$REORG group (optional)
This group controls the calculation of solvent
reorganization energy within the framework of IEF-PCM.
Presence of the $PCM group is a requirement for this group
to work. Specialized keywords in the $PCM group that work
with $REORG group are given below.
--------------
$PCM *** Only IEF=9,11,13,14 options are compatible ***
--------------
IEF=9 (models an environment with electrode and solvent
where the electrode is treated as a perfect
conductor => dielectric constant = infinity)
=11 (models an environment with electrode + self-
assembled monolayer (SAM) + solvent)
=13 (models an environment with electrode + double
layer (DL) + ionic solution)
=14 (models homogeneous solvent)
Note that extra keywords in the $REORG group are required
for the above keywords to work in the $PCM group. Also note
that IEF=14 option in $PCM along with an appropriate choice
of keywords in $REORG group may not reproduce the solution
phase free energies obtained with the IEF=3 keyword in $PCM
group because they use slightly different implementations
of IEF-PCM equation (See JCP 2002, 117, 7266).
--------------
$REORG
--------------
LAMDA = 1 (calculates solvent reorganization energies
with the total solvent polarization of the
product; not recommended)
= 2 (employs inertial polarization of the product)
The solvent reorganization energies for electron transfer
and proton-coupled electron transfer reactions are
calculated in a modular fashion. First, the equilibrium
solvent response is separated into the inertial and non-
inertial components and the corresponding surface charges
are written to the punch file (*.dat). This process needs
to be performed for both the oxidized and reduced states =>
separate inputfiles for oxidized and reduced states at the
same solute geometry. The surface charges of these 2 states
are then copied to a separate inputfile to calculate the
non-equilibrium solvent free energies. To calculate the
non-equilibrium solvent free energy for the oxidized state,
one needs to copy the surface charges corresponding to the
oxidized state first followed by the surface charges
corresponding to the reduced state. Similarly, for the
calculation of the non-equilibrium solvent free energy for
the reduced state the surface charges corresponding to the
oxidized state should follow the surface charges
corresponding to the reduced state.
An equilibrium calculation is implied by the presence of
IPCHG = 1
whereas a non-equilibrium calculation requires the
following
2 keywords instead:
IRCHG = 1
RLMIT = BO (Born-Oppenheimer limit)
= SC (Self-consistent limit)
In the BO limit, the non-inertial charges are read from the
inputfile (reactant state) and kept fixed during
calculation whereas in the SC limit, the non-inertial
charges are computed on-the-fly. In both cases, the
inertial charges are read from the inputfile (product
state).
A special type of calculation can be performed by taking
the inertial surface charges to be the average of the
reactant and product states. This calculation is triggered
by RLMIT = SCTS option.
****** Model Specific Keywords ******
|electrode + solvent: IEF=9 in $PCM|
DISIHP = distance of Inner Helmholtz Plane (IHP) from the
electrode in angstroms; The default value is
RSOLV (radius of a solvent molecule).
RADCAT = the radius of the solvated electrolyte ion
in angstroms; The default is 5.0 angstroms.
Note that the center of mass (COM)
of the molecule is placed at a distance "d"
(= 2*DISIHP + RADCAT) from the electrode-solvent
interface; this distance also defines the
location of the Outer Helmholtz Plane (OHP); In
principle, one can manipulate the distance of COM
of the molecule from the electrode-solvent
interface by changing the value of RADCAT.
For example, setting RADCAT = 0.0 will place the
COM at the outermost boundary of the 1st solvation
shell; alternatively, setting RADCAT = -RSOLV
will place the COM of the molecule at IHP. The
latter choice of keyword may, however, result in
an unphysical situation where a portion of
the solute molecule may penetrate the electrode.
To circumvent this situation, the distance between
the COM of the molecule and the electrode-solvent
interface is then reset to "d1" (= largest value
of the z-coordinates of the surface tesserae plus
10^(-5))
|electrode + SAM + solvent: IEF=11 in $PCM|
ESAM = dielectric constant of SAM; The default is 3.0
WSAM = width of SAM in angstroms; The default is 15.0
DISTMS = distance of COM of the molecule from the SAM-
solvent
interface in angstroms; The default is 5.0
|electrode + DL + ionic solution: IEF=13 in $PCM|
DISIHP = distance of IHP from the electrode in angstroms;
The default value is RSOLV
RADCAT = the radius of the solvated electrolyte ion
in angstroms. The default is 5.0 angstroms
DISM = ionic strength in Molar units (moles/Lt). The
default is 0.0
EPSOHP = dielectric constant of the solvent between the 1st
solvent sheath closest to the electrode and the
OHP. The default is EPS/2.0
EPSIOP = electronic dielectric constant of the solvent
between the 1st solvent sheath closest to the
electrode and the OHP. The default is EPSINF
EPSIHP = dielectric constant of the solvent between the
electrode and 2*DISIHP. The default is EPSINF.
