I am going to submit the calculation of the versatile Diels-Alder reaction of Furan and N-Phenyl Maleimide. I am inputting the function such as B3LYP, 6311+G**.
I want to apply the PCM model. Is it available in Spartan? If yes, then how shall I apply?
I am using Spartan Wavefunction.
Radwan Alnajjar
Cramer-Truhlar SM54 solvationWe currently implement the Cramer-Truhlar SM54P and SM54A solvation methods for water. This solvation calculation is done, by default, for all quantum mechanics calculations which have SM5 parameterized atoms. The energy of solvation predicted by this model can be found in the output text. The "solvated energy" (calculated by adding the electronic energy and the solvation energy) is labeled as "Energy(Aq)" in the spreadsheet window and in the molecule properties dialogue. Literature on these methods is extensive, some important articles are: MMFFaq mechanics forcefield (SM50R)SM50R is a solvation method derived from the semi-empirical SM54 approach described above. It is independent of the wavefunction and depends only on the geometry of the molecule. As such, it is very fast and is applicable to large systems and molecular mechanics calculations. This method can be accessed by using the POSTSOLVENT=SM50R keyword. MMFFaq is an extension to the MMFF94 forcefield, in which the SM50R energy term is added to the molecular mechanics energy. In Spartan, the MMFFaq forcefield is implemented such that the solvation energy is only added AFTER the geometry has been optimized. Thus the structures of molecules from MMFF94 and MMFFaq calculations will be the same, but their energies will be different. Thus, the MMFFaq method is most useful in the context of conformational searching or energy profile as the energy ordering of any conformers will likely be different in water (MMFFaq) than in vacuum (MMFF94). SM8 solvation calculation The SM8 model allows both water and organic solvents and treats both neutral and charged solutes. This method is notable for the large suite of experimental data used to parameterize the model and uses the HF or DFT wavefunctions. To run SM8 as a property calculation (to calculate the energy of solvation) use the keyword POSTSOLVENT=WATER where water can be replaced with many different organic solvents. The list of supported solvents is as follows: WATER, 111TRICHLOROETHANE, 112TRICHLOROETHANE, 11DICHLOROETHANE, 124TRIMETHYLBENZENE, 14DIOXANE, 1BROMO2METHYLPROPANE, 1BROMOPENTANE, 1BROMOPROPANE, 1BUTANOL, 1CHLOROPENTANE, 1CHLOROPROPANE, 1DECANOL, 1FLUOROOCTANE, 1HEPTANOL, 1HEXANOL, 1HEXENE, 1HEXYNE, 1IODOBUTANE, 1IODOPENTENE, 1IODOPROPANE, 1NITROPROPANE, 1NONANOL, 1OCTANOL, 1PENTANOL, 1PENTENE, 1PENTYNE, 1PROPANOL, 222TRIFLUOROETHANOL, 224TRIMETHYLPENTANE, 24DIMETHYLPENTANE, 24DIMETHYLPYRIDINE, 26DIMETHYLPYRIDINE, 2BROMOPROPANE, 2CHLOROBUTANE, 2HEPTANONE, 2HEXANONE, 2METHYLPENTANE, 2METHYLPYRIDINE, 2NITROPROPANE, 2OCTANONE, 2PENTANONE, 2PROPANOL, 