SM12: Solvation Model 12

Continuum solvation can be done with the Minnesota’s Solvation Model 12 (SM12) (JCTC,9,609,2013). Details on the implementation of SM12 in ADF can be found in Ref. (JCTC,12,4033,2016). The energetics of solvation is calculated using:

\[\Delta G_S^\otimes = \Delta E_E + G_P + G_{CDS} + \Delta G_N + \Delta G_{conc}^\otimes\]

where the symbol \(\otimes\) denotes an arbitrary choice of standard states, \(\Delta E_E\) is the change in the solute’s internal electronic energy in transferring from the gas phase to the liquid phase at the same geometry, \(G_P\) is the polarization free energy of the solute–solvent system when the solute is inserted, \(G_{CDS}\) is the component of the free energy that is nominally associated with cavitation, dispersion, and solvent structure, \(\Delta G_N\) is the change in \(\Delta G_S^0\) due to a change in nuclear coordinates, and \(\Delta G_{conc}^\otimes\) accounts for the difference in concentrations, if any, in the gas-phase standard state and the solution-phase one. In case of 1 M concentration in both solution and gas, then \(\Delta G_S^\otimes\) = 0 kcal/mol, which yields \(\Delta G_S^*\). If the same geometry is used in solution and gas phase calculation, then \(\Delta G_N\) is zero.

SM12 makes use of the Generalized Born approximation to calculate the bulk electrostatic contribution. This is comprised of several terms that are together known as the ENP (Electronic, Nuclear, and Polarization) term \(G_P\). The SM12 model in Band uses CM5. CM5 is a class 4 charge model, making use of both empirical and density related terms. It is comprised of Hirshfeld charges, a simple bond order calculation, atomic distances, and atom specific parameters. The covalent radii utilized are based on the atomic covalent radius from the Handbook of Chemistry and Physics. The Coulomb integral is described with the use of an approximation from Still et al.. Several parameters go into describing this, which include: inter atomic distance, an empirical Born constant, and the Born area, which is calculated with the Analytical Surface Area (ASA) algorithm. The Born area is calculated using Legendre-Gauss quadrature from the atomic radii to a sphere that encapsulates the entire molecule.

The ASA algorithm is also used to calculate the solvent accessible surface area (SASA), which is computed within the CDS (Cavitation, Dispersion, Solvation) term of SM12. The CDS term depends on three terms:

  • SASA (ASA Algorithm)
  • Atomic surface tension
  • Macroscopic surface tension

Atomic surface tension is based on atom-atom distances and the solvent. Macroscopic surface tension is solvent specific. The SM12 implementation in Band reports energies in an atom specific way. You can attribute exact CDS and polarization energies to each atom in your solute. The parameters for SM12 are derived to explicitly incorporate organic elements (N, C, O, F, Si, P, S, Cl, Br, I), with less emphasis on non-organics. Also, while most solvents have a generic atomic surface tension reliance for atoms, water has it’s own explicit set of parameters to better describe it.

Input

The minimal input for the SM12 method is the following:

