Protein structures and complexes: what they reveal about the interactions that stabilize them

Thornton, Janet M.; MacArthur, Malcolm W.; McDonald, Ian K.; Jones, David T.; Mitchell, John B. O.; Nandi, C. Lilian; Price, Sarah L.; Zvelebil, Marketa

doi:10.1098/rsta.1993.0123

Cited by 12 publications

(4 citation statements)

References 33 publications

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“…12 The electrostatic contribution to the intermolecular forces, which is the classical Coulombic interaction between the undistorted charge distributions of the molecules, dominates the intermolecular interaction at long range and generally determines the orientation dependence of the intermolecular potential in the van der Waals contact region. This was shown by the ability of an Ž accurate distributed multipole representation of .…”

Section: Ing Of CLmentioning

confidence: 99%

Hydrogen bonding properties of oxygen and nitrogen acceptors in aromatic heterocycles

et al. 1997

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The directionality and relative strengths of hydrogen bonds to monocyclic aromatic heterocycles were investigated using crystal structure data and theoretical calculations. Surveys of the Cambridge Structural Database for hydrogen bonds between C(sp3)(SINGLE BOND)O(SINGLE BOND)H and aromatic fragments containing one or more nitrogen and/or oxygen heteroatoms showed that hydrogen bonds to nitrogen atoms are much more abundant than to oxygen. Distinct preferred orientations were also revealed in these surveys. Theoretical calculations were performed on the interaction of methanol with pyridine, pyrimidine, pyrazine, pyridazine, oxazole, isoxazole, 1,2,4‐oxadiazole, and furan as models for the heterocyclic fragments. The intermolecular potential surface was thoroughly scanned using a model potential that accurately described the electrostatic forces (derived from distributed multipole analysis) with empirical parameters for the repulsion and dispersion terms. Minima on this surface agreed well with the observed orientations in the data base and they were typically deeper for nitrogen than for oxygen acceptors, although the hydrogen bond strength and geometry was influenced by other heteroatoms in the ring. These results were confirmed by highly accurate intermolecular perturbation theory calculations, which also estimated the deviations from hydrogen bonding in the traditional nitrogen lone pair direction that could occur with negligible reduction in the interaction energy. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 2060–2074, 1997

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Section: Ing Of CLmentioning

confidence: 99%

Hydrogen bonding properties of oxygen and nitrogen acceptors in aromatic heterocycles

et al. 1997

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“…These results could be called in to question by the work of Thornton et al, which suggests that all-atom models are insufficient for the modeling of the interactions of phenol. In their work on the interactions between phenol and a carboxylate group, they found that a model constructed using distributed multipole analysis 41 outperformed the CHARMM 42 force field, suggesting that higher-order multipole moments are required in order to model accurately even those aromatic compounds that possess a dipole moment.…”

Section: Introductionmentioning

confidence: 99%

Modeling Aromatic Liquids: Toluene, Phenol, and Pyridine

Baker

Grant

2007

J. Chem. Theory Comput.

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Aromatic groups are now acknowledged to play an important role in many systems of interest. However, existing molecular mechanics methods provide a poor representation of these groups. In a previous paper, we have shown that the molecular mechanics treatment of benzene can be improved by the incorporation of an explicit representation of the aromatic π electrons. Here, we develop this concept further, developing charge-separation models for toluene, phenol, and pyridine. Monte Carlo simulations are used to parametrize the models, via the reproduction of experimental thermodynamic data, and our models are shown to outperform an existing atom-centered model. The models are then used to make predictions about the structures of the liquids at the molecular level and are tested further through their application to the modeling of gas-phase dimers and cation-π interactions.

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“…Certainly we expect molecules with N−H and CO functional groups to form strong hydrogen bonds in crystals, with the classification “strong” implying that the hydrogen bond is dominated by the electrostatic interaction and the N···O separation is less than the sum of the van der Waals radii. Such hydrogen bonds typify the term, and their reliable formation, strength, and directionality are central to understanding biological structures − and strategies in crystal engineering. − There has been considerable research effort on defining hydrogen bonds and quantifying , their strength since Etter published general rules for hydrogen bonds as design elements in organic chemistry, and it is clear that CO and N−H are among the donors and acceptors to which these rules are expected to apply. The first rule, that “all good proton donors and acceptors are used in hydrogen bonding”, is so reliable that although exceptions have long been known, particularly for acceptors, they are sufficiently rare as to deserve comment .…”

Section: Introductionmentioning

confidence: 99%

Investigating Unused Hydrogen Bond Acceptors Using Known and Hypothetical Crystal Polymorphism

Lewis

Tocher

Price

2005

Crystal Growth & Design

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The crystal structures found in a manual search for polymorphs are discussed in conjunction with low energy crystal structures found in a computational search for minima in the lattice energy, for barbituric acid, cyanuric acid, alloxan, parabanic acid, and urazole. Since all these molecules, with the exception of urazole, have crystal structures in which there are carbonyl groups not used in conventional hydrogen bonding, these results and the electrostatic properties of the molecules are used to interpret this unusual behavior. It appears that there is no great difference between the strengths of the various N-H donors and CdO acceptors within these molecules, and the observed crystal structures result from the compromise between the intermolecular interactions of the molecules.

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Protein structures and complexes: what they reveal about the interactions that stabilize them

Cited by 12 publications

References 33 publications

Hydrogen bonding properties of oxygen and nitrogen acceptors in aromatic heterocycles

Hydrogen bonding properties of oxygen and nitrogen acceptors in aromatic heterocycles

Modeling Aromatic Liquids: Toluene, Phenol, and Pyridine

Investigating Unused Hydrogen Bond Acceptors Using Known and Hypothetical Crystal Polymorphism

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