AMBER-ii: New Combining Rules and Force Field for Perfluoroalkanes

Nikitin, Alexei; Milchevskiy, Yury V.; Lyubartsev, Alexander P.

doi:10.1021/acs.jpcb.5b07233

Cited by 23 publications

(21 citation statements)

References 50 publications

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“…Condensed-phase force fields such as CHARMM [5][6][7][8][9][10][11][12][13][14][15] , AMBER [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31] , OPLS 32-44 , TraPPE [45][46][47][48][49][50][51][52] and GROMOS [53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68] mainly aim at the description of solids, liquids and solutions, including solvated biomolecules as a particularly relevant special case. ...…”

Section: Introductionmentioning

confidence: 99%

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Horta

Merz

Fuchs

et al. 2016

J. Chem. Theory Comput.

144

287

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This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase. The calibration is based on 62 organic molecules spanning the chemical functions alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, and disulfide, as well as aromatic compounds and nucleic-acid bases. For 57 organic compounds, the calibration targets are the experimental pure-liquid density ρliq and the vaporization enthalpy ΔHvap, as well as the hydration free energy ΔGwat and the solvation free energy ΔGche in cyclohexane, at atmospheric pressure and at (or close to) room temperature. The final root-mean-square deviations (RMSD) for these four quantities over the set of compounds are 32.4 kg m(-3), 3.5 kJ mol(-1), 4.1 kJ mol(-1), and 2.1 kJ mol(-1), respectively, and the corresponding average deviations (AVED) are 1.0 kg m(-3), 0.2 kJ mol(-1), 2.6 kJ mol(-1), and 1.0 kJ mol(-1), respectively. For the five nucleic-acid bases, the parametrization is performed by transferring the final 2016H66 parameters from analogous organic compounds followed by a slight readjustment of the charges to reproduce the experimental water-to-chloroform transfer free energies ΔGtrn. The final RMSD for this quantity over the five bases is 1.7 kJ mol(-1), and the corresponding AVED is 0.8 kJ mol(-1). As an initial validation of the 2016H66 set, seven additional thermodynamic, transport, and dielectric properties are calculated for the 57 organic compounds in the liquid phase. The agreement with experiment in terms of these additional properties is found to be reasonable, with significant deviations typically affecting either a specific chemical function or a specific molecule. This suggests that in most cases, a classical force-field description along with a careful parametrization against ρliq, ΔHvap, ΔGwat, and ΔGche results in a model that appropriately describes the liquid in terms of a wide spectrum of its physical properties.

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Section: Introductionmentioning

confidence: 99%

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Horta

Merz

Fuchs

et al. 2016

J. Chem. Theory Comput.

144

287

View full text Add to dashboard Cite

show abstract

“…Such model has been developed by applying i) the MDEC concept for the modeling of the electrostatic part (i. e., the zinc ion point charge), and ii) force field optimization for the refinement of the Lennard‐Jones parameters. Intermolecular interactions between the zinc ion and neighboring atoms are modulated through the Waldman‐Hagler combination rule, which has been fruitfully applied in a previous work . We demonstrate that the same optimized model can well reproduce experimental quantities both in water and in the carbonic anhydrase enzyme cited above, and solving, in this last case, the wrong reproduction of structural properties deriving from the use of current literature parameters.…”

Section: Figurementioning

confidence: 82%

Including Electronic Screening in Classical Force Field of Zinc Ion for Biomolecular Simulations

Frate

Nikitin

2018

ChemistrySelect

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We present a new force field for zinc ion to be used in classical Molecular Dynamics. Such model has been developed according to an optimization procedure by fitting experimental quantities taken from the literature. The metal ion electrostatic charge has been scaled by a factor 0.75, according to a recently proposed polarization model which considers the electronic screening effects due to the surrounding environment. Zinc interatomic interactions have been modeled by means of the Waldman‐Hagler combination rule. It is demonstrated that the proposed force field for zinc is transferable from water solution to protein catalytic sites, offering in both the considered cases good performances in the reproduction of experimental quantities usually addressed in soft matter computer simulations.

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“…This principle has been chosen, since recent studies highlighted the more accuracy achievable for heavy elements when using the Waldman–Hagler rules, respect to other combining schemes . The last term of eq.…”

Section: Methodsmentioning

confidence: 99%

“…This principle has been chosen, since recent studies highlighted the more accuracy achievable for heavy elements when using the Waldman-Hagler rules, respect to other combining schemes. [34] The last term of eq. (2) represents the Coulomb potential, with ϵ 0 being the vacuum permittivity and q ECC M and q i the scaled charge of the metal ion and the atomic charge of atom i according to the employed water model, respectively.…”

Section: Potential Formmentioning

confidence: 99%

Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction

Nikitin

Frate

2019

J Comput Chem

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The parametrization of classical nonbonded models of metal ions has been widely addressed in the recent years. Despite the continuous development of novel and more physically inspired functional forms, the 12‐6 Lennard‐Jones plus Coulomb potential is still the most adopted force field in molecular dynamics (MD) codes, owing to its simple form and easy implementation. However, due to the integer formal charge, unpolarizable force fields of ions may suffer from overestimated interatomic electrostatic interactions, leading to nonphysical clustering or repulsion between such full charges. The electronic continuum correction (ECC) can fix this problem through a simple inclusion of solvent polarization effects via ionic charge rescaling. In this work, the development of novel nonbonded models for mono, divalent, and highly charged metal ions is presented. For each metal species, the ionic charge has been scaled, according to the ECC. Lennard‐Jones parameters have been optimized using experimental structural and thermodynamic properties as target quantities. Performances of the proposed models are discussed and compared with the literature data, while transferability attitudes among different and well‐known water models are evaluated. © 2019 Wiley Periodicals, Inc.

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AMBER-ii: New Combining Rules and Force Field for Perfluoroalkanes

Cited by 23 publications

References 50 publications

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Including Electronic Screening in Classical Force Field of Zinc Ion for Biomolecular Simulations

Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction

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