Release66:SMD Model
From NWChem
SMD (Solvation Model Based on Density) Model
SMD denotes “solvation model based on density” and it is described in detail in the following paper:
Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J. Phys. Chem. B 2009, 113, 6378-6396; http://dx.doi.org/10.1021/jp810292n.
The SMD model is a universal continuum solvation model where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known. The word “continuum” denotes that the solvent is not represented explicitly as a collection of discrete solvent molecules but rather as a dielectric medium with surface tensions at the solute-solvent interface.
SMD directly calculates the free energy of solvation of an ideal solvation process that occurs at fixed concentration (for example, from an ideal gas at a concentration of 1 mol/L to an ideal solution at a liquid-phase concentration of 1 mol/L) at 298 K, but this may converted by standard thermodynamic formulas to a standard-state free energy of solvation, which is defined as the transfer of molecules from an ideal gas at 1 bar to an ideal 1 molar solution.
The SMD model separates the fixed-concentration free energy of solvation into two components. The first component is the bulk-electrostatic contribution arising from a self-consistent reaction field (SCRF) treatment. The SCRF treatment involves an integration of the nonhomogeneous-dielectric Poisson equation for bulk electrostatics in terms of the COSMO model of Klamt and Schüürmann with the modified COSMO scaling factor suggested by Stefanovich and Truong and by using the SMD intrinsic atomic Coulomb radii. These radii have been optimized for H, C, N, O, F, Si, P, S, Cl, and Br. For any other atom the current implementation of the SMD model uses scaled values of the van der Waals radii of Mantina et al.
Mantina, M.; Valero, R.; Cramer, C. J.; Truhlar, D. G. “Atomic Radii of the Elements.” In CRC Handbook of Chemistry and Physics, 91st Edition, 2010-2011; Haynes, W. M., Ed.; CRC Press: Boca Raton, FL, 2010; pp 9-49 – 9-50.
The scaling factor equals 1.52 for group 17 elements heavier than Br (i.e., for I and At) and 1.18 for all other elements for which there are no optimized SMD radii.
The second contribution to the fixed-concentration free energy of solvation is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is called the cavity–dispersion–solvent-structure (CDS) term, and it is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas (SASAs) of the individual atoms of the solute.
At the moment the SMD model is available in NWChem only with the DFT block
The SMD input options are as follows:
do_cosmo_smd (logical input) .true. (perform a ground-state SMD calculation) or .false. (default)
solvent (keyword)
a solvent keyword from a list of available SMD solvent names below:
| Keyword | Name |
| h2o | water (default) |
| water | water (default) |
| acetacid | acetic acid |
| acetone | acetone |
| acetntrl | acetonitrile |
| acetphen | acetophenone |
| aniline | aniline |
| anisole | anisole |
| benzaldh | benzaldehyde |
| benzene | benzene |
| benzntrl | benzonitrile |
| benzylcl | benzyl chloride |
| brisobut | 1-bromo-2-methylpropane |
| brbenzen | bromobenzene |
| brethane | bromoethane |
| bromform | bromoform |
| broctane | 1-bromooctane |
| brpentan | 1-bromopentane |
| brpropa2 | 2-bromopropane |
| brpropan | 1-bromopropane |
| butanal | butanal |
| butacid | butanoic acid |
| butanol | 1-butanol |
| butanol2 | 2-butanol |
| butanone | butanone |
| butantrl | butanonitrile |
| butile | butyl acetate |
| nba | butylamine |
| nbutbenz | n-butylbenzene |
| sbutbenz | sec-butylbenzene |
| tbutbenz | tert-butylbenzene |
| cs2 | carbon disulfide |
| carbntet | carbon tetrachloride |
| clbenzen | chlorobenzene |
| secbutcl | sec-butyl chloride |
| chcl3 | chloroform |
| clhexane | 1-chlorohexane |
| clpentan | 1-chloropentane |
| clpropan | 1-chloropropane |
| ocltolue | o-chlorotoluene |
| m-cresol | m-cresol |
| o-cresol | o-cresol |
| cychexan | cyclohexane |
| cychexon | cyclohexanone |
| cycpentn | cyclopentane |
| cycpntol | cyclopentanol |
| cycpnton | cyclopentanone |
| declncis | cis-decalin |
| declntra | trans-decalin |
| declnmix | decalin (cis/trans mixture) |
| decane | n-decane |
| decanol | 1-decanol |
| edb12 | 1,2-dibromoethane |
| dibrmetn | dibromomethane |
| butyleth | dibutyl ether |
| odiclbnz | o-dichlorobenzene |
| edc12 | 1,2-dichloroethane |
| c12dce | cis-dichloroethylene |
| t12dce | trans-dichloroethylene |
| dcm | dichloromethane |
| ether | diethyl ether |
| et2s | diethyl sulfide |
| dietamin | diethylamine |
| mi | diiodomethane |
| dipe | diisopropyl ether |
| dmds | dimethyl disulfide |
| dmso | dimethyl sulfoxide |
| dma | N,N-dimethylacetamide |
