Assessment of the SM12, SM8, and SMD Solvation Models for Predicting Limiting Activity Coefficients at 298.15 K

The SMx (x= 12, 8, or D) universal solvent models are implicit solvent models which using electronic structure calculations can compute solvation free energies at 298.15 K. While solvation free energy is an important thermophysical property, within the thermodynamic modeling of phase equilibrium, limiting (or infinite dilution) activity coefficients are preferred since they may be used to parameterize excess Gibbs free energy models to model phase equilibrium. Conveniently, the two quantities are related. Therefore the present study was performed to assess the ability to use the SMx universal solvent models to predict limiting activity coefficients. Two methods of calculating the limiting activity coefficient where compared: 1) The solvation free energy and self-solvation free energy were both predicted and 2) the self-solvation free energy was computed using readily available vapor pressure data. Overall the first method is preferred as it results in a cancellation of errors, specifically for the case in which water is a solute. The SM12 model was compared to both UNIFAC and MOSCED. MOSCED was the highest performer, yet had the smallest available compound inventory. UNIFAC and SM12 exhibited comparable performance. Therefore further exploration and research should be conducted into the viability of using the SMx models for phase equilibrium calculations.

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Assessment of the SM12, SM8, and SMD Solvation Models for Predicting Limiting Activity Coefficients at 298.15 K

Processes ◽

10.3390/pr8050623 ◽

2020 ◽

Vol 8 (5) ◽

pp. 623 ◽

Cited By ~ 2

Author(s):

Sydnee N. Roese ◽

Justin D. Heintz ◽

Cole B. Uzat ◽

Alexa J. Schmidt ◽

Griffin V. Margulis ◽

...

Keyword(s):

Free Energy ◽

Phase Equilibrium ◽

Activity Coefficients ◽

Solvation Free Energy ◽

Excess Gibbs Free Energy ◽

Implicit Solvent ◽

Solvent Models ◽

Comparable Performance ◽

Solvation Models ◽

Solvation Free Energies

The SMx (x = 12, 8, or D) universal solvent models are implicit solvent models which using electronic structure calculations can compute solvation free energies at 298.15 K. While solvation free energy is an important thermophysical property, within the thermodynamic modeling of phase equilibrium, limiting (or infinite dilution) activity coefficients are preferred since they may be used to parameterize excess Gibbs free energy models to model phase equilibrium. Conveniently, the two quantities are related. Therefore the present study was performed to assess the ability to use the SMx universal solvent models to predict limiting activity coefficients. Two methods of calculating the limiting activity coefficient where compared: (1) the solvation free energy and self-solvation free energy were both predicted and (2) the self-solvation free energy was computed using readily available vapor pressure data. Overall the first method is preferred as it results in a cancellation of errors, specifically for the case in which water is a solute. The SM12 model was compared to both the Universal Quasichemical Functional-group Activity Coefficients (UNIFAC) and modified separation of cohesive energy density (MOSCED) models. MOSCED was the highest performer, yet had the smallest available compound inventory. UNIFAC and SM12 exhibited comparable performance. Therefore further exploration and research should be conducted into the viability of using the SMx models for phase equilibrium calculations.

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Assessment of the SM12, SM8, and SMD Solvation Models for Predicting Limiting Activity Coefficients at 298.15 K

10.26434/chemrxiv.12104058.v2 ◽

2020 ◽

Author(s):

Sydnee N. Roese ◽

Justin D. Heintz ◽

Cole B. Uzat ◽

Alexa J. Schmidt ◽

Griffin Margulis ◽

...

Keyword(s):

Free Energy ◽

Phase Equilibrium ◽

Activity Coefficients ◽

Solvation Free Energy ◽

Excess Gibbs Free Energy ◽

Implicit Solvent ◽

Solvent Models ◽

Comparable Performance ◽

Solvation Models ◽

Solvation Free Energies

The SMx (x= 12, 8, or D) universal solvent models are implicit solvent models which using electronic structure calculations can compute solvation free energies at 298.15 K. While solvation free energy is an important thermophysical property, within the thermodynamic modeling of phase equilibrium, limiting (or infinite dilution) activity coefficients are preferred since they may be used to parameterize excess Gibbs free energy models to model phase equilibrium. Conveniently, the two quantities are related. Therefore the present study was performed to assess the ability to use the SMx universal solvent models to predict limiting activity coefficients. Two methods of calculating the limiting activity coefficient where compared: 1) The solvation free energy and self-solvation free energy were both predicted and 2) the self-solvation free energy was computed using readily available vapor pressure data. Overall the first method is preferred as it results in a cancellation of errors, specifically for the case in which water is a solute. The SM12 model was compared to both UNIFAC and MOSCED. MOSCED was the highest performer, yet had the smallest available compound inventory. UNIFAC and SM12 exhibited comparable performance. Therefore further exploration and research should be conducted into the viability of using the SMx models for phase equilibrium calculations.

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Improved prediction of solvation free energies by machine-learning polarizable continuum solvation model

Nature Communications ◽

10.1038/s41467-021-23724-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Amin Alibakhshi ◽

Bernd Hartke

Keyword(s):

Machine Learning ◽

Free Energy ◽

Solvation Free Energy ◽

Continuum Solvation ◽

Free Energies ◽

Solvation Model ◽

Continuum Solvation Model ◽

Solvation Models ◽

Solvation Free Energies ◽

Polarizable Continuum

AbstractTheoretical estimation of solvation free energy by continuum solvation models, as a standard approach in computational chemistry, is extensively applied by a broad range of scientific disciplines. Nevertheless, the current widely accepted solvation models are either inaccurate in reproducing experimentally determined solvation free energies or require a number of macroscopic observables which are not always readily available. In the present study, we develop and introduce the Machine-Learning Polarizable Continuum solvation Model (ML-PCM) for a substantial improvement of the predictability of solvation free energy. The performance and reliability of the developed models are validated through a rigorous and demanding validation procedure. The ML-PCM models developed in the present study improve the accuracy of widely accepted continuum solvation models by almost one order of magnitude with almost no additional computational costs. A freely available software is developed and provided for a straightforward implementation of the new approach.

