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A theoretical, dynamical evaluation method of the steric hindrance in nitroxide radicals using transition states of model reactions.

ABSTRACT: Steric hindrance is known to affect the stability, reactivity, and radical trapping ability of stable nitroxide radicals. Therefore, a quantitative evaluation and prediction model of steric hindrance is needed to select and design the optimum nitroxide radicals for specific applications. In this study, a dynamic parameter of steric hindrance (DPSH) is proposed and its characteristics are investigated. Unlike using only the equilibrium structure to evaluate the steric hindrance, DPSH is a dynamic value calculated from the theoretical activation enthalpies for two model reactions of radical addition to olefins. Using DPSH, the steric hindrance was evaluated for a total of 43 alkyl radicals, nitroxide radicals, and radicals derived from phenols, and the results were compared with those of other methods. The DPSH values for radicals can vary when the energy barrier for structural change varies, even if the equilibrium structures of the radicals have the same steric shielding. Finally, for radicals other than nitroxide radicals, the DPSH values were consistent with the predictions from their structures, which suggests that the DPSH has a wide range of applications. We expect DPSH to be used and developed in the analysis of steric factors in various reactions.

SUBMITTER: Yamazaki Y

PROVIDER: S-EPMC6937270 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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A theoretical, dynamical evaluation method of the steric hindrance in nitroxide radicals using transition states of model reactions.

Yamazaki Yudai Y Naganuma Jun J Gotoh Hiroaki H

Scientific reports 20191230 1

Steric hindrance is known to affect the stability, reactivity, and radical trapping ability of stable nitroxide radicals. Therefore, a quantitative evaluation and prediction model of steric hindrance is needed to select and design the optimum nitroxide radicals for specific applications. In this study, a dynamic parameter of steric hindrance (DPSH) is proposed and its characteristics are investigated. Unlike using only the equilibrium structure to evaluate the steric hindrance, DPSH is a dynamic ...[more]

PMID: 31889058

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Project description:BackgroundIn computational structural biology, structure comparison is fundamental for our understanding of proteins. Structure comparison is, e.g., algorithmically the starting point for computational studies of structural evolution and it guides our efforts to predict protein structures from their amino acid sequences. Most methods for structural alignment of protein structures optimize the distances between aligned and superimposed residue pairs, i.e., the distances traveled by the aligned and superimposed residues during linear interpolation. Considering such a linear interpolation, these methods do not differentiate if there is room for the interpolation, if it causes steric clashes, or more severely, if it changes the topology of the compared protein backbone curves.ResultsTo distinguish such cases, we analyze the linear interpolation between two aligned and superimposed backbones. We quantify the amount of steric clashes and find all self-intersections in a linear backbone interpolation. To determine if the self-intersections alter the protein's backbone curve significantly or not, we present a path-finding algorithm that checks if there exists a self-avoiding path in a neighborhood of the linear interpolation. A new path is constructed by altering the linear interpolation using a novel interpretation of Reidemeister moves from knot theory working on three-dimensional curves rather than on knot diagrams. Either the algorithm finds a self-avoiding path or it returns a smallest set of essential self-intersections. Each of these indicates a significant difference between the folds of the aligned protein structures. As expected, we find at least one essential self-intersection separating most unknotted structures from a knotted structure, and we find even larger motions in proteins connected by obstruction free linear interpolations. We also find examples of homologous proteins that are differently threaded, and we find many distinct folds connected by longer but simple deformations. TM-align is one of the most restrictive alignment programs. With standard parameters, it only aligns residues superimposed within 5 Ångström distance. We find 42165 topological obstructions between aligned parts in 142068 TM-alignments. Thus, this restrictive alignment procedure still allows topological dissimilarity of the aligned parts.ConclusionsBased on the data we conclude that our program ProteinAlignmentObstruction provides significant additional information to alignment scores based solely on distances between aligned and superimposed residue pairs.

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A theoretical, dynamical evaluation method of the steric hindrance in nitroxide radicals using transition states of model reactions.

Publications

A theoretical, dynamical evaluation method of the steric hindrance in nitroxide radicals using transition states of model reactions.

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