scholarly journals “Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins

2017 ◽  
Vol 121 (27) ◽  
pp. 6538-6548 ◽  
Author(s):  
Clarisse G. Ricci ◽  
Bo Li ◽  
Li-Tien Cheng ◽  
Joachim Dzubiella ◽  
J. Andrew McCammon
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Solvent Method

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

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

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

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 SM<i>x</i> (<i>x</i>= 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 SM<i>x</i> 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 SM<i>x</i> models for phase equilibrium calculations.

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

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 SM<i>x</i> (<i>x</i>= 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 SM<i>x</i> 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 SM<i>x</i> models for phase equilibrium calculations.

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

Processes ◽  
2020 ◽  
Vol 8 (5) ◽  
pp. 623 ◽  
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.

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

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 SM<i>x</i> (<i>x</i>= 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 SM<i>x</i> 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 SM<i>x</i> models for phase equilibrium calculations.

To the fast calculation of the solvation free energy. Combining expanded ensembles with L2MC

2021 ◽  
Vol 42 (11) ◽  
pp. 787-792
Author(s):  
Alexei Nikitin ◽  
Vladislava Milchevskaya ◽  
Alexander Lyubartsev
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Fast Calculation
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