O-O bond formation in the S(4) state of the oxygen-evolving complex in photosystem II.

Based on recent X-ray structures of the oxygen-evolving complex in photosystem II, quantum chemical geometry optimizations of several thousand structures have been performed in order to elucidate the mechanism for dioxygen formation. Many of the results of these calculations have been presented previously. The energetically most stable structure of the S(4) state has been used in the present study to investigate essentially all the possible ways the O--O bond can be formed in this structure.

Ethylene biosynthesis by 1-aminocyclopropane-1-carboxylic acid oxidase: a DFT study.

The reaction catalyzed by the plant enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) was investigated by using hybrid density functional theory. ACCO belongs to the non-heme iron(II) enzyme superfamily and carries out the bicarbonate-dependent two-electron oxidation of its substrate ACC (1-aminocyclopropane-1-carboxylic acid) concomitant with the reduction of dioxygen and oxidation of a reducing agent probably ascorbate. The reaction gives ethylene, CO(2), cyanide and two water molecules.

Theoretical study of the catalytic reaction mechanism of MndD.

Manganese-dependent homoprotocatechuate 2,3-dioxygenase (MndD) is an enzyme taking part in the catabolism of aromatic compounds in the environment. It uses molecular oxygen to perform an extradiol cleavage of the ring of the ortho-dihydroxylated aromatic compound homoprotocatechuate. A theoretical investigation of the reaction path for MndD was performed using hybrid density functional theory with the B3LYP functional, and a catalytic mechanism has been suggested.

Hydroxide instead of bicarbonate in the structure of the oxygen evolving complex.

The energy diagram for the catalytic cycle of dioxygen evolution in photosystem II has been recomputed using a slightly different model than the one used previously, since the results showed an erroneous trend in the critical region from S(2) to S(3). By replacing the bicarbonate ligand, which was bridging between calcium and the outer manganese, by a hydroxide a significant improvement of the energy diagram is obtained. Most notably, the S(2) to S(3) transition is now exergonic as it should be.

Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study.

The mechanism of the unusual epimerization and desaturation reactions catalyzed by carbapenem synthase was investigated using the hybrid density functional method B3LYP. Several different models have been used in the calculations to study five component reactions. Both protonated and deprotonated models for the substrate have been explored so that the effects of hydrogen bonds could be characterized.

Theoretical studies of enzyme mechanisms involving high-valent iron intermediates.

Recent theoretical contributions to the elucidation of mechanisms for iron containing enzymes are reviewed. The method used in most of these studies is hybrid density functional theory with the B3LYP functional. Three classes of enzymes are considered, the mononuclear non-heme enzymes, enzymes containing iron dimers, and heme-containing enzymes.

Catalytic reaction mechanism of homogentisate dioxygenase: a hybrid DFT study.

Human homogentisate dioxygenase is an Fe(II)-dependent enzyme responsible for aromatic ring cleavage. The mechanism of its catalytic reaction has been investigated with the hybrid density functional method B3LYP. A relatively big model of the active site was first used to determine the substrate binding mode.

The mechanism for dioxygen formation in PSII studied by quantum chemical methods.

The availability of an X-ray structure for PSII including the water-oxidizing cluster, where the metal atoms and the amino acids are assigned, has opened up new possibilities to study the mechanism for dioxygen formation. In the present paper the main results of an ongoing hybrid DFT study are presented. The model used follows the structure suggested by the X-ray analysis as closely as possible.

Second-harmonic generation of solvated molecules using multiconfigurational self-consistent-field quadratic response theory and the polarizable continuum model.

We present the first implementation of the quadratic response function for multiconfigurational self-consistent-field wave functions of solvated molecules described by a polarizable continuum model employing a molecule-shaped cavity. We apply the methodology to the first hyperpolarizability beta and, in particular, the second-harmonic generation process for a series of conjugated push-pull oligomers, as well as for para-nitroaniline. The effect of solvation on the dispersion of the hyperpolarizability and the change in the hyperpolarizability for increasing chain length of the oligomers in vacuum and in solution is considered.

Two-photon absorption in solution by means of time-dependent density-functional theory and the polarizable continuum model.