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Publisher's Note: “Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations” [J. Chem. Phys. 139, 044119 (2013)]

The Journal of Chemical Physics ◽

10.1063/1.4819023 ◽

2013 ◽

Vol 139 (7) ◽

pp. 079901

Author(s):

Michael S. Lee ◽

Mark A. Olson

Keyword(s):

Free Energy ◽

Surface Area ◽

Solvation Free Energy ◽

Chem Phys ◽

Implicit Solvent ◽

Nonpolar Solvation

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‘Martinizing’ the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins

Biophysical Journal ◽

10.1016/j.bpj.2017.11.1922 ◽

2018 ◽

Vol 114 (3) ◽

pp. 344a-345a

Author(s):

Clarisse Gravina Ricci ◽

Bo Li ◽

Li-Tien Cheng ◽

Joachim Dzubiella ◽

J. Andrew McCammon

Keyword(s):

Free Energy ◽

Solvation Free Energy ◽

Coarse Grained ◽

Implicit Solvent ◽

Solvent Method

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Generalized Born implicit solvent models for small molecule hydration free energies

Physical Chemistry Chemical Physics ◽

10.1039/c6cp07347f ◽

2017 ◽

Vol 19 (2) ◽

pp. 1677-1685 ◽

Cited By ~ 2

Author(s):

Martin Brieg ◽

Julia Setzler ◽

Steffen Albert ◽

Wolfgang Wenzel

Keyword(s):

Free Energy ◽

Small Molecules ◽

Implicit Solvent ◽

Free Energies ◽

Hydration Free Energy ◽

Energy Estimation ◽

Generalized Born ◽

Solvent Models ◽

Molecular Force ◽

Implicit Solvent Models

Hydration free energy estimation of small molecules from all-atom simulations was widely investigated in recent years, as it provides an essential test of molecular force fields and our understanding of solvation effects.

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The Excess Gibbs Free Energy and the Activity Coefficients of the Nd(NO3)3—HNO3—H2O System at 25°C

Thermodynamic Behavior of Electrolytes in Mixed Solvents—II - Advances in Chemistry ◽

10.1021/ba-1979-0177.ch019 ◽

1979 ◽

pp. 299-321 ◽

Cited By ~ 5

Author(s):

WILLIAM G. O'BRIEN ◽

RENATO G. BAUTISTA

Keyword(s):

Free Energy ◽

Gibbs Free Energy ◽

Activity Coefficients ◽

Excess Gibbs Free Energy

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Thermodynamics of Helix formation in small peptides of varying lengthin vacuo, implicit solvent and explicit solvent: Comparison between AMBER force fields

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633619500159 ◽

2019 ◽

Vol 18 (03) ◽

pp. 1950015

Author(s):

Zhaoxi Sun ◽

Xiaohui Wang

Keyword(s):

Amino Acids ◽

Free Energy ◽

Hydrogen Bonds ◽

Force Fields ◽

Implicit Solvent ◽

Conformational Ensemble ◽

Helix Formation ◽

Solvent Models ◽

Explicit Solvent ◽

Amber Force Fields

Helix formation is of great significance in protein folding. The helix-forming tendencies of amino acids are accumulated along the sequence to determine the helix-forming tendency of peptides. Computer simulation can be used to model this process in atomic details and give structural insights. In the current work, we employ equilibrate-state free energy simulation to systematically study the folding/unfolding thermodynamics of a series of mutated peptides. Two AMBER force fields including AMBER99SB and AMBER14SB are compared. The new 14SB force field uses refitted torsion parameters compared with 99SB and they share the same atomic charge scheme. We find that in vacuo the helix formation is mutation dependent, which reflects the different helix propensities of different amino acids. In general, there are helix formers, helix indifferent groups and helix breakers. The helical structure becomes more favored when the length of the sequence becomes longer, which arises from the formation of additional backbone hydrogen bonds in the lengthened sequence. Therefore, the helix indifferent groups and helix breakers will become helix formers in long sequences. Also, protonation-dependent helix formation is observed for ionizable groups. In 14SB, the helical structures are more stable than in 99SB and differences can be observed in their grouping schemes, especially in the helix indifferent group. In solvents, all mutations are helix indifferent due to protein–solvent interactions. The decrease in the number of backbone hydrogen bonds is the same with the increase in the number of protein–water hydrogen bonds. The 14SB in explicit solvent is able to capture the free energy minima in the helical state while 14SB in implicit solvent, 99SB in explicit solvent and 99SB in implicit solvent cannot. The helix propensities calculated under 14SB agree with the corresponding experimental values, while the 99SB results obviously deviate from the references. Hence, implicit solvent models are unable to correctly describe the thermodynamics even for the simple helix formation in isolated peptides. Well-developed force fields and explicit solvents are needed to correctly describe the protein dynamics. Aside from the free energy, differences in conformational ensemble under different force fields in different solvent models are observed. The numbers of hydrogen bonds formed under different force fields agree and they are mostly determined by the solvent model.

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