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GAUSSIAN 03
E-mail: Ivan.Rostov@anu.edu.au
OUTLINE
Applications
Recommendations
2
SOLVENT EFFECTS
Nicolai Alexandrovich Menshutkin, Z. Physik. Chem. 1890, 5, 589
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SOLVENT EFFECTS
Spectra
Rotational (Microwave)
Vibrational (IR, Raman)
Electronic (UV, visible)
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METHODS FOR TREATMENT OF
SOLVATION
Supermolecule
Solute and some number of solvent molecules are included in one
large QM calculation
Molecular Mechanics Force Fields
Simple classical force fields allows us to include a large number of
solvent molecules
Continuum models
Explicit consideration of solvent molecules is neglected
Solvent effects are described in terms of macroscopic properties of
the chosen solvent (e, <Rsolvent>)
Hybrid/mixed:
Supermolecule + Continuum model
QM + MM
QM + MM + Continuum model
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SOLVATION PROCESS
disp.-rep. disp.-rep. elec
FiN FiN FiN
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BASICS OF THE CONTINUUM MODEL
THEORY
Solvent is described in terms of macroscopic
properties
Solvent is dielectric medium (uniform, normally),
characterized by the dielectric constant e0
Polarization of solvent is expressed in terms of the
surface charge density on the cavity surface
Polarization produces the electric field in the cavity
making an effect on solute
Dispersion-Repulsion and Cavitation are added
separately, or ignored
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THE ELECTROSTATIC PROBLEM
Poisson equations
- 4 r Vi
2
0 r Ve
with boundary conditions
on S:
in out
in
e= 1 e out
S n n
e= e0
Solution is calculated as
(r) (r)
(r) d r
3
d r
2
V
r - r S
r - r
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BORN MODEL
A single charge inside a spherical cavity
No constructing of the cavity surface elements, because
the Poisson equation is solved analytically
1 Q2
U solv -1 -
e0 R
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ONSAGER MODEL
Spherical cavity μ2 e 0 -1
E H- 3
Dipolar reaction field R 2e 0 1
No constructing of the cavity surface elements, because
the Poisson equation is solved analytically
Keywords in Gaussian:
SCRF(Dipole,A0=value,Dielectric=value)
Area of applicability:
Solute shape is close to spherical
Solute is polar (m >> 0)
References
L. Onsager, J. Am. Chem. Soc. 58, 1486 (1936).
M. Wong, M. Frisch, K. Wiberg, J. Am. Chem. Soc. 113, 4476
(1991).
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POLARIZED CONTINUUM MODEL (PCM)
Realistic molecular shape of the cavity (interlocking spheres
around each atom or group, or isodensity surface)
Induced surface charges represent solvent polarization
Includes free energy contributions from forming the cavity
and dispersion-repulsion
Comes in number of “flavours”:
IEFPCM, CPCM, DPCM, IPCM, or SCIPCM
Keywords in Gaussian:
SCRF(Solvent=, PCM specific options)
References:
E. Canses, B. Mennucci, J. Tomasi, J. Chem Phys. 107, 3032 (1997).
J. Tomasi, M. Persico, Chem. Rev. 94,2027 (1994).
J. Tomasi, B. Mennucci, R. Camm, Chem. Rev. 105, 2999 (2005).
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PCM, THE CAVITY CONSTRUCTION
Interlocking spheres around atomic groups
This is default in Gaussian 03
A choice of united atoms radii set, RADII=UAO (default), UAHF, UAKS,
or UFF
Interlocking spheres around each atom
Radii=Pauling (or Bondi)
Requires the scaling factor ALPHA by which the sphere radius is
multiplied. The default value is 1.0 though should be 1.2
A number of keywords is provided to add extraspheres when
necessary
A number of keyword is provided to govern the size and
number of surface elements (tesserae)
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PCM, THE CAVITY VIEW
Keyword: GeomView
Creates files in GeomView format to visualize the cavity
construction and the charge distribution on the cavity:
tesserae.off
charge.off
Files are readable by GeomView, JavaView and other visualization software.
(C5NH12+)
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PCM, METHODS OF SOLVING OF THE SCRF
PROBLEM TO CALCULATE SURFACE CHARGES
3
r r d r r 2 r
1 1 1
d r
2
Iterative
V f0 n (r ) r - r S
n (r ) r - r
Keyword: ITERATIVE
q
Solves the PCM electrostatic problem r i
through a linear scaling iterative Si
method using a Jacobi-like scheme
Advantageous when memory is
limited.
