Torsion angle fluctuations

Six homo- and heteronuclear Karplus relationships of vicinal couplings related to the

torsional angle have been analysed with MD/DFT calculations and model peptides by Case et It appeared that the average coupling values to the experimental ones. In addition, the authors have suggested that the / related Vnn coupling does not obey the usual Karplus type relationship. 

Photinos, D. J., Samulski, E. T., and Terzis, A. F, Conformations of n-hexane from proton dipolar couplings the role of torsion angle fluctuations, J. Phys. Chem., 96, 6979-6981... 

It is likely that local motions of the polymer chain are also important to penetrant diffusion. Removal of the torsional potential in polyethylene considerably increases the chain mobility and gave an increase of about a factor of two in the diffusion coefficient of 02. Conversely, decreasing the magnitude of the torsion angle fluctuations in the polyethylene model PE IV drastically reduces the diffusion coefficient of methane. ... 

Transitions of Leu. Another way to appreciate the fluctuations the molecule undergoes, and the difference between a dynamic and static representation of conformation is by examining the conformational states of the individual torsion angles in the molecule. The values of and any other torsion angle can be plotted as a function of time along the dynamic trajectory in order to observe their fluctuations and transitions. The example of Leu is given in Figure 4. 

Figure 4. A history of the fluctuations in torsion angles 0 and of the leucine residue as a function of the time elapsed during the molecular dynamics simulation of GnRH.

A theoretical analysis of the possible conformations of polylp-phenylene terephthalate) (PPTA) and polylp-phenylene isophthalate) (PPIA) is performed on the basis of molecular mechanics and molecular dynamics trajectories. The dependence of the persistence length on the fluctuations of the torsional angle around the ester bond is discussed for PPTA in the frame of the RIS model. Realistic parameters like bond length and bond angles are provided by computer simulations using MD. 

In considering the overall conformations of carbohydrate chains it is useful to start by distinguishing between (1) ordered conformations, in which the values of the torsion angles are fixed by cooperative interactions between residues and (2) disordered conformations, in which continuous fluctuation occurs. 

Figure 10. The Allan variances of the individual energy fluctuations of (a) bond energy Vr, (b) bending energy V (c) torsional angle energy Vtn, and (d) nonbonded vdW interaction energy Vr at T = 0.2,0.4,0.72, and 2.0 for the original BLN model.

The collapsing of the torsional angle energy fluctuations into these two families implies that, irrespective of the kinds of beads comprising the... 

Although the Allan variance of the individual nonbonded vdW interaction energy VRi t) fluctuations are not shown, the collapsing of VRi(t) into some small set of families at the transition temperature, as in the analyses of torsional angle energy fluctuation, was not found for either the BLN and Go-like BLN models. 

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