Dihedral angle

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

Molecular dynamics simulation of polymer liquid and glass. II. Short range order and orientation correlation

Abstract: Molecular dynamics simulation has been performed with an assembly of n‐alkane‐like chains subject to potentials restricting bond lengths, bond angles, and t r a n s–g a u c h e dihedral angles and interacting with neighboring chains according to a truncated Lennard‐Jones potential. The system, on stepwise cooling under constant pressure, undergoes a transition exhibiting characteristics of glass transition observable with laboratory polymers. The short range order in the system was monitored by evaluating the radial distribution functiong k (r), where r is the distance between two short subchains, each comprising k consecutive CH2 units. The orientation correlations between neighboring subchains were monitored by evaluating the function S k (r), giving the average cosine square of the angle between the end‐to‐end vectors of two neighboring subchains of k CH2 units separated by a scalar distance r. Integration of S k (r), weighted by g k (r), gives the correlation volume. Both the short range order and the orientation correlation are seen to improve steadily as the temperature is lowered. This increased order is brought about as a result of increased density, reduced thermal motion, and more extended chain conformation. Extrapolation of the orientation correlation against temperature predicts an isotropic–nematic transition temperature T c , as suggested by the Landau–deGennes theory. Isothermal annealing just below the predicted T c indeed produces a highly ordered structure.

Relaxed continuous random network models: (I). Structural characteristics☆

Abstract: Two elastic-energy-relaxed continuous random network (Polk) models for tetrahedrally bonded amorphous semiconductors have been obtained: a 201-atom model built entirely at Yale and a 519-atom model relaxed from a structure built by Polk and Boudreaux which originated at Harvard. In relaxing the coordinates to minimize the total energy the Keating potential was used for the interatomic interactions. The models are analyzed in terms of density, elastic distortion energy, elastic constants, numbers of five-, six- and seven-fold rings, distribution of dihedral angles, and radial distribution functions. We find that, despite their different origins, the models have essentially identical characteristics. Our principal conclusions are as follows: (a) The density of the CRN model is, to within 1%, that of diamond cubic. (b) The bulk modulus is about 3% lower than that for the diamond cubic structure and the shear modulus lies between the two diamond cubic shear moduli. (c) There are, to within ± 10% (and with corrections for surface effects), 0.38 five-fold, 0.91 six-fold and 1.04 seven-fold rings per atom. (d) For a reasonable value of the bond bending force constant, rms bond length distortions are about 1.0% and bond angle distortions are about 7.0°. (e) The radial distribution function agrees very well with experiment for all four principal peaks.

Time-resolved two-dimensional vibrational spectroscopy of a short α-helix in water

Abstract: Nonlinear two-dimensional (2D) vibrational spectroscopy has been used to investigate the amide I band of an alanine-based 21-residue α-helical peptide in aqueous solution. Whereas the linear absorption spectrum consists of a single, broad amide I band, the 2D vibrational spectrum clearly reveals that this band is composed of two amide I transitions, which are assigned to the A and E1 modes. The A–E1 frequency splitting is found to be approximately 10 cm−1. We find that the amide I band is inhomogeneously broadened due to conformational disorder of the helix. The 2D line shapes can be well described using distributions of the dihedral angles (φ,ψ) around their average values with a width of 20°, confirming previous molecular-dynamics studies. Time-resolved 2D measurements show that the conformation fluctuates on a time scale of picoseconds.

Gauche effect in 1,2-difluoroethane. Hyperconjugation, bent bonds, steric repulsion.

Abstract: Natural bond orbital deletion calculations show that whereas the gauche preference arises from vicinal hyperconjugative interaction between anti C-H bonds and C-F* antibonds, the cis C-H/C-F* interactions are substantial (approximately 25% of the anti interaction). The established significantly >60 degrees FCCF dihedral angle for the equilibrium conformer can then be rationalized in terms of the hyperconjugation model alone by taking into account both anti interactions that maximize near 60 degrees and the smaller cis interactions that maximize at a much larger dihedral angle. This explanation does not invoke repulsive forces to rationalize the 72 degrees equilibrium conformer angle. The relative minimum energy for the trans conformer is the consequence of a balance between decreasing hyperconjugative stabilization and decreasing steric destabilization as the FCCF torsional angle approaches 180 degrees . The torsional coordinate is predicted to be strongly contaminated by CCF bending, with the result that approximately half of the trans --> gauche stabilization energy stems from mode coupling.