2PROPEN1OL, 3METHYLPYRIDINE, 3PENTANONE, 4HEPTANONE, 4METHYL2PENTANONE, 4METHYLPYRIDINE, 5NONANONE, ACETICACID, ACETONE, ACETONITRILE, ANILINE, ANISOLE, BENZALDEHYDE, BENZENE, BENZONITRILE, BENZYLALCOHOL, BROMOBENZENE, BROMOETHANE, BROMOOCTANE, BUTANAL, BUTANOICACID, BUTANONE, BUTANONITRILE, BUTYLETHANOATE, BUTYLAMINE, BUTYLBENZENE, CARBONDISULFIDE, CARBONTET CHLOROBENZENE, CHLOROTOLUENE, CIS12DIMETHYLCYCLOHEXANE, DECALIN CYCLOHEXANE, CYCLOHEXANONE, CYCLOPENTANE, CYCLOPENTANOL, CYCLOPENTANONE, DECANE, DIBROMOMETHANE, DIBUTYLETHER, DICHLOROMETHANE, METHYLCHLORIDE, DIETHYLETHER, DIETHYLSULFIDE, DIETHYLAMINE, DIIODOMETHANE, DIMETHYLDISULFIDE, DIMETHYLACETAMIDE, DIMETHYLFORMAMIDE, DMF, DIMETHYLPYRIDINE, DMSO, DIMETHYLSULFOXIDE, DIPROPYLAMINE, DODECANE, E12DICHLOROETHENE, E2PENTENE, ETHANETHIOL, ETHANOL, ETHYLETHANOATE, ETHYLMETHANOATE, ETHYLPHENYLETHER, ETHYLBENZENE, ETHYLENEGLYCOL, FLUOROBENZENE, FORMAMIDE, FORMICACID, HEXADECYLIODIDE, HEXANOIC, IODOBENZENE, IODOETHANE, IODOMETHANE, ISOBUTANOL, ISOPROPYLETHER, ISOPROPYLBENZENE, ISOPROPYLTOLUENE, MCRESOL, MESITYLENE, METHANOL, METHYLBENZOATE, METHYLETHANOATE, METHYLMETHANOATE, METHYLPHENYLKETONE, METHYLPROPANOATE, METHYLBUTANOATE, METHYLCYCLOHEXANE, METHYLFORMAMIDE, MXYLENE, HEPTANE, HEXADECANE, HEXANE, NITROBENZENE, NITROETHANE, NITROMETHANE, METHYLANILINE, NONANE, OCTANE, PENTANE, OCHLOROTOLUENE, OCRESOL, ODICHLOROBENZENE, ONITROTOLUENE, OXYLENE, PENTADECANE, PENTANAL, PENTANOICACID, PENTYLETHANOATE, PENTYLAMINE, PERFLUOROBENZENE, PHENYLETHER, PROPANAL, PROPANOICACID, PROPANONITRILE, PROPYLETHANOATE, PROPYLAMINE, PXYLENE, PYRIDINE, PYRROLIDINE, SECBUTANOL, TBUTANOL, TBUTYLBENZENE, TETRACHLOROETHENE, THF, TETRAHYDROFURAN, TETRAHYROTHIOPHENEDIOXIDE, TETRALIN, THIOPHENE, THIOPHENOL, TOLUENE, TRANSDECALIN, TRIBROMOMETHANE, TRIBUTYLPHOSPHATE, TRICHLOROETHENE, TRICHLOROMETHANE, TRIETHYLAMINE, UNDECANE, Z12DICHLOROETHENE The solvents in bold are availble from the pull-down'in-solvent' menu. It is important to notice that no spaces are allowed in the name, thus "acetic acid" is spelled "ACETICACID". The reference for SM8 is A.V. Marenich, R.M. Olson, C.P. Kelly, C.J. Cramer, D.G. Truhlar, "Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges," J. Chem. Theory Comput. 3, 2011 (2007) SS(V)PE solvation calculation The Surface and Simulations of Volume Polarization for Electrostatics (SS(V)PE) method treats the solvent as as a continuum dielectric, solving Poisson's equation on the boundary. A dielectric constant is needed for the calculation. For example, POSTSOLVENT=SVP,78.39 would be use for water. References for this method can be found in SM3 solvation method For legacy purposes Spartan also implements the Cramer-Truhlar SM3 method. The SM54P and SM8 method are much improved over SM3 and should not be used in the future, but can be accessed with the POSTSOLVENT=SM3 keyword.
you may find this helpful
- What solvation models does Spartan provide?
