Molecular Quantum Chemistry Gaussian and all that… Herbert Früchtl

Molecular Quantum Chemistry
Gaussian and all that…
Herbert Früchtl
Overview
Using Gaussian on the cluster
Computational methods overview
Basis sets
Calculation of different properties
Gaussview 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 format
babel –i<fmt> <inputfile> -og03 <input>.gjf
babel –H


Build molecule with builder software
Molden, Maestro, Gaussview
Don’t run long calculations from Gaussview on
cluster!
Notation: replace <something> with actual argument
Elements of G09 Input
Checkpoint file (for restart or orbital analysis)
Memory requirement (too much may slow
calculation 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 queue
for execution when a
compute node is available
Job script with SLURM
directives at the start:
Name of job
SLURM directives
Commands to
execute when job
starts
Request one node
Use 12 cores
Run for 48h max
Use complete nodes
Script to run Gaussian
Analysis of Results





Text output: <input>.log
Energy, final geometry, …
Checkpoint file (name specified in input)
Additional information (orbitals, …)
formchk <file>.chk
Creates “formatted checkpoint” for transfer to different
computer
cubegen <file>.fchk
Creates density map to be displayed with various other
programs
.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 transferable
between machines. Create them with formchk.
Gaussview 4 can not read frequencies from Gaussian 09 log
files. Translate to G03 format with g09tog03.
Modelling Methods for Molecules
FCI
Accuracy
CCSD(T)
MP2
DFT
Hartree-Fock
QM/MM
Semiempirical Methods
Molecular Mechanics
1
10
100
1000
10000
Number of Atoms
100000
1000000
Molecular Mechanics






Parametrised forces between
atoms or groups
No description of electronic
structure
Cheap  large systems and/or
long dynamics simulations
Not good for change in bond
structure
Force Fields:
UFF
AMBER
CHARMM
OPLS
Dreiding
For dynamics use
Often problems associating atom an MD program
types
(AMBER, DL_POLY, …)
Force fields optimised for certain
class of molecule
Semiempirical Methods




Fastest electronic structure method!
Electronic structure with severe
approximations and parametrised
integrals
Originally optimised for small(ish)
organic molecules
Only PM6/7 (not in Gaussian)
parametrised for all elements.
Methods:
AM1
PM3
PM6
PM7
Often good for
initial optimisation.
For many purposes
a good Force Field
is better.
Consider QM/MM
Density Functional Theory



All ground state properties can be
determined as a functional of the electron
density (Hohenberg-Kohn Theorem)
This functional is not known. Many model
functionals in use.
Current functionals do not describe static
correlation (London dispersion), although
some are parametrised to experimental
results. Empirical corrections for forces
available.
VWN5
BLYP
HCTH
BP86
TPSS
M06-L
B3LYP
B97/2
MPW1K
MPWB1K
M05-2X
M06-2X
Increasing quality and computational cost
Density Functionals
LDA
local density
GGA
gradient corrected
Meta-GGA
kinetic energy density
included
Hybrid
“exact” HF exchange
component
Hybrid-meta-GGA
Better scaling with system
size
Allow density fitting for even
better scaling
Meta-GGA is “bleeding
edge”, but M06-2X slowly
replacing B3LYP as “gold
standard”
Hybrid makes bigger
difference in cost and
accuracy than meta-GGA
Look at literature if
somebody has compared
functionals for systems
similar to yours!
Post-HF Methods


MP2

Similar to DFT in total accuracy

Describes all kinds of correlation
energy

Scales n5 with basis functions
Many more Methods:
MP3, MP4
QCISD, BD
CCSDT(Q)
CCSD(T)

Best feasible black-box method
for small molecules

Scaling n7
MP2 may be necessary
in case of dispersion
dominated interactions
(e.g. -)
QM/MM
Treat “interesting” region with
higher accuracy
Anything not part of the reaction
treated on lower level (typically
MM)
Boundary atoms saturated with H
atoms
Careful where you cut!
Gaussian keyword:
ONIOM(HF/631G(d):AM1:UFF)
Up to 3 layers
Gaussian Basis Sets
Pople split
valence

