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:
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 [True | False]
Solv [...]
End
SolvationSM12Type: Block Description: Options for Solvation Model 12 (SM12). EnabledType: Bool Default value: False GUI name: Include SM12 solvation Description: Whether to use the Solvation Model 12 (SM12) in the calculation. SolvType: 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 [True | False]
End
Chgal float
Cust string
Debug string
EPS float
Enabled [True | False]
HALO float
Kappa float
PostSCF [True | False]
PrintSM12 [True | False]
RadSolv float
Ref float
Solv [...]
Tens float
TopologicalExtrapolation
FirstCell integer
LastCell integer
Order integer
End
End
SolvationSM12Type: Block Description: Options for Solvation Model 12 (SM12). AROType: Float Default value: 0.0 Description: Square of the fraction of non-hydrogen atoms in the solvent that are aromatic carbon atoms (carbon aromaticity) AcidType: Float Default value: 0.82 Description: Abraham hydrogen bond acidity parameter BaseType: Float Default value: 0.35 Description: Abraham hydrogen bond bacicity parameter BornCType: Float Default value: 3.7 Description: Coulomb constant for General Born Approximation BornRadiusConfigType: Block Description: MaxCellDistanceType: Float Default value: 30.0 Unit: Bohr Description: Max distance from the centra cell used when computing the Born radii for periodic systems PointsPerBohrType: Integer Default value: 10 Description: UseLegendreGridType: Bool Default value: True Description:
ChgalType: Float Default value: 2.474 Description: Exponential of Pauli’s bond order CustType: String Description: Custom solvent input DebugType: String Description: Prints a lot of information about every pass on CDS and ENP code, keywords: ENP, CDS EPSType: Float Default value: 78.36 Description: The dielectric constant EnabledType: Bool Default value: False GUI name: Include SM12 solvation Description: Whether to use the Solvation Model 12 (SM12) in the calculation. HALOType: 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) KappaType: Float Default value: 0.0 Description: Factor for Debye screening PostSCFType: Bool Default value: False Description: Whether to apply the solvation potential during the SCF or only calculate the solvation energy after the SCF. PrintSM12Type: Bool Default value: False Description: Prints out an in-depth breakdown of solvation energies RadSolvType: Float Default value: 0.4 Description: The radius distance between the solute and solvent RefType: Float Default value: 1.3328 Description: Refractive index of solvent SolvType: 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 TensType: Float Default value: 103.62 Description: Macroscopic surface tension of the solvent at the air/solvent interface at 298K (cal*mol^-1*Ang^-2) TopologicalExtrapolationType: Block Description: Method to extrapolate the long range Coulomb potential, needed for periodic calculations FirstCellType: Integer Default value: 5 Description: First cell for the topological extrapolation of the long range part of the Coulomb Potential. LastCellType: Integer Default value: 10 Description: Last cell for the topological extrapolation of the long range part of the Coulomb Potential. OrderType: Integer Default value: 3 Description: Order of the topological extrapolation of the long range part of the Coulomb Potential.