Dihedral angle

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

An ab initio investigation of the torsional potential function of n-butane

Abstract: The rotational potential function of n-butane has been calculated as a function of the dihedral angle of the skeletal carbon–carbon bonds using a 4–31 Gaussian basis set. Relaxation of the central C—C bond by up to 0.03 A and of the CCC angles by 2.8° accompanies the rotation. Apart from a vertical displacement in energy, the potential curve, when all coordinates are released, is closely similar to that obtained when the HCC angles are held to tetrahedral values and the C—H bond lengths are fixed at as much as 0.1 A greater than their equilibrium values. This suggests that the potential curves of more complex systems may be adequately reproduced in this simplifying approximation of not releasing the hydrogen coordinates. The calculated potential curves reproduce the experimental anti to gauche energy differences as well as the optimum gauche dihedral angle of 67°. Significant differences exist between the ab initio curve and the frequently used Scott and Scheraga curves. In particular the energy of the eclipsed configuration over the anti form is reduced from 45 to 27 kJ mol–1.

Identification of secondary structures in globular proteins--a new algorithm.

Abstract: A new algorithm has been developed for identifying helices, extended structures, and bends from the positions of the alpha-carbon atoms using the virtual bond approach. The parameters used are two virtual bond angles (delta 1 and delta 2), the virtual dihedral angle (theta), and the distance (D) between the terminal alpha-carbon atoms of the tripeptide. The criteria for classification have been worked out by model building as well as from proteins whose complete secondary structures are known. These criteria are as follows: (i) magnitude of theta less than or equal to 60 degrees and (delta 1 + delta 2) less than or equal to 230 degrees for a bend, (ii) for a helix, successive thetas should not differ by more than 30 degrees, and (iii) for an extended structure, the cumulative deviation of the above parameters should not vary by more than 20% from the ideal extended chain. The method developed has been applied successfully to three proteins wherein the coordinates of alpha-carbon atoms alone are known and a complete mapping of the secondary structures has now been obtained. One interesting observation is that the percentage of residues not taking part in helices, extended structures, and bends is very small--of the order of 4%.

A theoretical model of phospholipid dynamics in membranes

Abstract: Static and dynamic properties related to the internal configurational motions have been calculated for the alkyl chains of phospholipid molecules in a membrane environment in the liquid crystal phase The calculations have been performed for the chain 1 of 1,2‐dipalmitoyl 3‐sn‐phosphatidylcholine (DPPC), a typical constituent of phospholipid membranes Under the assumption of fixed bond lengths and bond angles, the internal dynamics of the chain is described in terms of 15 dihedral angles The time evolution of the angular variables is assumed to be diffusional in character, and a master equation for transitions among the stable conformers is constructed from the energetics and hydrodynamics of the chain This method is an extension to the time domain of the rotational isomeric state (RIS) approximation, which has been widely used to compute static properties of the chains After calculation of the suitable correlation functions, effective rate constants relevant for spectroscopic and kinetic observables have been computed, and the results have been compared with those obtained by recent Brownian dynamics (BD) calculations The position dependence of the rate constants along the chain has been examined with special reference to understanding the effects resulting from cooperativity in the conformational transitions The overall spinning and tumbling of the chain has also been described by a diffusive model The calculated spectral densities for the composite motional process have been used to rationalize the behavior of the relaxation times T1, T2, and T1ρ measured in deuterium nuclear magnetic resonance (NMR) experiments

The internal coordinate path Hamiltonian; application to methanol and malonaldehyde

Abstract: The internal coordinate path Hamiltonian is introduced for the study of the vibrations of molecules which have one large amplitude motion. The Hamiltonian is represented in terms of a one path coordinate and 3N—7 normal coordinates. The variational method is used to solve the Schrodinger equation. The molecules studied are methanol and malonaldehyde. For methanol the internal coordinate is a dihedral angle, for malonaldehyde it is the difference in the distances between the migrating hydrogen and the neighbouring oxygen atoms. For methanol there is little coupling between the path and the normal coordinates and so no complications were encountered in the calculations which used harmonic surfaces generated by density functional and M⊘ller—Plesset theory. Fundamental frequencies were predicted. Malonaldehyde is a different story. There is substantial coupling between the path coordinate and several of the normal coordinates. This introduces many complications: an anharmonic surface is essential and large va...