scispace - formally typeset
Search or ask a question
Topic

Dihedral angle

About: Dihedral angle is a research topic. Over the lifetime, 15718 publications have been published within this topic receiving 174904 citations.


Papers
More filters
Journal ArticleDOI
TL;DR: This study of the observed side-chain conformations has led to a refinement of one of the energy parameters used in empirical conformational energy computations.
Abstract: The distributions of side-chain conformations in 258 crystal structures of oligopeptides have been analyzed. The sample contains 321 residues having side chains that extend beyond the C beta atom. Statistically observed preferences of side-chain dihedral angles are summarized and correlated with stereochemical and energetic constraints. The distributions are compared with observed distributions in proteins of known X-ray structures and with computed minimum-energy conformations of amino acid derivatives. The distributions are similar in all three sets of data, and they appear to be governed primarily by intraresidue interactions. In side chains with no beta-branching, the most important interactions that determine chi 1 are those between the C gamma H2 group and atoms of the neighboring peptide groups. As a result, the g- conformation (chi 1 congruent to -60 degrees) occurs most frequently for rotation around the C alpha-C beta bond in oligopeptides, followed by the t conformation (chi 1 congruent to 180 degrees), while the g+ conformation (chi 1 congruent to 60 degrees) is least favored. In residues with beta-branching, steric repulsions between the C gamma H2 or C gamma H3 groups and backbone atoms govern the distribution of chi 1. The extended (t) conformation is highly favored for rotation around the C beta-C gamma and C gamma-C delta bonds in unbranched side chains, because the t conformer has a lower energy than the g+ and g- conformers in hydrocarbon chains. This study of the observed side-chain conformations has led to a refinement of one of the energy parameters used in empirical conformational energy computations.

225 citations

Journal ArticleDOI
TL;DR: In this paper, the product rotational polarization is reported using the quasiclassical trajectory method for the photo-initiated bimolecular reaction A+BC→AB+C. The model takes the form of a 3D quasico-clique study of a hypothetical exothermic reaction employing combinations of three different potential energy surfaces (attractive, mixed and repulsive), three markedly different reagent mass combinations (H+HL, H+LL and H+HH, where L≡1 amu and H≡80 amu).
Abstract: The product rotational polarization is reported using the quasiclassical trajectory method for the photoinitiated bimolecular reaction A+BC→AB+C. The model takes the form of a 3D quasiclassical trajectory study of a hypothetical exothermic reaction employing combinations of (a): three different potential energy surfaces (attractive, mixed and repulsive), (b): three markedly different reagent mass combinations (H+HL, H+LL and H+HH, where L≡1 amu and H≡80 amu). Four PDDCSs (2π/σ) (dσ00/dωt), (2π/σ) (dσ20/dωt), (2π/σ) (dσ22+/dωt), and (2π/σ) (dσ21−/dωt) which are usually sensitive to many photoinitiated bimolecular reaction experiments are presented. Furthermore, the distribution of dihedral angle P(φr) and the distribution of angle between K and J′ P(θr) are discussed. Moreover, the angular distribution of product rotational vectors in the form of polar plots in θr and φr is calculated.

225 citations

Journal ArticleDOI
TL;DR: In this article, a data file was created containing internal coordinates and derived parameters for 178 β-D-furanoside fragments, occurring in X-ray structures of ribo-, 2′-deoxyribo- and arabinonucleoside derivatives.
Abstract: A data file was created containing internal coordinates and derived parameters for 178 β-D-furanoside fragments, occurring in X-ray structures of ribo-, 2′-deoxyribo- and arabinonucleoside derivatives. The variability in bond angles and torsion angles can be described by four conformational parameters; the kind and degree of ring puckering as expressed in phase angle of pseudorotation P and puckering amplitude vm, the conformation of the side-chain δ and the glycosidic torsion angle χ. Comparison between out-of-plane and torsion angle methods for calculation of pseudorotation parameters revealed that the latter method is better suited to describe the internal coordinates of the non-equilateral five-membered ring. Inspection of the distribution of phase angles and puckering amplitudes lends additional support to the hypothesis that conformational interconversion of the familiar N and S type ring conformers is a process of hindered pseudorotation, proceeding through the O4′endo conformation (P = 90°) and maintaining a constant puckering amplitude. Both syn-anti distribution and preferred ranges of χ are correlated with furanose conformation in ribonucleosides; the distribution is also affected by the type of base, purines showing higher syn/anti ratios than pyrimidines. Three modes are observed for the backbone torsion angle δ(C4′–C5′); the most abundant rotamer is δ+, followed by δa. The δ− rotamer has so far been found only in S-type furanosides. Regressions based on existing or modified equations were used to express variations in internal coordinates in terms of the four parameters involved. As a consequence of its anomeric character, the glycosidic bond length can be described by a cyclic function of χ. Endocyclic bond angles' and torsion angles show small but systematic deviations from the pseudorotation equations derived for equilateral rings. Based on observed correlations with the four parameters, reasonably accurate coordinates for exocyclic atoms, including hydrogen atoms, could also be obtained. Coordinates for model β-D-furanoside fragments with preferred χ and δ orientations and variable pseudorotation parameters, covering a part of the N ⇌ S interconversion pathway, are presented. Their usefulness in future theoretical and experimental studies on nucleic acid conformations, both in the solid state and in solution, is discussed.

224 citations

Journal ArticleDOI
TL;DR: In this article, a simple and versatile method for the conformational assessment of this class of compounds is reported, which has been quite successfully tested on about 10 compounds derived from 2,2‘-dimethyl-1,1'binaphthyl derivatives.
Abstract: The dihedral angle θ of 1,1‘-binaphthyl derivatives is quantitatively related to the wavelength splitting Δλmax of the 220 nm couplet of the CD spectra. This relation is almost independent of measurement conditions (solvent, concentration). Its reliability has been quite successfully tested on about 10 compounds derived from 2,2‘-dimethyl-1,1‘-binaphthyl. A simple and versatile method for the conformational assessment of this class of compounds is reported.

221 citations

Journal ArticleDOI
TL;DR: DANGLE, a new algorithm that employs Bayesian inference to estimate the likelihood of all possible values of the backbone dihedral angles phi and psi for each residue in a query protein, based on observed chemical shifts and the conformational preferences of each amino acid type, is introduced.

220 citations


Network Information
Related Topics (5)
Hydrogen bond
57.7K papers, 1.3M citations
88% related
Crystal structure
100.9K papers, 1.5M citations
85% related
Ligand
67.7K papers, 1.3M citations
80% related
Molecule
52.4K papers, 1.2M citations
79% related
Intramolecular force
41.6K papers, 772.2K citations
77% related
Performance
Metrics
No. of papers in the topic in previous years
YearPapers
2023203
2022473
2021160
2020195
2019193
2018216