$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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generated on 7/7/2017