Conformational isomerism

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

Helically chiral ferrocene peptides containing 1'-aminoferrocene-1-carboxylic acid subunits as turn inducers.

Abstract: We present a detailed structural study of peptide derivatives of 1'-aminoferrocene-1-carboxylic acid (ferrocene amino acid, Fca), one of the simplest organometallic amino acids. Fca was incorporated into di- to pentapeptides with D- and L-alanine residues attached to either the carboxy or amino group, or to both. Crystallographic and spectroscopic studies (circular dicroism (CD), IR, and NMR) of about two dozen compounds were used to gain a detailed insight into their structures in the solid state as well as in solution. Four derivatives were characterized by single crystal X-ray analysis, namely Boc-Fca-Ala-OMe (16), Boc-Fca-D-Ala-OMe (17), Boc-Fca- -Ala-OMe (18), and Boc-Ala-Fca-Ala-Ala-OMe (21). CD spectroscopy is an extremely useful tool to elucidate the helical chirality of the metallocene core. Unlike in all other known ferrocene peptides, the helical chirality of the ferrocene is governed solely by the chirality of the amino acid attached to the N-terminus of Fca. Depending on the degree of substitution of both cyclopentadiene (Cp) rings, different hydrogen-bonding patterns are realized. 1H NMR and IR spectroscopy, together with the results from X-ray crystallography, give detailed information regarding not only the hydrogen-bonding patterns of the compounds, but also the equilibria between different conformers in solution. Differences in chemical shifts of NH-protons in dimethyl sulfoxide ([D6]DMSO and CDCl3, that is, the variation ratio (vr), is used for the first time as a measure of the hydrogen-bonding strength of individual CO   HN bonds in ferrocenoyl peptides. In dipeptides with one intramolecular hydrogen bond between the pendant chains, for example in dipeptide 16, an equilibrium between hydrogen bonded and open forms is observed, as testified by a vr value around 0.5. Higher peptides, such as tetrapeptide 21, are able to form two intramolecular hydrogen bonds stabilizing one single conformation in CDCl3 solution (vr  0). Due to the low barrier of Cp-ring rotation, new and unnatural hydrogen-bonding patterns are emerging. The systematic work described herein lays a solid foundation for the rational design of metallocene peptides with unusual structures and properties.

Infrared and ultraviolet spectroscopy of water-containing clusters of indole, 1-methylindole, and 3-methylindole

Abstract: A combination of resonant two-photon ionization (R2PI), resonant ion-dip infrared spectroscopy (RIDIRS), and infrared−ultraviolet (IR−UV) hole-burning spectroscopy is used to characterize the hydrogen-bonding topologies of indole−(water)1,2, 1-methylindole−(water)1-3, and 3-methylindole−(water)1 clusters formed and cooled in a supersonic expansion. The combination of methods provides a means of disentangling R2PI spectra that contain contributions from more than one species in the same mass channel due either to fragmentation or to the presence of conformational isomers. Density functional theory calculations (DFT Becke3LYP/6-31+G*) of the structures, harmonic vibrational frequencies, and infrared intensities provide a basis for distinguishing which structures are observed experimentally. The clusters studied exhibit a range of solvation structures around indole. In the indole−(water)1 and 3-methylindole−(water)1 complexes, the RIDIR spectra provide a benchmark frequency shift for the N−H···OH2 H-bonds in...

Spectroscopy and conformational preferences of gas-phase helices

Abstract: We describe here a study of the spectroscopy of two peptides that we expect to be helical, Ac-Phe-(Ala)5-Lys-H+ and Ac-Phe-(Ala)10-Lys-H+, and one that we expect to be globular, Ac-Lys(H+)-Phe-(Ala)10, with the goal of identifying the spectral features characteristic of their secondary structure. Conformation-specific IR-UV double resonance spectroscopy in a cold ion trap, together with nitrogen-15 isotopic substitution, allow us to identify four conformers of the smaller helix. Infrared spectra in the OH and amide NH stretch regions, together with theoretical calculations, provide diagnostics of the presence of helical structure as well as details of the specific hydrogen bonding patterns within the helix. The assigned vibrational spectra presented here provide a benchmark for the ability of theory to predict the spectrum of a helical peptide.

A tale of two ions: the conformational landscapes of bis(trifluoromethanesulfonyl)amide and N,N-dialkylpyrrolidinium.

Abstract: The conformational landscapes of two commonly used ionic liquid ions, the anion bis(trifluoromethanesulfonyl)amide (Ntf2) and the cations N-propyl- and N-butyl-N-methylpyrrolidinium, were investigated using data obtained from Raman spectroscopy, molecular dynamics, and ab initio techniques. In the case of Ntf2, the plotting of three-dimensional potential energy surfaces (PES) and the corresponding molecular dynamics (MD) simulations confirmed the existence of two stable isomers (each existing as a pair of enantiomers) and evidenced the nature of the anion as a flexible, albeit hindered, molecule capable of interconversion between conformers in the liquid state, a result confirmed by the Raman data. In the case of the N,N-dialkylpyrrolidinium cations, the PES show a much more limited conformational behavior of the pyrrolidinium ring (pseudorotation). Nevertheless, such pseudorotation produces two stable isomers with the propyl and butyl side chains in completely different positions (axial-envelope and equa...