Dihedral angle

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

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

Abstract: We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A “projection” approach (Katritch et al. J Comput Chem 2003, 24, 254–265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone ϕ/ψ and side chain χ1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1565–1578, 2005

Structural studies of bis-catecholate, bis-dithiocatecholate, and tetraalkoxy diborane(4) compounds

Abstract: X-ray structures are described for the bis-catecholate, bis-dithiocatecholate, and tetraalkoxy diborane(4) compounds B2(1,2-O2C6H4)2 (1), B2(1,2-O2-4-ButC6H3)2 (2), B2(1,2-O2-3,5-But2C6H2)2 (3), B2(1,2-S2C6H4)2 (4), B2(1,2-S2-4-MeC6H3)2 (5), and B2(OCH2CMe2CH2O)2 (6). All the compounds adopt structures in the solid-state in which the B2O4 or B2S4 units are planar or very nearly so. In compounds 2 and 3, the dihedral angles between the two BO2C2 planes are 17.3 and 31.8° respectively whereas in 1, 4 and 5 these angles are exactly 0°. In 6, a 3-fold disorder precluded our obtaining accurate positions for the two boron atoms, yet a dihedral angle of 0° is required by the 3 site symmetry. The structure of the bis(Lewis base) adduct of B2Cl4, [B2Cl4(NHMe2)2] (7), is also described and structures of the salt [NH2Me2][B(1,2-O2C6H4)2] (8) and the NMe2-bridged dimer [{BCl2(μ-NMe2)}2] (9) are available in the Supporting Information. Compound 1 crystallized in the monoclinic space group P21/c with a = 4.746(1) A, b...

A solid state NMR study on crystalline forms of nylon 6

Abstract: High-resolution 13C-NMR spectra were studied for two different crystalline structures of nylon 6 in the solid state by the cross polarization/magic angle spinning (CP/MAS) method. Two crystalline structures, α-form and γ-form, gave different chemical shifts for methylene carbons. The results showed that the hydrogen bonds between intermolecular chains are stronger in the γ-form than in the α-form. This strongly supports the results of the X-ray study of nylon 6 by Malta et al. Our results also showed that interamolecular delocalization of positive charges occurs in the γ-form through hyperconjugation in which the dihedral angle between the π bond and neighboring σ bonds is 30° while no such effect can be expected in the α-form in which the angle is 0°.