Conformational analysis nonbonded interactions

In a similar way the potential constant method as described here allows the simultaneous vibrational analysis of systems which differ in other strain factors. Furthermore, conformations and enthalpies (and other properties see Section 6.5. for examples) may be calculated with the same force field. For instance, vibrational, conformational, and energetic properties of cyclopentane, cyclohexane and cyclodecane can be analysed simultaneously with a single common force field, despite the fact that these cycloalkanes involve different distributions of angle and torsional strain, and of nonbonded interactions 8, 17). This is not possible by means of conventional vibrational spectroscopic calculations. 

Results of INDO calculations for staggered and eclipsed CH3COX are shown above and support our analysis. Specifically, a lower energy of the eclipsed conformation can be attributed to pi nonbonded interaction since the total pi overlap population is larger in the conformation relative to the S conformation. 

By following the same arguments as before, we conclude that the conformation will be lower in energy than the Cee conformation. The same analysis can be used to compare the relative energetics of the and Cx conformations. In conclusion, we can say that the C conformation will be favored over the Cee and Cx conformations due to a larger pi attractive nonbonded interaction which obtains in the 6 pi electron aromatic geometry of the conformation. 

One may gather from the preceding discussion that the application of conformational analysis to the determination of the geometry of these transition states is in an early stage of development. However further studies coupled with refinements in the theory of interaction between nonbonded groups can be expected to lead to a clearer picture of these important structures. 

The configurational assignment can be made indirectly by the analysis of Cotton effects due to enone helicity. Thus, while in the parent molecule 1 the enone chromophore is slightly twisted in the sense opposite to that shown in Figure 7 (ra > 0), nonbonded interactions further stabilize the half-chair conformer with > Oof the a-methyl derivative 2a, while an inverted half-chair conformer (w < 0) is preferred for the /i-methyl derivative 2b55. 

The polydihalophosphazenes are examined by conformational analysis using nonbonding intramolecular interactions based on a 6-12 Lennard-Jones potential and a Coulombic term. The results provide an insight into the reasons for the low glass transition temperatures, the high chain flexibilities, and the conformational preferences of these molecules. Minimum energy conformations are discussed. 

The conformational analysis of oxepane conducted within the MM2 and MM3 force fields shows a preference for the twist-chair conformation, which can be explained based on nonbonding interactions between hydrogen atoms <1994JST247>. 

It is becoming apparent that nonbonding interactions play a greater role than previously appreciated in determining the structures of both main-group and transition-metal metallocenes. Molecular mechanics are particularly efficient in describing such interactions and can be readily applied to much larger systems than traditional MO methods. The analysis of structural conformations of bis(cyclopentadienyl) compounds used in stereoselective synthesis can be expected to benefit from wider applications of MM methods. 

The series of linear polystannanes represented by compounds 31, 33, 35, 48, and 49 have also been the subject of spectroscopic analysis. In this case, a similar trend is observed, although the magnitude of the red-shift per tin atom is less than that observed for the previous series (Fig. 6). This discrepency between the two series of linear polystannanes is likely to be a result of the strong nonbonded interactions in the former (i.e., 39, 40, 50, and 51), which severely restrict conformational mobility... 

Intramolecular nonbonding interactions 3.13.3.5 Application of conformational analysis... 

Tsuzuki, S., Uchimaru, T., Tanabe, K., and Hirano, T. (1993) Conformational analysis of 1,2-dimethoxyethane by ab initio molecular orbital and molecular mechanics calculations stabilization of the TGG rotamer by the 1,5 CH3/O nonbonding attractive interaction, J. Phys. Chem. 97, 1346-1350. 

Bruno I J, J C Cole, J P M Lommerse, R S Rowland, R Taylor and M L Verdonk 1997. Isostar A Library of Information about Nonbonded Interactions. Journal of Computer-Aided Molecular Design 11 525-53I. Chang G, W C Guida and W C Still 1989. An Internal Coordinate Monte Carlo Method for Searching Conformational Space Journal of the American Chemical Scociefi/111 4379-4386 Chatfield C and A J Collins 1980. Introduction to Multivariate Analysis. London, Chapman Hall Chung C-W, R M Cooke, A E I Proudfoot and T N C Wells 1995 The Three-dimensional Structure of RANTES Biochemistry 34 9307-9314... 

The study of the conformations of cyclic sugars was developed more fully by Reeves in a series of papers, beginning in 1949, dealing with the formation of complexes of sugars and their derivatives in cuprammonia solution. Reeves was able to provide experimental evidence to indicate that some pyranoid sugars indeed adopt chair conformations in solution, and that, in such cases, one chair form usually appeared to preponderate over the other. Boat or skew conformations were considered possible if the nonbonded interactions between the substituents in the chair conformation became too large. " Reeves s investigations have formed the basis of much subsequent work in the conformational analysis of cyclic carbohydrate... 

The reader who is familiar with qualitative MO theory will have no difficulty recognizing the ominous forebodings of the analysis presented above for we have hardly ever incorporated nonbonded interaction effects in qualitative MO models except when discussing problems such as the rotational barrier of ethane, where consideration of nonbonded interaction is actually inevitable since the staggered and eclipsed conformers are differentiable only if vicinal nonbonded interaction is assumed to be nonzero. 

Structural phase diagram for a flexible, elastic polymer with 90 monomers, parametrized by temperature T and nonbonded Interaction range 8. The transition lines (solid lines) were obtained by inflection-point microcanonical analysis. The crossover between collapse transition and nucleation cross is enlarged in the inset. The dashed vertical line separates solid phases that cannot be discriminated thermodynamically. The bottom figure shows for T = 02 the (canonical) probability that a conformation in these solid phases contains nic icosahedral cores, thereby separating fee or decahedral crystalline structures with Oje = 0 from Mackay icosahedral shapes (Ok > 1). From [136]. 

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