Gaussian Solvent

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Gaussian Input file: Section layout

Example of CH2O 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

PCM in Gaussian 03PCM in Gaussian 03

Gcav + Gelec + Gdis-rep

Cavitationfree energy

Electrostaticfree energy

Disp-rep free energy

Energy and cavityEnergy 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

cavspheres

i i

icav RGR

AG =Exposed surface of sphere i

Single sphere contribution

( )

solvent soluteatom atom tesserae

dis rep dis reps s i ms mi i

s m i

G N a A r n = G G G(6)

6( ) 3dis msms ms ms

ms

dA r rr

= G G(12)

12( ) 9rep msms ms ms

ms

dA r rr

= G G

Cavitation term: van der Waals surface (VDW) with unscaled radii

Disp-rep terms: solvent-accessible surface (SAS) with radii scaled to account forthe 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

Spherescentered on solute atoms

Electrostatic interactions:Solvent-excluded surface (SES)


Probe sphererepresenting the

solvent

Added spherenot centered on

atoms



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

vdWRR f =Atom

Scaling factor :

f can be optimized; often for small-medium size solvents: f = 1.2

fRvdW

1.21.21.21.0-1.21.551.521.71.2

NitrogenOxygenCarbonHydrogenFor example

Electrostatic interactions:The boundary element method

Electrostatic interactions:The boundary element method

si

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

( )is G constant on eachelement of area ai ( )i i iq a s=G

A sphere: the mesh or tessellationA sphere: the mesh or tessellation

Polyhedron withn number of

faces

Projectionon a sphere: n triangular

sphericalelements(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 tesserainside the sphere is

eliminated

The area ai 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=itemIf 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 1solute geom

Gaussian Input for PCMGaussian Input for PCM

#p scrf=(iefpcm,solvent=item,read) hf/3-21G

title

0 1solute geom

PCM keywords

Gaussian Input for PCMGaussian 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)

CavitiesCavities

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

OAceto-phenone

------------------------------------------------------------------------------United Atom Topological 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 Atom Topological 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 = 2.023000Eps(inf)= 2.028000RSolv = 2.815000 Ang.

------------------------------------------------------------------------------GePol: Number of tesserae being generated = 1185GePol: Average area of tesserae = 0.15 Ang**2GePol: Minimum area of tessera = 0.12D-02 Ang**2GePol: Maximum area of tessera = 0.30586 Ang**2GePol: Number of small tesserae = 16GePol: Fraction of small tesserae (

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 1C -1.70224259 0.12750348 0.11298551O -2.28678088 1.19484792 -0.04380417C -0.20894647 0.05080826 0.00724215C 0.50951011 1.22655781 -0.27366334C 1.89851189 1.19842744 -0.38034127C 2.59066606 -0.00676889 -0.20769622C 1.88685577 -1.18183291 0.07185998C 0.49446587 -1.15391970 0.17894851H -0.04009200 2.15431340 -0.40529346H -0.03600514 -2.07642759 0.39663425O -2.44243558 -1.06194043 0.39975636H -3.37923874 -0.85540077 0.43637888O 2.58890857 -2.41498234 0.24895983H 3.53135335 -2.26504814 0.14447268O 4.01617040 -0.03602505 -0.31715599H 4.34088853 0.84642460 -0.51065213O 2.61592210 2.40192899 -0.66635985H 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 1.212 1.000 1.213 1.520 1.214 1.000 1.215 1.520 1.216 1.000 1.217 1.520 1.218 1.000 1.2

O

O

O

O

OH

H

H

H

From UA0

vdWRR f =

0 RH H V E = + =

0

0

1 12 2

12

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

0el elG G G = Electrostatic solvation free energy:

Electrostatic interactionsGaussian OutputGaussian Output

--------------------------------------------------------------------

Variational PCM results

=======================

(a.u.) = -98.568013

(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

--------------------------------------------------------------------

OutputOutput

12

RV

0 12

el RG H V= +

Nonelectrostaticterms

E H=

By doing first a gas-phase calculation: keyword = scfvac

Variational PCM results======================= (a.u.) = -509.799632 (a.u.) = -509.821720 (a.u.) = -509.823898 (a.u.) = -509.797139 (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 0H H

12

RV

0 012

RV

0 0 0el elG G H =

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