EPSIIP = electronic dielectric constant of the solvent
between the electrode and the 1st solvent sheath
closest to the electrode. The default is EPSINF
DLDIST = measure of the distance of the COM of the molecule
from the DL-ionic solution interface in angstroms.
The default is 0.0, which puts the COM of the
molecule at a distance "d1" (=largest value of the
z-coordinates of the surface tesserae + 10^(-5))
from the DL-ionic solution interface.
RECOMMENDED KEYWORDS FOR OTHER $ GROUPS
(for less computation time/faster convergence)
--------------
$CONTRL
--------------
COORD=UNIQUE
UNITS=ANGS
RUNTYP=ENERGY
*** RUNTYP=OPTIMIZE is incompatible ***
--------------
$SCF
--------------
DIRSCF=.T.
DIIS=.T.
DAMP=.T.
*** For transition metal complexes ETHRSH = 2.0 is strongly
recommended ***
--------------
$TESCAV
--------------
MTHALL=4 (strongly recommended)
NTSALL=60
--------------
$PCMCAV
--------------
RADII=VANDW (or SUAHF)
For transition metal complexes (strongly recommended)
--------------
$DFT
--------------
JANS=1
*********** Example ***************
A typical set of keywords for the equilibrium calculation
of the oxidized state during the reduction of quinone in
DMF solvent with IEF=13 model is given by:
***********************************
$CONTRL
COORD=UNIQUE UNITS=ANGS
ISPHER=-1 MAXIT=200
ICHARG=0 MULT=1 RUNTYP=ENERGY EXETYP=RUN
SCFTYP=RHF DFTTYP=B3LYPV3 NPRINT=9
$END
$SYSTEM MWORDS=1000 $END
$SCF DIIS=.T. DAMP=.T. DIRSCF=.T. $END
$BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 $END
$PCM IEF=13 SOLVNT=DMSO EPS=37.219 EPSINF=2.046 $END
$TESCAV MTHALL=4 NTSALL=60 $END
$PCMCAV RADII=VANDW $END
$REORG
LAMDA=2 IPCHG=1
RADCAT=4.0
DISM=0.1 EPSOHP=18.6095
$END
$DATA
solvent dmf, double layer + ionic solution
C1
C 6.0 -0.62400 -0.02800 -0.34790
C 6.0 0.71910 -0.02690 -0.34810
C 6.0 1.49200 1.24330 -0.34830
C 6.0 0.71700 2.51230 -0.34810
C 6.0 -0.62610 2.51120 -0.34790
H 1.0 -1.21110 -0.94200 -0.34770
H 1.0 1.30760 -0.94000 -0.34830
H 1.0 1.30410 3.42630 -0.34830
H 1.0 -1.21460 3.42430 -0.34770
C 6.0 -1.39900 1.24100 -0.34770
O 8.0 -2.62410 1.24000 -0.34740
O 8.0 2.71710 1.24440 -0.34860
$END
***********************************
-----------------------------------------------------------
-
The two most important solvent parameters required to
calculate solvent reorganization energies are 1) EPS
(static dielectric constant of the solvent) and 2) EPSINF
(optical dielectric constant). In the above example, DMF is
not present in the standard GAMESS solvent database and so,
the radius a DMF molecule is approximated with the radius
of a DMSO molecule whereas the static and optical
dielectric constants (EPS and EPSINF) are provided
explicitly in the inputfile via keywords.
** Note also that a similar set of keywords as above can be
employed to compute just the solution phase free energy in
certain non-standard environments (IEF=9,11,13) **
-----------------------------------------------------------
-
The inputfile for the corresponding reduced state is
obtained by setting ICHARG=-1; MULT=2; SCFTYP=UHF.
Inputfile for the calculation of the corresponding non-
equilibrium free energy of the oxidized state is obtained
by replacing IPCHG=1 with IRCHG=1 and adding RLMIT=SC (or
BO) to the $REORG group. In addition, the user has to copy
the surface charges of the oxidized and reduced states from
the corresponding .dat files and place the surface charges
at the end of the inputfile. Note that the order in which
the surface charges are placed in the input file matters.
A python script is provided with the GAMESS code that runs
the equilibrium calculations, generates the inputfiles for
the non-equilibrium calculations, runs them and finally
prints out the solvent reorganization energies.
*** The above group of keywords may also be employed to
generate potential energy scans in the presence of
the solvent if the user wants to keep the inertial
solvent polarization fixed during the scan. In this
case, the solute cavity is also assumed to be unchanged
during the scan. ***
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Edited by Shiro KOSEKI on Thu Mar 5 10:25:38 2020.