Potential energy maps, conformational

Figure 4. Conformational potential energy maps for rotation...

Figure 6. Conformational potential energy map from sucrose parameters with hydrogens of intramolecular H-bonds removed...

Figure 2. Potential energy maps of a) GalA(l->2)Rha as a function of the glycosidic dihedrals, b) the same disaccharide with the galacturonic acid acetylated at 02 and 03. The conformation used to build integer helices is indicated.

The concept of conformational Probability Density Map often is improperly associated with that of potential energy map. The potential energy map indeed gives a relatively good image of the probability density map of finding a molecule in a given conformation [53,54]. To determine the conformational chemical physic properties of a molecule, as a function of temperature, statistical methods have to be used. 

An adiabatic potential energy map for sucrose and molecular dynamics simulations applied to the minimum energy conformations indicated by this map have been reported. An anafysis of sucrose, maltose, and lactose by n.m.r. spectroscopy, differential scanning calorimetry (DSC), and x-ray diffraction was aimed at an understanding of molecular behaviour in the ciystals. ... 

Fig. 3. Projections on the (<1>, maps of the CICADA conformational search of the pentasaccharide. The dots indicate the values of all the optimized conformations determined by CICADA at each glycosidic linkange in 8 kcal/mol energy window For comparison, the isocontours, drawn in 1 Kcal/mol steps with an outer limit of 8 kcal/mol, represent the energy level of each disaccharide and calculated with the relaxed grid search approach. Dashed regions represent the locations of the low energy conformation of the pentasaccharide plotted on the potential energy surfaces of the constituting disaccharide segments...

Fig. 15. Conformational map of cyclohexane. The diagram represents a partial qualitative pictorial polar projection of the conformational globe of Pickett and Strauss (106) it may be completed by rotating around 120 and 240°, respectively. Relative potential energies are given (kcal mole-1 force field of ref. 19 reference chair conformation). The lines inside the six-membered rings represent mirror planes (solid) and twofold axes (dotted), respectively.

Fig. 16. Three dimensional conformational map of cyclohexane. The representation is analogous to that of Fig. 15 the third (vertical) coordinate is the potential energy. The given calculated potential energy differences (kcal mole-1) of the minima and transition states are drawn to scale. The interconnecting curves are drawn qualitatively they are merely meant to indicate the absence of intermediate further minima and maxima. See ref. 106 for details of analytical representations of conformational maps of cyclohexane...

A short presentation of the Consistent Force Field is given, with emphasis on parametrization and optimization of energy function parameters. For best possible calculation of structure, potential energy functions with parameter values optimized on both structural and other properties must be used. Results from optimization with the Consistent Force Field on alkanes and ethers are applied to glucose, gentiobiose, maltose and cellobiose. Comparison is made with earlier and with parallel work. The meaning and use of conformational maps is discussed shortly. 

A review of the Journal of Physical Chemistry A, volume 110, issues 6 and 7, reveals that computational chemistry plays a major or supporting role in the majority of papers. Computational tools include use of large Gaussian basis sets and density functional theory, molecular mechanics, and molecular dynamics. There were quantum chemistry studies of complex reaction schemes to create detailed reaction potential energy surfaces/maps, molecular mechanics and molecular dynamics studies of larger chemical systems, and conformational analysis studies. Spectroscopic methods included photoelectron spectroscopy, microwave spectroscopy circular dichroism, IR, UV-vis, EPR, ENDOR, and ENDOR induced EPR. The kinetics papers focused on elucidation of complex mechanisms and potential energy reaction coordinate surfaces. 

Steric information is most easily summarised in a conformational energy map. Such calculations have been made by a number of workers but they require semi-empirical potentials or the effective van der Waals radii which are subject to error and dispute. We have carried out calculations of this sort for polyethylene units using different potentials and find that although the relative energies of the minima vary considerably, their locations are not particularly sensitive to the different potentials. Thus the conformations for which the scattering will be calculated may be restricted to those of low energy without loss of generality. 

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