Conformations, potential energy

Jensen, J.H. Gordon, M.S. The conformational potential energy surface of glycine A... 

The researchers established that the potential energy surface is dependent on the basis set (the description of individual atomic orbitals). Using an ab initio method (6-3IG ), they found eight Cg stationary points for the conformational potential energy surface, including four minima. They also found four minima of Cg symmetry. Both the AMI and PM3 semi-empirical methods found three minima. Only one of these minima corresponded to the 6-3IG conformational potential energy surface. 

Lelj, F., C. Adamo, and V. Barone. 1994. Role of Hartree-Fock exchange in density functional theory. Some aspects of the conformational potential energy surface of glycine in the gas phase. Chem. Phys. Lett. 230, 189. 

Perczel, A., W. Viviani, and I. G. Csizmadia. 1992. Peptide Conformational Potential Energy Surfaces and Their Relevance to Protein Folding in Molecular Aspects of Biotechnology Computational Models and Theories, Bertran, J., ed., Kluwer Academic Publishers, 39-82. 

Viviani, W., J.-L. Rivail, A. Perczel, and I. G. Csizmadia. 1993b. Peptide Models. 3. Conformational Potential Energy Hypersurface of Formyl-L-valinamide. J. Am. Chem. Soc. 115, 8321-8329. 

This section presents X-ray diffraction, dynamic NMR and theoretical data on the conformations of heterocyclic eight-membered rings. Ideally, it would be desirable to know the whole conformational potential energy surface of the ground electronic state of a molecule. In practice, the lowest (and perhaps the second lowest) energy conformation can be more or less characterized, and some conformational energy barriers can be determined and calculated. 

A semiempirical force field is constructed for the calculation of conformational potential energies of unstrained, acyclic, aliphatic aldehydes and ketones, taking solvent effects into consideration. Detailed conformational calculations for fitting and testing the necessary parameters are done. The results are incorporated into a RIS scheme for polylmethyl vinyl ketonels. 

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

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

Butane can exist in an infinite number of conformations (we have chosen to show only the six most significant) but has only three conformers (potential energy minima)— the two synclinal (gauche) conformations and the anti-periplanar conformation. 

Conformation Potential Energy Vibrational Energy °W T Vibrational Entropy (TS) Free Energy AAtot... 

Monosaccharides exist chiefly in the six-membered pyranose form and in the flve-membered furanose form, both of which adopt puckered shapes to minimize eclipsing interactions. These puckered shapes are most commonly described in terms of the shapes of the symmetrical conformations adopted by the analogous hydrocarbons, cyclohexane and cyclopentane [8,9,10,11], but may also be described in terms of puckering parameters [12,13,14]. Minima on the conformational potential energy surface are called conformers. 

Since classical-type calculations cannot intrinsically reproduce such effects as atomic orbital interactions, it is necessary to adjust the conformational potential energy terms to accurately reproduce experimentally observed torsional barrier heights. Harmonic torsional correction functions are incorporated in the repetoire of classical potential energy terms in order to economically satisfy this requirement. These functions may be described in several ways. Sets of parameters may be given to fit a general purpose torsional correction term which includes provisions for describing cis/trans barriers. The general form of this equation is... 

The conformational potential energy of a molecule is, in general, given by ... 

DNA supercoiling provides conformational potential energy for DNA tertiary structure formation such as the development of DNA cruciform structures (Figure 1.77). Supercoiling also leads to the creation of DNA triple helix (DNA triplex) structures, which form when an oligodeoxynucleotide chain, with an appropriately complementary deoxynucleotide residue... 

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