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 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 basicity 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.