Solvation¶
CENSO uses several QM-packages and not all solvents are available for all solvation models throughout the QM-codes. For this reason a user editable file is created in the folder ~/.censo_assets:
$ ~/.censo_assets/censo_solvents.json
{
"acetone":{
"cosmors": ["propanone_c0", "propanone_c0"],
"dcosmors": ["propanone", "propanone"],
"xtb": ["acetone", "acetone"],
"cpcm": ["acetone", "acetone"],
"smd": ["ACETONE", "ACETONE"],
"DC": 20.7
},
"chcl3":{
"cosmors": ["chcl3_c0", "chcl3_c0"],
"dcosmors": ["chcl3", "chcl3"],
"xtb": ["chcl3", "chcl3"],
"cpcm": ["chloroform","chloroform"],
"smd": ["CHLOROFORM", "CHLOROFORM"],
"DC": 4.8
},
"acetonitrile":{
"cosmors": ["acetonitrile_c0", "acetonitrile_c0"],
"dcosmors": ["acetonitrile", "acetonitrile"],
"xtb": ["acetonitrile", "acetonitrile"],
"cpcm": ["acetonitrile", "acetonitrile"],
"smd": ["ACETONITRILE", "ACETONITRILE"],
"DC": 36.6
},
"ch2cl2":{
"cosmors": ["ch2cl2_c0", "ch2cl2_c0"],
"dcosmors": [null, "chcl3"],
"xtb": ["ch2cl2", "ch2cl2"],
"cpcm": ["CH2Cl2", "CH2Cl2"],
"smd": ["DICHLOROMETHANE", "DICHLOROMETHANE"],
"DC": 9.1
},
"dmso":{
"cosmors": ["dimethylsulfoxide_c0", "dimethylsulfoxide_c0"],
"dcosmors": ["dimethylsulfoxide", "dimethylsulfoxide"],
"xtb": ["dmso", "dmso"],
"cpcm": ["DMSO", "DMSO"],
"smd": ["DIMETHYLSULFOXIDE", "DIMETHYLSULFOXIDE"],
"DC": 47.2
},
"h2o":{
"cosmors": ["h2o_c0", "h2o_c0"],
"dcosmors": ["h2o", "h2o"],
"xtb": ["h2o", "h2o"],
"cpcm": ["Water", "Water"],
"smd": ["WATER", "WATER"],
"DC": 80.1
},
"methanol":{
"cosmors": ["methanol_c0", "methanol_c0"],
"dcosmors": ["methanol", "methanol"],
"xtb": ["methanol", "methanol"],
"cpcm": ["Methanol", "Methanol"],
"smd": ["METHANOL", "METHANOL"],
"DC": 32.7
},
"thf":{
"cosmors": ["thf_c0", "thf_c0"],
"dcosmors": ["thf", "thf"],
"xtb": ["thf", "thf"],
"cpcm": ["THF", "THF"],
"smd": ["TETRAHYDROFURAN", "TETRAHYDROFURAN"],
"DC": 7.6
},
"toluene":{
"cosmors": ["toluene_c0", "toluene_c0"],
"dcosmors": ["toluene", "toluene"],
"xtb": ["toluene", "toluene"],
"cpcm": ["Toluene", "Toluene"],
"smd": ["TOLUENE", "TOLUENE"],
"DC": 2.4
},
"octanol":{
"cosmors": ["1-octanol_c0", "1-octanol_c0"],
"dcosmors": ["octanol", "octanol"],
"xtb": ["octanol", "octanol"],
"cpcm": ["Octanol", "Octanol"],
"smd": ["1-OCTANOL", "1-OCTANOL"],
"DC": 9.9
},
"woctanol":{
"cosmors": [null, "woctanol"],
"dcosmors": ["wet-otcanol", "wet-octanol"],
"xtb": ["woctanol", "woctanol"],
"cpcm": [null, "Octanol"],
"smd": [null, "1-OCTANOL"],
"DC": 8.1
},
"hexadecane":{
"cosmors": ["n-hexadecane_c0", "n-hexadecane_c0"],
"dcosmors": ["hexadecane", "hexadecane"],
"xtb": ["hexadecane", "hexadecane"],
"cpcm": [null, "Hexane"],
"smd": ["N-HEXADECANE", "N-HEXADECANE"],
"DC": 2.1
},
"dmf":{
"cosmors": ["dimethylformamide_c0","dimethylformamide_c0"],
"dcosmors": [null, "dimethylsulfoxide"],
"xtb": ["dmf", "dmf"],
"cpcm": ["DMF", "DMF"],
"smd": ["N,N-DIMETHYLFORMAMIDE", "N,N-DIMETHYLFORMAMIDE"],
"DC": 38.3
},
"aniline":{
"cosmors": ["aniline_c0", "aniline_c0"],
"dcosmors": ["aniline", "aniline"],
"xtb": ["aniline", "aniline"],
"cpcm": [null,"Pyridine"],
"smd": ["ANILINE", "ANILINE"],
"DC": 6.9
},
"cyclohexane":{
"cosmors": ["cyclohexane_c0", "cyclohexane_c0"],
"dcosmors": ["cyclohexane", "cyclohexane"],
"xtb": [null, "hexane"],
"cpcm": ["Cyclohexane", "Cyclohexane"],
"smd": ["CYCLOHEXANE", "CYCLOHEXANE"],
"DC": 2.0
},
"ccl4":{
"cosmors": ["ccl4_c0", "ccl4_c0"],
"dcosmors": ["ccl4", "ccl4"],
"xtb": ["ccl4", "ccl4"],
"cpcm": ["CCl4", "CCl4"],
"smd": ["CARBON TETRACHLORIDE", "CARBON TETRACHLORIDE"],
"DC": 2.2
},
"diethylether":{
"cosmors": ["diethylether_c0", "diethylether_c0"],
"dcosmors": ["diethylether", "diethylether"],
"xtb": ["ether", "ether"],
"cpcm": [null, "THF"],