SolvationSM12
   Enabled Yes/No
   Solv [...]
End
SolvationSM12
Type:Block
Description:Options for Solvation Model 12 (SM12).
Enabled
Type:Bool
Default value:No
GUI name:Include SM12 solvation
Description:Whether to use the Solvation Model 12 (SM12) in the calculation.
Solv
Type:Multiple Choice
Default value:WATER
Options:[ACETICACID, ACETONITRILE, ACETOPHENONE, ANILINE, ANISOLE, BENZENE, BENZONITRILE, BENZYLALCOHOL, BROMOBENZENE, BROMOETHANE, BROMOFORM, BROMOOCTANE, N-BUTANOL, SEC-BUTANOL, BUTANONE, BUTYLACETATE, N-BUTYLBENZENE, SEC-BUTYLBENZENE, T-BUTYLBENZENE, CARBONDISULFIDE, CARBONTETRACHLORIDE, CHLOROBENZENE, CHLOROFORM, CHLOROHEXANE, M-CRESOL, CYCLOHEXANE, CYCLOHEXANONE, DECALIN, DECANE, DECANOL, 1-2-DIBROMOETHANE, DIBUTYLETHER, O-DICHLOROBENZENE, 1-2-DICHLOROETHANE, DIETHYLETHER, DIISOPROPYLETHER, N-N-DIMETHYLACETAMIDE, N-N-DIMETHYLFORMAMIDE, 2-6-DIMETHYLPYRIDINE, DIMETHYLSULFOXIDE, DODECANE, ETHANOL, ETHOXYBENZENE, ETHYLACETATE, ETHYLBENZENE, FLUOROBENZENE, 1-FLUORO-N-OCTANE, HEPTANE, HEPTANOL, HEXADECANE, HEXADECYLIODIDE, HEXANE, HEXANOL, IODOBENZENE, ISOBUTANOL, ISOOCTANE, ISOPROPANOL, ISOPROPYLBENZENE, P-ISOPROPYLTOLUENE, MESITYLENE, METHANOL, METHOXYETHANOL, METHYLENECHLORIDE, N-METHYLFORMAMIDE, 2-METHYLPYRIDINE, 4-METHYL-2-PENTANONE, NITROBENZENE, NITROETHANE, NITROMETHANE, O-NITROTOLUENE, NONANE, NONANOL, OCTANE, OCTANOL, PENTADECANE, PENTANE, PENTANOL, PERFLUOROBENZENE, PHENYLETHER, PROPANOL, PYRIDINE, TETRACHLOROETHENE, TETRAHYDROFURAN, TETRAHYDROTHIOPHENEDIOXIDE, TETRALIN, TOLUENE, TRIBUTYLPHOSPHATE, TRIETHYLAMINE, 1-2-4-TRIMETHYLBENZENE, UNDECANE, WATER, XYLENE, 1-2-DIBROMOETHANE_WATER, 1-2-DICHLOROETHANE_WATER, BENZENE_WATER, CARBONTETRACHLORIDE_WATER, CHLOROBENZENE_WATER, CHLOROFORM_WATER, CYCLOHEXANE_WATER, DIBUTYLETHER_WATER, DIETHYLETHER_WATER, ETHYLACETATE_WATER, HEPTANE_WATER, HEXANE_WATER, NITROBENZENE_WATER, OCTANOL_WATER]
GUI name:Solvent
Description:List of predefined solvents

This is the full list of input options for the SM12 method:

