Tip
All input files can be downloaded: Files
.
pcm
Options
This option controls the polarized continuum model.
- solvent
Value
7 real numbers
water
acetic acid
acetone
acetonitrile
acetophenone
aniline
anisole
benzaldehyde
benzene
benzonitrile
benzyl chloride
1-bromo-2-methylpropane
bromobenzene
bromoethane
bromoform
1-bromooctane
1-bromopentane
2-bromopropane
1-bromopropane
butanal
butanoic acid
1-butanol
2-butanol
butanone
butanonitrile
butyl acetate
butylamine
n-butylbenzene
sec-butylbenzene
tert-butylbenzene
carbon disulfide
carbon tetrachloride
chlorobenzene
sec-butyl chloride
chloroform
1-chlorohexane
1-chloropentane
1-chloropropane
o-chlorotoluene
m-cresol
o-cresol
cyclohexane
cyclohexanone
cyclopentane
cyclopentanol
cyclopentanone
cis-decalin
trans-decalin
decalin (cis/trans mixture)
n-decane
1-decanol
1,2-dibromoethane
dibromomethane
dibutyl ether
o-dichlorobenzene
1,2-dichloroethane
cis-dichloroethylene
trans-dichloroethylene
dichloromethane
diethyl ether
diethyl sulfide
diethylamine
diiodomethane
diisopropyl ether
dimethyl disulfide
dimethyl sulfoxide
n,n-dimethylacetamide
cis-1,2-dimethylcyclohexane
n,n-dimethylformamide
2,4-dimethylpentane
2,4-dimethylpyridine
2,6-dimethylpyridine
1,4-dioxane
diphenyl ether
dipropylamine
n-dodecane
1,2-ethanediol
ethanethiol
ethanol
ethyl acetate
ethyl formate
ethylbenzene
ethylphenyl ether
fluorobenzene
1-fluorooctane
formamide
formic acid
n-heptane
1-heptanol
2-heptanone
4-heptanone
n-hexadecane
n-hexane
hexanoic acid
1-hexanol
2-hexanone
1-hexene
1-hexyne
iodobenzene
1-iodobutane
iodoethane
1-iodohexadecane
iodomethane
1-iodopentane
1-iodopropane
isopropylbenzene
p-isopropyltoluene
mesitylene
methanol
2-methoxyethanol
methyl acetate
methyl benzoate
methyl butanoate
methyl formate
4-methyl-2-pentanone
methyl propanoate
2-methyl-1-propanol
2-methyl-2-propanol
n-methylaniline
methylcyclohexane
n-methylformamide (e/z mixture)
2-methylpentane
2-methylpyridine
3-methylpyridine
4-methylpyridine
nitrobenzene
nitroethane
nitromethane
1-nitropropane
2-nitropropane
o-nitrotoluene
n-nonane
1-nonanol
5-nonanone
n-octane
1-octanol
2-octanone
n-pentadecane
pentanal
n-pentane
pentanoic acid
1-pentanol
2-pentanone
3-pentanone
1-pentene
e-2-pentene
pentyl acetate
pentylamine
perfluorobenzene
phenylmethanol
propanal
propanoic acid
1-propanol
2-propanol
propanonitrile
2-propen-1-ol
propyl acetate
propylamine
pyridine
tetrachloroethene
tetrahydrofuran
tetrahydrothiophene-s,s-dioxide
tetralin
thiophene
thiophenol
toluene
tributyl phosphate
1,1,1-trichloroethane
1,1,2-trichloroethane
trichloroethene
triethylamine
2,2,2-trifluoroethanol
1,2,4-trimethylbenzene
2,2,4-trimethylpentane
n-undecane
m-xylene
o-xylene
p-xylene
xylene (mixture)
1,1-dichloroethane
1-iodopentene
1-pentyne
2-chlorobutane
benzyl alcohol
Default
None
The solvent name. It can be one of the string given in the table above, or 7 real numbers, which are:
dielectric_constant refraction_index Abraham_alpha Abraham_beta abomaticity halogenicity macro_surface_tension
.
If some properties are unknown, you can set them to 0
.
- radius
Value
UFF
. Will use UFF atomic radii for tesselation.Bondi
. Will use UFF atomic radii for tesselation.Default
UFF
This determines the radius type used for tesselation.
UFF
is highly recommended, since Bondi radii data is not complete for some common elements, like Fe.
- tss_method
Value
Swig
. Will use Swig algorithm for tesselation.Switching
. Will use Switching algorithm for tesselation.Sphere
. Will use sphere algorithm for tesselation.Default
Swig
The algorithm for tesselation.
Swig
is recommended.Sphere
is useful in the study of electron transfer.
- grid_accuracy
Value
An integer
6
,14
,26
,38
,50
,86
,110
146
,170
,194
,302
,350
,434
,590
770
,974
,1202
,1454
,1730
,2030
,2354
2702
,3074
,3470
,3890
,4334
,4802
,5294
Default
302
The number of Lebedev points generated for tesselation. Usually
302
is enough. For higher accuracy, ``590``can be used.