6-31g
6-31+g*
6-31++g**
Pople
valence triple
zeta
Dunning correlation
consistent
cc-pvdz
aug-cc-pvdz

6-311g
cc-pvtz
aug-cc-pvtz

6-311+g*
cc-pvqz
aug-cc-pvqz

6-311++g**
Diffuse functions
long-distance interactions
anions
Many more basis sets
Post-HF methods need larger basis than DFT
Polarisation functions
Flexibility in angular
charge distribution
Geometry Optimisation
• Find (local) minimum (equilibrium
structure) or saddle point (transition
state) on potential energy surface
• No guarantee to find “correct”
minimum or TS
• TS considerably more difficult
• Most methods are quasi-Newton with
updated Hessian
 Need good initial guess of curvature
– Frequency calculation at lower level
– Optimisation at lower level (ReadFC)
– In extreme cases, calculate Hessian in
every step
Opt=CalcFC in Gaussian
Expensive!
Transition State Optimisation


Transition state:
1st order saddle point on
potential energy surface
Method:
follow Eigenvector of negative
Eigenvalue uphill
all other directions downhill
Considerably more difficult
than minimisation
Need good Hessian
Need starting point where Hessian
has correct structure: one negative
Eigenvalue
Solvation
Explicit Solvent
Continuum Solvation Models
+ +
+
-- -
Expensive
Solvent may be treated at lower
level (QM/MM)
In Gaussian:
SCRF=(PCM,Solvent=H2O)
(various models and solvents
available)
Solvent treatment is essential for Zwitterions and many ions
Geometry optimisation more difficult with both approaches
Infrared Spectroscopy
Frequencies are
Eigenvalues of massweighted force constant
matrix (Hessian)
Harmonic approximation
(and therefore too high)
Anharmonic frequencies
possible, but expensive
(Gaussian keyword
Frequency=Anharmonic)
UV/Visible Spectroscopy
Electronically excited states vertical excitation
energies





HOMO-LUMO gap (Koopman’s Theorem)
Bad; virtual HF/DFT orbital energies unreliable,
no orbital relaxation
ZINDO
semiempirical, limited selection of atoms;
fast, qualitatively OK
CIS
HF based; rather inaccurate (but better than Koopman)
TD-DFT
DFT equivalent of CIS (but founded in different theory);
better than CIS
CIS(D)
CIS with approximate doubles
based on MP2; accurate but expensive
NMR Properties
Shielding Tensor
(keyword NMR)
Spin-Spin couplings
(NMR=SpinSpin)
Expensive!
Requires good basis set
at nucleus
Consider uncontracting basis
functions or
NMR=(SpinSpin,Mixed)
(uncontracts basis and adds
functions around nucleus for part
of the calculation)
Atom
Isotropic shielding in ppm
Needs to be compared to value
from TMS optimised and
calculated with same method
and basis set
Thermochemistry
Frequency calculation gives zero-point correction
to Energy, Enthalpy and Gibbs Free Energy
Properties calculated at 298.15K (default) or
user-specified temperature
Thermodynamic reaction properties can be
determined in a “model chemistry” (CBS-QB3,
G2, …)
(expensive!)
Atomic Charges
Mulliken

There is no such
thing as an
atom…



Projection of electron
density on AO basis
Calculated by default
Not very reliable
Diffuse basis functions
make things worse!
NBO


Natural Bond Orbitals
Better…

Atoms in Molecules

Cut molecule at surface of
“minimum flux”

Requires separate
program to calculate
AIM
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 if
that’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.htm
http://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)
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
Sign up to mailing list with Tanja van Mourik
Postgrad course on computational chemistry
Email your name and supervisor to Tanja van Mourik
[email protected]
Not only for postgrads!