Extension of the MST model to the IEF formalism: HF and B3LYP parametrizations

Soteras, Ignacio; Curutchet, Carles; Bidon‐Chanal, Axel; Orozco, Modesto; Luque, F. Javier

doi:10.1016/j.theochem.2005.02.029

Cited by 87 publications

(125 citation statements)

References 55 publications

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“…Because the separation of the full free energy of solvation into bulk-electrostatic and non-bulkelectrostatic components is not well defined 44 and because GB and NPE predictions for the bulk-electrostatic component can differ markedly for molecules decorated with polar functionality (although this dependence is reduced by using different atomic radii in the two formalisms), we consider it valuable to compare predictions from these alternative electrostatic formalisms on this demanding test set. When restricted to water as solvent, we note that the SMD model and the MST solvation model of Soteras et al 45 are functionally very similar to one another. The MST model combines IEF-PCM electrostatics with a cavitation term based on scaled-particle theory [46][47][48] (not separately present in SMD but included implicitly in eq 1) and a van der Waals term computed from water-specific atomic or group surface tensions precisely as in eq 1.…”

Section: Methodsmentioning

confidence: 58%

Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the Prediction of Small-Molecule Solvation Free Energies

2009

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The SM6, SM8, and SMD quantum mechanical aqueous continuum solvation models are applied to predict free energies of aqueous solvation for 61 molecules in the SAMPL1 test set described elsewhere (Guthrie. J. Phys. Chem. B 2009, 113, 4501-4507). For direct comparison to other models, frozen geometries, provided by Guthrie, were used together with the M06-2X density functional and the 6-31G(d) basis set. For the bulk electrostatic component of the solvation free energy, SM6 and SM8 employ a generalized Born model that uses polarized discrete partial atomic charges to model the electron density, with these charges being calculated by the CM4 and CM4M class IV charge models, respectively; SMD uses the polarized continuous quantum mechanical charge density. If five sulfonylureas are removed from the SAMPL1 set, the root-mean-square deviations (RMSDs) of SM6, SM8, and SMD on the remaining 56 molecules are 2.4, 2.6, and 2.5 kcal mol -1 , respectively. The SM6, SM8, and SMD RMSDs on the five sulfonylureas are 14.2, 12.6, and 11.1 kcal mol -1 , respectively; however, we suggest that the uncertainty in the target solvation free energies for these molecules may be quite large.

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Section: Methodsmentioning

confidence: 58%

Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the Prediction of Small-Molecule Solvation Free Energies

2009

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“…Solvation free energies were determined at the MST/ HF/6-31G(d) and MST/B3LYP/6-31G(d) levels. [55][56][57] Electrostatic and nonelectrostatic terms were considered to evaluate the solvation free energy. The electrostatic contribution was determined by using the integral equation formalism.…”

Section: Methodsmentioning

confidence: 99%

“…Cavitation was determined by using the Claverie-Pierotti formalism, and the van der Waals term was computed by using a linear relationship for the solventexposed surface with the atomic tensions obtained by fitting the experimental solvation free energies (see refs. [55][56][57] for details). In particular, calculations were carried out in four different solvents (water, octanol, carbon tetrachloride, and chloroform) for which MST parameters are available.…”

Section: Methodsmentioning

confidence: 99%

Nature of Base Stacking: Reference Quantum‐Chemical Stacking Energies in Ten Unique B‐DNA Base‐Pair Steps

Šponer

Jurečka

Marchán

et al. 2006

Chemistry A European J

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214

307

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Base-stacking energies in ten unique B-DNA base-pair steps and some other arrangements were evaluated by the second-order Møller-Plesset (MP2) method, complete basis set (CBS) extrapolation, and correction for triple (T) electron-correlation contributions. The CBS(T) calculations were compared with decade-old MP2/6-31G*(0.25) reference data and AMBER force field. The new calculations show modest increases in stacking stabilization compared to the MP2/6-31G*(0.25) data and surprisingly large sequence-dependent variation of stacking energies. The absolute force-field values are in better agreement with the new reference data, while relative discrepancies between quantum-chemical (QM) and force-field values increase modestly. Nevertheless, the force field provides good qualitative description of stacking, and there is no need to introduce additional pair-additive electrostatic terms, such as distributed multipoles or out-of-plane charges. There is a rather surprising difference of about 0.1 A between the vertical separation of base pairs predicted by quantum chemistry and derived from crystal structures. Evaluations of different local arrangements of the 5'-CG-3' step indicate a sensitivity of the relative stacking energies to the level of calculation. Thus, describing quantitative relations between local DNA geometrical variations and stacking may be more complicated than usually assumed. The reference calculations are complemented by continuum-solvent assessment of solvent-screening effects.

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“…The aforementioned PCMs, however, treat only the bulk electrostatic contributions to solvation, neglecting other contributions such as dispersion, exchange repulsion, and solute-induced changes in the solvent structure. Although non-electrostatic corrections to PCMs can be put in 'by hand' [286,287] to obtain accurate free energies of solvation [288], a more universal approach is offered by the so-called SMx models developed by Cramer and Truhlar [283]. The SMx models use a variety of macroscopic solvent descriptors (surface tension, refractive index, acid/base parameters, etc.)…”

Section: Continuum Solvationmentioning

confidence: 99%

“…Results in Table 6 demonstrate that the SM8 model achieves sub-kcal/mol accuracy for neutral molecules, although average errors for ions are more like ∼4 kcal/mol [283]. Non-electrostatic terms appropriate for IEF-PCM are available for a few solvents [286,287], and when these are included, the 'IEF-PCM+non-elst.' errors (Table 7) are comparable to those obtained using SM8 [288].…”

Section: Continuum Solvationmentioning

confidence: 99%

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Shao¹,

Gan²,

Epifanovsky³

et al. 2014

Molecular Physics

2,746

2,077

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A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and openshell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr 2 dimer, exploring zeolitecatalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.Keywords quantum chemistry, software, electronic structure theory, density functional theory, electron correlation, computational modelling, Q-Chem Disciplines Chemistry CommentsThis article is from Molecular Physics: An International Journal at the Interface Between Chemistry and Physics 113 (2015): 184, doi:10.1080/00268976.2014. RightsWorks produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted. Authors 185A summary of the technical advances that are incorporated in the fourth major release of the Q-CHEM quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly corre...

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Extension of the MST model to the IEF formalism: HF and B3LYP parametrizations

Cited by 87 publications

References 55 publications

Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the Prediction of Small-Molecule Solvation Free Energies

Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the Prediction of Small-Molecule Solvation Free Energies

Nature of Base Stacking: Reference Quantum‐Chemical Stacking Energies in Ten Unique B‐DNA Base‐Pair Steps

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

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