Dihedral angle

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

Crystal and molecular structure of hydrogen peroxide$. A neutron- diffraction study

Abstract: The coordinates and thermal parameters of the O and H atoms in solid H2O2 have been determined by a single‐crystal neutron‐diffraction study. Final values were obtained by least‐squares refinement based on 91 observed intensities of the hk0, hhl, and h0l reflections. The molecular parameters (uncorrected for the effect of thermal motion) are as follows: O–O distance, 1.453±0.007 A; O–H distance, 0.988±0.005 A; O–O–H angle, 102.7±0.3°; dihedral angle between the two O–O–H planes, 90.2±0.6°. Hydrogen bonding occurs with an O–H···O distance of 2.799±0.008 A. The O–H bond distance corrected for thermal motion is 1.008±0.005 A.Comparison of these results with those reported by others from studies of H2O2 vapor and of various crystals containing H2O2 indicates that the dihedral angle is quite sensitive to the environment of the molecule.

Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution.

Abstract: The conformational behavior of the title compounds has been investigated by Hartree–Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed γ turn (γl), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4–0.5 kcal/mol for helical structures and about 2 kcal/mol for γl structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for γl structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 341–350, 2002

The Structure of Alanine Based Tripeptides in Water and Dimethyl Sulfoxide Probed by Vibrational Spectroscopy

Abstract: We have measured the band profile of amide I in the infrared, isotropic, and anisotropic Raman spectra of cationic l-alanyl-d-alanyl-l-alanine, l-lysyl-l-alanine-l-alanine, and l-seryl-l-alanine-l-alanine in D2O. Additionally, we recorded spectra of N-acetyl-l-alanyl-l-alanine in D2O and in DMSO-d6. The respective intensity ratios of the two amide I bands depend on excitonic coupling between the amide I modes of the two peptides. These intensity ratios were obtained from a spectral decomposition and then used to determine the dihedral angles between the peptide groups by means of a recently developed algorithm (Schweitzer-Stenner, Biophys. J., 83, 83, 523, 2002). The validity of the obtained structures was checked by measuring the vibrational circular dichroism of the amide I bands. l-Lysyl-l-alanyl-l-alanine, l-seryl-l-alanyl-l-alanine, and acetyl-l-alanyl-l-alanine adopt structures similar to that observed for l-alanyl-l-alanyl-l-alanine. This suggests that the N-terminal residues do not significantly i...

Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c.

Abstract: A new approach to NMR solution structure refinement is introduced that uses paramagnetic effects on nuclear chemical shifts as constraints in energy minimization or molecular dynamics calculations. Chemical shift differences between oxidized and reduced forms of horse cytochrome c for more than 300 protons were used as constraints to refine the structure of the wild-type protein in solution and to define the structural changes induced by a Leu 94 to Val mutation. A single round of constrained minimization, using the crystal structure as the starting point, converged to a low-energy structure with an RMS deviation between calculated and observed pseudo-contact shifts of 0.045 ppm, 7.5-fold lower than the starting structure. At the same time, the procedure provided stereospecific assignments for more than 45 pairs of methylene protons and methyl groups. Structural changes caused by the mutation were determined to a precision of better than 0.3 A. Structure determination based on dipolar paramagnetic (pseudocontact) shifts is applicable to molecules containing anisotropic paramagnetic centers with short electronic relaxation times, including numerous naturally occurring metalloproteins, as well as proteins or nucleic acids to which a paramagnetic metal ion or ligand may be attached. The long range of paramagnetic shift effects (up to 20 A from the iron in the case of cytochrome c) provides global structural constraints, which, in conjunction with conventional NMR distance and dihedral angle constraints, will enhance the precision of NMR solution structure determination.