"smd": ["DIETHYL ETHER", "DIETHYL ETHER"],
"DC": 4.4
},
"ethanol":{
"cosmors": ["ethanol_c0", "ethanol_c0"],
"dcosmors": ["ethanol", "ethanol"],
"xtb": ["ethanol", "ethanol"],
"cpcm": [null, "Methanol"],
"smd": ["ETHANOL", "ETHANOL"],
"DC": 24.6
},
"hexane":{
"cosmors": ["hexane_c0", "hexane_c0"],
"dcosmors": ["hexane", "hexane"],
"xtb": ["hexane", "hexane"],
"cpcm": ["Hexane", "Hexane"],
"smd": ["N-HEXANE", "N-HEXANE"],
"DC": 1.9
},
"nitromethane":{
"cosmors": ["nitromethane_c0", "nitromethane_c0"],
"dcosmors": ["nitromethane", "nitromethane"],
"xtb": ["nitromethane", "nitromethane"],
"cpcm": [null, "methanol"],
"smd": "",
"DC": 38.2
},
"benzaldehyde":{
"cosmors": ["benzaldehyde_c0", "benzaldehyde_c0"],
"dcosmors": [null, "propanone"],
"xtb": ["benzaldehyde", "benzaldehyde"],
"cpcm": [null, "Pyridine"],
"smd": ["BENZALDEHYDE", "BENZALDEHYDE"],
"DC": 18.2
},
"benzene":{
"cosmors": ["benzene_c0", "benzene_c0"],
"dcosmors": [null, "toluene"],
"xtb": ["benzene", "benzene"],
"cpcm": ["Benzene", "Benzene"],
"smd": ["BENZENE", "BENZENE"],
"DC": 2.3
},
"cs2":{
"cosmors": ["cs2_c0", "cs2_c0"],
"dcosmors": [null, "ccl4"],
"xtb": ["cs2", "cs2"],
"cpcm": [null, "CCl4"],
"smd": ["CARBON DISULFIDE", "CARBON DISULFIDE"],
"DC": 2.6
},
"dioxane":{
"cosmors": ["dioxane_c0", "dioxane_c0"],
"dcosmors": [null, "diethylether"],
"xtb": ["dioxane", "dioxane"],
"cpcm": [null, "Cyclohexane"],
"smd": ["1,4-DIOXANE", "1,4-DIOXANE"],
"DC": 2.2
},
"ethylacetate":{
"cosmors": ["ethylacetate_c0", "ethylacetate_c0"],
"dcosmors": [null, "diethylether"],
"xtb": ["ethylacetate", "ethylacetate"],
"cpcm": [null, "THF"],
"smd": ["ETHYL ETHANOATE", "ETHYL ETHANOATE"],
"DC": 5.9
},
"furan":{
"cosmors": ["furane_c0", "furane_c0"],
"dcosmors": [null, "diethylether"],
"xtb": ["furane", "furane"],
"cpcm": [null, "THF"],
"smd": [null, "THF"],
"DC": 3.0
},
"phenol":{
"cosmors": ["phenol_c0", "phenol_c0"],
"dcosmors": [null, "thf"],
"xtb": ["phenol", "phenol"],
"cpcm": [null, "THF"],
"smd": [null, "THIOPHENOL"],
"DC": 8.0
}
}
The file contains a dictionary of all available solvent models and solvents. If a solvent is not available with a certain solvent model, the user can then choose a replacement solvent within the same solvation model. E.g. if benzene is not available in DCOSMO-RS choose toluene in DCOSMO-RS.
{ # EXAMPLE
"solvent-name-in-CENSO":{
"solvent-model1": ["solvent-name in solvent model","solvent-name USED in solvent model"],
"solvent-model2": ["null = solvent not found"," replacement solvent USED"],
"xtb represents ALPB or GBSA" : ["solvent", "solvent],
"DC = Dielectric Constant: Used for COSMO and DCOSMO-RS
},
# END EXAMPLE
"acetonitrile":{
"cosmors": ["acetonitrile_c0", "acetonitrile_c0"],
"dcosmors": ["acetonitrile", "acetonitrile"],
"xtb": ["acetonitrile", "acetonitrile"],
"cpcm": ["acetonitrile", "acetonitrile"],
"smd": ["ACETONITRILE", "ACETONITRILE"],
"DC": 36.6
},
"ch2cl2":{
"cosmors": ["ch2cl2_c0", "ch2cl2_c0"],
"dcosmors": [null, "chcl3"],
"xtb": ["ch2cl2", "ch2cl2"],
"cpcm": ["CH2Cl2", "CH2Cl2"],
"smd": ["DICHLOROMETHANE", "DICHLOROMETHANE"],
"DC": 9.1
},
}
Warning
The solvent file is directly used in censo and typos will cause the calculations to crash!
Adding a new solvent is as easy as adding a new dictionary entry to the file.
In CENSO several solvent models can be applied. The intention is either a good description of the free energy (keyword: smgsolv) or an implicit effect on a property or geometry (keyword: sm).
(sm) implicit solvation for properties:
COSMO [TM]
CPCM [ORCA]
DCOSMO-RS [TM]
ALPB [xtb]
GBSA [xtb]
SMD [ORCA]
(smgsolv) implicit solvation for free energies:
COSMO-RS [COSMO-RS]
SMD_Gsolv [ORCA]
ALPB_Gsolv [xtb]
GBSA_Gsolv [xtb]