Dihedral angle

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

Medium-range order in v-SiO2

Abstract: A computer algorithm has been developed to generate fully valence-satisfied models of amorphous AX 2 chemically ordered continuous random networks. The specific application here is the successive addition of rigid corner-sharing AX 4 tetrahedral units and the networks produced are analyzed with reference to the structure of v-SiO 2 . Control over parameters such as bond angles, minimum ring size and dihedral angle is possible while short-range order is ensured by using rigid AX 4 tetrahedral units as the basic building block. Models have been generated to investigate a region of parameter space with minimum ring size and equilibrium SiOSi bond angles as variables. Careful considerations is given to the effects of experimental resolution, thermal broadening and finite model-size correction when comparing the models with experimental data. It is found that a comparatively narrow region of parameter space gives rise to good models assessed in terms of their fit to experimentally derived real-space distribution functions, bond-angle distributions, reciprocal space scattering data and, in particular, the relative intensity of the first sharp diffraction peak (FSDP).

Determination of internuclear distances and the orientation of functional groups by solid-state NMR: rotational resonance study of the conformation of retinal in bacteriorhodopsin.

Abstract: We have used a new solid-state NMR technique--rotational resonance--to determine both internuclear distances and the relative orientations of chemical groups (dihedral angles) in retinal bound to bacteriorhodopsin (bR) and in retinoic acid model compounds. By matching the rotational resonance condition (delta = n omega r/2 pi, where delta is the difference in isotropic chemical shifts for two dipolar coupled spins, omega r/2 pi is the mechanical rotational frequency of the sample in the MAS experiment, and n is a small integer denoting the order of the resonance), we selectively reintroduce the dipolar coupling and enhance the rate of magnetization exchange. Spectroscopic data and theoretical simulations of the magnetization exchange trajectories for the 8,18-13C dipolar coupled pair in retinoic acid model compounds, crystallized in both the 6-s-cis and 6-s-trans forms, indicate that an accurate determination of the internuclear distance is possible. For the n = 1 resonance we find the distance determination to be reasonably independent of the relative orientation of the groups. In contrast, for the n = 2 resonance, there is a more pronounced dependence on the relative orientation of the groups which permits an estimate of the angle around the 6-s bond for the cis and trans forms to be 42 +/- 5 degrees and 90 +/- 10 degrees, respectively, in good agreement with crystallography. In bR we demonstrate that the 8-13C-18-13C distance is 4.1 A and the average 8-13C-16-13C/8-13C-17-13C distance is 3.3-3.5 A.(ABSTRACT TRUNCATED AT 250 WORDS)

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations

Abstract: Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules. To improve the stability and accuracy of coarse-grained molecular dynamics simulations, we propose two approaches. The first makes use of improved forms for the angle potentials: the restricted bending (ReB) potential prevents torsion angles from visiting unstable or unphysical configurations and the combined bending-torsion (CBT) potential smoothly flattens the interactions when such configurations are sampled. In the second approach, dummy-assisted dihedral (DAD), the torsion potential is applied differently: instead of acting directly on the beads, it acts on virtual beads, bound to the real ones. For simple geometrical reasons, the unstable region is excluded from the accessible conformational space. The benefits of the new approaches are demonstrated in simulations of polyethylene glycol (PEG), polystyrene (PS), and polypeptide molecules described by the MARTINI coarse-grained force field. The new potentials are implemented in an in-house version of the Gromacs package, publicly available.

Rotational isomerism in acrylic acid. A combined matrix-isolated IR, Raman and ab initio molecular orbital study

Abstract: The results of a combined vibrational and structural study of the acrylic acid monomer undertaken by matrix-isolated low-temperature IR spectroscopy and ab initio SCF-HF and MP2 MO calculations are presented. In addition, both Raman and IR spectra of liquid acrylic acid and the Raman spectrum of the crystal are also reported and interpreted. It is shown that in both argon and krypton matrices acrylic acid monomer exists as a mixture of two conformers of similar energies, differing by the relative orientation of the CC—CO axis. Upon irradiation at λ= 243 nm by a xenon lamp, the s-cis form (CC—CO dihedral angle equal to 0 °), corresponding to the conformational ground state, converts to the s-trans form (CC—CO dihedral angle equal to 180 °). In the liquid phase, dimeric structures strongly predominate, but the existence in this phase of the two conformational states referred to above can also be inferred from the corresponding vibrational spectra. In turn, in the crystal only the thermodynamically most stable form (s-cis) exists. Results of ab initio SCF-HF and MP2 molecular orbital (MO) calculations, in particular optimised geometries, relative stabilities, dipole moments and harmonic force fields, for the relevant conformational states of acrylic acid are also presented and the conformational dependence of some relevant structural parameters is used to characterise the most important intramolecular interactions present in the studied conformers. Finally, the calculated vibrational spectra and both the results of a normal-mode analysis based on the theoretical harmonic force fields and of IR intensity studies based on the charge–charge flux–overlap (CCFO) model were used to help interpret the experimental vibrational data, enabling a detailed assignment of the acrylic acid spectra obtained in the different conditions considered.

Structure Analysis of Dipeptides in Water by Exploring and Utilizing the Structural Sensitivity of Amide III by Polarized Visible Raman, FTIR−Spectroscopy and DFT Based Normal Coordinate Analysis

Abstract: A series of dipeptides AX and XA (X = G, K, L, S, and V) were investigated by polarized visible Raman and FTIR-spectroscopy to examine the conformational determinants of the amide III band. A spectral decomposition combined with density functional calculations revealed that the amide III band has a multicomponent structure in that three different modes contribute to amide III vibrations. One of them (amide III2) dominates the Raman spectra particularly of the cationic species. Its normal mode displays an in-phase combination of NH and Cα1H in plane bending vibrations, which makes it sensitive to changes of the dihedral angle ψ. Indeed, our Raman data show that amide III2 varies with ψ but remains practically unaffected by variation of φ in the region between −95° and −75°, which is sampled by the investigated AX peptides. Our data support the Lord hypothesis that amide III depends solely on ψ (Lord, R. Appl. Spectrosc. 1977, 31, 187) but specifies to which of the amide III modes this statement applies. Ou...