Spartan includes a number of ways to examine solvation.
- Chistopher J. Cramer, Donald G. Truhlar J. Comp. Chem, Vol. 13, no. 9, 1089-1097 (1992) "PM3-SM3: A General Parameterization for Including aqueous Solvation Effects in the PM3 Molecular Orbital Model"
- Candee C. Chambers, Gregory D. Hawkins, Christopher J. Cramer Donald G. Truhlar J. Phys. Chem. Vol 100, 16385-16398 (1996) "Model for Aqueous Solvation Based on Class IV Atomic Charges and First Solvation Shell Effects"
- D. M. Chipman, J. Chem. Phys. 112, 5558, (2000)
- D. M. Chipman, Theor. Chem. Acc. 107, 80, (2002)
- D. M. Chipman, Theor. Chem. Acc. 107, 90, (2002)
- It should be noted that analytical gradients are not available, so transition state searches with this solvent model should only be applied to small molecules. Another important constraint of our implementation is that only molecules with 'star-like' volumes are allowed. Any ray emanating out from the center can only pass through the surface once. Our implmentation has been designed for small molecules. So for larger molecules one may have to modify internal parameters to get good results. Specifically NPTLEB=, which controls the number of Lebedev points set to 1202. This has been shown to be precise enough for .1 kcal/mol on solutes the size of monosubstituted benzenes. Other possible lvalues are (974,1202,1454,1730,2030,2354,2702,3074,3470,3890,4334,4801,5294).
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Radwan Alnajjar
C-PCMThe default solvation model which we advise for geometry and frequency calculations is the C-PCM model (Conductor like Polarizable continuum model). This depends on the shape and charge distribution of the molecule (solute) and the dielectric of the solvent. Continuum models such as C-PCM do not account for explicit solvent-solute interactions such as hydrogen bonding or 'explicit hydrophobic'. For this reason we do not report an "energy of solvation". Spartan gives easy access to three different dielectrics: "NonPolar" (7.43 same as THF), "Polar" (37.22, same as dimethylformamide), and "Water" (78.3). From the pull-down menu in the Calculations dialogue. You can add another solvent by appending a dielectric constant or a solvent name, i.e.: SOLVENT=CPCM:1BROMOPENTANE or SOLVENT=CPCM:DIELECTRIC~10.3(You can type the SOLVENT keyword in the option line, but when you hit return it will move to the pull-down menu.) Some references for C-PCM models are: C-PCM variations.There is a large and diverse literature on C-PCM methods. Spartan's defaults should probably be used as these have been tested and are reasonable for organic systems. However for those familiar with the C-PCM literature we allow some access to the variations. There are 3 main "methods" to treat the polarizable continuum. One can replace the CPCM in the SOLVENT= keyword above with CPCM which uses a dielectric screening factor of fe=(ε-1)/ε. COSMO for a COSMO like implementation using a screening factor of fe=(ε-1)/(ε+1/2). SSVPE which is a symmetrized version of an integral equation formalism (IEF-PCM) model with a screening factor of fe=(ε-1)/(ε+1/2). By appendingSOLVENT=SSVPE:DIELECTRIC~10.3 SSVPE has been argued to be the best method for solvated excited states. an example of using SSVPE that might be appropriate for excited states is ADDSOLVENT=SSVPE:DIETHYLETHER,STATESPECIFIC~PERTURB,CHARGESEPARATION~MARCUS(The ADDSOLVENT= is a pseudonym for SOLVENT= but this keyword stays in the Options line as opposed to popping over to