Dihedral angle

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

Prediction of methyl-side chain dynamics in proteins.

Abstract: A simple analytical model is presented for the prediction of methyl-side chain dynamics in comparison with S2 order parameters obtained by NMR relaxation spectroscopy. The model, which is an extension of the local contact model for backbone order parameter prediction, uses a static 3D protein structure as input. It expresses the methyl-group S2 order parameters as a function of local contacts of the methyl carbon with respect to the neighboring atoms in combination with the number of consecutive mobile dihedral angles between the methyl group and the protein backbone. For six out of seven proteins the prediction results are good when compared with experimentally determined methyl-group S2 values with an average correlation coefficient \(\bar r\)=0.65±0.14. For the unusually rigid cytochrome c2 no significant correlation between prediction and experiment is found. The presented model provides independent support for the reliability of current side-chain relaxation methods along with their interpretation by the model-free formalism.

Onset of 310-Helical Secondary Structure in Aib Oligopeptides Probed by Coherent 2D IR Spectroscopy

Abstract: We have investigated the onset of the secondary structure and the evolution of two-dimensional infrared (2D IR) spectral patterns as a function of chain length with a study of 310-helical peptides. The results show that 2D IR is highly sensitive to peptide conformation, disorder, and size. An extensive set of 2D IR spectra of Cα-methylated homopeptides, Z-(Aib)n-OtBu (n = 3, 5, 8, and 10), in CDCl3 was measured in the amide-I region. The 2D spectral patterns of the tripeptide are quite different from those of the longer peptides. The spectral signatures begin to converge at the pentapeptide and become almost the same for the octa- and decapeptide. Simulations employing a vibrational exciton model were performed, with the local mode frequency shifts estimated from the intramolecular hydrogen bond electrostatic energies. The 2D spectra are well simulated using dihedral angle distributions around the average values (ϕ, ψ) ≈ (−57°, −31°) with a width of ∼21°. The simulated site-dependent amide-I local mode fr...

Effects of boron doping on the structural and optoelectronic properties of 9,10-diarylanthracenes

Abstract: Key structural and optoelectronic properties of 9,10-dihydro-9,10-diboraanthracene (DBA) derivatives carrying mesityl (2a), 2-methylnaphthyl- (2b) and 9-phenyl-2,7-di-tert-butylanthryl (2c) substituents at the boron atoms have systematically been compared with the properties of their all-carbon congeners 4a–c. The experimental investigations have been augmented by quantum-chemical calculations. Steric repulsion leads to large dihedral angles between the aryl substituents and the DBA (2a–c) or anthrylene (4a–c) cores; as a result, the B–C bonds of 2a–c are kinetically shielded from hydrolysis and oxidative degradation. Lithium metal reduces the mesityl derivative 2a to the inverse sandwich complexes [Li(OR2)n]2[2a] (X-ray crystallography; OR2 = THF, n = 2; Et2O, n = 1). In line with the nodal structures of the LUMO of 2a/HOMO of [Li(THF)2]2[2a], the C–C bond lengths of the anionic fragment [2a]2− show characteristic differences to those of 2a and come close to the C–C bond lengths of the isoelectronic species 4a. X-ray crystallography on anti-2b × 2 C6H6 and anti-4b × 2 C6H6 reveals an essentially identical packing of the main molecules. The benzene solvate molecules, however, interact in a very different manner with anti-2b or anti-4b, which can be traced down to subtle disparities between the electron density distributions of the two compounds. 2a–c undergo a photoinduced aryl-to-DBA charge transfer; the back electron transfer results in blue (2a), green (2b) and red (2c) emission, albeit with low quantum yields. 4a–c are characterised by a local π–π* photoexcitation of the central 9,10-anthrylene fragments and corresponding blue emission. Each of the compounds 2a–c gives rise to two reversible DBA-centred one-electron transitions in the cyclic voltammogram.

Couplings into Methylene Groups: a New Nuclear Magnetic Resonance Approach to Stereochemistry

Abstract: A method of assigning dihedral angles to hydrogens adjacent to a methylene function by using computer analyzed n.m.r. coupling constants in a modified Karplus equation is presented. The "Dihedral Angle Estimation by the Ratio Method" (DAERM) is based on the assumption that, although the magnitudes of the Karplus constants, k1 and k2, vary, the ratio of k1 to k2 is a constant. Dihedral angles computed in this way seem not to be influenced by the effects of ring strain and substituent electronegativity. The conformational preferences of several four- to six-membered ring Systems, some containing oxygen and sulfur atoms, have been investigated by this method. Molecular features such as ring puckering and flattening are indicated by DAERM as are some subtle electrostatic influences.