Dihedral angle

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

Molecular dynamics with internal coordinate constraints

Abstract: The method of Ryckaert, Ciccotti, and Berendsen [J. Comp. Phys. 23, 327 (1977)] for integrating the Cartesian equations of motion of a system with holonomic constraints, has been extended to allow the independent constraint of arbitrary internal coordinates. To illustrate this new methodology, and to investigate the effects of dihedral angle constraints on the equilibrium and dynamical properties of macromolecules, we have carried out parallel sets of molecular dynamics simulations and normal mode analyses of a small dipeptide: one without constraints, and one with a single backbone dihedral angle constrained. We find that the averages and the fluctuations of the energies, and of the internal degrees of freedom are not significantly modified by the constraint. However, in the region between 100 and 1400 cm−1 of the normal mode spectrum, the constraint shifts the frequencies of the modes, and modifies their contributions to the spectra of the internal coordinates. Except for the lowest frequency torsional ...

Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L.

Abstract: Traditional protein force fields use one set of parameters for most of the 20 amino acids (AAs), allowing transferability of the parameters. However, a significant shortcoming is the difficulty to fit the Ramachandran plots of all AA residues simultaneously, affecting the accuracy of the force field. In this Feature Article, we report a new strategy for protein force field parametrization. Backbone and side-chain conformational distributions of all 20 AA residues obtained from protein coil library were used as the target data. The dihedral angle (torsion) potentials and some local nonbonded (1-4/1-5/1-6) interactions in OPLS-AA/L force field were modified such that the target data can be excellently reproduced by molecular dynamics simulations of dipeptides (blocked AAs) in explicit water, resulting in a new force field with AA-specific parameters, RSFF1. An efficient free energy decomposition approach was developed to separate the corrections on ϕ and ψ from the two-dimensional Ramachandran plots. RSFF1 ...

Molecular structure and puckering potential function of cyclobutane studied by gas electron diffraction and infrared spectroscopy

Abstract: The electron diffraction intensity of cyclobutane was measured and analyzed conjointly with the rotational constant, B0=0.355 82(11) cm−1, determined by an analysis of FTIR spectra of the ν14 (CH2 scissoring, B1g) and ν16 (CH2 rocking, A2u) bands. The rz structure was determined to be rz (C–C)=1.552±0.001 A, rz (C–H)=1.093±0.003 A, αz (∠HCH)=106.4±1.3°, and the ring dihedral angle, θz =27.9±1.6°; the rg distances of the C–C and C–H bonds are 1.554±0.001 and 1.109±0.003 A, respectively. The uncertainties represent estimated limits of error. The rocking angle βz between the bisectors of the adjacent H–C–H and C–C–C angles was found to be 6.2±1.2°, the axial C–H bonds in the 1,3 positions being tilted towards each other. The coefficient of coupling of the ring‐puckering and CH2‐rocking motions was estimated to be βz/θz =0.22±0.05. The combination and difference sideband structures appearing in the ν14 band due to the puckering mode ν6 were analyzed. The puckering energy levels thus obtained were consistent w...

Toward understanding the nature of internal rotation barriers with a new energy partition scheme: ethane and n-butane.

Abstract: On the basis of an alternative energy partition scheme where density-based quantification of the steric effect was proposed [Liu, S. B. J. Chem. Phys. 2007, 126, 244103], the origin of the internal rotation barrier between the eclipsed and staggered conformers of ethane and n-butane is systematically investigated in this work. Within the new scheme, the total electronic energy is decomposed into three independent components, steric, electrostatic, and fermionic quantum. The steric energy defined in this way is repulsive, exclusive, and extensive and intrinsically linked to Bader's atoms in molecules approach. Two kinds of differences, adiabatic (with optimal structure) and vertical (with fixed geometry), are considered for the molecules in this work. We find that in the adiabatic case the eclipsed conformer possesses a larger steric repulsion than the staggered conformer for both molecules, but in the vertical cases the staggered conformer retains a larger steric repulsion. For ethane, a linear relationship between the total energy difference and the fermionic quantum energy difference is discovered. This linear relationship, however, does not hold for n-butane, whose behaviors in energy component differences are found to be more complicated. The impact of basis set and density functional choices on energy components from the new energy partition scheme has been investigated, as has its comparison with another definition of the steric effect in the literature in terms of the natural bond orbital analysis through the Pauli Exclusion Principle. In addition, profiles of conceptual density functional theory reactivity indices as a function of dihedral angle changes have been examined. Put together, these results suggest that the new energy partition scheme provides insights from a different perspective of internal rotation barriers.