.. tip:: All input files can be downloaded: :download:`Files `. pcm ====== .. contents:: :local: Options ------------ This option controls the polarized continuum model. .. contents:: :local: .. option:: solvent .. list-table:: :stub-columns: 1 :widths: 5 20 * - 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``. .. option:: radius .. list-table:: :stub-columns: 1 :widths: 5 20 * - 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. .. option:: tss_method .. list-table:: :stub-columns: 1 :widths: 5 20 * - 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. .. option:: grid_accuracy .. list-table:: :stub-columns: 1 :widths: 5 20 * - 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 CH\ :sub:`3`\ Cl ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ To use PCM in Qbics, we need to add the ``pcm`` keyword in the input file. There are two ways to use PCM: 1. Use the built-in solvent list shown above. 2. 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: .. tabs:: .. tab:: pcm-1.inp .. code-block:: bash :caption: pcm-1.inp :linenos: basis cc-pvdz end pcm solvent aniline # Use aniline as solvent. end mol C -0.43654823 1.13197968 0.00000000 H -0.07987539 1.63637787 0.87365150 H -0.07987539 1.63637787 -0.87365150 H -1.50654823 1.13199286 0.00000000 Cl 0.15009830 -0.52737135 0.00000000 end task energy b3lyp end .. tab:: pcm-2.inp .. code-block:: bash :caption: pcm-2.inp :linenos: basis cc-pvdz end pcm solvent 6.8882 1.5863 0.2600 0.4100 0.8570 0.0000 60.6200 # Explicitly define the solvent. end mol C -0.43654823 1.13197968 0.00000000 H -0.07987539 1.63637787 0.87365150 H -0.07987539 1.63637787 -0.87365150 H -1.50654823 1.13199286 0.00000000 Cl 0.15009830 -0.52737135 0.00000000 end task energy b3lyp end In the output file ``pcm-1.out`` and ``pcm-2.out``, you will find the solvent definitions and PCM energies: .. tabs:: .. tab:: pcm-1.out .. code-block:: bash :caption: pcm-1.out :linenos: Polarized continuum model is applied. Solvent: aniline Dielectric constant: 6.8882 Refraction index: 1.5863 Abraham alpha: 0.2600 Abraham beta: 0.4100 Abomaticity: 0.8570 Halogenicity: 0.0000 Macro surface tension: 60.6200 Tesselation: ..omitted.. SCF Energies ============ Kinetic energy: 499.00382795 Hartree Electron-nuclear attraction energy: -1290.65493694 Hartree Pseudopotential energy: 0.00000000 Hartree Exchange-correlation energy: -28.07548686 Hartree Electron Coulomb energy: 274.37629685 Hartree Electron exchange energy: -6.76432588 Hartree Nuclear repulsion energy: 51.98869889 Hartree PCM solvation energy: -0.00201126 Hartree Grimme dispersion energy: 0.00000000 Hartree ---------------------------------------------------------------- SCF energy (E): -500.12793727 Hartree Virial quotien (V/T): -2.00225271 .. tab:: pcm-2.out .. code-block:: bash :caption: pcm-2.out :linenos: Polarized continuum model is applied. Solvent: defined by user Dielectric constant: 6.8882 Refraction index: 1.5863 Abraham alpha: 0.2600 Abraham beta: 0.4100 Abomaticity: 0.8570 Halogenicity: 0.0000 Macro surface tension: 60.6200 Tesselation: Method: Swig Radius type: UFF ..omitted.. SCF Energies ============ Kinetic energy: 499.00382490 Hartree Electron-nuclear attraction energy: -1290.65493976 Hartree Pseudopotential energy: 0.00000000 Hartree Exchange-correlation energy: -28.07548686 Hartree Electron Coulomb energy: 274.37630261 Hartree Electron exchange energy: -6.76432590 Hartree Nuclear repulsion energy: 51.98869889 Hartree PCM solvation energy: -0.00201136 Hartree Grimme dispersion energy: 0.00000000 Hartree ---------------------------------------------------------------- SCF energy (E): -500.12793747 Hartree Virial quotien (V/T): -2.00225271