A force field for monosaccharides and (1 → 4) linked polysaccharides

Glennon, Timothy M.; Zheng, Ya-Jun; Grand, Scott M. Le; Shutzberg, Brad A.; Merz, Kenneth M.

doi:10.1002/jcc.540150910

Cited by 117 publications

(105 citation statements)

References 67 publications

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“…For both the ␣ and ␤ anomer, these structures cover the three orientations of the hydroxymethylene group with the clockwise and counterclockwise hydrogen-bond networks. The AMBER 1 and CHARMM 12 force fields give RMS deviations of 2.82 and 1.54 kcalrmol to the RHFr6᎐31G U results, respectively. The RMS error for the OPLS force field is 0.81 kcalrmol, which shows important and expected improvement.…”

Section: Comparison Of Force Field and Ab Initio Relative Energiesmentioning

confidence: 94%

“…As noted above, such charges have been used in earlier force fields. 1,5,6 Because CHELPG charges depend on the investigated conformation, it was also interesting to check the range of the CHELPG charges for the hexopyranoses. Comparison of the OPLS-AA charges in Figure 5 and the ranges covered by the CHELPG charges in Figure 6 shows that the magnitudes of the OPLS-AA charges are generally on the low end of the range.…”

Section: Nonbonded Parametersmentioning

confidence: 99%

“…Hartree᎐Fock RHF r6᎐31G calculations have been reported for 16 different conformers of D-glucopyranose by Glennon et al, 1 Brown and Wladkoski, 2 and Salzner and Schleyer. 3 Brown and Wladkoski also optimized three conformers of ␣-D-glucose at the MP2r6᎐31G U and BLYPr6᎐31G U levels and found that inclusion of the correlation effects led to variations in relative energies of less than 0.5 kcalrmol.…”

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confidence: 91%

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OPLS all-atom force field for carbohydrates

et al. 1997

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The OPLS all‐atom (AA) force field for organic and biomolecular systems has been expanded to include carbohydrates. Starting with reported nonbonded parameters of alcohols, ethers, and diols, torsional parameters were fit to reproduce results from ab initio calculations on the hexopyranoses, α,β‐d‐glucopyranose, α,β‐d‐mannopyranose, α,β‐d‐galactopyranose, methyl α,β‐d‐glucopyranoside, and methyl α,β‐d‐mannopyranoside. In all, geometry optimizations were carried out for 144 conformers at the restricted Hartree–Fock (RHF)/6–31G* level. For the conformers with a relative energy within 3 kcal/mol of the global minima, the effects of electron correlation and basis‐set extension were considered by performing single‐point calculations with density functional theory at the B3LYP/6–311+G** level. The torsional parameters for the OPLS‐AA force field were parameterized to reproduce the energies and structures of these 44 conformers. The resultant force field reproduces the ab initio calculated energies with an average unsigned error of 0.41 kcal/mol. The α/β ratios as well as the relative energies between the isomeric hexopyranoses are in good accord with the ab initio results. The predictive abilities of the force field were also tested against RHF/6–31G* results for d‐allopyranose with excellent success; a surprising discovery is that the lowest energy conformer of d‐allopyranose is a β anomer. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1955–1970, 1997

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Section: Comparison Of Force Field and Ab Initio Relative Energiesmentioning

confidence: 94%

Section: Nonbonded Parametersmentioning

confidence: 99%

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confidence: 91%

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OPLS all-atom force field for carbohydrates

et al. 1997

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“…298 Glennon and Merz developed an hexapyronse force field in which semiempirical calculations were used to assign partial atomic charges to each atom (vs. all secondary hydroxyls having the same charge). 299,300 Woods and coworkers have developed the GLY-CAM force field 301 again by considering the unique partial atomic charges for the individual atoms, including ensemble averaging in the charge determination 302,303 as well as additional optimization of internal parameters. Recent updates of the GLYCAM force field have included use of a 1,4 scale factor of 1.0 304 vs. 1/1.2 common to the remainder of the AMBER force fields and a general carbohydrate model that avoids anomeric carbon specific terms is available (R. Woods, personal communication).…”

Section: Carbohydratesmentioning

confidence: 99%

Empirical force fields for biological macromolecules: Overview and issues

2004

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Empirical force field-based studies of biological macromolecules are becoming a common tool for investigating their structure-activity relationships at an atomic level of detail. Such studies facilitate interpretation of experimental data and allow for information not readily accessible to experimental methods to be obtained. A large part of the success of empirical force field-based methods is the quality of the force fields combined with the algorithmic advances that allow for more accurate reproduction of experimental observables. Presented is an overview of the issues associated with the development and application of empirical force fields to biomolecular systems. This is followed by a summary of the force fields commonly applied to the different classes of biomolecules; proteins, nucleic acids, lipids, and carbohydrates. In addition, issues associated with computational studies on "heterogeneous" biomolecular systems and the transferability of force fields to a wide range of organic molecules of pharmacological interest are discussed.

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“…At the QM level, we test both semiempirical molecular orbital theory 35,36 and lower-level ab initio approaches 37 -the latter continue to find use in force-field development, 13,23,38 so it is critical to evaluate their quality. At the MM level, we test the predictive capabilities of the MM3 24,26 force field w Ž .…”

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confidence: 99%