Introduction to

Introduction to
Gaussian
Gaussian
03 Package
03 Package
http://ww.gaussian.com
Gaussian Input file: Section layout
Example of CH
2
O with HF/STO-3G: Input file
More About Gaussian Input file
An array of ab initio methods are available
Gaussian job Route: a sequence of links
Output file
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PCM in Gaussian 03
PCM in Gaussian 03
G
cav
+ G
elec
+ G
dis-rep
Cavitation
free energy
Electrostatic
free energy
Disp-rep
free energy
Energy and cavity
Energy and cavity
Electrostatic term: solvent-excluded surface (SES) with scaled radii
Cavitation term: van der Waals surface (VDW) with unscaled radii
Disp-rep terms: solvent-accessible surface (SAS) with scaled radii.
) (
4
2
i
cav
spheres
i
i
i
cav
R G
R
A
G

=
Exposed surface of sphere i
Single sphere contribution
( )
solvent solute
atom atom
tesserae
dis rep dis rep
s s i ms mi i
s m i
G N a A r n

=



(6)
6
( )
3
dis
ms
ms ms ms
ms
d
A r r
r
=

(12)
12
( )
9
rep
ms
ms ms ms
ms
d
A r r
r
=

Cavitation term: van der Waals surface (VDW) with unscaled radii
Disp-rep terms: solvent-accessible surface (SAS) with radii scaled to account for
the solvent. A different cavity has to be built for each different solvent atom (s)
Non-Electrostatic terms
Connolly: formal definition
GePol: computational definition
Reentrant (concave) surface Convex surface
Spheres
centered on
solute atoms
Electrostatic interactions:
Solvent-excluded surface (SES)
Electrostatic interactions:
Solvent-excluded surface (SES)
Probe sphere
representing the
solvent
Added sphere
not centered on
atoms
Electrostatic interactions:
Solvent-excluded surface (SES)
Electrostatic interactions:
Solvent-excluded surface (SES)
Which Radii for the spheres centered on the atoms?
van der Waals radius
atomic bond or lone pair charge centers of the
solvent molecules are normally located a bit
further from the solute atoms
vdW
R R f

=
Atom
Scaling factor :
f can be optimized; often for small-medium size solvents:
f = 1.2
f
R
vdW
1.2 1.2 1.2 1.0-1.2
1.55 1.52 1.7 1.2
Nitrogen Oxygen Carbon Hydrogen For
example
Electrostatic interactions:
The boundary element method
Electrostatic interactions:
The boundary element method
s
i
1. Partition of the cavity surface into N finite
elements (tesserae) (Boundary Element
Method, BEM)
2. Discretization of the apparent surface charge into N point-
like charges q
( )
i
s

