Dihedral angle

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

Conformation-dependent dipoles of liquid crystal molecules and fragments from first principles

Abstract: We determine accurate molecular dipole moments for mesogenic fragments and liquid crystal molecules from quantum mechanical computer simulations adapted from large-scale electronic structure calculations on periodic solids. We employ density functional theory and use ab initio pseudopotentials for the interaction between valence electrons and ions and the generalized gradient approximation to account for the many-body effects of exchange and correlation. Periodic boundary conditions are enforced so that the molecular electronic wave function can be expanded in terms of a plane wave basis set. We test our method on several small molecules and then apply it to determine the direction, position and dipole moment magnitude for 4-4' pentyl-cyanobiphenyl (5CB) (and related fragments), phenyl benzoate, and 2-2'difluorobiphenyl. For the latter compound, we parametrize a torsional potential for rotation about the dihedral bond. We perform full structural optimization, and find that the torsional barrier heights for fully relaxed molecular structures are substantially reduced relative to nonoptimized geometries. We then demonstrate the influence of conformation and temperature on the molecular dipole moment. We also find that simple vector addition of dipole moments of fragments provides a good estimate of the total dipole moment of the complete molecule. We compare our results to experiment and to conventional quantum chemistry methods where data is available.

N-Acetylated amino sugars: the dependence of NMR 3J(HNH2)-couplings on conformation, dynamics and solvent

Abstract: N-Acetylated amino sugars are essential components of living organisms, but their dynamic conformational properties are poorly understood due to a lack of suitable experimental methodologies. Nuclear magnetic resonance (NMR) is ideally suited to these conformational studies, but accurate equations relating the conformation of key substituents (e.g., the acetamido group) to NMR observables are unavailable. To address this, density functional theory (DFT) methods have been used to calculate vicinal coupling constants in N-acetylated amino sugars and derive empirical Karplus equations for 3J(HNH2) of N-acetyl-D-glucosamine (GlcNAc) and N-acetyl-D-galactosamine (GalNAc). The fitted Karplus parameters were found to be similar to those previously derived for peptide amide groups, but are consistently larger in magnitude. Local intramolecular interactions had a small effect on the calculated J-couplings and comparison with experimental data suggested that DFT slightly overestimated them. An implicit solvation model consistently lowered the magnitude of the calculated values, improving the agreement with the experimental data. However, an explicit solvent model, while having a small effect, worsened the agreement with experimental data. The largest contributor to experimentally-determined 3J(HNH2)-couplings is proposed to be librations of the amide group, which are well approximated by a Gaussian distribution about a mean dihedral angle. Exemplifying the usefulness of our derived Karplus equations, the libration of the amide group could be estimated in amino sugars from experimental data. The dynamical spread of the acetamido group in free α-GlcNAc, β-GlcNAc and α-GalNAc was estimated to be 32°, 42° and 20°, with corresponding mean dihedral angles of 160°, 180° and 146°, respectively.

Base pair analogs in the gas phase

Abstract: A rotationally resolved electronic spectrum of the gas-phase dimer 2-aminopyridine·2-pyridone, an analog of the adenine·thymine base pair, has been observed and assigned, leading to precise measurements of its moments of inertia and preliminary determinations of its structure. A Watson–Crick configuration results, with N···H—N and N—H···O hydrogen bond lengths of 2.898 and 2.810 A, respectively. The two bases are found not to be coplanar; a dihedral angle of 6.1° between the base planes is also estimated from the measured moments of inertia. Possible chemical and biological implications of these results are discussed.

Improved molecular dynamics simulations for the determination of peptide structures

Abstract: In this article a few methods or modifications proven to be useful in the conformational examination of peptides and related molecules by molecular dynamics are illustrated. The first is the explicit use of organic solvents in the simulations. For many cases such solvents are appropriate since the nmr measurements (or other experimental observations) were carried out in the same solvent. Here, the use of dimethylsulfoxide and chloroform in molecular dynamics is described, with some advantages of the use of these solvents highlighted. A constant allowing for the scaling of the nonbonded interactions of the force field, an idea previously employed in distance geometry and simulated annealing, has been implemented. The usefulness of this method is that when the nonbonded term is turned to zero, atoms can pass through each other, while the connectivity of the molecule is maintained. It will be shown that such simulations, if a sufficient driving force is present (i.e., nuclear Overhauser effects restraints), can produce the correct stereoconfiguration (i.e., chiral center) as well as configurational isomer (i.e., cis/trans isomers). Lastly, a penalty term for coupling constants directly related to the Karplus curve has been plemented into the potential energy force field. The advantages of this method over the commonly used dihedral angle restraining are discussed. In particular, it is shown that with more than one coupling constant about a dihedral angle a great reduction of the allowed conformational space is obtained. © 1993 John Wiley & Sons, Inc.