The Consistent Force Field. 2. An Optimized Set of Potential Energy Functions for the Alkanes.

Engelsen, Søren Balling; Fabricius, Jesper; Rasmussen, Kjeld; Klæboe, P.; Nielsen, Carl; Kondow, A. J.; Bisht, Kirpal S.; Parmar, Virinder S.; Francis, George W.

doi:10.3891/acta.chem.scand.48-0553

Cited by 19 publications

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“…The choice of the potential energy functions is the same as in the previously described and analyzed model, except that the Morse potential is chosen instead of a harmonic function for modeling the bond potential. The reasons for selecting the Morse potential over the quadratic function are: the harmonic potential could not reproduce the diversities in the Cu−N and Cu−O bond lengths, and the satisfactory performance of several force fields which use Morse potentials. ,− …”

Section: Methods and Calculationsmentioning

confidence: 99%

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Why Are Copper(II) Amino Acid Complexes Not Planar in Their Crystal Structures? An ab Initio and Molecular Mechanics Study

Sabolović

Liedl

1999

Inorg. Chem.

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This paper presents geometries of copper(II) chelates with l-alanine, l-leucine, and l-N,N-dimethylvaline optimized by the hybrid density functional method B3LYP. According to the molecular quantum mechanics results, a square-planar copper(II) coordination geometry is electronically favored in vacuo. Deviations from the planar configuration observed in the crystal state should be attributed to sterical intramolecular and/or intermolecular effects. This paper proposes a new molecular mechanics model for tetracoordinated copper(II) amino acidates to investigate these effects in detail. The empirical parameter set for the selected potential energy functions was optimized both with respect to the X-ray crystal structures (internal coordinates and unit cell constants) and with respect to the quantum mechanically derived valence angles around copper. To test this newly developed force field (FF), the equilibrium geometries of 10 molecules are predicted in vacuo and in approximate crystalline surrounding. The results were compared with their ab initio and experimental crystal structures, respectively. The unit cell volumes were reproduced in a range from −7.0% to 2.1%. The total root-mean-square deviations between the experimental and FF in crystal internal coordinates were 0.017 Å in the bond lengths, 2.2° in the valence angles, and 3.6° in the torsion angles. The force field is capable of reproducing the changes in the chelate rings' torsion angles caused by the crystal packing forces and successfully explains the nonplanarity of Cu(II) amino acid complexes in their crystal structures.

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Section: Methods and Calculationsmentioning

confidence: 99%

“…The reasons for selecting the Morse potential over the quadratic function are: the harmonic potential could not reproduce the diversities in the Cu-N and Cu-O bond lengths, and the satisfactory performance of several force fields which use Morse potentials. 45,[66][67][68][69]…”

Section: Methods and Calculationsmentioning

confidence: 99%

Why Are Copper(II) Amino Acid Complexes Not Planar in Their Crystal Structures? An ab Initio and Molecular Mechanics Study

Sabolović

Liedl

1999

Inorg. Chem.

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“…A coarse distinction of available force fields can be made based on the purpose of the force field, which determines the underlying parametrization strategy. Spectroscopic force fields − are designed to investigate gas-phase molecular properties, and their parametrization aims at the accurate representation of molecular geometric, energetic, and vibrational properties, while thermodynamic force fields − are designed to investigate condensed-phase properties, the parametrization accordingly aiming at the accurate representation of bulk thermodynamic properties such as, e.g., densities, vaporization enthalpies, or solvation free energies. The present study is concerned with the GROMOS force field for (bio)molecular simulation.…”

