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Dihedral angle

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


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Journal ArticleDOI
16 Feb 2004
TL;DR: In this paper, the characteristics of the 2D-IR rephasing and non-rephasing, absorptive and dispersive spectra of model helical polypeptides in the amide-I region are examined by simulation in the frequency domain, based on a vibrational exciton Hamiltonian matrix approach.
Abstract: The characteristics of the two-dimensional infrared (2D-IR) rephasing, non-rephasing, absorptive and dispersive spectra of model helical polypeptides in the amide-I region are examined by simulation in the frequency domain, based on a vibrational exciton Hamiltonian matrix approach Analytical models and solutions of the exciton band structure, the density of states, and the allowed IR transitions for the simplest cases are presented and compared with simulations The through space and through bond vibrational anharmonic coupling energies between pair-wise amide units are evaluated by using ab initio density functional theory calculations on glycine di-, tri- and tetrapeptides, and by using the transition charge–transition charge interactions including charge-fluxes A contour diagram at 5° interval of the nearest neighbor coupling energies for the right-handed helices in the region of −25° to −70° for both φ and ψ dihedral angles is provided The static diagonal disorder is introduced into the Hamiltonian diagonal frequency through statistical models and is used to account for localizations of the excitations and the inhomogeneous broadening associated with the conformational fluctuations and local interactions with solvent The role of the anharmonicity in constructing the 2D-IR spectra is described qualitatively, and the manifestations of the given anharmonicity in the 2D-IR spectra under various line broadening conditions are examined The absorptive and dispersive 2D-IR spectra under several experimental polarization conditions have been examined, and spectral features for the 3 10 -and α-helices have been illustrated

88 citations

Journal ArticleDOI
TL;DR: In this paper, the crystal structure of cytidylic acid b, cytidine-3′-phosphate, has been refined by the method of full matrix least squares to an R factor of 0·045, where R is the observed and calculated diffraction amplitudes.

88 citations

Journal ArticleDOI
TL;DR: Damrauer et al. as discussed by the authors investigated the effect of steric bulk on electron delocalization in 4-arylpyridines and showed that the steric effect of the ortho-methyl groups serves to increase the dihedral angle between the pyridyl and phenyl rings of the neutral compounds from ca. 45° to ca. 65° and 90° in the mono-and dimethylated compounds, respectively.
Abstract: The effect of steric bulk on electron delocalization in 4-arylpyridines has been studied by computational methods. Ab initio (HF, UHF, ROHF, MP2, UMP2, and ROMP2) as well as density functional theory (USVWN and UB-LYP) approaches were applied to a series of molecules and their corresponding anions. These molecules are put forth as models for the ground and MLCT excited states of three polypyridyl ligands that were the subject of a recent report on the effects of sterics and delocalization on the photophysics of several Ru II complexes (Damrauer, et al. J. Am. Chem. Soc.1997, 119, 8253). The present study finds that, in the series 4-phenylpyridine, 4-(o-tolyl)pyridine, and 4-(2,6-dimethylphenyl)pyridine, the steric effect of the ortho-methyl groups serves to increase the dihedral angle between the pyridyl and phenyl rings of the neutral compounds from ca. 45° in the case of 4-phenylpyridine to ca. 65° and 90° in the mono- and dimethylated compounds, respectively. These results are generally consistent with the single-crystal X-ray structures of the three corresponding bipyridines, also reported herein. Upon one-electron reduction, calculations on all three model ligands reveal a preference for a coplanar structure, with the optimized geometries reflecting a balance between an energetic stabilization gained via conjugation in the planar form and unfavorable steric interactions between the methyl group(s) of the 4-aryl substituent and the pyridyl protons ortho to the central C-C bond. Calculated dihedral angles were 0°,25°, and45° for 4-phenyl-, 4-(o-tolyl)-, and 4-(2,6dimethyl)pyridine, respectively. Finally, a simulation of the Franck -Condon state evolution of MLCT states of molecules containing the bipyridyl analogues of the three models was carried out by computing singlepoint energies of each compound as its monoanion in the optimized neutral geometry. Comparison of these energies with those of the fully optimized anions revealed effective reorganization energies of 4 -7 kcal/mol for 4-phenylpyridine, 4-7 kcal/mol for 4-(o-tolyl)pyridine, and ca. 6 kcal/mol for 4-(2,6-dimethylphenyl)pyridine. The implications of these results as they pertain to ultrafast spectroscopic studies of MLCT excitedstate evolution in the corresponding Ru II bipyridyl complexes are discussed.

87 citations

Journal ArticleDOI
TL;DR: In this article, the parameters which affect the strength and sign of the magnetic superexchange interaction via non-bonding contacts between bromide ions are described and a system for describing the topology of the interaction between tetrahedra is proposed.

87 citations

Journal ArticleDOI
TL;DR: The use of 8-bromodeoxyguanosine (8-Br-dG) as a modification that is directly sensitive to a dihedral angle should prove useful as a chemical probe for the conformation about glycosidic bonds in unusual nucleic acid structures.
Abstract: Chemical modifications are powerful tools to probe nucleic acid structure and protein-nucleic acid interactions. Nucleic acids can be modified either randomly by a variety of chemical reagents or site-specifically with synthetic base analog substitutions. We report here the use of 8-bromodeoxyguanosine (8-Br-dG) as a modification that is directly sensitive to a dihedral angle. 8-Br-dG should prove useful as a chemical probe for the conformation about glycosidic bonds in unusual nucleic acid structures.

87 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
2023203
2022473
2021160
2020195
2019193
2018216