For dynamics usean MD program(AMBER, DL_POLY, …)
Semiempirical Methods
Fastest electronic structure method!
Electronic structure with severeapproximations and parametrisedintegrals
Originally optimised for small(ish)organic molecules
Only PM6/7 (not in Gaussian)parametrised for all elements.
Methods:AM1PM3PM6PM7
Often good forinitial optimisation.
For many purposesa good Force Fieldis better.
Consider QM/MM
Density Functional Theory
All ground state properties can bedetermined as a functional of the electrondensity (Hohenberg-Kohn Theorem)
This functional is not known. Many modelfunctionals in use.
Current functionals do not describe staticcorrelation (London dispersion), althoughsome are parametrised to experimentalresults. Empirical corrections for forcesavailable.
Density Functionals
LDAlocal density
GGAgradient corrected
Meta-GGAkinetic energy densityincluded
Hybrid“exact” HF exchangecomponent
Hybrid-meta-GGA
VWN5
BLYPHCTHBP86
TPSSM06-L
B3LYPB97/2MPW1K
MPWB1KM05-2XM06-2X
Better scaling with system
size
Allow density fitting for even
better scaling
Meta-GGA is “bleeding
edge”, but M06-2X slowlyreplacing B3LYP as “goldstandard”
Hybrid makes bigger
difference in cost andaccuracy than meta-GGA
Look at literature if
somebody has comparedfunctionals for systemssimilar to yours!
Incr
easi
ng
qualit
yand
com
puta
tionalco
st
Post-HF Methods
MP2
Similar to DFT in total accuracy
Describes all kinds of correlationenergy
Scales n5 with basis functions
CCSD(T)
Best feasible black-box methodfor small molecules
Scaling n7
Many more Methods:MP3, MP4QCISD, BDCCSDT(Q)
MP2 may be necessaryin case of dispersiondominated interactions(e.g. -)
QM/MM
Treat “interesting” region withhigher accuracy
Anything not part of the reactiontreated on lower level (typicallyMM)
Boundary atoms saturated with Hatoms
Careful where you cut!
Gaussian keyword:ONIOM(HF/6-31G(d):AM1:UFF)Up to 3 layers
Gaussian Basis Sets
Pople splitvalence
6-31g
6-31+g*
6-31++g**
Poplevalence triplezeta
6-311g
6-311+g*
6-311++g**
Dunning correlationconsistent
cc-pvdz aug-cc-pvdz
cc-pvtz aug-cc-pvtz
cc-pvqz aug-cc-pvqz
Diffuse functions
long-distance interactionsanions
Polarisation functions
Flexibility in angularcharge distribution
Many more basis sets
Post-HF methods need larger basis than DFT
Geometry Optimisation
• Find (local) minimum (equilibriumstructure) or saddle point (transitionstate) on potential energy surface
• No guarantee to find “correct”minimum or TS
• TS considerably more difficult
• Most methods are quasi-Newton withupdated Hessian Need good initial guess of curvature
– Frequency calculation at lower level
– Optimisation at lower level (ReadFC)
– In extreme cases, calculate Hessian inevery stepOpt=CalcFC in GaussianExpensive!
Transition State Optimisation
Transition state:1st order saddle point onpotential energy surface
Method:follow Eigenvector of negativeEigenvalue uphillall other directions downhill
Considerably more difficultthan minimisation
Need good Hessian
Need starting point where Hessianhas correct structure: one negativeEigenvalue
Solvation
Explicit Solvent
Expensive
Solvent may be treated at lowerlevel (QM/MM)
Continuum Solvation Models
In Gaussian:SCRF=(PCM,Solvent=H2O)(various models and solventsavailable)
++
-
+
--
Solvent treatment is essential for Zwitterions and many ionsGeometry optimisation more difficult with both approaches
Infrared Spectroscopy
Frequencies are
Eigenvalues of mass-weighted force constantmatrix (Hessian)
Harmonic approximation(and therefore too high)
Anharmonic frequenciespossible, but expensive(Gaussian keyword
Frequency=Anharmonic)
UV/Visible SpectroscopyElectronically excited states vertical excitation
energies HOMO-LUMO gap (Koopman’s Theorem)
Bad; virtual HF/DFT orbital energies unreliable,no orbital relaxation
ZINDOsemiempirical, limited selection of atoms;fast, qualitatively OK
CISHF based; rather inaccurate (but better than Koopman)
TD-DFTDFT equivalent of CIS (but founded in different theory);better than CIS
CIS(D)CIS with approximate doublesbased on MP2; accurate but expensive
NMR Properties
Shielding Tensor(keyword NMR)
Spin-Spin couplings(NMR=SpinSpin)
Expensive!
Requires good basis setat nucleus
Consider uncontracting basisfunctions orNMR=(SpinSpin,Mixed)(uncontracts basis and addsfunctions around nucleus for partof the calculation)
Atom Isotropic shielding in ppm
Needs to be compared to valuefrom TMS optimised andcalculated with same methodand basis set
Thermochemistry
Frequency calculation gives zero-point correctionto Energy, Enthalpy and Gibbs Free Energy
Properties calculated at 298.15K (default) oruser-specified temperature
Thermodynamic reaction properties can bedetermined in a “model chemistry” (CBS-QB3,G2, …)(expensive!)
Atomic Charges
There is no suchthing as anatom…
Mulliken
Projection of electrondensity on AO basis
Calculated by default
Not very reliable
Diffuse basis functionsmake things worse!
NBO
Natural Bond Orbitals
Better…
AIM
Atoms in Molecules
Cut molecule at surface of“minimum flux”
Requires separateprogram to calculate
Gaussview
Graphical user interface for Gaussian
Can be used to
build molecules
analyse results
run calculations (not on cluster!)
Have site licence for any University-owned PC(Windows or Linux)
Problems with cygwin seem to be resolved. Tell me ifthat’s not the case…
Gaussview Screenshot
And Finally
Gaussian is not the only program
B3LYP is not the only functional
6-31g* is not the only basis set
More information:
http://www.gaussian.com/g_tech/1.htmhttp://www.gaussian.com/g_ur/g03mantop.htm
(we have G03 on PCs, but G09 on clusters)
Ask me! (or TvM, or MBuehl, or any of our postgrads)
Postgrad course on computational chemistry
Email your name and supervisor to Tanja van Mourik
Not only for postgrads!
Other Lectures and Seminars
Lectures on
Introduction to using the EaStCHEM cluster (previous)
DFT on Periodic Systems (next)
Available on School website (Current Students -> Undergrads -> Course resources)
Computation in Chemistry Seminars
See Chemistry Newsletter
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