| cisdmchx | cis-1,2-dimethylcyclohexane |
| dmf | N,N-dimethylformamide |
| dmepen24 | 2,4-dimethylpentane |
| dmepyr24 | 2,4-dimethylpyridine |
| dmepyr26 | 2,6-dimethylpyridine |
| dioxane | 1,4-dioxane |
| phoph | diphenyl ether |
| dproamin | dipropylamine |
| dodecan | n-dodecane |
| meg | 1,2-ethanediol |
| etsh | ethanethiol |
| ethanol | ethanol |
| etoac | ethyl acetate |
| etome | ethyl formate |
| eb | ethylbenzene |
| phenetol | ethyl phenyl ether |
| c6h5f | fluorobenzene |
| foctane | 1-fluorooctane |
| formamid | formamide |
| formacid | formic acid |
| heptane | n-heptane |
| heptanol | 1-heptanol |
| heptnon2 | 2-heptanone |
| heptnon4 | 4-heptanone |
| hexadecn | n-hexadecane |
| hexane | n-hexane |
| hexnacid | hexanoic acid |
| hexanol | 1-hexanol |
| hexanon2 | 2-hexanone |
| hexene | 1-hexene |
| hexyne | 1-hexyne |
| c6h5i | iodobenzene |
| iobutane | 1-iodobutane |
| c2h5i | iodoethane |
| iohexdec | 1-iodohexadecane |
| ch3i | iodomethane |
| iopentan | 1-iodopentane |
| iopropan | 1-iodopropane |
| cumene | isopropylbenzene |
| p-cymene | p-isopropyltoluene |
| mesityln | mesitylene |
| methanol | methanol |
| egme | 2-methoxyethanol |
| meacetat | methyl acetate |
| mebnzate | methyl benzoate |
| mebutate | methyl butanoate |
| meformat | methyl formate |
| mibk | 4-methyl-2-pentanone |
| mepropyl | methyl propanoate |
| isobutol | 2-methyl-1-propanol |
| terbutol | 2-methyl-2-propanol |
| nmeaniln | N-methylaniline |
| mecychex | methylcyclohexane |
| nmfmixtr | N-methylformamide (E/Z mixture) |
| isohexan | 2-methylpentane |
| mepyrid2 | 2-methylpyridine |
| mepyrid3 | 3-methylpyridine |
| mepyrid4 | 4-methylpyridine |
| c6h5no2 | nitrobenzene |
| c2h5no2 | nitroethane |
| ch3no2 | nitromethane |
| ntrprop1 | 1-nitropropane |
| ntrprop2 | 2-nitropropane |
| ontrtolu | o-nitrotoluene |
| nonane | n-nonane |
| nonanol | 1-nonanol |
| nonanone | 5-nonanone |
| octane | n-octane |
| octanol | 1-octanol |
| octanon2 | 2-octanone |
| pentdecn | n-pentadecane |
| pentanal | pentanal |
| npentane | n-pentane |
| pentacid | pentanoic acid |
| pentanol | 1-pentanol |
| pentnon2 | 2-pentanone |
| pentnon3 | 3-pentanone |
| pentene | 1-pentene |
| e2penten | E-2-pentene |
| pentacet | pentyl acetate |
| pentamin | pentylamine |
| pfb | perfluorobenzene |
| benzalcl | phenylmethanol |
| propanal | propanal |
| propacid | propanoic acid |
| propanol | 1-propanol |
| propnol2 | 2-propanol |
| propntrl | propanonitrile |
| propenol | 2-propen-1-ol |
| propacet | propyl acetate |
| propamin | propylamine |
| pyridine | pyridine |
| c2cl4 | tetrachloroethene |
| thf | tetrahydrofuran |
| sulfolan | tetrahydrothiophene-S,S-dioxide |
| tetralin | tetralin |
| thiophen | thiophene |
| phsh | thiophenol |
| toluene | toluene |
| tbp | tributyl phosphate |
| tca111 | 1,1,1-trichloroethane |
| tca112 | 1,1,2-trichloroethane |
| tce | trichloroethene |
| et3n | triethylamine |
| tfe222 | 2,2,2-trifluoroethanol |
| tmben124 | 1,2,4-trimethylbenzene |
| isoctane | 2,2,4-trimethylpentane |
| undecane | n-undecane |
| m-xylene | m-xylene |
| o-xylene | o-xylene |
| p-xylene | p-xylene |
| xylenemx | xylene (mixture) |
When a solvent is specified by name, the descriptors for the solvent are based on the Minnesota Solvent Descriptor Database:
Winget, P.; Dolney, D. M.; Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. Minnesota Solvent Descriptor Database. University of Minnesota: Minneapolis, MN, 2010. http://comp.chem.umn.edu/solvation/mnsddb.pdf
The user can specify a solvent that is not on the list by omitting the solvent keyword and instead introducing user-provided values for the following solvent descriptors:
dielec (real input) dielectric constant at 298 K
sola (real input) Abraham’s hydrogen bond acidity
solb (real input) Abraham’s hydrogen bond basicity solc (real input) aromaticity as a fraction of non-hydrogenic solvent atoms that are aromatic carbon atoms solg (real input) macroscopic surface tension of the solvent at an air/solvent interface at 298 K in units of cal mol–1 Å–2 (note that 1 dyne/cm = 1.43932 cal mol–1 Å–2)
solh (real input) electronegative halogenicity as the fraction of non-hydrogenic solvent atoms that are F, Cl, or Br
soln (real input) index of refraction at optical frequencies at 293 K
An example of an SMD input file is as follows:
echo title 'SMD/M06-2X/6-31G(d) solvation free energy for CF3COO- in water' start charge -1 geometry nocenter C 0.512211 0.000000 -0.012117 C -1.061796 0.000000 -0.036672 O -1.547400 1.150225 -0.006609 O -1.547182 -1.150320 -0.006608 F 1.061911 1.087605 -0.610341 F 1.061963 -1.086426 -0.612313 F 0.993255 -0.001122 1.266928 symmetry c1 end basis * library 6-31G* end dft XC m06-2x end cosmo do_cosmo_smd true solvent water end task dft energy