Theoretical Background
The Polarizable Continuum Model (PCM) is a widely used implicit solvation model in computational chemistry. In PCM, the solute molecule is placed inside a cavity embedded in a continuous dielectric medium that represents the solvent. Instead of explicitly simulating individual solvent molecules, PCM treats the solvent as a polarizable continuum characterized by its dielectric constant and other macroscopic properties.
The interaction between the solute and the solvent is described by the polarization of the continuum in response to the solute’s charge distribution. This polarization, in turn, affects the electronic structure of the solute. PCM enables the calculation of solvation effects on molecular properties, such as energies, geometries, and spectra, with relatively low computational cost compared to explicit solvent models.
PCM is particularly useful for studying systems in solution, where solvent effects play a significant role in chemical reactivity, stability, and spectroscopic behavior. The model can be combined with various quantum chemical methods, such as Hartree-Fock and Density Functional Theory, to provide a more realistic description of molecules in their solvated environment.
Input Examples
Example: Use Built-in and Self-defined Solvents for CH3Cl
To use PCM in Qbics, we need to add the pcm
keyword in the input file. There are two ways to use PCM:
Use the built-in solvent list shown above.
Explicitly give 7 numbers: dielectric_constant, refraction_index, Abraham_alpha, Abraham_beta, abomaticity, halogenicity, and macro_surface_tension. If some properties are unknown, you can set them to
0
, but “dielectric_constant” must be at least given.
In the following, in pcm-1.inp
, we use aniline
as solvent; in pcm-2.inp
, we explicitly give the dielectric constant, refraction index, Abraham alpha, Abraham beta, abomaticity, and halogenicity:
1basis
2 cc-pvdz
3end
4
5pcm
6 solvent aniline # Use aniline as solvent.
7end
8
9mol
10 C -0.43654823 1.13197968 0.00000000
11 H -0.07987539 1.63637787 0.87365150
12 H -0.07987539 1.63637787 -0.87365150
13 H -1.50654823 1.13199286 0.00000000
14 Cl 0.15009830 -0.52737135 0.00000000
15end
16
17task
18 energy b3lyp
19end
1basis
2 cc-pvdz
3end
4
5pcm
6 solvent 6.8882 1.5863 0.2600 0.4100 0.8570 0.0000 60.6200 # Explicitly define the solvent.
7end
8
9mol
10 C -0.43654823 1.13197968 0.00000000
11 H -0.07987539 1.63637787 0.87365150
12 H -0.07987539 1.63637787 -0.87365150
13 H -1.50654823 1.13199286 0.00000000
14 Cl 0.15009830 -0.52737135 0.00000000
15end
16
17task
18 energy b3lyp
19end
In the output file pcm-1.out
and pcm-2.out
, you will find the solvent definitions and PCM energies:
1Polarized continuum model is applied.
2 Solvent: aniline
3 Dielectric constant: 6.8882
4 Refraction index: 1.5863
5 Abraham alpha: 0.2600
6 Abraham beta: 0.4100
7 Abomaticity: 0.8570
8 Halogenicity: 0.0000
9 Macro surface tension: 60.6200
10 Tesselation:
11..omitted..
12SCF Energies
13============
14Kinetic energy: 499.00382795 Hartree
15Electron-nuclear attraction energy: -1290.65493694 Hartree
16Pseudopotential energy: 0.00000000 Hartree
17Exchange-correlation energy: -28.07548686 Hartree
18Electron Coulomb energy: 274.37629685 Hartree
19Electron exchange energy: -6.76432588 Hartree
20Nuclear repulsion energy: 51.98869889 Hartree
21PCM solvation energy: -0.00201126 Hartree
22Grimme dispersion energy: 0.00000000 Hartree
23----------------------------------------------------------------
24SCF energy (E): -500.12793727 Hartree
25Virial quotien (V/T): -2.00225271
1Polarized continuum model is applied.
2 Solvent: defined by user
3 Dielectric constant: 6.8882
4 Refraction index: 1.5863
5 Abraham alpha: 0.2600
6 Abraham beta: 0.4100
7 Abomaticity: 0.8570
8 Halogenicity: 0.0000
9 Macro surface tension: 60.6200
10 Tesselation:
11 Method: Swig
12 Radius type: UFF
13..omitted..
14SCF Energies
15============
16Kinetic energy: 499.00382490 Hartree
17Electron-nuclear attraction energy: -1290.65493976 Hartree
18Pseudopotential energy: 0.00000000 Hartree
19Exchange-correlation energy: -28.07548686 Hartree
20Electron Coulomb energy: 274.37630261 Hartree
21Electron exchange energy: -6.76432590 Hartree
22Nuclear repulsion energy: 51.98869889 Hartree
23PCM solvation energy: -0.00201136 Hartree
24Grimme dispersion energy: 0.00000000 Hartree
25----------------------------------------------------------------
26SCF energy (E): -500.12793747 Hartree
27Virial quotien (V/T): -2.00225271