Inversion
Keyword: INVERSION
r ˆ -1 (r, r ' )Vˆ (r, r' ) (r )
D
Solve the PCM electrostatic problem to
calculate polarization charges through
the inversion matrix D with dimension
of NtesxNtes
Gaussian 03 uses Inversion by default.
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DIELECTRIC PCM
The original version of PCM
Electrostatics directly from the cavity model
Charges produces by discontinuity in the electric field
across the boundary created by the cavity
Very sensitive to solute charge outside the cavity
Only single point calculations
No longer recommended
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INTEGRAL EQUATION FORMALISM PCM
(IEFPCM)
Default in Gaussian 03
Less sensitive to diffuse solute charge
distributions
PCM + careful outlying charge corrections =>
IEFPCM
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CPCM (COSMO)
Uses the assumption that the cavity surface to be
conductor-like
This assumption simplifies the solution of Poisson
equation and calculation of the surface charges
Results can be outputted in COSMO RS format
Not recommended for solvents with low polarity
It is more efficient in iterative regime
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ISODENSITY PCM (IPCM) AND
SELF-CONSISTENT ISODENSITY PCM (SCIPCM)
Cavity formed using gas-phase static electronic isodensity
surface (IPCM)
Less arbitrary than spheres on atoms
Cavity changes with electron density and environment
The default density value is 0.0004
only single point calculations
Self-Consistent Isodensity (SCIPCM)
iterations are folded in SCF
issues regarding scaling of charges still remain
References
J. Foresman, T.Keith, K. Wiberg, J. Snoonian, M. Frisch,
J. Phys. Chem. 100,16098 (1996).
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GAUSSIAN 03 KEYWORD EXAMPLES
SCRF(Dipole,A0=5.5,eps=78.39)
SCRF(CPCM,Solvent=THF,Read)
SCRF(IPCM)
SCRF(SCIPCM)
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SAMPLE INPUT FOR PCM CALCULATIONS
PCM solvation is
%chk=pip-pcm
#P HF/6-31g(d) SCRF(PCM,Solvent=Water,Read) test
requested. Solvent is
Water. Additional PCM
Piperidinium cation specific keywords are
provided
1 1
N
C 1 1.50977268
C 2 1.52365511 1 109.63925419
C 3 1.53136665 2 111.56508108 1 -55.04631728
C 1 1.50978576 2 113.42079276 3 57.07092348
C 4 1.53134037 3 110.99585756 2 54.90811126
H 1 1.00969298 5 109.64667654 6 -179.99768911
H 1 1.01028619 5 109.06107319 6 64.67690355
H 2 1.08151743 1 106.09798567 5 -64.03241054
H 2 1.08069845 1 107.09512052 5 179.68520816
H 3 1.08732966 2 109.45874935 1 67.33780856
H 3 1.08342937 2 107.81444282 1 -177.04873713
H 4 1.08661607 3 109.70973952 2 -66.50424273
H 4 1.08269752 3 109.4557835 2 176.38517116
H 5 1.08069728 1 107.09836585 2 -179.68240007
H 5 1.08151732 1 106.09918524 2 64.03563496
H 6 1.08732304 4 110.31444998 3 66.98445589
H 6 1.08344075 4 110.90163383 3 -175.10999479
PCMDOC
ITERATIVE PCM specific keywords
GEOMVIEW 20
SAMPLE OUTPUT
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APPLICATIONS
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+
PIPEREDIN CATION (C5NH12 ),
FREE ENERGY OF HYDRATION
QM: HF/6-31G(d)
Method Gsolv, kcal/mol
SP SCRF(Dipole,A0=5.5) -30.6
SP SCRF(PCM) -56.0
SP SCRF(CPCM) -56.1
SP SCRF(IPCM) -59.4
SP SCRF(SCIPCM) -60.9
D-SA → DSA-
Spacer: 5-a-androstane
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- -
ET system D SA → DSA
ET SYSTEM
D: 4-Biphenyl
A: 2-Naphthyl
S:5-a-androstane
87 atoms in total,
5158 tesserae created
D: 4-Biphenyl
A: 2-Naphthyl
S:5-a-androstane
87 atoms in total,
5158 tesserae created
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MENSHUTKIN REACTION
Model G≠ G
Gas 43.7 120.0
Onsager 18.2 10.0
DPCM@Onsager 24.2 -21.0
CPCM 24.8 -21.5
Experiment – for CH3I
Gas ? 110
Solution 24 -30
Energies in kcal/mol
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MENSHUTKIN REACTION: TRANSITION STATE
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RECOMMENDATIONS
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