Comparison of conformational energies

Gundertofte, K., Liljefors, T., Norrby, P.-O., Pettersson, I. A comparison of conformational energies calculated by several molecular mechanics methods. 

In this section we provide a short comparison of conformational energies for a set of nitrogen-containing molecules as obtained by several commonly used molecular mechanics force fields and by experiment. The data, collected in Table 22, were mostly taken from Reference 60 but several were calculated for this work. 

Gundertofte K, Palm J, Pettersson I Stamvik A (1991) A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, ChemX) and semiempirical (AMI and PM3) methods, J Comp Chem, 12 200-208... 

Comparison of Conformational Energies Calculated by Molecular Mechanics (MM2(85), SYBYL 5.1, SYBYL 5.21, and Chem-X) and Semiempirical (AMI and PM3) Methods. 

A Comparison of Conformational Energies Calculated by Several Molecular Mechanics Methods. 

Variations of these releases are implemented in almost every commercial or academic software package, which cannot be fisted in this context. A comprehensive comparison of several force fields focusing the calculation of conformational energies of organic molecules has been published by Pettersson and liljefors [1]. 

Table 3.8. Comparison of Conformational Free-Energy Values for Substituents on Tetrahydropyran, 1,3-Dioxane, and 1,3-Dithiane Rings with Those for Cyclohexane...

One of the common features of the growing number of studies on conformational polymorphs is the utilization of a number of analytical and computational techniques to characterize the systems (e.g. Bauer et al. 2001). The emphasis differs from study to study, as demonstrated below, but these multidisciplinary approaches are to be encouraged and hopefully expanded. Another common feature of these investigations is the nature of the molecules investigated—relatively small molecules, with a limited number of conformational parameters. This allows a more direct comparison of conformational differences and the energies associated with those differences. As our understanding of the phenomenon increases and the computational capabilities to deal with larger systems improve, we can expect that more and more complex systems will be studied. 

Allen, F. H., Harris, S. E. and Taylor, R. (1996). Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques. J. Comput. Aided Mol. Des., 10,247-54. [155]... 

D.A. Rees and P.J.C. Smith, Polysaccharide conformation. Part IX. Monte Carlo calculation of conformational energies for disaccharides and comparison with experiment. J. Chem. Soc., Perkin Trans. II, (1975) 836. 

Molecular Mechanics (MM) Fair to good depends on atom parameterization Energy comparison of conformers and diastereomers Good if augmented parameters for transition metals are used Low Upto thousands of atoms... 

Fig. 53. Comparison between exact electrostatic and approximate descriptions of conformational energy for an aziridine-water associate. Solid, line "exact electrostatic potential — expansion truncated after dipole terms - — after quadrupole terms - -----after octopole terms ------after hexadecapole terms. From Ref. B0>...

Figure 2 Comparison of mean absolute errors (in kcal/mol) for different structural classes of organic compounds obtained in calculations of conformational energy differences by using different commonly used force fields.

Roe, D.R., Okur, A., Wickstrom, L., Hornak, V., Simmerling, C. Secondary stmcture bias in Generalized Born solvent models Comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. J. Phys. Chem. B 2007, 111, 1846-57. 

Comparison of conformational free-energy values for substituents on tetrahydropyran, 1,3-dioxane, and 1,3-dithiane rings with those for cyclohexane... 

A perspective of the minimum energy conformation of the complex is shown in Figure 6. We observe from theoretical studies that the Cu(II) atom prefers a square planar environment. Detailed account of our study and a comparison of conformations of the synthetic molecule glycylglycyl-L-histidine-N-methyl amide with the natural analogue L-aspartyl-L-alanly-L-histidyl-N-methyl amide will be presented elsewhere. 

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