modified on 11 September 2014 at 15:03 ••• 4,312 views

Release66:SMD Model

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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;

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.

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:

title 'SMD/M06-2X/6-31G(d) solvation free energy for CF3COO- in water'
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
* library 6-31G*
 XC m06-2x
 do_cosmo_smd true
 solvent water
task dft energy