Dihedral angle

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

Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum.

Abstract: A three-dimensional solution structure for the self-complementary dodecanucleotide [d-(GCCTGATCAGGC)]2 has been determined by distance geometry with further refinements being performed after back-calculation of the NOESY spectrum. This DNA dodecamer contains the hexamer [d(TGATCA)]2 recognized and cut by the restriction endonuclease BclI, and its structure was determined in hopes of obtaining a better understanding of the sequence-specific interactions which occur between proteins and DNA. Preliminary examination of the structure indicates the structure is underwound with respect to idealized B-form DNA though some of the local structural parameters (glycosyl torsion angle and pseudorotation angle) suggest a B-family type of structure is present. This research demonstrates the requirements (resonance assignments, interproton distance measurements, distance geometry calculations, and NOESY spectra back-calculation) to generate experimentally self-consistent solution structures for short DNA sequences.

Molecular orbital calculations on the conformation of nucleic acids and their constituents

Abstract: The conformational properties of the furanose ring of purine- and pyrimidine-β-nucleosides and-nucleotides are studied quantum-mechanically with the help of the PCILO method, using the pseudorotational concept. The computations point to the existence of two stable conformational zones centered around the C(3′)-endo and C(2′)-endo conformations which in the isolated furanose ring are separated by barriers of the order of 4 kcal/mole. In nucleosides one of the barriers (the one running through the O(1′)-exo-C(2′)-exo path) becomes very high. A detailed study is made of the relation between the phase angle of pseudorotation, P, and the torsion angle about the glycosyl bond, χ CN. A very satisfactory agreement with the available experimental data is observed.

van der Waals–Lifshitz forces in lyotropic polypeptide liquid crystals

Abstract: The McLachlan susceptibility theory is used to calculate the van der Waals–Lifshitz forces betwen two chiral, rodlike dielectric particles embedded in an isotropic dielectric medium. The resulting interparticle potential contains an asymmetric term in φ, the mutual dihedral angle between the major axes of the particles. The variations of the free energy of interaction with respect to the mutual orientation of the particles and the relative magnitudes of the medium and particle dielectric permittivities can explain the origin and unusual solvent dependence of the cholesteric twist exhibited by lyotropic polypeptide liquid crystals.

Modulation of sensitivity to mechanical stimulus in mechanofluorochromic properties by altering substituent positions in solid-state emissive diiodo boron diiminates

Abstract: This manuscript describes modulation of the sensitivity to mechanical forces in diiodo boron diiminates by altering the substituent position of iodine groups. A series of modified complexes were prepared, and their solid-state luminescence properties based on aggregation and crystallization-induced emission mechanisms were observed. By adding mechanical forces to the crystalline samples of each complex, changes in the optical properties were monitored. Interestingly, peak shift degree of the emission bands was varied. From X-ray crystallographic analyses, it was shown that molecular distributions in the crystal packing significantly depended on the positions of the iodine groups in the complex. In particular, it was found that by increasing the dihedral angles between the phenyl substituents and the boron-containing six-membered ring, a larger peak shift width was obtained. Finally, the most planar conformation of the complexes was detected from the complex insensitive to mechanical forces. It was suggested that intramolecular electronic conjugation in the initial crystalline state could be responsible for the degree of peak shift. This is the first example, to the best of our knowledge, to offer regulation of sensitivity to mechanical forces in a series of structural isomers with the same chemical component.