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Ring Orientation (ring + orientation)

Distribution by Scientific Domains
Chemistry75%

Selected Abstracts

Molecular Dynamics Simulations of the Orientation and Reorientational Dynamics of Water and Polypyrrole Rings as a Function of the Oxidation State of the Polymer

MACROMOLECULAR THEORY AND SIMULATIONS, Issue 1 2005
Jose J. López Cascales
Abstract Summary: Polypyrrole is one of the most widely-studied conducting polymers due to its steady electrochemical response and good chemical stability in different solvents, including organic and inorganic ones. In this work, we provide for the first time valuable information in atomic detail concerning the steady and dynamic properties of pyrrole rings as a function of the oxidation state of the polymer. The study was carried out by Classical molecular dynamics simulation, where the system was modelled by 256 polypyrrole chains of 10 pyrrole rings each. Water was explicitly introduced in our simulations. Besides the uncharged or reduced state, two steady oxidation states of the polymer have been simulated by introducing a net charge (+1) on 85 and 256 of the polypyrrole chains. To balance the charges emerging in these oxidised states, 85 and 256 chloride ions (Cl,1) respectively, were introduced into the system. From an analysis of the simulated trajectories, the orientation and relaxation times of water and pyrrole rings were evaluated for the different oxidation states of the polymer across the polypyrrole/water interface. The calculated densities for different oxidation states describe the swelling or shrinking process during electrochemical oxidation or reduction respectively. The rotational relaxation times calculated for the polypyrrole rings decrease with increasing oxidation of the polymer, which is in a good agreement with experimental electrochemical data. Almost no variation in pyrrole ring orientation was measured for the different oxidation states of the polymer, even compared with polypyrrole bulk. As regards the water structure in the vicinity of the polypyrrole/water interface, both the orientation and orientation relaxation time were strongly affected by the presence of charges in the polymer. Thus, the water dipole was strongly orientated in the vicinity of the water/polypyrrole interface and its orientational relaxation time increased by one order of magnitude compared with bulk water, even when only one-third of the total polymer chains were oxidised. The results attained in this work were validated with experimental results, when they were available. Polypyrrole ring orientation and water orientation at the polypyrrole/water interface. (a) 256 rPPy and (b)171 rPPy,+,85 oPPy. [source]

High-resolution structure of human carbonic anhydrase II complexed with acetazolamide reveals insights into inhibitor drug design

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2009
Katherine H. Sippel
The crystal structure of human carbonic anhydrase II (CA II) complexed with the inhibitor acetazolamide (AZM) has been determined at 1.1,Ĺ resolution and refined to an Rcryst of 11.2% and an Rfree of 14.7%. As observed in previous CA II,inhibitor complexes, AZM binds directly to the zinc and makes several key interactions with active-site residues. The high-resolution data also showed a glycerol molecule adjacent to the AZM in the active site and two additional AZMs that are adventitiously bound on the surface of the enzyme. The co-binding of AZM and glycerol in the active site demonstrate that given an appropriate ring orientation and substituents, an isozyme-specific CA inhibitor may be developed. [source]

Indole ring orientations of Trp189 in the ground and M intermediate states of bacteriorhodopsin as studied by polarized UV resonance Raman spectroscopy,

JOURNAL OF RAMAN SPECTROSCOPY, Issue 1-3 2006
Kazuhiro Asakawa
Abstract Polarized resonance Raman spectroscopy provides a means for orientation analysis of proteins in aligned samples. Previously, we developed a Raman linear intensity difference (RLID) method to determine the orientations of aromatic amino acid side chains in flow-oriented or membrane-bound proteins. In this study, we have applied the RLID method to Trp189 in bacteriorhodopsin (BR), a transmembrane protein that acts as a light-driven proton pump. Among the eight Trp residues in BR, the Raman spectrum of Trp189 has been extracted by subtracting the spectrum of the Trp189 , Phe mutant from that of wild-type BR. By examining the 251.3-nm-exited polarized resonance Raman intensities of two indole ring vibrations of Trp189, the directions of the La and Bb transition moments have been determined with respect the membrane normal in the light-adapted ground state (BR568) and a photo-excited intermediate (M). Comparison of the orientations of the Trp189 indole ring derived from the La and Bb inclination angles has shown that the indole ring slightly but significantly reorients toward the ionone ring of the retinal chromophore in the M intermediate. The reorientation of Trp189 is consistent with the previous observation that helix F, on which Trp189 is located, undergoes an outward tilt and the hydrophobic interaction of Trp189 increases in the M intermediate. The RLID method combined with 251.3 nm excitation and point mutation is useful for detecting even a small reorientation of a targeted Trp residue. Copyright © 2006 John Wiley & Sons, Ltd. [source]

Sterically Crowded peri -Substituted Naphthalene Phosphines and their PV Derivatives

CHEMISTRY - A EUROPEAN JOURNAL, Issue 25 2010
Fergus
Abstract Three sterically crowded peri -substituted naphthalene phosphines, Nap[PPh2][ER] (Nap=naphthalene-1,8-diyl; ER=SEt, SPh, SePh) 1,3, which contain phosphorus and chalcogen functional groups at the peri positions have been prepared. Each phosphine reacts to form a complete series of PV chalcogenides Nap[P(E,)(Ph2)(ER)] (E,=O, S, Se). The novel compounds were fully characterised by using X-ray crystallography and multinuclear NMR spectroscopy, IR spectroscopy and MS. X-ray data for 1, 2, n,O, n,S, n,Se (n=1,3) are compared. Eleven molecular structures have been analysed by naphthalene ring torsions, peri -atom displacement, splay angle magnitude, X,,,E interactions, aromatic ring orientations and quasi-linear arrangements. An increase in the congestion of the peri region following the introduction of heavy chalcogen atoms is accompanied by a general increase in naphthalene distortion. P,,,E distances increase for molecules that contain bulkier atoms at the peri positions and also when larger chalcogen atoms are bound to phosphorus. The chalcogenides adopt similar conformations that contain a quasi-linear E,,,PC fragment, except for 3,O, which displays a twist-axial-twist conformation resulting in the formation of a linear O,,,SeC alignment. Ab initio MO calculations performed on 2,O, 3,O, 3,S and 3,Se reveal Wiberg bond index values of 0.02 to 0.04, which indicates only minor non-bonded interactions; however, calculations on radical cations of 3,O, 3,S and 3,Se reveal increased values (0.14,0.19). [source]