Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model

2017 ◽  
Vol 13 (12) ◽  
pp. 6146-6157 ◽  
Author(s):  
Mohamad Mohebifar ◽  
Erin R. Johnson ◽  
Christopher N. Rowley
Keyword(s):  
Dipole Moment ◽  
Force Field ◽  
Dispersion Coefficients ◽  
London Dispersion

Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model

2018 ◽  
Author(s):  
Evan T. Walters ◽  
Mohamad Mohebifar ◽  
Erin R. Johnson ◽  
Christopher Rowley
Keyword(s):  
Dipole Moment ◽  
Force Fields ◽  
Higher Order ◽  
Side Chain ◽  
Dispersion Interactions ◽  
Dispersion Coefficients ◽  
Hydration Energies ◽  
London Dispersion ◽  
Higher Order Dispersion ◽  
Order Dispersion

<div>London dispersion is one of the fundamental intermolecular interactions involved in protein folding and dynamics. The popular CHARMM36, Amber ff14sb, and OPLS-</div><div>AA force fields represent these interactions through the C6 /r 6 term of the Lennard-Jones potential. The C6 parameters are assigned empirically, so these parameters are</div><div>not necessarily a realistic representation of the true dispersion interactions. In this work, dispersion coefficients of all three force fields were compared to corresponding</div><div>values from quantum-chemical calculations using the exchange-hole dipole moment (XDM) model. The force field values were found to be roughly 50% larger than the XDM values for protein backbone and side-chain models. The CHARMM36 and Amber OL15 force fields for nucleic acids were also found to exhibit this trend. To explore how these elevated dispersion coefficients affect predicted properties, the hydration energies of the side-chain models were calculated using the staged REMD-TI method of Deng and Roux for the CHARMM36, Amber ff14sb, and OPLS-AA force fields. Despite having large C 6 dispersion coefficients, these force fields predict side-chain hydration energies that are in generally good agreement with the experimental values, including for hydrocarbon residues where the dispersion component is the dominant attractive solute–solvent interaction. This suggests that these force fields predict the correct total strength of dispersion interactions, despite C6 coefficients that are considerably larger than XDM predicts. An analytical expression for the water–methane dispersion energy using XDM dispersion coefficients shows that that higher-order dispersion terms(i.e., C 8 and C 10 ) account for roughly 37.5% of the hydration energy of methane. This suggests that the C 6 dispersion coefficients used in contemporary force fields are</div><div>elevated to account for the neglected higher-order terms. Force fields that include higher-order dispersion interactions could resolve this issue.</div>

Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model

2017 ◽  
Author(s):  
Mohamad Mohebifar ◽  
Erin R. Johnson ◽  
Christopher Rowley
Keyword(s):  
Dipole Moment ◽  
Density Functional ◽  
Force Fields ◽  
Mechanical Force ◽  
Pharmaceutical Chemistry ◽  
Dispersion Coefficients ◽  
Innovative Strategy ◽  
London Dispersion ◽  
Improved Accuracy ◽  
Mechanical Force Fields

<p>The exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields…..(see full abstract). Finally, XDM-derived dispersion coefficients were used to parameterize molecular-mechanical force fields for five liquids – benzene, toluene, cyclohexane, n-pentane, and n-hexane – which resulted in improved accuracy in the computed enthalpies of vaporization despite only having to evaluate a much smaller section of the parameter space.</p>

Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model

2018 ◽  
Vol 122 (26) ◽  
pp. 6690-6701 ◽  
Author(s):  
Evan T. Walters ◽  
Mohamad Mohebifar ◽  
Erin R. Johnson ◽  
Christopher N. Rowley
Keyword(s):  
Dipole Moment ◽  
Force Fields ◽  
Dispersion Coefficients ◽  
London Dispersion ◽  
Protein Force Fields

Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model

2018 ◽  
Author(s):  
Evan T. Walters ◽  
Mohamad Mohebifar ◽  
Erin R. Johnson ◽  
Christopher Rowley
Keyword(s):  
Dipole Moment ◽  
Force Fields ◽  
Higher Order ◽  
Side Chain ◽  
Dispersion Interactions ◽  
Dispersion Coefficients ◽  
Hydration Energies ◽  
London Dispersion ◽  
Higher Order Dispersion ◽  
Order Dispersion

