The Consistent Force Field. 1. Methods and Strategies for Optimization of Empirical Potential Energy Functions.

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.48-0548

Cited by 19 publications

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“…The following discussion refers frequently to information contained in Tables 1 and 2. These tables contain an annotated bibliography of as many CarbFFs14–92 as the authors were able to find using a comprehensive literature search. If any have been omitted, the omission was accidental with the exception that the tables are limited to all‐atom and united‐atom classical FFs intended for molecular mechanics (MM) and MD.…”

Section: History and Classificationsmentioning

confidence: 99%

Carbohydrate force fields

Foley

Tessier

Woods

2011

WIREs Comput Mol Sci

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Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.

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Section: History and Classificationsmentioning

confidence: 99%

Carbohydrate force fields

Foley

Tessier

Woods

2011

WIREs Comput Mol Sci

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“…In the case of PEF91L we developed the following strategy of optimization: 8 (1) An initial potential energy function with "reasonable" parameter values is neces- For PEF95SAC we changed the strategy: We kept the charge parameters fixed all way through, after having adapted them to Mulliken charges at the Hartree-Fock level at the outset. Dipole moments were kept in the gas phase optimization database.…”

Section: Main Approachesmentioning

confidence: 99%

“…7 Our work over the years had shown that it was of overriding importance to model the non-bonded interactions adequately. We developed a new and more rational strategy of optimization, 8 involving heavy optimization on crystal structures, which resulted in our best potential energy function so far, with the parameter set PEF95SAC. This has been documented in much detail.…”

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confidence: 99%

Consistent Force Fields for Saccharides

Rasmussen

1999

Journal of Carbohydrate Chemistry

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Consistent force fields for carbohydrates were hitherto developed by extensive optimization of potential energy function parameters on experimental data and on ab initio results. A wide range of experimental data is used: internal structures obtained from gas phase electron diffraction and from x-ray and neutron diffraction, vibrational frequencies, dipole moments, unit cell dimensions and lattice energies. The range of model compounds covered so far includes alkanes, ethers, alcohols, ketones and mono-and disaccharides. Electrostatic interactions are handled by fractional charges assigned to individual atoms. Charges are modeled such that Mulliken population analyses are reproduced. Morse functions are used for all bonded interactions; experimentally derived dissociation energies are used as parameters. Van der Waals interactions are modeled with Lennard-Jones 12-6 functions. The anomeric and exo-anomeric effects are accounted for without addition of specific terms. The work is done in the framework of the Consistent Force Field which originated in Israel and was further developed in Denmark. The actual methods and strategies employed have been described previously. Extensive testing of the force field is reported, and ways and means of improvement are indicated. Principles of mapping of conformational space are discussed, and a discussion on which properties to preferentially reproduce in modeling is invited. SHORT HISTORY OF THE CFF ATTEMPTSWe have worked on the Consistent Force Field 3 for thirty years, 4 and tried to apply the method to saccharides for twenty; the previous history has been published. 5 The full power of the CFF was not available in its updated form until 1985, 6 and then optimization 789 T 790 RASMUSSEN was undertaken. In 1991 we finished the first serious bid for an optimized force field for carbohydrates and their derivatives, PEF91L. 7Until then we had worked with hand-fitted force fields like most other researchers in modeling, and our main results were the demonstration that relaxation in all internal degrees of freedom is necessary for meaningful calculation of conformations of disaccharides and, by implication, of oligosaccharides; and the proof that quite good results can be provided even with rather primitive potential energy functions, if their parameters are judiciously chosen.PEF91L was applied to a variety of problems, notably the charting of the conformational space of gentiobiose. 7Our work over the years had shown that it was of overriding importance to model the non-bonded interactions adequately. We developed a new and more rational strategy of optimization, 8 involving heavy optimization on crystal structures, which resulted in our best potential energy function so far, with the parameter set PEF95SAC. This has been documented in much detail. 9The present paper records further tests of the force fields, and directions for improvement are indicated.

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“…All molecules included in this study have been subjected to the conformational analysis described previously, where a method of selecting the most important molecular conformers (equilibrium conformations) has been developed. For each individual molecule, the possible conformers within the selection scheme described by Dyekjær et al have been minimized with the molecular mechanics program CFF (Consistent Force Field), − using the parameter set PEF95SAC. − The Gibbs free energy at 298.16 K, calculated with CFF, is used to Boltzmann weight the calculated descriptors for all important conformers of each compound. From this set, the conformers with a relative probability above 10% are kept; all other conformers are excluded from further analysis.…”

Section: Computational Detailsmentioning

confidence: 99%

QSPR Models Based on Molecular Mechanics and Quantum Chemical Calculations. 2. Thermodynamic Properties of Alkanes, Alcohols, Polyols, and Ethers

and

Jónsdóttir

2003

Ind. Eng. Chem. Res.

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Quantitative Structure-Property Relationship (QSPR) models for prediction of various thermodynamic properties of simple organic compounds have been developed. A number of new descriptors are proposed and used alongside with descriptors available within the Codessa program. An important feature in this work has been to include the most probable molecular conformers in the model development and thus account for the conformational flexibility of the molecules. The models cover the properties boiling points, melting points, enthalpies of vaporization, enthalpies of fusion, and liquid densities for alkanes, alcohols, diols, ethers, and oxyalcohols, including cyclic alkanes and alcohols. Several good models, having good predictability, have been developed. To enhance the applicability of the QSPR models, simpler expressions for each descriptor have also been developed. This allows for the prediction of the physical properties by knowledge of the molecular constitution only.

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The Consistent Force Field. 1. Methods and Strategies for Optimization of Empirical Potential Energy Functions.

Cited by 19 publications

References 0 publications

Carbohydrate force fields

Carbohydrate force fields

Consistent Force Fields for Saccharides

QSPR Models Based on Molecular Mechanics and Quantum Chemical Calculations. 2. Thermodynamic Properties of Alkanes, Alcohols, Polyols, and Ethers

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