An efficient implementation for determining volume polarization in self-consistent reaction field theory

Vilkas, Marius J.; Zhan, Chang-Guo

doi:10.1063/1.3020767

Cited by 17 publications

(20 citation statements)

References 40 publications

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“…All calculations were carried out by using a local version [38] of the Gaussian03 program [39] in which the SVPE solvation model was implemented. All of the computations in this study were carried out on a Dell supercomputer cluster with 384 nodes or 4,768 processors at the Computer Center of the University of Kentucky.…”

Section: Methodsmentioning

confidence: 99%

Reaction pathway and free energy barrier for urea elimination in aqueous solution

Yao

Chen

2015

Chemical Physics Letters

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To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. The free energy barrier of 25.3 kcal/mol predicted for the dominant reaction pathway of urea elimination in aqueous solution is in good agreement with available experimental kinetic data.

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Section: Methodsmentioning

confidence: 99%

Reaction pathway and free energy barrier for urea elimination in aqueous solution

Yao

Chen

2015

Chemical Physics Letters

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“…All calculations were performed by using a local version 45 of the Gaussian 03 program 46 in which the SVPE solvation model was implemented. All of the computations in this study were carried out on a Dell supercomputer cluster with 384 nodes or 4,768 processors at the Computer Center of the University of Kentucky.…”

Section: Methodsmentioning

confidence: 99%

Reaction pathways and free energy profiles for spontaneous hydrolysis of urea and tetramethylurea: unexpected substituent effects

Yao

Chen

et al. 2013

Org. Biomol. Chem.

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It has been difficult to directly measure the spontaneous hydrolysis rate of urea and, thus, 1,1,3,3-tetramethylurea (Me4U) was used as a model to determine the “experimental” rate constant for urea hydrolysis. The use of Me4U was based on an assumption that the rate of urea hydrolysis should be 2.8 times that of Me4U hydrolysis because the rate of acetamide hydrolysis is 2.8 times that of N,N-dimethyl-acetamide hydrolysis. The present first-principles electronic-structure calculations on the competing non-enzymatic hydrolysis pathways have demonstrated that the dominant pathway is the neutral hydrolysis via the CN addition for both urea (when pH<~11.6) and Me4U (regardless of pH), unlike the non-enzymatic hydrolysis of amides where alkaline hydrolysis is dominant. Based on the computational data, the substituent shift of free energy barrier calculated for the neutral hydrolysis is remarkably different from that for the alkaline hydrolysis, and the rate constant for the urea hydrolysis should be ~1.3×109-fold lower than that (4.2×10−12 s−1) measured for the Me4U hydrolysis. As a result, the rate enhancement and catalytic proficiency of urease should be 1.2×1025 and 3×1027 M−1, respectively, suggesting that urease surpasses proteases and all other enzymes in its power to enhance the rate of reaction. All of the computational results are consistent with available experimental data for Me4U, suggesting that the computational prediction for urea is reliable.

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“…The bulk electrostatics were calculated by the SVPE method by using a local version10 of Gaussian03 57. The SVPE results depend only on the level and basis set of the quantum mechanical calculation and the isodensity contour value that defines the solute cavity.…”

Section: Methodsmentioning

confidence: 99%

Free Energies of Solvation with Surface, Volume, and Local Electrostatic Effects and Atomic Surface Tensions to Represent the First Solvation Shell

Liu

Kelly

Goren

et al. 2010

J. Chem. Theory Comput.

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Building on the SVPE (surface and volume polarization for electrostatics) model for electrostatic contributions to the free energy of solvation with explicit consideration of both surface and volume polarization effects, on the SMx approach to including first-solvation-shell contributions, and on the linear relationship between the electric field and short-range electrostatic contributions found by Chipman, we have developed a new method for computing absolute aqueous solvation free energies by combining the SVPE method with semiempirical terms that account for effects beyond bulk electrostatics. The new method is called SMVLE, and the elements it contains are denoted by SVPE-CDSL where SVPE denotes accounting for bulk electrostatic interactions between solute and solvent with both surface and volume contributions, CDS denotes the inclusion of solvent cavitation, changes in dispersion energy, and possible changes in local solvent structure by a semiempirical term utilizing geometry-dependent atomic surface tensions as implemented in SMx models, and L represents the local electrostatic effect derived from the outward-directed normal electric field on the cavity surface. The semiempirical CDS and L terms together represent the deviation of short-range contributions to the free energy of solvation from those accounted for by the SVPE term based on the bulk solvent dielectric constant. A solute training set containing a broad range of molecules used previously in the development of SM6 is used here for SMVLE model calibration. The aqueous solvation free energies predicted by the parameterized SMVLE model correlate exceedingly well with experimental values. The square of the correlation coefficient is 0.9949 and the slope is 1.0079. Comparison of the final SMVLE model against the earlier SMx solvation model shows that the parameterized SMVLE model not only yields good accuracy for neutrals but also significantly increases the accuracy for ions, making it the best implicit solvation model to date for aqueous solvation free energies of ions. The semiempirical terms associated with the outward-directed electric field account

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An efficient implementation for determining volume polarization in self-consistent reaction field theory

Cited by 17 publications

References 40 publications

Reaction pathway and free energy barrier for urea elimination in aqueous solution

Reaction pathway and free energy barrier for urea elimination in aqueous solution

Reaction pathways and free energy profiles for spontaneous hydrolysis of urea and tetramethylurea: unexpected substituent effects

Free Energies of Solvation with Surface, Volume, and Local Electrostatic Effects and Atomic Surface Tensions to Represent the First Solvation Shell

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