the pull-down menu. This has the advantage of being able to more easily edit the line if needed.) There are a number of other parameters which can be changed in C-PCM models which can be added as comma separated options appended to the keyword after the dielectric. These are: Cramer-Truhlar SM5.4 solvationWe currently implement the Cramer-Truhlar SM5.4P and SM5.4A solvation methods for water, and is available to any molecule SM5 parameterized atoms. This is a very fast method and is appropriate to get quick "energy of solvation" energies at a given geometry. To use this model, for "solvation energy" calculations use the SM54 keyword in the option line. The energy of solvation predicted by this model can be found in the output text. You can print this in the spreadsheet with the equation Solve.E.=@prop(SOLV_CORRECTION)*@hart2kj, In Spartan "10 and Spartan "14 this calculation was done by default for all HF and DFT jobs. Literature on these methods is extensive, some important articles are: MMFFaq mechanics force field (SM5.0R)SM5.0R is a solvation method derived from the semi-empirical SM54 approach described above. It is independent of the wave function and depends only on the geometry of the molecule. As such, it is very fast and is applicable to large systems and molecular mechanics calculations. This method can be accessed by using the POSTSOLVENT=SM50R keyword. MMFFaq is an extension to the MMFF94 forcefield, in which the SM50R energy term is added to the molecular mechanics energy. In Spartan, the MMFFaq forcefield is implemented such that the solvation energy is only added AFTER the geometry has been optimized. Thus the structures of molecules from MMFF94 and MMFFaq calculations will be the same, but their energies will be different. The MMFFaq method is most useful in the context of conformational searching or in an energy profile as the energy ordering of any conformers will likely be different in water (MMFFaq) than in vacuum (MMFF94). The reference for SM5.0R is SM8 and SM12 solvation calculation The SM8 and SM12 model allow both water and a number of organic solvents and treats both neutral and charged solutes. This method is notable for the large suite of experimental data used to parameterize the model and uses the HF or DFT wave functions. To run SM8 as a property calculation (to calculate the energy of solvation) use the keyword POSTSOLVENT=SM8:WATER (and POSTSOLVENT=SM12 where water can be replaced with many different organic solvents. This method is dependent on the basis set, and is parameterized for the 6-31G* sets. (While the method will function for other variants in the 6-31G series, experience has shown that using larger basis sets worsens the results. Technically, it is possible to do geometry optimizations with these models, but because of the discontinuous nature of the derivatives (due to the SCF like nature of solvated charge calculation) optimizations and frequency are problematic except for the simplest of molecules. Use the SOLVENT=SM12:WATER keyword for optimizations. (When you type in this keyword and hit 'enter'; the keyword will replace the "in Gas" pull-down menu in the upper right of the Calculations dialogue.) For SM8 and SM12 you can use a number of different solvents in place of water. The list of supported solvents follows: WATER, 111TRICHLOROETHANE, 112TRICHLOROETHANE, 11DICHLOROETHANE, 124TRIMETHYLBENZENE, 14DIOXANE, 1BROMO2METHYLPROPANE, 1BROMOPENTANE, 1BROMOPROPANE, 1BUTANOL, 1CHLOROPENTANE, 