Dihedral angle distributions

Detailed calculations on the condensed phases of biphenyl have been carried out by the variable shape isothermal-isobaric ensemble Monte Carlo method. The study employs the Williams and the Kitaigorodskii intermolecular potentials with several intramolecular potentials available from the literature. Thermodynamic and structural properties including the dihedral angle distributions for the solid phase at 300 K and 110 K are reported, in addition to those in the liquid phase. In order to get the correct structure it is necessary to carry out calculations in the isothermal-isobaric ensemble. Overall, the Williams model for the intermolecular potential and Williams and Haigh model for the intramolecular potential yield the most satisfactory results. In contrast to the results reported recently by Baranyai and Welberry, the dihedral angle distribution in the solid state is monomodal or weakly bimodal. There are interesting correlations between the molecular planarity, the density and the intermolecular interaction. 

Dihedral angle distribution functions for the various models are shown in figure 5. Models using the Bartell and BHS intramolecular potential functions show a clear bimodal distribution. The former shows a zero intensity near 9 = 0°. The latter shows a small non-zero intensity near 9 = 0°. The Haigh potential shows a distribution which may be described as lying somewhere between bimodal and monomodal. Both the WW and KK models show a monomodal function with a maximum near 9 = 0°, suggesting the most probable conformation is the planar conformation in the room temperature solid phase. The RDFs for these two models show well defined features which seem to be correlated with the monomodal S(9) exhibited by them. 

Figure 5. Dihedral angle distribution function for solid biphenyl at 300 K for models containing the intermolecular potential given by (a) Williams and Cox, and by (b) Kitaigorodskii.

Figure 8. Dihedral angle distribution function for liquid biphenyl at 400 K for the WW and...

Fig. 12.2. Population density map for the dihedral angle distributions obtained from MD simulations for trehalose (a) and neotrehalose (b) in aqueous solution...

Side-chain prediction methods can be classified in terms of how they treat side-chain dihedral angles (rotamer library, grid, or continuous dihedral angle distribution), potential energy function used to evaluate proposed conformations, and search strategy. These factors are summarized in Table... 

The distribution of dihedral angles in hexacycles is also analyzed. Using dihedral angle distribution it is possible to define some known hexacycles ... 

The dihedral angles distribution for collagen and ubiquitin shows three maxima in ubiquitin water shell and a wide and not sharp maxima in collagen shell. These maxima are the same that in boat hexacycle, so it seems to be ice-like. Ubiquitin water shell seems to be more iee-like than collagen water shell. 

J.M. Schmidt, Conformational equflibria in polypeptides. II. Dihedral-angle distribution in antamanide based on three-bond coupling information, J. Magn. Reson. 124 (1997) 310-322. 

It is interesting to look at the dihedral angles for the alkyl chains in 5CB and CCH5. In the nematic phase at 350 K, Wilson and Allen found that almost 50% of molecules have the fully extended all-tran (ttt) conformation. However, dihedral angle distributions are temperature-dependent. The observed dihedral angle distribution 5(0) can be written in terms of an effective torsional potential eff( ) (conformational free energy) [22, 28] ... 

When working with iterative structural coarse-graining techniques, we limit ourselves to potentials and distribution functions that depend only on a single coordinate like radial distribution functions (RDFs), bond distance, bond angle, or dihedral angle distributions. These distribution functions are convenient for describing the structure of polymers, and they enable the use of the to reproduce the structure. As this procedure is iterative,... 

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