Conformational isomerism

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

Intra- and Intermolecular π-Type Hydrogen Bonding in Aryl Alcohols: UV and IR-UV Ion Dip Spectroscopy

Abstract: The structures of benzyl alcohol, its 1:1 water complex, and its dimer have been investigated by R2PI spectroscopy and IR−UV ion dip spectroscopy, combined with ab initio computation. The sole molecular conformer observed in the jet has a gauche arrangement of the gauche arrangement of the OH group relative to the C1−Cα bond, but the extent of π-type intramolecular H-bonding is small. Analysis of its rotational band contours suggests the incidence of vibronic coupling involving motion of the side chain and also leads to an estimate for the dihedral angle τ1(OCCC) lying in the range 35°−60°, in good agreement with the values (50°−60°) indicated by high-level ab initio calculations. The 1:1 water complex is assigned to a structure in which water binds as a proton acceptor to the alcohol group, and as a weak proton donor to the π-system of the aromatic ring. The arrangement of H-bonds is similar within the dimer: the OH of one molecule acts as both acceptor to the alcohol group and as donor to the π-system ...

Conformers of Gaseous Proline

Abstract: Accurate geometries, relative energies, rotational and quartic centrifugal distortion constants, dipole moments, harmonic vibrational frequencies, and infrared intensities were determined from ab initio electronic structure calculations for eighteen conformers of the neutral form of the amino acid L-proline. Only four conformers have notable population at low and moderate temperature. The second most stable conformer is only 2+/-2 kJ mol(-1) above the global minimum, while the third and fourth conformers are nearly degenerate and have an excess energy of 7+/-2 kJ mol(-1) relative to the global minimum. All four conformers have one hydrogen bond: N.HO in the lower energy pair of conformers, and NH.O in the higher energy pair of conformers. The conformer pairs differ only in their ring puckering. The relative energies of the conformers include corrections for valence electron correlation, extrapolated to the complete basis set limit, as well as core correlation and relativistic effects. Structural features of the pyrrolidine ring of proline are discussed by using the concept of pseudorotation. The accurate rotational and quartic centrifugal distortion constants as well as the vibrational frequencies and infrared intensities should aid identification and characterization of the conformers of L-proline by rotational and vibrational spectroscopy, respectively. Bonding features of L-proline, especially intramolecular hydrogen bonds, were investigated by the atoms-in-molecules (AIM) technique.

Hydrogen exchange properties of proteins in native and denatured states monitored by mass spectrometry and NMR

Abstract: The extent of deuterium labeling of hen lysozyme, its three-disulfide derivative, and the homologous alpha-lactalbumins, has been measured by both mass spectrometry and NMR. Different conformational states of the proteins were produced by varying the solution conditions. Alternate protein conformers were found to contain different numbers of 2H atoms. Furthermore, measurement in the gas phase of the mass spectrometer or directly in solution by NMR gave consistent results. The unique ability of mass spectrometry to distinguish distributions of 2H atoms in protein molecules is exemplified using samples prepared to contain different populations of 2H-labeled protein. A comparison of the peak widths of bovine alpha-lactalbumin in alternate solution conformations but containing the same average number of 2H atoms showed dramatic differences due to different 2H distributions in the two protein conformers. Measurement of 2H distributions by ESI-MS enabled characterization of conformational averaging and structural heterogeneity. In addition, a time course for hydrogen exchange was examined and the variation in distributions of 2H atom compared with simulations for different hydrogen exchange models. The results clearly show that exchange from the native state of bovine alpha-lactalbumin at 15 degrees C is dominated by local unfolding events.

United Atom Force Field for Molecular Dynamics Simulations of 1,4-Polybutadiene Based on Quantum Chemistry Calculations on Model Molecules

Abstract: We present a united atom force field for simulations of 1,4-polybutadiene based on ab initio quantum chemistry calculations on model molecules. The geometries and energies of conformers and rotational energy barriers in model alkenes and dienes have been determined from high-level quantum chemistry calculations. A rotational isomeric state (RIS) model for 1,4-polybutadiene based on the conformer geometries and energies of the model molecules has been derived. The characteristic ratio and its temperature dependence for cis-1,4-polybutadiene and trans-1,4-polybutadiene, and the characteristic ratio of a random copolymer of cis and trans units, as predicted by the RIS model, are in good agreement with experimental values, thereby supporting the accuracy of the quantum chemistry calculations. Torsional potentials for the united atom force field have been parametrized to reproduce the quantum chemistry conformer energies and rotational energy barriers for rotations about the C(sp2)−C(sp2), C(sp2)−C(sp3), and C...

Solution Conformations, Photophysics, and Photochemistry of Bile Pigments; Bilirubin and Biliverdin, Dimethyl Esters and Related Linear Tetrapyrroles

Abstract: Bilirubin and biliverdin dimethyl esters (BRE and BVE, respectively) and related linear tetrapyrroles have been studied using a combination of photochemical and spectroscopic techniques, the latter including absorption, fluorescence fluorescence excitation, medium-induced circular dichroism, and proton magnetic resonance. Both types of tetrapyrroles form mixtures of different topological isomers in very dilute solutions. In the case of the bilirubins the heterogeneity of the solutions is caused by two coexisting conformers with different orientations of the A/B and C/D pyrromethenone moieties with repect to each other. The spectral properties of one conformer resemble the isolated parent pyrromethenone, whereas those of the other result from electronic coupling of the two subchromophores presumably held in a “ridge tile” -like orientation. CC rotations at the C-5 and C-15 bridges substantially compete in both components with the photochemical channels (EZ isomerization and lumirubin formation) for the radiationless deactivation of the excited singlet state. The more rigid “ridge tile” component additionally undergoes hydrogen bond-mediated deactivation, and it photoisomerizes more efficiently. The situation is markedly more complex with the biliverdins. In order to obtain a more detailed insight into the mechanisms of the radiationless excited-state processes, time-resolved optoacoustic spectroscopy and ultrafast absorption (pump-probe) and fluorescence detection (single-photon-timing) techniques were used to supplement the stationary methods. The solution mixtures are composed of a (family of) helically coiled all-Z, all-syn species, and of species differing from the former by stretched arrangements of the rings B and C around the central C-10 bridge (E-anti, E-syn, and Z-anti). Two excited singlet states with picosecond lifetimes are attributed to either one or two coiled ground-state forms, and two remarkably long-lived nanosecond excited states arise each from a stretched ground state. The radiationless deactivation of the shorter-lived of the picosecond states is brought about by ultrafast intramolecular proton transfer between the B/C nitrogen atoms, in addition to the CC rotational modes operative in both. ZE photoisomerization is also an appreciable deactivation channel of excited biliverdin dimethyl ester. It is confined to the central C-10 double bond and selectively affords a stretched isomer (10E-anti), which thermally reforms the coiled starting meterial at room temperature via a sequence of tautomerization and CC rotation. Heating or ultrasonic treatment can reverse this sequence and drive it farther to populate another stretched isomer (10E-syn) which is thermally stable at room temperature. This stretched form aggregates (presumably to dimers) already at concentrations at which the coiled species still appears to be fully monomeric.