| Chapter 15. AMSOL Model Module | ||
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Part I. AMPAC™ 10 User Guide |  |
| Chapter 15. AMSOL Model Module | ||
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Part I. AMPAC™ 10 User Guide | |
Table of Contents
The AMSOL models in AMPAC™ allow for the calculation of free energies of solvation for compounds containing H, C, N, O, F, P, S, Cl, Br, and I in water and organic solvents. Geometry optimization within a solvated environment is also supported.
The AMSOL Model Module (AMM) in AMPAC contains two universal solvation models, SM5.2 and SM5C. Universal solvation models are parameterized for aqueous solution or any organic solvent as well as other solvents or media for which certain solvent descriptors are known. SM5.2 is based on the generalized Born approximation for bulk electrostatics augmented by geometry-dependent atomic surface tensions for cavitation, dispersion, and solvent structure and is parameterized for AM1, PM3, MNDO, and MNDO/d. SM5C is based on the COSMO algorithm for solving the nonhomogeneous Poisson equation for bulk electrostatics augmented by geometry-dependent atomic surface tensions for cavitation, dispersion, and solvent structure and is parameterized for AM1, PM3, and MNDO/d. When the models are used with gas-phase geometries, they are called SM5.2R and SM5CR. The solvation models in AMM are the only SMx solvation models that have been parameterized for MNDO/d, and the implementation for semiempirical molecular orbital theory with d functions is not present in any other program.
AMPAC™ 10's advanced CI (configuration interaction) capability has also been integrated with AMSOL. This allows efficient treatment of open-shell systems in a solvated environment.
The original version of the AMM was contributed to Semichem by its authors, namely, D. A. Liotard, G. D. Hawkins, D. M. Dolney, D. Rinaldi, C. J. Cramer, and D. G. Truhlar. The following references should be cited in any research publications using the methods:
For publications based on SM5.2R or SM5.2: "Universal Quantum Mechanical Model for Solvation Free Energies Based on Gas-Phase Geometries," G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry B, 102 3257-3271 (1998).
For publications based on SM5CR or SM5C: "A Universal Solvation Model Based on the Conductor-like Screening Model," D. M. Dolney, G. D. Hawkins, P. Winget, D. A. Liotard, C. J. Cramer, and D. G. Truhlar, Journal of Computational Chemistry 21, 340-366 (2000).
The SM5.2R model has been parameterized for four Hamiltonians (AM1, PM3, MNDO, and MNDO/d), and it is described by Truhlar et al.[42] That publication should be considered a part of the (This model can also be used with MNDOC.) AMPAC documentation.
The SM5.2R model was parameterized for water using a training set containing 248 neutral solutes with a variety of functional groups. The SM5.2R model was parameterized using gas-phase geometries calculated at the Hartree-Fock level with a heteroatom-polarized valence-double-zeta basis set (HF/MIDI!), and it achieves a mean unsigned error of 0.47 kcal/mol when the model is applied using HF/MIDI! gas-phase geometries, and a mean unsigned error of 0.66 kcal/mol when it is applied using gas-phase geometries from MNDO/d.
Although the parameterization of SM5.2R employed HF/MIDI! gas-phase geometries, the SM5.2R model may be used with any realistic gas-phase geometry.
SM5.2R/X implies that the liquid-phase calculation is carried out with Hamiltonian X (where X = AM1, PM3, MNDO, MNDOC, or MNDO/d) at a gas-phase geometry optimized by that same method. Thus SM5.2R/X is shorthand for SM5.2R/X//X, since when another method is used to obtain the gas-phase geometry, it is indicated as, e.g., SM5.2R/AM1//HF/MIDI! or SM5.2R/PM3//MP2/cc-pVDZ. Finally, if liquid-phase optimization is carried out with the SM5.2R keyword, the resulting calculation should be labeled SM5.2/X rather than SM5.2R/X.
The SM5.2 model uses the same parameters as the SM5.2R model, but the deletion of the R in the application means that the geometry is optimized in the liquid-phase.
The SM5.2 model is available in the current version of AMPAC. Molecular gradients are implemented analytically at the SCF level.
The SM5CR model has been parameterized for three Hamiltonians (AM1, PM3, and MNDO/d), and is described by Truhlar,et al.[43] That publication should also be considered part of the AMPAC documentation. (This model can also be used with MNDOC.) The C in SM5C comes from denotes the conductor-like algorithm devised by Klamt and Schuurmann for approximate solutions of the non-homogeneous Poisson equastion. SM5CR uses an SM5-type approach but with COSMO-based electrostatics.