constant on each
element of area a
i
( )
i i i
q a s =

A sphere: the mesh or tessellation
A sphere: the mesh or tessellation
Polyhedron with
n number of
faces
Projection
on a sphere:
n triangular
spherical
elements
(tesserae)
Refinement of
the mesh
A polyhedron with a
larger number of faces
A sphere intersects a
tessera placed on
another sphere
The part of the tessera
inside the sphere is
eliminated
The area a
i
of all the tesserae
(original or cut) can be calculated
analytically
Cut tessera
A more general cavity: the mesh or
tessellation
A more general cavity: the mesh or
tessellation
Solvent=item
If unspecified, the solvent defaults to water.
Item is a solvent name chosen from the list:
Water or H2O, Acetonitrile or CH3CN, DiMethylSulfoxide or DMSO, Methanol or CH3OH,
Ethanol or CH3CH2OH, Isoquinoline, Quinoline, Chloroform or CHCl3, Ether or DiEthylEther or
CH3CH2OCH2CH3, DiChloroMethane or MethyleneChloride or CH2Cl2, DiChloroEthane or
CH2ClCH2Cl, CarbonTetrachloride or CCl4, Benzene or C6H6, Toluene or C6H5CH3,
ChloroBenzene or C6H5Cl, NitroMethane or CH3NO2, Heptane or C7H16, CycloHexane or
C6H12, Aniline or C5H5NH2, Acetone or CH3COCH3, TetraHydroFuran or THF,
DiMethylSulfoxide or DMSO or CH3SOCH3, Argon or Ar, Krypton or Kr, Xenon or Xe
#p scrf=(iefpcm,solvent=item) hf/3-21G
title
0 1
solute geom
Gaussian Input for PCM
Gaussian Input for PCM
#p scrf=(iefpcm,solvent=item,read) hf/3-21G
title
0 1
solute geom
PCM keywords
Gaussian Input for PCM
Gaussian Input for PCM
PCM keywords:
norep, nodis, nocav: to skip nonelectrostatic terms
scfvac: to do a gas-phase calculation first
eps=XX, epsinf=YY, Rsolv=ZZ, : to change solvent parameters
NOADDSPH, Radii=XX, tsare=YY, nsfe=NN, : to change cavity and meshing
..
Default (UA0): Spheres centered only
on heavy atoms (effective radii)
Cavities
Cavities
Rmin=0. ofac=0.8
simplified scheme for
the added spheres:
computationally more
efficient
Radii=bondi : spheres centered on
each atom including the hydrogens
Simplification
of the topology
Further
simplification
of the topology
Green spheres are centered on
carbons, red spheres on oxygens,
white spheres on hydrogens and
added spheres are in black
O
Aceto-phenone
------------------------------------------------------------------------------
United AtomTopological Model (UA0 parameters set).
Nord Group Hybr Charge Alpha Radius Bonded to
1 C * 0.00 1.00 1.925 C2 [s] O3 [d] C4 [s]
2 CH3 * 0.00 1.00 2.525 C1 [s]
3 O * 0.00 1.00 1.750 C1 [d]
4 C * 0.00 1.00 1.925 C1 [s] C5 [s] C9 [s]
5 CH * 0.00 1.00 2.125 C4 [s] C6 [s]
6 CH * 0.00 1.00 2.125 C5 [s] C7 [s]
7 CH * 0.00 1.00 2.125 C6 [s] C8 [s]
8 CH * 0.00 1.00 2.125 C7 [s] C9 [s]
9 CH * 0.00 1.00 2.125 C4 [s] C8 [s]
------------------------------------------------------------------------------
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : UA0 (Simple United AtomTopological Model).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity : GePol (RMin=0.500 OFac=0.800).
Default sphere list used, NSphG= 9.
Tesserae with average area of 0.200 Ang**2.
Solvent : Cyclohexane, Eps = 2.023000
Eps(inf)= 2.028000
RSolv = 2.815000 Ang.
------------------------------------------------------------------------------
GePol: Number of tesserae being generated = 1185
GePol: Average area of tesserae = 0.15 Ang**2
GePol: Minimum area of tessera = 0.12D-02 Ang**2
GePol: Maximumarea of tessera = 0.30586 Ang**2
GePol: Number of small tesserae = 16
GePol: Fraction of small tesserae (<1% of avg) = 1.35%
GePol: Total count of vertices = 3905
GePol: Maximumnumber of vertices in a tessera = 6
GePol: Cavity surface area = 175.984 Ang**2
GePol: Cavity volume = 182.113 Ang**3
In the output
In the output
#p scrf=(iefpcm, solvent=cyclohexane, read) ....
title
0 1
solute geom
nodis nocav norep rmin=0.5 ofac=0.8
Input
Spheres centered only on heavy atoms.
Computationally efficient but it loses accuracy in describing
the interaction of acidic hydrogens with solvent
When the default (UA0) cavity is not sufficient?
Default: UA0
When hydrogens play a role
OH
OH
OH
O
HO
+
rmin=0.5 ofac=0.8
Gallic acid
When the default (UA0) cavity is not sufficient?
When hydrogens play a role
OH
OH
OH
O
HO
Mixed
Spheres centered on the heavy atoms and on acidic hydrogens
More accurate in the description of solute-solvent interactions
Gallic acid
Gallic acid
#p scrf=(iefpcm,read) ....
Gallic acid
0 1
C -1.70224259 0.12750348 0.11298551
O -2.28678088 1.19484792 -0.04380417
C -0.20894647 0.05080826 0.00724215
C 0.50951011 1.22655781 -0.27366334
C 1.89851189 1.19842744 -0.38034127
C 2.59066606 -0.00676889 -0.20769622
C 1.88685577 -1.18183291 0.07185998
C 0.49446587 -1.15391970 0.17894851
H -0.04009200 2.15431340 -0.40529346
H -0.03600514 -2.07642759 0.39663425
O -2.44243558 -1.06194043 0.39975636
H -3.37923874 -0.85540077 0.43637888
O 2.58890857 -2.41498234 0.24895983
H 3.53135335 -2.26504814 0.14447268
O 4.01617040 -0.03602505 -0.31715599
H 4.34088853 0.84642460 -0.51065213
O 2.61592210 2.40192899 -0.66635985
H 1.99714443 3.13057680 -0.75460133
rmin=0.5 ofac=0.8 nsfe=16
1 1.925
2 1.750
3 1.925
4 2.125
5 1.925
6 1.925
7 1.925
8 2.125
11 1.520 1.2
12 1.000 1.2
13 1.520 1.2
14 1.000 1.2
15 1.520 1.2
16 1.000 1.2
17 1.520 1.2
18 1.000 1.2
O
O
O
O
O
H
H
H
H
From UA0
vdW
R R f

=
0 R
H H V E

= + =

0
0
1 1
2 2
1
2
el R R R
R
G E V H V V
H V
= = +
= +
To get the free energy we have to subtract the work spent in polarizing the solvent
By solving the equation we get
E H =
The internal energy of
the solvated system
0 el el
G G G =
Electrostatic solvation free energy:
Electrostatic interactions
Gaussian Output
Gaussian Output
--------------------------------------------------------------------
Variational PCM results
=======================
<psi(f)| H |psi(f)> (a.u.) = -98.568013
<psi(f)|H+V(f)/2|psi(f)> (a.u.) = -98.573228
Total free energy in solution:
with all non electrostatic terms (a.u.) = -98.569083
--------------------------------------------------------------------
(Polarized solute)-Solvent (kcal/mol) = -3.27
--------------------------------------------------------------------
Cavitation energy (kcal/mol) = 5.34
Dispersion energy (kcal/mol) = -3.08
Repulsion energy (kcal/mol) = 0.34
Total non electrostatic (kcal/mol) = 2.60
--------------------------------------------------------------------
Output
Output
1
2
R
V
0
1
2
el R
G H V = +
Nonelectrostatic
terms
E H =
By doing first a gas-phase calculation: keyword = scfvac
Variational PCM results
=======================
<psi(0)| H |psi(0)> (a.u.) = -509.799632
<psi(0)|H+V(0)/2|psi(0)> (a.u.) = -509.821720
<psi(0)|H+V(f)/2|psi(0)> (a.u.) = -509.823898
<psi(f)| H |psi(f)> (a.u.) = -509.797139
<psi(f)|H+V(f)/2|psi(f)> (a.u.) = -509.823917
(Unpolarized solute)-Solvent (kcal/mol) = -13.86
(Polarized solute)-Solvent (kcal/mol) = -16.80
Solute polarization (kcal/mol) = 1.56
Total electrostatic (kcal/mol) = -15.24
0 0 0 0
H H
1
2
R
V
0 0
1
2
R
V
0 0 0 el el
G G H =