We present the first study of two-photon absorption (TPA) of solvated molecules based on direct evaluation of TPA cross sections from the quadratic response of time-dependent perturbations. A set of prototypical two-photon (TP) chromophores has been selected and analyzed: a pure pi system (t-stilbene) and its substituted homologs obtained employing a donor (D) and an acceptor (A) group to probe the solvent effects along the series pi, D-pi-D, A-pi-D, and A-pi-A. For the selected systems we have calculated the TPA cross sections in different environments by means of the polarizable continuum model.

Catalytic Reaction Mechanism of Oxalate Oxidase (Germin). A Hybrid DFT Study.

The mechanism of the catalytic reaction for oxalate oxidase has been investigated with the hybrid density functional method B3LYP. The models used in the calculations comprise of the manganese ion, three imidazoles, and one acetate, which model the active-site Mn(II) and its first-shell protein ligands. Moreover, the reactants, i.

Methods and models for studying mechanisms of redox-active enzymes.

Methods and models used in recent quantum chemical studies of redox-active enzymes are described. Only density functional methods are able to treat these systems with sufficient accuracy. For the most accurate of these methods, the so-called hybrid methods, a fraction of exact exchange is included and the deviation from experimental energies is usually not higher than 5 kcal mol-1.

4-Hydroxyphenylpyruvate dioxygenase: a hybrid density functional study of the catalytic reaction mechanism.

Density functional calculations using the B3LYP functional has been used to study the reaction mechanism of 4-hydroxyphenylpyruvate dioxygenase. The first part of the catalytic reaction, dioxygen activation, is found to have the same mechanism as in alpha-ketoglutarate-dependent enzymes; the ternary enzyme-substrate-dioxygen complex is first decarboxylated to the iron(II)-peracid intermediate, followed by heterolytic cleavage of the O-O bond yielding an iron(IV)-oxo species. This highly reactive intermediate attacks the aromatic ring at the C1 position and forms a radical sigma complex, which can either form an arene oxide or undergo a C1-C2 side-chain migration.

A hybrid density functional study of O-O bond cleavage and phenyl ring hydroxylation for a biomimetic non-heme iron complex.

Density functional calculations using the B3LYP functional have been used to study the reaction mechanism of [Fe(Tp(Ph2))BF] (Tp(Ph2) = hydrotris(3,5-diphenylpyrazol-1-yl)borate; BF = benzoylformate) with dioxygen. This mononuclear non-heme iron(II) complex was recently synthesized, and it proved to be the first biomimetic complex reproducing the dioxygenase activity of alpha-ketoglutarate-dependent enzymes. Moreover, the enthalpy and entropy of activation for this biologically interesting process were derived from kinetic experiments offering a unique possibility for direct comparison of theoretical and experimental data.

Network analysis of metabolic enzyme evolution in Escherichia coli.

Background: The two most common models for the evolution of metabolism are the patchwork evolution model, where enzymes are thought to diverge from broad to narrow substrate specificity, and the retrograde evolution model, according to which enzymes evolve in response to substrate depletion. Analysis of the distribution of homologous enzyme pairs in the metabolic network can shed light on the respective importance of the two models. We here investigate the evolution of the metabolism in E.

A theoretical study of the cis-dihydroxylation mechanism in naphthalene 1,2-dioxygenase.

The catalytic mechanism of naphthalene 1,2-dioxygenase has been investigated by means of hybrid density functional theory. This Rieske-type enzyme, which contains an active site hosting a mononuclear non-heme iron(II) complex, uses dioxygen and two electrons provided by NADH to carry out the cis-dihydroxylation of naphthalene. Since a (hydro)peroxo-iron(III) moiety has been proposed to be involved in the catalytic cycle, it was probed whether and how this species is capable of cis-dihydroxylation of the aromatic substrate.

Identification of medically important fungi by the Pyrosequencing technology.

The Pyrosequencing technology was used for identification of different clinically relevant fungi. The tests were performed on amplicons derived from the 18S rRNA gene using polymerase chain reaction (PCR) universal primers for amplification. Sequencing was performed up to 40 bases in a variable region with a designed general sequencing primer and the Pyrosequence data were analyzed by BLAST sequence search in the GenBank database.

