On I-fuzzy topologies derived from a decreasing family of I-topologies

The aim of this paper is to study I-fuzzy topologies (fuzzy topologies in ostak's sense) derived from decreasing families of I-topologies (fuzzy topologies in Chang's sense), defined on a set X.     

A theoretical evaluation of steric and electronic effects on the structure of [OSO4 (NR3)] (NR3 = bulky chiral alkaloid derivative) complexes

Summary The novel theoretical scheme IMOMM, integrating ab initio and molecular mechanics contributions in a single geometry optimization process, is applied to the structural determination of different [OsO₄(NR₃)] (NR₃ = bulky chiral alkaloid derivative) species closely related to active catalysts for the asymmetric dihydroxylation of olefins. Computed values compare in a satisfactory way with available X-ray data, the relationship between the Os-N distance and the nature of the NR₃, ligand being properly reproduced. The computational scheme allows the separate quantification of electronic and steric effects, as well as the identification of the specific steric repulsions responsible for the difference.     

Models of the low-spin iron(III) hydroperoxide intermediate of heme oxygenase: magnetic resonance evidence for thermodynamic stabilization of the d(xy) electronic state at ambient temperatures

The (13)C pulsed ENDOR and NMR study of [meso-(13)C-TPPFe(OCH(3))(OO(t)Bu)](-) performed in this work shows that although the unpaired electron in low-spin ferrihemes containing a ROO(-) ligand resides in a d(pi) orbital at 8 K, the d(xy) electron configuration is favored at physiological temperatures. The variable temperature NMR spectra indicate a dynamic situation in which a heme with a d(pi) electron configuration and planar porphyrinate ring is in equilibrium with a d(xy) electron configuration that has a ruffled porphyrin ring. Because of the similarity in the EPR spectra of the hydroperoxide complexes of heme oxygenase, cytochrome P450, and the model heme complex reported herein, it is possible that these two electron configurations and ring conformations may also exist in equilibrium in the enzymatic systems. The ruffled porphyrinate ring would aid the attack of the terminal oxygen of the hydroperoxide intermediate of heme oxygenase (HO) on the meso-carbon, and the large spin density at the meso-carbons of a d(xy) electron configuration heme suggests the possibility of a radical mechanism for HO. The dynamic equilibrium between the ruffled (d(xy)) and planar (d(pi)) conformers observed in the model complexes also suggests that a flexible heme binding cavity may be an important structural motif for heme oxygenase activity.     

Catalysis on the coastline: theozyme,molecular dynamics,and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole

Antibody 21D8 catalyzes the decarboxylation of 5-nitro-3-carboxybenzisoxazole. The hapten used was designed to induce an antibody binding site with anion binders for the carboxylate, plus a nonpolar environment to accelerate decarboxylation. A recent X-ray crystal structure of 21D8 has shown that the binding pocket contains an array of both polar and charged residues. Nevertheless, 21D8 is able to catalyze a reaction that involves a decrease in polarity from reactant to transition state. The origins of this phenomenon were explored using various computational strategies-quantum mechanics, theozyme models, docking, molecular dynamics, free energy perturbation, and linear interaction energy-the combination of which has produced a consistent picture of catalysis. By partially desolvating the charged carboxylate, 21D8 manages to effect "catalysis on the coastline," without burying the carboxylate in a nonpolar region of the binding pocket. The results have implications for that broad class of enzyme and antibody catalyzed reactions that involve the conversion of a substrate with a relatively localized charge into a transition state with a highly dispersed charge.     

Oxidation of heme to beta- and delta-biliverdin by Pseudomonas aeruginosa heme oxygenase as a consequence of an unusual seating of the heme

The origin of the unusual regioselectivity of heme oxygenation, i.e. the oxidation of heme to delta-biliverdin (70%) and beta-biliverdin (30%), that is exhibited by heme oxygenase from Pseudomonas aeruginosa (pa-HO) has been studied by (1)H NMR, (13)C NMR, and resonance Raman spectroscopies. Whereas resonance Raman indicates that the heme-iron ligation in pa-HO is homologous to that observed in previously studied alpha-hydroxylating heme oxygenases, the NMR spectroscopic studies suggest that the heme in this enzyme is seated in a manner that is distinct from that observed for all other alpha-hydroxylating heme oxygenase enzymes for which a structure is known. In pa-HO, the heme is rotated in-plane approximately 110 degrees, so the delta-meso-carbon of the major orientational isomer is located within the HO-fold in the place where the alpha-hydroxylating enzymes typically place the alpha-meso-carbon. The unusual heme seating displayed by pa-HO places the heme propionates so that these groups point in the direction of the solvent-exposed heme edge and appears to originate in large part from the absence of stabilizing interactions between the polypeptide and the heme propionates, which are typically found in alpha-hydroxylating heme oxygenase enzymes. These interactions typically involve Lys-16 and Tyr-112, in Neisseriae meningitidis HO, and Lys-16 and Tyr-134, in human and rat HO-1. The corresponding residues in pa-HO are Asn-19 and Phe-117, respectively. In agreement with this hypothesis, we found that the Asn-19 Lys/Phe-117 Tyr double mutant of pa-HO exists as a mixture of molecules exhibiting two distinct heme seatings; one seating is identical to that exhibited by wild-type pa-HO, whereas the alternative seating is very similar to that typical of alpha-hydroxylating heme oxygenase enzymes and is related to the wild-type seating by approximately 110 degrees in-plane rotation of the heme. Furthermore, each of these heme seatings in the pa-HO double mutant gives rise to a subset of two heme isomeric orientations that are related to each other by 180 degrees rotation about the alpha-gamma-meso-axis. The coexistence of these molecules in solution, in the proportions suggested by the corresponding area under the peaks in the (1)H NMR spectrum, explains the unusual regioselectivity of heme oxygenation observed with the double mutant, which we found produces alpha- (55%), delta- (35%), and beta-biliverdin (10%). Alpha-biliverdin is obtained by oxidation of the heme seated similar to that of alpha-hydroxylating enzymes, whereas beta- and delta-biliverdin are formed from the oxidation of heme seated as in wild-type pa-HO.     

Simulation of laser-driven,ablated plasma flows in collisionless shock experiments on OMEGA and the NIF

Experiments investigating the physics of interpenetrating, collisionless, ablated plasma flows have become an important area of research in the high-energy-density field. In order to evaluate the feasibility of designing experiments that will generate a collisionless shock mediated by the Weibel instability on the National Ignition Facility (NIF) laser, computer simulations using the Center for Radiative Shock Hydrodynamics (CRASH) radiation-hydrodynamics model have been carried out. This paper reports assessment of whether the experiment can reach the required scale size while maintaining the low interflow collisionality necessary for the collisionless shock to form. Comparison of simulation results with data from Omega experiments shows the ability of the CRASH code to model these ablated systems. The combined results indicate that experiments on the NIF are capable of reaching the regimes necessary for the formation of a collisionless shock in a laboratory experiment.     

Electromechanical phase transition in hexacyanometallate nanostructure (Prussian Blue)

This paper demonstrates the importance of the structural changeover in controlling the physical-chemical properties of hexacyanometalate-like materials (Prussian Blue). A meticulous in situ study of compositional variations using electroacoustic impedance techniques associated to electrogravimetric techniques in hexacyanoferrates containing K+ alkali metals reveals the existence of a nanostructural changeover coupled to a change of the magnetic properties of these electromagnetic materials. In the same way, the electroacoustic impedance techniques can be useful both in the understanding and in the in situ monitoring of the structural changeovers and the magnetic behavior of all kinds of materials.