Conformational isomerism

About: Conformational isomerism is a research topic. Over the lifetime, 11563 publications have been published within this topic receiving 199312 citations.

IR spectroscopy and theoretical vibrational calculation of the melamine molecule

Abstract: We have observed the IR spectra of the melamine molecule and its deuteriated counterpart in the gas phase at ca. 150°C and in a solid argon-matrix at 10 K. The assignment of the vibrations of melamine has been facilitated by the calculated thirty nine normal modes using several abinitio and density functional methods. By scaling the calculated vibrational frequencies, the theoretical computations have been demonstrated to be in good agreement with the experimental observations. The optimized equilibrium structure of melamine has been shown to be a planar but distorted-hexagonal triazine ring with three pyramidal amino groups, which result in different conformers. This has been supported by the comparison between the observed and the calculated spectra for non-planar conformers 1 and 2 vs. the planar D3h structure 3. In view of the small energy differences between the calculated conformers 1 and 2 and the ‘transition state’ 3 (corresponding to a third-order saddle point on the potential-energy hypersurface), the melamine molecule has a flat potential-energy hypersurface near the equilibrium structures and the conformers can rapidly rearrange.

Global search for minimum energy (H2O)n clusters, n = 3-5.

Abstract: The Gaussian-3 (G3) model chemistry method has been used to calculate the relative deltaG(o) values for all possible conformers of neutral clusters of water, (H2O)n, where n = 3-5. A complete 12-fold conformational search around each hydrogen bond produced 144, 1728, and 20,736 initial starting structures of the water trimer, tetramer, and pentamer. These structures were optimized with PM3, followed by HF/6-31G* optimization, and then with the G3 model chemistry. Only two trimers are present on the G3 potential energy hypersurface. We identified 5 tetramers and 10 pentamers on the potential energy and free-energy hypersurfaces at 298 K. None of these 17 structures were linear; all linear starting models folded into cyclic or three-dimensional structures. The cyclic pentamer is the most stable isomer at 298 K. On the basis of this and previous studies, we expect the cyclic tetramers and pentamers to be the most significant cyclic water clusters in the atmosphere.

Conformational Behavior of Serine: An Experimental Matrix-Isolation FT-IR and Theoretical DFT(B3LYP)/6-31++G** Study

Abstract: The conformational equilibria of neutral serine are studied by experimental matrix-isolation Fourier transform infrared spectroscopy in combination with density functional theory (DFT) calculations. The geometries and energies of the low-energy conformers of serine were optimized using the DFT(B3LYP)/6-31++G** method. In addition, we calculated the infrared frequencies and intensities of the most stable conformers in order to assist in the assignment of the vibrational bands in the experimental spectrum. The calculated relative energies suggest that four conformers are sufficiently stable to appear in the gas phase and all could be distinguished in the experimental matrix infrared spectra. We also calculated theoretical rotamerization constants and compared these with experimental determined constants. For the equilibria SER2/SER1 and SER3/SER1, a deviation between the experimental rotamerization constant and the theoretical constant was found. A relatively strong intramolecular H-bond in conformers SER2 ...

Solution structure of a trisaccharide-antibody complex: comparison of NMR measurements with a crystal structure.

Abstract: NMR and crystallography have been used to study antigen conformational changes that occur in a trisaccharide-Fab complex in solution and in the solid state. NOE buildup rates from transferred NOE experiments show that the antigenic determinant of a Salmonella lipopolysaccharide, represented by the trisaccharide methyl glycoside alpha-D-Galp(1-->2 [alpha-D-Abep(1-->3)]- alpha-D-Manp1-->OMe (1), undergoes a protein-induced conformational shift about the Gal-->Man glycosidic linkage when it is bound by a monoclonal antibody in aqueous solution. The same trisaccharide was crystallized with Fab, and a solved structure at 2.1-A resolution revealed that the conformation of the trisaccharide ligand was similar to that seen in a dodesaccharide-Fab complex [Cygler et al. (1991) Science 253, 442-445), where the Gal-Man linkage also experienced a similar conformational shift. Distance constraints derived from the TRNOE buildup curves are consistent with two bound trisaccharide conformations, one of which correlates with the ligand conformation of the crystalline Fab-trisaccharide complex. In this bound conformation, short interatomic distances between Abe O-2 and Gal O-2 permit an oligosaccharide intramolecular hydrogen bond. Despite its relatively low energy, a preponderance of this conformer could not be detected in aqueous or DMSO solutions of free trisaccharide by either 1H or 13C NMR experiments. In DMSO, a different intramolecular hydrogen bond between Abe O-2 and Man O-4 was observed due to a solvent-induced shift in the conformational equilibria (relative to aqueous solution). Molecular modeling of the trisaccharide in the binding site and as the free ligand suggested that the protein imposes an induced fit on the antigen, primarily resulting in a shift of the Gal-Man phi torsional angle. This reduces the interproton separation between Abe H-3 and Gal H-1 with a marked increase in the intensity of the previously weak NOEs between the protons of the noncovalently linked galactose and abequose residues. The impact of the conformational shift on gross trisaccharide topology is sufficiently small that binding modes inferred from functional group replacements are not impaired.