<div>London dispersion is one of the fundamental intermolecular interactions involved in protein folding and dynamics. The popular CHARMM36, Amber ff14sb, and OPLS-</div><div>AA force fields represent these interactions through the C6 /r 6 term of the Lennard-Jones potential. The C6 parameters are assigned empirically, so these parameters are</div><div>not necessarily a realistic representation of the true dispersion interactions. In this work, dispersion coefficients of all three force fields were compared to corresponding</div><div>values from quantum-chemical calculations using the exchange-hole dipole moment (XDM) model. The force field values were found to be roughly 50% larger than the XDM values for protein backbone and side-chain models. The CHARMM36 and Amber OL15 force fields for nucleic acids were also found to exhibit this trend. To explore how these elevated dispersion coefficients affect predicted properties, the hydration energies of the side-chain models were calculated using the staged REMD-TI method of Deng and Roux for the CHARMM36, Amber ff14sb, and OPLS-AA force fields. Despite having large C 6 dispersion coefficients, these force fields predict side-chain hydration energies that are in generally good agreement with the experimental values, including for hydrocarbon residues where the dispersion component is the dominant attractive solute–solvent interaction. This suggests that these force fields predict the correct total strength of dispersion interactions, despite C6 coefficients that are considerably larger than XDM predicts. An analytical expression for the water–methane dispersion energy using XDM dispersion coefficients shows that that higher-order dispersion terms(i.e., C 8 and C 10 ) account for roughly 37.5% of the hydration energy of methane. This suggests that the C 6 dispersion coefficients used in contemporary force fields are</div><div>elevated to account for the neglected higher-order terms. Force fields that include higher-order dispersion interactions could resolve this issue.</div>

Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model

2017 ◽  
Author(s):  
Mohamad Mohebifar ◽  
Erin R. Johnson ◽  
Christopher Rowley
Keyword(s):  
Dipole Moment ◽  
Density Functional ◽  
Force Fields ◽  
Mechanical Force ◽  
Pharmaceutical Chemistry ◽  
Dispersion Coefficients ◽  
Innovative Strategy ◽  
London Dispersion ◽  
Improved Accuracy ◽  
Mechanical Force Fields

<p>The exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields…..(see full abstract). Finally, XDM-derived dispersion coefficients were used to parameterize molecular-mechanical force fields for five liquids – benzene, toluene, cyclohexane, n-pentane, and n-hexane – which resulted in improved accuracy in the computed enthalpies of vaporization despite only having to evaluate a much smaller section of the parameter space.</p>

Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model

2018 ◽  
Author(s):  
Evan T. Walters ◽  
Mohamad Mohebifar ◽  
Erin R. Johnson ◽  
Christopher Rowley
Keyword(s):  
Dipole Moment ◽  
Force Fields ◽  
Higher Order ◽  
Side Chain ◽  
Dispersion Interactions ◽  
Dispersion Coefficients ◽  
Hydration Energies ◽  
London Dispersion ◽  
Higher Order Dispersion ◽  
Order Dispersion

<div>London dispersion is one of the fundamental intermolecular interactions involved in protein folding and dynamics. The popular CHARMM36, Amber ff14sb, and OPLS-</div><div>AA force fields represent these interactions through the C6 /r 6 term of the Lennard-Jones potential. The C6 parameters are assigned empirically, so these parameters are</div><div>not necessarily a realistic representation of the true dispersion interactions. In this work, dispersion coefficients of all three force fields were compared to corresponding</div><div>values from quantum-chemical calculations using the exchange-hole dipole moment (XDM) model. The force field values were found to be roughly 50% larger than the XDM values for protein backbone and side-chain models. The CHARMM36 and Amber OL15 force fields for nucleic acids were also found to exhibit this trend. To explore how these elevated dispersion coefficients affect predicted properties, the hydration energies of the side-chain models were calculated using the staged REMD-TI method of Deng and Roux for the CHARMM36, Amber ff14sb, and OPLS-AA force fields. Despite having large C 6 dispersion coefficients, these force fields predict side-chain hydration energies that are in generally good agreement with the experimental values, including for hydrocarbon residues where the dispersion component is the dominant attractive solute–solvent interaction. This suggests that these force fields predict the correct total strength of dispersion interactions, despite C6 coefficients that are considerably larger than XDM predicts. An analytical expression for the water–methane dispersion energy using XDM dispersion coefficients shows that that higher-order dispersion terms(i.e., C 8 and C 10 ) account for roughly 37.5% of the hydration energy of methane. This suggests that the C 6 dispersion coefficients used in contemporary force fields are</div><div>elevated to account for the neglected higher-order terms. Force fields that include higher-order dispersion interactions could resolve this issue.</div>

A Generally Applicable Atomic-Charge Dependent London Dispersion Correction Scheme

2019 ◽  
Author(s):  
Eike Caldeweyher ◽  
Sebastian Ehlert ◽  
Andreas Hansen ◽  
Hagen Neugebauer ◽  
Sebastian Spicher ◽  
...  
Keyword(s):  
Density Functional ◽  
Dispersion Model ◽  
Low Cost ◽  
Atomic Charge ◽  
Body Part ◽  
Dispersion Interactions ◽  
Dispersion Coefficients ◽  
Charge Dependence ◽  
London Dispersion ◽  
Dynamic Polarizabilities