1CHLOROPROPANE, 1DECANOL, 1FLUOROOCTANE, 1HEPTANOL, 1HEXANOL, 1HEXENE, 1HEXYNE, 1IODOBUTANE, 1IODOPENTENE, 1IODOPROPANE, 1NITROPROPANE, 1NONANOL, 1OCTANOL, 1PENTANOL, 1PENTENE, 1PENTYNE, 1PROPANOL, 222TRIFLUOROETHANOL, 224TRIMETHYLPENTANE, 24DIMETHYLPENTANE, 24DIMETHYLPYRIDINE, 26DIMETHYLPYRIDINE, 2BROMOPROPANE, 2CHLOROBUTANE, 2HEPTANONE, 2HEXANONE, 2METHYLPENTANE, 2METHYLPYRIDINE, 2NITROPROPANE, 2OCTANONE, 2PENTANONE, 2PROPANOL, 2PROPEN1OL, 3METHYLPYRIDINE, 3PENTANONE, 4HEPTANONE, 4METHYL2PENTANONE, 4METHYLPYRIDINE, 5NONANONE, ACETICACID, ACETONE, ACETONITRILE, ANILINE, ANISOLE, BENZALDEHYDE, BENZENE, BENZONITRILE, BENZYLALCOHOL, BROMOBENZENE, BROMOETHANE, BROMOOCTANE, BUTANAL, BUTANOICACID, BUTANONE, BUTANONITRILE, BUTYLETHANOATE, BUTYLAMINE, BUTYLBENZENE, CARBONDISULFIDE, CARBONTET CHLOROBENZENE, CHLOROTOLUENE, CIS12DIMETHYLCYCLOHEXANE, DECALIN CYCLOHEXANE, CYCLOHEXANONE, CYCLOPENTANE, CYCLOPENTANOL, CYCLOPENTANONE, DECANE, DIBROMOMETHANE, DIBUTYLETHER, DICHLOROMETHANE, DIETHYLETHER, DIETHYLSULFIDE, DIETHYLAMINE, DIIODOMETHANE, DIMETHYLDISULFIDE, DIMETHYLACETAMIDE, DIMETHYLFORMAMIDE, DMF, DIMETHYLPYRIDINE, DMSO, DIMETHYLSULFOXIDE, DIPROPYLAMINE, DODECANE, E12DICHLOROETHENE, E2PENTENE, ETHANETHIOL, ETHANOL ETHYLETHANOATE, ETHYLMETHANOATE, ETHYLPHENYLETHER, ETHYLBENZENE, ETHYLENEGLYCOL, FLUOROBENZENE, FORMAMIDE, FORMICACID, HEXADECYLIODIDE, HEXANOIC, IODOBENZENE, IODOETHANE, IODOMETHANE, ISOBUTANOL, ISOPROPYLETHER, ISOPROPYLBENZENE, ISOPROPYLTOLUENE, MCRESOL, MESITYLENE, METHANOL, METHYLBENZOATE, METHYLETHANOATE, METHYLMETHANOATE, METHYLPHENYLKETONE, METHYLPROPANOATE, METHYLBUTANOATE, METHYLCYCLOHEXANE, METHYLFORMAMIDE, MXYLENE, HEPTANE, HEXADECANE, HEXANE, NITROBENZENE, NITROETHANE, NITROMETHANE, METHYLANILINE, NONANE, OCTANE, PENTANE, OCHLOROTOLUENE, OCRESOL, ODICHLOROBENZENE, ONITROTOLUENE, OXYLENE, PENTADECANE, PENTANAL, PENTANOICACID, PENTYLETHANOATE, PENTYLAMINE, PERFLUOROBENZENE, PHENYLETHER, PROPANAL, PROPANOICACID, PROPANONITRILE, PROPYLETHANOATE, PROPYLAMINE, PXYLENE, PYRIDINE, PYRROLIDINE, SECBUTANOL, TBUTANOL, TBUTYLBENZENE, TETRACHLOROETHENE, THF, TETRAHYDROFURAN, TETRAHYROTHIOPHENEDIOXIDE, TETRALIN, THIOPHENE, THIOPHENOL, TOLUENE TRANSDECALIN, TRIBROMOMETHANE, TRIBUTYLPHOSPHATE, TRICHLOROETHENE, TRICHLOROMETHANE, TRIETHYLAMINE, UNDECANE, Z12DICHLOROETHENE It is important to notice that no spaces are allowed in the name, thus "acetic acid" is spelled "ACETICACID". SM12 has been defined for multiple charge models. The default uese Charge Model 5 (CM5) but Merz-Singh-Kollman (MK) and ChElpG (CHELPG) charges are also available. You can access these by adding to the end of the POSTSOLVENT= keyword. For example: POSTSOLVENT=SM12:1OCTANOL,CHARGES:chelpg Some useful reference are (iso)SS(V)PE solvation calculation (In Spartan'14 this was called SS(V)PE but has been renamed to distinguish it from the SS(V)PE variants of C-PCM model The Surface and Simulations of Volume Polarization for Electrostatics (SS(V)PE) method treats the solvent as a continuum dielectric, solving Poisson's equation on the boundary. A dielectric constant is needed for the calculation. For example, POSTSOLVENT=ISOSVP,78.39 would be use for water. References for this method can be found in SM3 solvation method For legacy purposes Spartan also implements the Cramer-Truhlar SM3 method. The SM54P and SM8 method are much improved over SM3 and should not be used in the future, but can be accessed with the POSTSOLVENT=SM3 keyword.
hat solvation models does Spartan provide?