Mechanism of dioxygen activation in 2-oxoglutarate-dependent enzymes: a hybrid DFT study.

The reaction mechanism for dioxygen activation in 2-oxoglutarate-dependent enzymes has been studied by means of hybrid density functional theory. The results reported here support a mechanism in which all chemical transformations take place on a quintet potential-energy surface. More specifically, the activated dioxygen species attacks the carbonyl group of the co-substrate producing the Fe(II)-persuccinate-CO(2) complex, which readily releases the carbon dioxide molecule.

Pyrosequencing trade mark technology at elevated temperature.

To date, the Pyrosequencing trade mark technology has been performed at 28 degrees C due to the low thermostability of the firefly luciferase. In this study, firefly luciferase was stabilized in the presence of glycine betaine, allowing DNA sequencing at 37 degrees C. By increasing the temperature to 37 degrees C, false signals due to primer-dimers and loop-structures were decreased significantly.

Oxyl radical required for o-o bond formation in synthetic Mn-catalyst.

DFT calculations using the B3LYP functional support the suggestion that the [(terpy)(H(2)O)Mn(IV)(micro-O)(2)Mn(III)(H(2)O)(terpy)](3+) (terpy=2,2':6,2' '-terpyridine) complex functions as a synthetic O(2) catalyst. The calculated barrier for O-O bond formation with water is 23 kcal/mol. In this complex, as well as in models of the oxygen evolving complex in PSII, the active species is a Mn(IV)-oxyl radical.

Viral and microbial genotyping by a combination of multiplex competitive hybridization and specific extension followed by hybridization to generic tag arrays.

Detection and identification of microbial pathogens are important for disease diagnosis, treatment and prophylaxis measurements. By introducing an innovative technique, we show a robust, reliable and accurate microarray-based method for identification of microbial pathogens. The technique utilizes a unique combination of multiplex competitive hybridization, which enhances hybridization accuracy of oligonucleotides to the specific target, and apyrase-mediated allele-specific extension, which improves specific extension.

Mechanism of aromatic hydroxylation by an activated FeIV=O core in tetrahydrobiopterin-dependent hydroxylases.

The chemical pathways leading to the hydroxylated aromatic amino acids in phenylalanine and tryptophan hydroxylases have been investigated by means of hybrid density functional theory. In the catalytic core of these non-heme iron enzymes, dioxygen reacts with the pterin cofactor and is likely to be activated by forming an iron(IV)=O complex. The capability of this species to act as a hydroxylating intermediate has been explored.

Multiple group-specific sequencing primers for reliable and rapid DNA sequencing.

Pyrosequencing technology is a bioluminometric DNA sequencing method that employs a cascade of four enzymes to deliver sequence signals. To date this technology has been limited to the sequencing of short stretches of DNA. As an improvement to this technique, we have introduced a bacterial group-specific, multiple sequencing primer approach that circumvents sequencing of less informative semi-conservative regions of the 16S rRNA gene.

Catalysis by methyl-coenzyme M reductase: a theoretical study for heterodisulfide product formation.

Hybrid density functional theory has been used to investigate the catalytic mechanism of methyl-coenzyme M reductase (MCR), an essential enzyme in methanogenesis. In a previous study of methane formation, a scheme was suggested involving oxidation of Ni(I) in the starting square-planar coordination to the high-spin Ni(II) form in the CoM-S-Ni(II)F(430) octahedral intermediate. The methyl radical, concomitantly released by methyl-coenzyme M (CoM), is rapidly quenched by hydrogen atom transfer from the coenzyme B (CoB) thiol group, yielding methane as the first product of the reaction.

Multiple-primer DNA sequencing method.

A multiple-primer DNA sequencing approach suitable for genotyping, detection and identification of microorganisms and viruses has been developed. In this new method two or more sequencing primers, combined in a pool, are added to a DNA sample of interest. The oligonucleotide that hybridizes to the DNA sample will function as a primer during the subsequent DNA sequencing procedure.