A molecular mechanics force field (MM3) for alcohols and ethers

Allinger, Norman L.; Rahman, Mita; Lii, Jenn Huei

doi:10.1021/ja00179a012

Cited by 337 publications

(128 citation statements)

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“…The molecular mechanics program MM3 (92) (QCPE, Indiana University, USA), developed by Allinger and coworkers was used, 8,9 modified as the MM3 (2000) version in the O-C-C-O and O-C-O-H torsional parameters, O-H hydrogen bonding parameters, and C-H electronegativity correction. 31 Besides, a suggested modification of the MM3 routines 32 was made, by changing the maximum atomic movement from 0.25 to 0.10 Å.…”

Section: Methodsmentioning

confidence: 99%

“…Flexible-residue molecular modeling was systematically used for many different disaccharides, [1][2][3][4][5][6][7] especially after the appearance of MM3, 8,9 a force-field with good parameterization for carbohydrates. Those studies were recently extended to different trisaccharides, [12][13][14][15] in an attempt to achieve a better knowledge of the conformational features of polysaccharides.…”

Section: Introductionmentioning

confidence: 99%

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MM3 Potential energy surfaces of β-4-linked mannobiose and mannotriose at different dielectric constants

Stortz¹

2005

Arkivoc

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The adiabatic potential energy surface (PES) of β-4-linked mannobiose was obtained using the MM3 force field at ε=3 and ε=80, and plotted as contour maps and as 2D graphs representing the energy vs. the ψ angle. The surfaces of the corresponding trisaccharide were also obtained and represented by a single 3D contour map for which the energy is plotted against the two ψ glycosidic angles. The PES of the disaccharide contains a low-energy well comprising two different minima, and three more minima in different locations. No major change was observed by changing the dielectric constant. For the trisaccharide, four main minima were observed, located within one minimum-energy region. The minima have a geometry close to that experimentally obtained for mannobiose, mannotriose and mannan I in solid state, but differ from that expected in aqueous solutions. The flexibility of the glycosidic linkage increases at higher dielectric constant, whereas it decreases for the linkage closer to the reducing end when passing from the di-to the trisaccharide.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

MM3 Potential energy surfaces of β-4-linked mannobiose and mannotriose at different dielectric constants

Stortz¹

2005

Arkivoc

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“…Energy Calculations-All geometry optimization steps were performed using the molecular mechanics program, MM3 (22,23). The block-diagonal minimization method was used for geometry optimization, with the default energy-convergence criterion (0.00008*n kcal/mol per five iterations, n ϭ number of atoms).…”

Section: Methodsmentioning

confidence: 99%

“…The 3 J C,H coupling constants were determined by two different techniques, EXSIDE (excitation-sculptured indirect-detection experiments) (19) and gradient-selected J-HMBC experiments (gs-J-HMBC) (20). The molecular modeling of the pentasaccharides involved a complete conformational search with the CI-CADA algorithm (21) interfaced with MM3 force field (22,23), which is very efficient for exploring the conformational space of flexible molecules (21), including oligosaccharides (24 -26). Boltzmann-averaged inter-residue distances and 3 J C,H coupling constants were calculated for the conformers generated and compared with NMR data for all frame-shifted pentasaccharides.…”

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confidence: 99%

Conformational Studies of the O-specific Polysaccharide of Shigella flexneri 5a and of Four Related Synthetic Pentasaccharide Fragments Using NMR and Molecular Modeling

Clément

Imberty

Phalipon

et al. 2003

Journal of Biological Chemistry

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As part of a program for the development of synthetic vaccines against the pathogen Shigella flexneri, we used a combination of NMR and molecular modeling methods to study the conformations of the O-specific polysaccharide (O-SP) of S. flexneri 5a and of four related synthetic pentasaccharide fragments. The NMR study, based on the analysis of 1 H and 13 C chemical shifts, the evaluation of inter-residue distances, and the measurement of oneand three-bond heteronuclear coupling constants, showed that the conformation of one of the four pentasaccharides is similar to that of the native O-SP in solution. Interestingly, inhibition enzyme-linked immunosorbent assay demonstrated that a protective monoclonal antibody specific for S. flexneri 5a has a greater affinity for this pentasaccharide than for the others. We carried out a complete conformational search on the pentasaccharides using the CICADA algorithm interfaced with MM3 force field. We calculated Boltzmann-averaged inter-residue distances and 3 J C,H coupling constants for the different conformational families and compared the results with NMR data for all pentasaccharides. Our experimental data are consistent with only one conformational family. We also used molecular modeling data to build models of the O-SP with the molecular builder program POLYS. The models that are in agreement with NMR data adopt right-handed 3-fold helical structures in which the branched glucosyl residue points outwards.

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“…We have thoroughly investigated ten tautomers (Fig. 1), including six of gossypol, three of gossypolone, and the one of anhydrogossypol, with MM3, version 2000 [19][20][21]. Three N-gossypol tautomers were also studied but in less detail.…”

Section: Introductionmentioning

confidence: 99%

Conformational analysis of gossypol and its derivatives by molecular mechanics

Beisel

Dowd

Reilly

2005

Journal of Molecular Structure: THEOCHEM

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Conformations and inversion pathways leading to racemization of all the tautomers of gossypol, gossypolone, anhydrogossypol, and a diethylamine Schiff 's base of gossypol were investigated with MM3(2000). All forms have hindered rotation because of clashes between the methyl carbon atom and oxygen-containing moieties ortho to the bond linking the two naphthalene rings. Inversion energies generally agree with available experimental data. Gossypol preferentially inverts in its dihemiacetal tautomeric form through the cis pathway (where similar groups clash). Gossypolone inverts more easily than gossypol, and preferentially through the trans pathway (where dissimilar groups clash) when one of its outer rings has an enol-keto group and the other has an aldehyde group. Anhydrogossypol racemizes through the cis pathway. The bridge bond and the ortho exo-cyclic bonds in all the structures bend from planarity, and the inner naphthalene rings pucker to accommodate the inversion. For gossypol, the transition is achieved through greater bending of the exo-cyclic bonds (up to 12°) and less distortion of the inner benzyl rings (q≤0.34 Å), (up to 12.7°) . For gossypolone the transition occurs with greater distortion of the inner benzyl rings (q≤0.63 Å) and less out-of-plane bending (up to 8.4°). By isolating individual clashes, their contribution to the overall barrier can be analyzed, as shown for the dialdehyde tautomer of gossypol.

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A molecular mechanics force field (MM3) for alcohols and ethers

Cited by 337 publications

References 0 publications

MM3 Potential energy surfaces of β-4-linked mannobiose and mannotriose at different dielectric constants

MM3 Potential energy surfaces of β-4-linked mannobiose and mannotriose at different dielectric constants

Conformational Studies of the O-specific Polysaccharide of Shigella flexneri 5a and of Four Related Synthetic Pentasaccharide Fragments Using NMR and Molecular Modeling

Conformational analysis of gossypol and its derivatives by molecular mechanics

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