Spartan includes a number of ways to examine solvation.
- X. Zhang and J. M. Herbert, J. Phys. Chem. B 118, 7806 (2014) "Excited-State Deactivation Pathways in Uracil versus Hydrated Uracil: Solvatochromatic Shift in the 1nπ* State is the Key"
- A. W. Lange, J. M. Herbert, Chem. Phys. Lett. 509 77-87 (2011) "Symmetric versus asymmetric discretization of the integral equations in polarizable continuum solvation models"
- T. N. Truong and E. V. Stefanovich, Chem. Phys. Lett. 240, 253 (1995)
- V. Barone and M. Cossi, J. Phys. Chem. A 102, 1995 (1998)
- DIELECTRIC (If using a solvent name this is not required)
- OPTICALDIELECTRIC While formally required for excited state calculations we use an appropriate value if using a solvent name)
- TEMPERATURE
- PRESSURE
- SOLVENTRHO
- STATESPECIFIC
- CHARGESEPARATION
- For a full list and more in depth discussion we follow the notation and keywords found in the Q-Chem 4.0 Manual.
- Christopher J. Cramer, Donald G. Truhlar J. Comp. Chem. 13, no. 9, 1089-1097 (1992) "PM3-SM3: A General Parameterization for Including aqueous Solvation Effects in the PM3 Molecular Orbital Model"
- Candee C. Chambers, Gregory D. Hawkins, Christopher J. Cramer Donald G. Truhlar J. Phys. Chem. 100, 16385-16398 (1996) "Model for Aqueous Solvation Based on Class IV Atomic Charges and First Solvation Shell Effects"
- G.D. Hawkins, C.J. Cramer, D.G. Truhlar J. Phys. Chem. B 101, 7147-7157 (1997) "Parameterized Model for Aqueous Free Energies of Solvation using Geometry-dependent Atomic Surface Tensions with Implicit Electrostatics"
- A.V. Marenich, R.M. Olson, C.P. Kelly, C.J. Cramer, D.G. Truhlar, "Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges," J. Chem. Theory Comput. 3, 2011-2033 (2007)
- A.V. Marenich, C.J. Cramer, D.G. Truhlar, "Generalized Born Solvation Model SM12" J. Chem. Theory Comput. 9, 609-620 (2013)
- D. M. Chipman, J. Chem. Phys. 112, 5558, (2000)
- D. M. Chipman, Theor. Chem. Acc. 107, 80, (2002)
- D. M. Chipman, Theor. Chem. Acc. 107, 90, (2002)
- It should be noted that analytical gradients are not available, so transition state searches with this solvent model should only be applied to small molecules. Another important constraint of our implementation is that only molecules with 'star-like' volumes are allowed. Any ray emanating out from the center can only pass through the surface once. Our implementation has been designed for small molecules. So for larger molecules one may have to modify internal parameters to get good results. Specifically NPTLEB=, which controls the number of Lebedev points set to 1202. This has been shown to be precise enough for .1 kcal/mol on solutes the size of monosubstituted benzenes. Other possible values are (974,1202,1454,1730,2030,2354,2702,3074,3470,3890,4334,4801,5294).
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Radwan Alnajjar
if you need fast information,
yes spartan use PCM model as default.
so just choose your solvent from the solvent menu
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Prantik Mondal
Ok that's great! Actually I had went through out the brochure but didn't found much ideas regarding PCM model! Thanks a lot!
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