The SM5CR model was parameterized using a training set containing neutral and ionic solutes with a variety of functional groups for which either experimental solvation free energies or experimental water/solvent partition coefficients were available. The training set contains experimental solvation free energies for 327 solutes in water and 90 organic solvents and partition coefficients for 54 solutes between water and one of 12 organic solvents. A total of 2141 experimental solvation free energies for 243 neutral solutes and 76 experimental water/solvent partition coefficients for 54 neutral solutes were used in the parameterization. The SM5CR model was parameterized using gas-phase geometries calculated at the Hartree-Fock level with a heteroatom-polarized valence-double-zeta basis set (HF/MIDI!). The SM5CR model achieves a mean unsigned error of 0.55 kcal/mol when the model is applied using gas-phase HF/MIDI! geometries.
We define a notation analogous to that applied used SM5.2R models. SM5CR/X implies that the liquid-phase calculation is carried out with Hamiltonian X (where X = AM1, PM3, MNDO, MNDOC, or MNDO/d) at a gas-phase geometry optimized by that same method. Thus SM5CR/X is shorthand for SM5CR/X//X, since when another method is used to obtain the gas-phase geometry, it should be indicated e.g., SM5CR/AM1//HF/MIDI! or SM5CR/PM3//MP2/cc-pVDZ. Finally, if liquid-phase optimization is carried out with the SM5CR keyword, the resulting calculation should be labeled SM5C/X rather than SM5CR/X.
The SM5C solvation model uses the same parameters as the SM5CR model, but the deletion of the R in the application means that the geometry is optimized in the liquid phase. Geometry optimization with SM5C is included in the present version of AMPAC, with analytical molecular gradients at the SCF level.
This section contains an alphabetical list of all keywords used with the AMSOL models. SM5C and SM5CR also use certain COSMO dedicated keywords (See Chapter 14, COSMO Solvation Model), which are included in this list.
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Specify alpha of the desired solvent. |
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Set level of AMSOL printout. |
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Specify beta of the desired solvent. |
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Specify the effective molecular radius of the desired solvent. |
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Specify the dielectric constant for desired solvent. (Equivalent to EPS) |
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Distance threshold for using two-point interaction approximation. |
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Specify the dielectric constant for desired solvent. (Equivalent to DIELEC) |
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Specify the fraction of non-hydrogenic solvent atoms that are carbon atoms contained in an aromatic ring. |
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Specify the fraction of non-hydrogenic solvent atoms that are electronegative halogen atoms. |
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Specify the macroscopic surface tension of the desired solvent. |
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Specify the heat of formation (kcal/mol) of the solute in the gas phase. |
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Specify the index of refraction of the desired solvent. (Equivalent to REFRACT) |
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Specify the number of segments per atom. |
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Specify the index of refraction of the desired solvent. (Equivalent to IOFR) |
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Specify the molecular radius of the desired solvent. |
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Request a calculation using the SM5.2 model. |
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Request a calculation using the SM5.2R model. |
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Request a calculation using the SM5C model. |
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Request a calculation using the SM5CR model. |
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Indicate which parameter set will be used in the SM5 calculation. |
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Solvation trapezoidal integration shell growth factor. |
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Solvation trapezoidal integration shell thickness. |
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Calculate the true solvation free energy. |
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Specify an element’s van der Waals radius. |
The standard output file of an AMPAC calculation using the AMSOL models includes:
An echo of the keywords that were input on the keyword line(s).
A summary of the recognized keywords. This can be used to determine whether a keyword was mis-typed and therefore not recognized by the program.
(SOLVNT='name' only) The values of the solvent
descriptors as extracted from the data statements corresponding to the file
solvent.data
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A table of the atom-by-atom solvent-accessible surface area and the atom-by-atom solvation free energy (unless AMSPRNT=0).
A statement of the total predicted solvation free energy.
The free energy of a system in solution is defined by the SM5 models to be the sum of the
electronic-nuclear energy of solute, the polarization free energy of solvation, and the
cavity-dispersion-solvent structure free energy. In order to calculate the free energy of
solvation, we must subtract from this sum the electronic-nuclear energy of the solute in the
gas phase. The keywords used for accomplishing this are TRUES and HGAS=n.n, where n.n is the
so called heat of formation (kcal/mol) in the gas phase. (Recall that the semiempirical
electronic structure packages refer to the electronic-nuclear energy as heat of formation,
although this is not correct.) If the TRUES keyword is not used, the output contains only the
free energy of the system in solution.
NOTE: All solvation free energies predicted by the SM5 models are standard-state values and are printed in kcal/mol. They correspond to standard state for which the molar concentration of the solute is the same in the gas and in the liquid solution, for example, a concentration of 1 mole per liter in both the gas phase and liquid solution. To re-express standard-state solvation free energies at 298 K to the gas phase at 1 atmosphere of pressure, add 1.89 kcal/mol.
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Copyright © 1992-2013 Semichem, Inc. All rights reserved. |
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| Chapter 14. COSMO Solvation Model |  |
Chapter 16. Package Administration |