SolvationSM12
   ARO float
   Acid float
   Base float
   BornC float
   BornRadiusConfig
      MaxCellDistance float
      PointsPerBohr integer
      UseLegendreGrid Yes/No
   End
   Chgal float
   Cust string
   Debug string
   EPS float
   Enabled Yes/No
   HALO float
   Kappa float
   PostSCF Yes/No
   PrintSM12 Yes/No
   RadSolv float
   Ref float
   Solv [...]
   Tens float
   TopologicalExtrapolation
      FirstCell integer
      LastCell integer
      Order integer
   End
End
SolvationSM12
Type:Block
Description:Options for Solvation Model 12 (SM12).
ARO
Type:Float
Default value:0.0
Description:Square of the fraction of non-hydrogen atoms in the solvent that are aromatic carbon atoms (carbon aromaticity)
Acid
Type:Float
Default value:0.82
Description:Abraham hydrogen bond acidity parameter
Base
Type:Float
Default value:0.35
Description:Abraham hydrogen bond bacicity parameter
BornC
Type:Float
Default value:3.7
Description:Coulomb constant for General Born Approximation
BornRadiusConfig
Type:Block
Description:
MaxCellDistance
Type:Float
Default value:30.0
Unit:Bohr
Description:Max distance from the centra cell used when computing the Born radii for periodic systems
PointsPerBohr
Type:Integer
Default value:10
Description:
UseLegendreGrid
Type:Bool
Default value:Yes
Description:
Chgal
Type:Float
Default value:2.474
Description:Exponential of Pauli’s bond order
Cust
Type:String
Description:Custom solvent input
Debug
Type:String
Description:Prints a lot of information about every pass on CDS and ENP code, keywords: ENP, CDS
EPS
Type:Float
Default value:78.36
Description:The dielectric constant
Enabled
Type:Bool
Default value:No
GUI name:Include SM12 solvation
Description:Whether to use the Solvation Model 12 (SM12) in the calculation.
HALO
Type:Float
Default value:0.0
Description:Square of the fraction of non-hydrogen atoms in the solvent molecule that are F, Cl, or Br (electronegative halogenicity)
Kappa
Type:Float
Default value:0.0
Description:Factor for Debye screening
PostSCF
Type:Bool
Default value:No
Description:Whether to apply the solvation potential during the SCF or only calculate the solvation energy after the SCF.
PrintSM12
Type:Bool
Default value:No
Description:Prints out an in-depth breakdown of solvation energies
RadSolv
Type:Float
Default value:0.4
Description:The radius distance between the solute and solvent
Ref
Type:Float
Default value:1.3328
Description:Refractive index of solvent
Solv
Type:Multiple Choice
Default value:WATER
Options:[ACETICACID, ACETONITRILE, ACETOPHENONE, ANILINE, ANISOLE, BENZENE, BENZONITRILE, BENZYLALCOHOL, BROMOBENZENE, BROMOETHANE, BROMOFORM, BROMOOCTANE, N-BUTANOL, SEC-BUTANOL, BUTANONE, BUTYLACETATE, N-BUTYLBENZENE, SEC-BUTYLBENZENE, T-BUTYLBENZENE, CARBONDISULFIDE, CARBONTETRACHLORIDE, CHLOROBENZENE, CHLOROFORM, CHLOROHEXANE, M-CRESOL, CYCLOHEXANE, CYCLOHEXANONE, DECALIN, DECANE, DECANOL, 1-2-DIBROMOETHANE, DIBUTYLETHER, O-DICHLOROBENZENE, 1-2-DICHLOROETHANE, DIETHYLETHER, DIISOPROPYLETHER, N-N-DIMETHYLACETAMIDE, N-N-DIMETHYLFORMAMIDE, 2-6-DIMETHYLPYRIDINE, DIMETHYLSULFOXIDE, DODECANE, ETHANOL, ETHOXYBENZENE, ETHYLACETATE, ETHYLBENZENE, FLUOROBENZENE, 1-FLUORO-N-OCTANE, HEPTANE, HEPTANOL, HEXADECANE, HEXADECYLIODIDE, HEXANE, HEXANOL, IODOBENZENE, ISOBUTANOL, ISOOCTANE, ISOPROPANOL, ISOPROPYLBENZENE, P-ISOPROPYLTOLUENE, MESITYLENE, METHANOL, METHOXYETHANOL, METHYLENECHLORIDE, N-METHYLFORMAMIDE, 2-METHYLPYRIDINE, 4-METHYL-2-PENTANONE, NITROBENZENE, NITROETHANE, NITROMETHANE, O-NITROTOLUENE, NONANE, NONANOL, OCTANE, OCTANOL, PENTADECANE, PENTANE, PENTANOL, PERFLUOROBENZENE, PHENYLETHER, PROPANOL, PYRIDINE, TETRACHLOROETHENE, TETRAHYDROFURAN, TETRAHYDROTHIOPHENEDIOXIDE, TETRALIN, TOLUENE, TRIBUTYLPHOSPHATE, TRIETHYLAMINE, 1-2-4-TRIMETHYLBENZENE, UNDECANE, WATER, XYLENE, 1-2-DIBROMOETHANE_WATER, 1-2-DICHLOROETHANE_WATER, BENZENE_WATER, CARBONTETRACHLORIDE_WATER, CHLOROBENZENE_WATER, CHLOROFORM_WATER, CYCLOHEXANE_WATER, DIBUTYLETHER_WATER, DIETHYLETHER_WATER, ETHYLACETATE_WATER, HEPTANE_WATER, HEXANE_WATER, NITROBENZENE_WATER, OCTANOL_WATER]
GUI name:Solvent
Description:List of predefined solvents
Tens
Type:Float
Default value:103.62
Description:Macroscopic surface tension of the solvent at the air/solvent interface at 298K (cal*mol^-1*Ang^-2)
TopologicalExtrapolation
Type:Block
Description:Method to extrapolate the long range Coulomb potential, needed for periodic calculations
FirstCell
Type:Integer
Default value:5
Description:First cell for the topological extrapolation of the long range part of the Coulomb Potential.
LastCell
Type:Integer
Default value:10
Description:Last cell for the topological extrapolation of the long range part of the Coulomb Potential.
Order
Type:Integer
Default value:3
Description:Order of the topological extrapolation of the long range part of the Coulomb Potential.