The D4 model is presented for the accurate computation of London dispersion interactions in density functional theory approximations (DFT-D4) and generally for atomistic modeling methods. In this successor to the DFT-D3 model, the atomic coordination-dependent dipole polarizabilities are scaled based on atomic partial charges which can be taken from various sources. For this purpose, a new charge-dependent parameter-economic scaling function is designed. Classical charges are obtained from an atomic electronegativity equilibration procedure for which efficient analytical derivatives are developed. A numerical Casimir-Polder integration of the atom-in-molecule dynamic polarizabilities yields charge- and geometry-dependent dipole-dipole dispersion coefficients. Similar to the D3 model, the dynamic polarizabilities are pre-computed by time-dependent DFT and elements up to radon are covered. For a benchmark set of 1225 dispersion coefficients, the D4 model achieves an unprecedented accuracy with a mean relative deviation of 3.8% compared to 4.7% for D3. In addition to the two-body part, three-body effects are described by an Axilrod-Teller-Muto term. A common many-body dispersion expansion was extensively tested and an energy correction based on D4 polarizabilities is found to be advantageous for some larger systems. Becke-Johnson-type damping parameters for DFT-D4 are determined for more than 60 common functionals. For various energy benchmark sets DFT-D4 slightly outperforms DFT-D3. Especially for metal containing systems, the introduced charge dependence improves thermochemical properties. We suggest (DFT-)D4 as a physically improved and more sophisticated dispersion model in place of DFT-D3 for DFT calculations as well as for other low-cost approaches like semi-empirical models.<br><br>

A Generally Applicable Atomic-Charge Dependent London Dispersion Correction Scheme

2019 ◽  
Author(s):  
Eike Caldeweyher ◽  
Sebastian Ehlert ◽  
Andreas Hansen ◽  
Hagen Neugebauer ◽  
Sebastian Spicher ◽  
...  
Keyword(s):  
Density Functional ◽  
Dispersion Model ◽  
Low Cost ◽  
Atomic Charge ◽  
Body Part ◽  
Dispersion Interactions ◽  
Dispersion Coefficients ◽  
Charge Dependence ◽  
London Dispersion ◽  
Dynamic Polarizabilities

The D4 model is presented for the accurate computation of London dispersion interactions in density functional theory approximations (DFT-D4) and generally for atomistic modeling methods. In this successor to the DFT-D3 model, the atomic coordination-dependent dipole polarizabilities are scaled based on atomic partial charges which can be taken from various sources. For this purpose, a new charge-dependent parameter-economic scaling function is designed. Classical charges are obtained from an atomic electronegativity equilibration procedure for which efficient analytical derivatives are developed. A numerical Casimir-Polder integration of the atom-in-molecule dynamic polarizabilities yields charge- and geometry-dependent dipole-dipole dispersion coefficients. Similar to the D3 model, the dynamic polarizabilities are pre-computed by time-dependent DFT and elements up to radon are covered. For a benchmark set of 1225 dispersion coefficients, the D4 model achieves an unprecedented accuracy with a mean relative deviation of 3.8% compared to 4.7% for D3. In addition to the two-body part, three-body effects are described by an Axilrod-Teller-Muto term. A common many-body dispersion expansion was extensively tested and an energy correction based on D4 polarizabilities is found to be advantageous for some larger systems. Becke-Johnson-type damping parameters for DFT-D4 are determined for more than 60 common functionals. For various energy benchmark sets DFT-D4 slightly outperforms DFT-D3. Especially for metal containing systems, the introduced charge dependence improves thermochemical properties. We suggest (DFT-)D4 as a physically improved and more sophisticated dispersion model in place of DFT-D3 for DFT calculations as well as for other low-cost approaches like semi-empirical models.<br><br>

London dispersion coefficients from static multipole polarizabilities

1983 ◽  
Vol 50 (5) ◽  
pp. 1173-1187 ◽  
Author(s):  
Giuseppe Figari ◽  
Gian Franco Musso ◽  
Valerio Magnasco
Keyword(s):  
Dispersion Coefficients ◽  
London Dispersion

Computation of Nonretarded London Dispersion Coefficients and Hamaker Constants of Copper Phthalocyanine

2010 ◽  
Vol 6 (2) ◽  
pp. 491-498 ◽  
Author(s):  
Yan Zhao ◽  
Hou T. Ng ◽  
Eric Hanson ◽  
Jiannan Dong ◽  
David S. Corti ◽  
...  
Keyword(s):  
Copper Phthalocyanine ◽  
Dispersion Coefficients ◽  
London Dispersion ◽  
Hamaker Constants
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