Topic
Conformational isomerism
About: Conformational isomerism is a research topic. Over the lifetime, 11563 publications have been published within this topic receiving 199312 citations.
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TL;DR: The origin of the altered electronic properties of meso-tetrathien-2'-ylporphyrins are mainly due to the contribution of conformations in which the thienyl groups adopt idealized co-planar arrangements with the porphyrin ring.
Abstract: The UV-Vis and fluorescence spectra of free base and diprotonated meso-tetrathien-2′-ylporphyrins are, when compared to the spectra of meso-tetra-phenyl- or even -thien-3′-ylporphyrins, characterized by surprisingly large red-shifts. A comparison of the optical spectra and the computed rotational barriers for these meso-aryl-substituted porphyrins and a detailed conformational analysis of the single crystal X-ray structure of a diprotonated meso-tetrathien-2′-ylporphyrin suggest that the origin of the altered electronic properties of meso-tetrathien-2′-ylporphyrins are mainly due to the contribution of conformations in which the thienyl groups adopt idealized co-planar arrangements with the porphyrin ring. These conformations allow an efficient extension of the porphyrinic π-system through conjugation. We synthesized a meso-tetrathien-2′-ylporphyrin with methyl groups in the o-position, thus preventing the formation of conformers with co-planar thienyl groups and a corresponding thien-2′-ylporphyrin with methyl substituents in a distal position that possesses the same steric requirements for thienyl group rotation as the parent compound, to conclusively deduce the influence of the conformers on the electronic structure. A MNDO-PSDCI computation of their optical spectra further supports our key hypothesis. DFT computations of the total energies of the hypothetical diprotonated thien-2′-ylporphyrin conformer with perpendicular thienyl groups and the conformer containing near-co-planar thienyl groups quantify the resonance stabilization energy. Our results support and complement recent photophysical and theoretical studies by Gupta and Ravikanth and Friedlein et al. on thien-2′-yl-substituted core-modified porphyrins and [meso-tetra(5′-bromothien-2′-yl)porphyrinato]Zn(II), respectively.
71 citations
TL;DR: Single-molecule nanopore measurements have revealed ligand-induced conformational changes in the catalytic cycle of dihydrofolate reductase, and showed that the enzyme adopts distinctive conformers, which have different affinities for substrates and products.
Abstract: Conformational heterogeneity is emerging as a defining characteristic of enzyme function. However, understanding the role of protein conformations requires their thermodynamic and kinetic characterization at the single-molecule level, which remains extremely challenging. Here we report the ligand-induced conformational changes of dihydrofolate reductase (DHFR) by measuring the modulation of the nanopore currents. The long observation time of the electrical recordings enabled the detection of rare conformational transitions hidden in ensemble measurements. We show that DHFR exists in at least four ground-state configurations or conformers with different affinities for its ligands. Unliganded DHFR adopted low-affinity conformers, whereas the binding of substrates promoted the switch to the high-affinity conformer. Conversion between the conformers was accelerated by molecules that stabilized the transition state of DHFR, which suggests that the reaction lowers the energy barrier for conformer exchange and thus facilitates product release. This mechanism might be a general feature in enzymatic reactions affected by product inhibition or when the release of products is the rate-limiting step.
71 citations
TL;DR: In this paper, the energy pathways between the αR, β, β′, C, and β-regions of the conformational energy surface of N-acetyl-N′-methylalanyl amide were obtained by SCF ab initio calculations on the 4-21G level, with gradient geometry optimization at each point.
Abstract: Energy pathways between the αR, β′, C, and β-regions of the conformational energy surface of N-acetyl-N′-methylalanyl amide were obtained by SCF ab initio calculations on the 4-21G level, with gradient geometry optimization at each point. The calculations indicate that no barrier exists at this computational level between αR and β′. The variation of geometry (bond distances and bond angles) with conformation is analyzed in detail, and the most important geometrical parameters that should be treated as variables in both empirical energy calculations and in the fitting of polypeptide chains in proteins by x-ray methods are identified. In addition to the ϕ,ψ correlation discussed previously for the helical state, a correlation of these dihedral angles in the β-region is described.
71 citations
TL;DR: In this article, the internal coordinates of the disaccharide Man-α(1 → 3)-Man-α-O-Me were relaxed and minimized through an extensive molecular mechanics scheme.
Abstract: We report calculations of potential energy surfaces where all the internal coordinates of the disaccharide Man-α(1 → 3)-Man-α-O-Me were relaxed and minimized through an extensive molecular mechanics scheme. Flexibility within the mannopyranose rings plays a crucial role. Introduction of the relaxed principle into the conformational description of the disaccharide does not greatly alter the overall shape of the low-energy domains but it reveals new local minima. However, its principle effect is the lowering of energy barriers in the potential energy surface. New conformational transitions about the glycosidic bonds appear, permiting pathways among the low energy sections. This occurs with only little variation of the classical 4C1 conformation of the mannopyranose residues. All the conformations observed in the solid state, along with those already predicted through the joint use of NMR and modeling techniques, fall into the populations of stable conformers calculated in the present work. Moreover, a satisfactory agreement is reached between previously observed NOE values, and the theoretical one, calculated from the averaging of more than 500 microstates. The present results reconciliate most of the apparently conflicting data previously reported; they provide strong support for the application of the concept of conformational averaging to solution behavior. Some limitations of the proposed methodology are also discussed.
71 citations
TL;DR: The structures, energies, and rotational profiles of 17 heterobutadienes have been studied at the MP2/6-31G * theoretical level, with additional single point calculations at MP3/ 6-311++G * level as discussed by the authors.
Abstract: The structures, energies, and rotational profiles of 17 heterobutadienes have been studied at the MP2/6-31G * theoretical level, with additional single point calculations at the MP3/6-311++G ** level. The rotational profiles are, in part, determined by steric interactions between groups or between lone pairs. The magnitudes of these energies have been studied by examining the rotational profiles for some N-protonated derivatives which serve to minimize lone pair interactions
71 citations