Conformational isomerism

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

Conformational preferences of non-prolyl and prolyl residues.

Abstract: The conformational study on Ac-Ala-NHMe (the alanine dipeptide) and Ac-Pro-NHMe (the proline dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in the backbone conformational preference and the cis−trans isomerization for the non-prolyl and prolyl residues in the gas phase and in the solutions (chloroform and water). For the alanine and proline dipeptides, with the increase of solvent polarity, the populations of the conformation tC with an intramolecular C7 hydrogen bond significantly decrease, and those of the polyproline II-like conformation tF and the α-helical conformation tA increase, which is in good agreement with the results from circular dichroism and NMR experiments. For both the dipeptides, as the solvent polarity increases, the relative free energy of the cis conformer to the trans conformer decreases and the rotational barrier to the cis−trans isomerization increases. It is found that the cis−t...

Conformation and anion binding properties of cyclic hexapeptides containing l-4-hydroxyproline and 6-aminopicolinic acid subunits

Abstract: Two cyclic hexapeptides containing alternating all R and all S configured l-(4R/S)-hydroxyproline and 6-aminopicolinic acid subunits are presented, and the influence of the hydroxyl groups on the solubility, conformation, and receptor properties is investigated. Cyclopeptide 2, containing the natural 4R configured hydroxyproline, adopts a conformation similar to that of the unsubstituted peptide 1, which is able to bind anions such as halides and sulfate in aqueous solution. 2 also interacts with these anions, but whereas 1 forms sandwich type 2:1 complexes, in which the anion is bound by two cyclopeptide moieties, 2 forms 1:1 complexes. The stabilities of the halide and sulfate complexes of 2 range between 100 and 102 M−1 in 80% D2O/CD3OD. Complex formation is detectable even in water, but with slightly smaller stability constants. Using this information a quantitative evaluation of the stability of the 2:1 complexes of 1, for which overall stability constants in the order 104 to 105 M−2 in 80% D2O/CD3OD were observed, was made. In contrast to 2, the conformation of 3, containing the non-natural 4S configured hydroxyproline, is strongly affected by the presence of the hydroxyl groups. In d6-DMSO and methanol/water mixtures a slow conformational equilibrium between two C3-symmetrical conformers is observed, and 3 is thus much less preorganized for anion binding than either 1 or 2.

Currents through single molecular junction of Au/hexanedithiolate/Au measured by repeated formation of break junction in STM under UHV: Effects of conformational change in an alkylene chain from gauche to trans and binding sites of thiolates on gold

Abstract: The currents through single molecular bridges of 1,6-hexanedithiolate sandwiched between two gold protruded electrodes were measured by scanning tunneling microscopy (STM) under ultrahigh vacuum. The currents through the single molecules were measured by repeating formation of break junction between an Au(111) substrate covered with 1,6-hexanedithiolate and a gold STM tip, while current–separation (i–s) curves were repeatedly recorded. The gradual increase in the tunneling currents through the single molecules was observed almost every time (ca. 80%) during stretching of the molecular bridges. The increase in the tunneling currents can be attributed to the increase in the single molecular conductivity caused by the change in alkylene chains of 1,6-hexanedithiolate from gauche to trans conformations. The change from the gauche rich (4–5 gauche content in a single hexylene chain) to all-trans conformation resulted in one order of magnitude increase in the observed currents. Between the extreme gauche rich (5 gauche content) and all-trans (0 gauche content) conformations, there are many kinds of conformers (i.e., rotamers) with different gauche contents having different single molecular conductivities. Complexity of the observed currents due to such conformational changes made the study of the effect of Au–S contacts on single molecular conductivities difficult, although the effect was observed clearly for single molecular bridges with a previous rigid π-conjugated system without the conformational effect (K. Ishizuka et al., Jpn. J. Appl. Phys., 2006, 45, 2037). To solve this problem, new methods are proposed and their usefulness is demonstrated.

Theoretical Evaluation of Solvent Effects on the Conformational and Tautomeric Equilibria of 2-(2'-Hydroxyphenyl)benzimidazole and on Its Absorption and Fluorescence Spectra

Abstract: The effect of the solvent on the ground state free energy differences of three enol conformers of 2-(2‘-hydroxyphenyl)benzimidazole and its keto tautomer has been examined by means of Monte Carlo simulations and continuum model calculations. In agreement with the experimental data, calculations show that the trans enol and keto forms are stabilized by polar solvents, leading to a conformational and tautomeric equilibrium with the closed cis enol conformer in water, the only single species in apolar solvents. Monte Carlo simulations have also been used to examine the influence of the solvent on the absorption band of the closed cis enol structure and the fluorescence band of the keto form generated by photoinduced intramolecular proton transfer. In concordance with the experimental spectra, absorption and fluorescence band maxima for the closed cis enol and keto forms, respectively, are found to be blue-shifted with increasing polarity and hydrogen bonding capacity of the solvent.