Spectroscopic and electronic structure studies of intermediate X in ribonucleotide reductase R2 and two variants: a description of the FeIV-oxo bond in the FeIII-O-FeIV dimer

Spectroscopic and electronic structure studies of the class I Escherichia coli ribonucleotide reductase (RNR) intermediate X and three computationally derived model complexes are presented, compared, and evaluated to determine the electronic and geometric structure of the FeIII-FeIV active site of intermediate X. Rapid freeze-quench (RFQ) EPR, absorption, and MCD were used to trap intermediate X in R2 wild-type (WT) and two variants, W48A and Y122F/Y356F. RFQ-EPR spin quantitation was used to determine the relative contributions of intermediate X and radicals present, while RFQ-MCD was used to specifically probe the FeIII/FeIV active site, which displayed three FeIV d-d transitions between 16,700 and 22,600 cm(-1), two FeIV d-d spin-flip transitions between 23,500 and 24,300 cm(-1), and five oxo to FeIV and FeIII charge transfer (CT) transitions between 25,000 and 32,000 cm(-1). The FeIV d-d transitions were perturbed in the two variants, confirming that all three d-d transitions derive from the d-pi manifold. Furthermore, the FeIV d-pi splittings in the WT are too large to correlate with a bis-mu-oxo structure. The assignment of the FeIV d-d transitions in WT intermediate X best correlates with a bridged mu-oxo/mu-hydroxo [FeIII(mu-O)(mu-OH)FeIV] structure. The mu-oxo/mu-hydroxo core structure provides an important sigma/pi superexchange pathway, which is not present in the bis-mu-oxo structure, to promote facile electron transfer from Y122 to the remote FeIV through the bent oxo bridge, thereby generating the tyrosyl radical for catalysis.     

CD and MCD of CytC3 and taurine dioxygenase: role of the facial triad in alpha-KG-dependent oxygenases

The alpha-ketoglutarate (alpha-KG)-dependent oxygenases are a large and diverse class of mononuclear non-heme iron enzymes that require FeII, alpha-KG, and dioxygen for catalysis with the alpha-KG cosubstrate supplying the additional reducing equivalents for oxygen activation. While these systems exhibit a diverse array of reactivities (i.e., hydroxylation, desaturation, ring closure, etc.), they all share a common structural motif at the FeII active site, termed the 2-His-1-carboxylate facial triad. Recently, a new subclass of alpha-KG-dependent oxygenases has been identified that exhibits novel reactivity, the oxidative halogenation of unactivated carbon centers. These enzymes are also structurally unique in that they do not contain the standard facial triad, as a Cl- ligand is coordinated in place of the carboxylate. An FeII methodology involving CD, MCD, and VTVH MCD spectroscopies was applied to CytC3 to elucidate the active-site structural effects of this perturbation of the coordination sphere. A significant decrease in the affinity of FeII for apo-CytC3 was observed, supporting the necessity of the facial triad for iron coordination to form the resting site. In addition, interesting differences observed in the FeII/alpha-KG complex relative to the cognate complex in other alpha-KG-dependent oxygenases indicate the presence of a distorted 6C site with a weak water ligand. Combined with parallel studies of taurine dioxygenase and past studies of clavaminate synthase, these results define a role of the carboxylate ligand of the facial triad in stabilizing water coordination via a H-bonding interaction between the noncoordinating oxygen of the carboxylate and the coordinated water. These studies provide initial insight into the active-site features that favor chlorination by CytC3 over the hydroxylation reactions occurring in related enzymes.     

Skew loops in flat tori

We produce skew loops—loops having no pair of parallel tangent lines—homotopic to any loop in a flat torus or other quotient of R ⁿ . The interesting case here is n = 3. More subtly for any n, we characterize the homotopy classes that will contain a skew loop having a specified loop as tangent indicatrix. A fellowship from the Lady Davis foundation helped support this work.     

Optimal interleaving schemes for correcting two-dimensional cluster errors

We present an elementary theory of optimal interleaving schemes for correcting cluster errors in two-dimensional digital data. It is assumed that each data page contains a fixed number of, say n, codewords with each codeword consisting of m code symbols and capable of correcting a single random error (or erasure). The goal is to interleave the codewords in the m×n array such that different symbols from each codeword are separated as much as possible, and consequently, an arbitrary error burst with size up to t can be corrected for the largest possible value of t. We show that, for any given m, n, the maximum possible interleaving distance, or equivalently, the largest size of correctable error bursts in an m×n array, is given by if n?⌈m²/2⌉, and t=m+⌊(n-⌈m²/2⌉)/m⌋ if n?⌈m²/2⌉. Furthermore, we develop a simple cyclic shifting algorithm that can provide a systematic construction of an m×n optimal interleaving array for arbitrary m and n. This extends important earlier work on the complementary problem of constructing interleaving arrays that, given the burst size t, minimize the interleaving degree, that is, the number of different codewords in a 2-D (or 3-D) array such that any error burst with given size t can be corrected. Our interleaving scheme thus provides the maximum burst error correcting power without requiring prior knowledge of the size or shape of an error burst.     

