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 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.