Section: Introductionmentioning

confidence: 99%

Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins

Reif

Winger

Oostenbrink

2013

J. Chem. Theory Comput.

101

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The GROMOS 54A8 force field [Reif et al. J. Chem. Theory Comput.2012, 8, 3705–3723] is the first of its kind to contain nonbonded parameters for charged amino acid side chains that are derived in a rigorously thermodynamic fashion, namely a calibration against single-ion hydration free energies. Considering charged moieties in solution, the most decisive signature of the GROMOS 54A8 force field in comparison to its predecessor 54A7 can probably be found in the thermodynamic equilibrium between salt-bridged ion pair formation and hydration. Possible shifts in this equilibrium might crucially affect the properties of electrolyte solutions or/and the stability of (bio)molecules. It is therefore important to investigate the consequences of the altered description of charged oligoatomic species in the GROMOS 54A8 force field. The present study focuses on examining the ability of the GROMOS 54A8 force field to accurately model the structural properties of electrolyte solutions, lipid bilayers, and proteins. It is found that (i) aqueous electrolytes involving oligoatomic species (sodium acetate, methylammonium chloride, guanidinium chloride) reproduce experimental salt activity derivatives for concentrations up to 1.0 m (1.0-molal) very well, and good agreement between simulated and experimental data is also reached for sodium acetate and methylammonium chloride at 2.0 m concentration, while not even qualitative agreement is found for sodium chloride throughout the whole range of examined concentrations, indicating a failure of the GROMOS 54A7 and 54A8 force-field parameter sets to correctly account for the balance between ion–ion and ion–water binding propensities of sodium and chloride ions; (ii) the GROMOS 54A8 force field reproduces the liquid crystalline-like phase of a hydrated DPPC bilayer at a pressure of 1 bar and a temperature of 323 K, the area per lipid being in agreement with experimental data, whereas other structural properties (volume per lipid, bilayer thickness) appear underestimated; (iii) the secondary structure of a range of different proteins simulated with the GROMOS 54A8 force field at pH 7 is maintained and compatible with experimental NMR data, while, as also observed for the GROMOS 54A7 force field, α-helices are slightly overstabilized with respect to 310-helices; (iv) with the GROMOS 54A8 force field, the side chains of arginine, lysine, aspartate, and glutamate residues appear slightly more hydrated and present a slight excess of oppositely-charged solution components in their vicinity, whereas salt-bridge formation properties between charged residues at the protein surface, as assessed by probability distributions of interionic distances, are largely equivalent in the GROMOS 54A7 and 54A8 force-field parameter sets.

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“…From a broad perspective, one may distinguish between two main classes of force fields, involving different scopes and design strategies. On one hand, molecular mechanics or spectroscopic force fields, e.g., CFF, , CVFF, MM3, − and MM4, mainly aim at an accurate description of molecular properties in the gas phase, e.g., geometries, energies, and vibrational properties. They usually involve few atom types, a complex functional form, e.g., including anharmonicities and couplings in the bonded terms, largely automatized parametrization procedures, and parameters mainly derived on the basis of spectroscopic measurements and QM calculations in the gas phase.…”

Section: Introductionmentioning

confidence: 99%

New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters

Horta

Fuchs

Gunsteren

et al. 2011

J. Chem. Theory Comput.

111

193

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A new parameter set (53A6OXY) is developed for the GROMOS force field, that combines reoptimized parameters for the oxygen-containing chemical functions (alcohols, ethers, aldehydes, ketones, carboxylic acids, and esters) with the current biomolecular force field version (53A6) for all other functions. In the context of oxygen-containing functions, the 53A6OXY parameter set is obtained by optimization of simulated pure-liquid properties, namely the density ρliq and enthalpy of vaporization ΔHvap, as well as solvation properties, namely the free energies of solvation in water ΔGwat and in cyclohexane ΔGche, against experimental data for 10 selected organic compounds, and further tested for 25 other compounds. The simultaneous refinement of atomic charges and Lennard-Jones interaction parameters against the four mentioned types of properties provides a single parameter set for the simulation of both liquid and biomolecular systems. Small changes in the covalent parameters controlling the geometry of the oxygen-containing chemical functions are also undertaken. The new 53A6OXY force-field parameters reproduce the mentioned experimental data within root-mean-square deviations of 22.4 kg m(-3) (ρliq), 3.1 kJ mol(-1) (ΔHvap), 3.0 kJ mol(-1) (ΔGwat), and 1.7 kJ mol(-1) (ΔGche) for the 35 compounds considered.

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The Consistent Force Field. 2. An Optimized Set of Potential Energy Functions for the Alkanes.

Cited by 19 publications

References 0 publications

Why Are Copper(II) Amino Acid Complexes Not Planar in Their Crystal Structures? An ab Initio and Molecular Mechanics Study

Why Are Copper(II) Amino Acid Complexes Not Planar in Their Crystal Structures? An ab Initio and Molecular Mechanics Study

Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins

New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters

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