NBO analysis, hybrid density functional theory (B3LYP/6-311+G**) based methods were used to study the anomeric effects (AE), Stereoelectronic interactions, dipole-dipole interactions on the conformational properties of 1-Fluoro-N, N-dimethylmethanamine (1) and phosphorus (2) and arsenic (3) analogues.Moreover, relationships between stability of the anti-conformations of 1-Fluoro-N, N-dimethylme...

It is well known that small molecules (ligands) do not necessarily adopt their lowest potential energy conformations when binding to proteins. Analyses of protein-bound ligand crystal structures have reportedly shown that many of them do not even adopt the conformations at local minima of their potential energy surfaces (local minimum conformations). The results of these analyses raise a concer...

Preview You learned in the Chapter 1 that all organic molecules have carbon skeletons. These carbon skeletons show great diversity in the ways that C atoms bond to each other, and in their three-dimensional shapes. Alkanes and cycloalkanes consist entirely of carbon skeletons bonded to H atoms since they have no functional groups. As a result, they serve as a basis for understanding the structu...

We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic expressions leading to the spatial configuration of a family of solutions representing distortions that interpolate between the circular form of DNA and a figur...

High-resolution ion mobility measurements and molecular dynamics simulations have been used to probe the conformations of protonated polyglycine and polyalanine (GlynH 1 and AlanH , n 5 3–20) in the gas phase. The measured collision integrals for both the polyglycine and the polyalanine peptides are consistent with a self-solvated globule conformation, where the peptide chain wraps around and s...

The geometries and energies of the conformers of oxocane, the isomeric diand trioxocanes, and of 1,3,5,7-tetroxocane were calculated by molecular mechanics. A boat-chair conformation was preferred by all molecules. From the preference of oxygen in the boat-chair conformations of oxocane (position 3 over 1 over 4) the preferred boat-chair form of all other oxocanes can be derived. The results ar...