On Local Coefficients for Non-generic Representations of Some Classical Groups

This paper is concerned with representations of split orthogonal and quasi-split unitary groups over a nonarchimedean local field which are not generic, but which support a unique model of a different kind, the generalized Bessel model. The properties of the Bessel models under induction are studied, and an analogue of Rodier's theorem concerning the induction of Whittaker models is proved for Bessel models which are minimal in a suitable sense. The holomorphicity in the induction parameter of the Bessel functional is established. Local coefficients are defined for each irreducible supercuspidal representation which carries a Bessel functional and also for a certain component of each representation parabolically induced from such a supercuspidal. The local coefficients are related to the Plancherel measures, and their zeroes are shown to be among the poles of the standard intertwining operators.     

Resonant solutions and breathers to the BKP equation

In this paper, we derive resonant and breather solutions from multi-soliton solutions of the B-type Kadomtsev–Petviashvili (BKP) equation of fourth order via the Hirota bilinear method. We first discuss N-soliton solutions of the BKP equation and use the linear superposition principle to generate N-resonant solutions. Subsequently, we construct complexiton and breather solutions and finally, study the dynamics of some selected solutions with the aid of 3D plots, contour plots and density plots.

     

Chemistry of novolac resins. X. Polymerization studies of HMTA and strategically synthesized model compounds

The reactions between hexamethylenetetramine (HMTA) and compounds which model novolac resins have been studied by ¹³C‐ and ¹⁵N‐NMR techniques. The dimer and tetramer compounds vary in molecular size and structure and react with HMTA to yield benzylamines and benzoxazine as the major initial‐formed intermediates and convert to methylene linked compounds at increased temperatures. The reaction of the compounds with only ortho reactive sites paralleled the 2,4‐xylenol–HMTA case reported by us previously; however, increasing molecular weight favored the formation of benzylamines and not benzoxazines. Those compounds with only para reactive sites paralleled the 2,6‐xylenol–HMTA case. The reactivity of the systems containing both ortho and para reactive sites depends on the ratio of ortho/para sites and various aspects such as the chemical structure and molecular weight of the compound, the HMTA level, and the melting point and pH of the system. These results parallel those obtained from novolac/HMTA systems. The xylenol/HMTA reactions formed similar products but showed quite different relative reaction rates by varying the HMTA ratio and structures of the materials. The importance of careful selection of model systems is also discussed. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 1347–1355, 1999     

The isomeric compounds nimbolide and isonimbolide

Nimbolide [systematic name: (4α,5α,6α,7α,15β,17α)‐7,15:21,23‐diepoxy‐6‐hydroxy‐4,8‐dimethyl‐1‐oxo‐18,24‐dinor‐11,12‐secochola‐2,13,20,22‐tetraene‐4,11‐dicarboxylic acid γ‐lactone methyl ester], C₂₇H₃₀O₇, was isolated from the leaves of Azadirachta indica, and its isomer, isonimbolide [systematic name: (4α,5α,6α,7α,15α)‐7,15:21,23‐diepoxy‐6‐hydroxy‐4,8‐dimethyl‐1‐oxo‐18,24‐dinor‐11,12‐secochola‐2,16,20,22‐tetra­ene‐4,11‐dicarboxylic acid γ‐lactone methyl ester], was prepared from a novel rearrangement reaction of nimbolide, using boron trifluoride etherate and tetra­butyl­ammonium bromide. The reaction conditions are probably responsible for the ether cleavage, double‐bond rearrangement and reformation of the ether linkage. As a result, there are conformational changes in two cyclo­pentane rings and the side‐chain –CH₂COOMe group. In isonimbolide, an (24) hydrogen‐bond motif is observed.     

Mechanism of N2O reduction by the mu4-S tetranuclear CuZ cluster of nitrous oxide reductase

Reaction thermodynamics and potential energy surfaces are calculated using density functional theory to investigate the mechanism of the reductive cleavage of the N-O bond by the mu(4)-sulfide-bridged tetranuclear Cu(Z) site of nitrous oxide reductase. The Cu(Z) cluster provides an exogenous ligand-binding site, and, in its fully reduced 4Cu(I) state, the cluster turns off binding of stronger donor ligands while enabling the formation of the Cu(Z)-N(2)O complex through enhanced Cu(Z) --> N(2)O back-donation. The two copper atoms (Cu(I) and Cu(IV)) at the ligand-binding site of the cluster play a crucial role in the enzymatic function, as these atoms are directly involved in bridged N(2)O binding, bending the ligand to a configuration that resembles the transition state (TS) and contributing the two electrons for N(2)O reduction. The other atoms of the Cu(Z) cluster are required for extensive back-bonding with minimal sigma ligand-to-metal donation for the N(2)O activation. The low reaction barrier (18 kcal mol(-)(1)) of the direct cleavage of the N-O bond in the Cu(Z)-N(2)O complex is due to the stabilization of the TS by a strong Cu(IV)(2+)-O(-) bond. Due to the charge transfer from the Cu(Z) cluster to the N(2)O ligand, noncovalent interactions with the protein environment stabilize the polar TS and reduce the activation energy to an extent dependent on the strength of proton donor. After the N-O bond cleavage, the catalytic cycle consists of a sequence of alternating protonation/one-electron reduction steps which return the Cu(Z) cluster to the fully reduced (4Cu(I)) state for future turnover.