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Oxygen Atoms (oxygen + atom)

Distribution by Scientific Domains

Chemistry	90%
Polymers and Materials Science	5%
Physics and Astronomy	2%
3 Other Domains	3%

Distribution within Chemistry

General & Introductory Chemistry	27%
Organic Chemistry	8%
Computational Chemistry & Molecular Modeling	3%
Biochemistry	2%
15 Other Subdomains	57%

Kinds of Oxygen Atoms

bridging oxygen atom

carbonyl oxygen atom

phosphonate oxygen atom

Terms modified by Oxygen Atoms

oxygen atom transfer

Selected Abstracts

Reductions of Benzene Derivatives Whose Benzylic Positions Bear Oxygen Atoms under Mild Conditions

HELVETICA CHIMICA ACTA, Issue 12 2008
Abdullah Menzek
Abstract Reductions of compounds whose benzylic positions bear O-atoms, such as benzyl alcohol, dibenzyl ether, styrene oxide, benzaldehyde, acetophenone, and benzophenone, to the corresponding non-conjugated dienes were performed by using t -BuOH, Li, and gaseous NH3 in THF at room temperature. In these reductions, it was observed that the functional groups at benzylic positions were reduced first. [source]

Highly Selective Acylation of Dimethylamine Mediated by Oxygen Atoms on Metallic Gold Surfaces,

ANGEWANDTE CHEMIE, Issue 2 2010
Bingjun Xu
Komplett gekuppelt: Die Acylierung von Dimethylamin durch Kupplung mit Formaldehyd gelingt mit fast kompletter Selektivität bei niedriger Aktivierungsenergie und niedrigen Bedeckungen mit adsorbierten O-Atomen auf metallischem Gold. Der Sauerstoff erzeugt die aktivierte Zwischenstufe (CH3)2N(a), die das Carbonyl-Kohlenstoffatom des Aldehyds angreift (siehe Bild). Ein allgemeiner Mechanismus für die effiziente und selektive Acylierung von Aminen durch Au wird vorgeschlagen. [source]

Interactions between Oxygen Atoms on Pt(100): Implications for Ordering during Chemisorption and Catalysis

CHEMPHYSCHEM, Issue 10 2010
Da-Jiang Liu
Abstract We present a DFT analysis of the interactions between chemisorbed oxygen on the unreconstructed (1×1)-Pt(100) surface. These interactions control ordering of O not just for single-species adsorption, but also within O domains during coadsorption and reaction with other species such as CO. The calculations indicate that O prefers bridge sites, as deduced previously. In addition, we find a large difference in the interactions between O at different types of bridge site pairs separated by one lattice constant. There is strong repulsion for pairs separated by a Pt atom, but only a weak interaction for pairs separated by a fourfold hollow site. This finding elucidates the tendency for striped (n×1)-O ordering often observed in chemisorption and reaction studies. [source]

Nitrosyl Ruthenium Diolato Complexes

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 7 2005
Michael Barth
Abstract [mer -(dien)(NO)Ru(AnErytH,2)]BPh4·2,H2O (1), [mer -(dien)(NO)Ru(R,R -ChxdH,2)]BPh4 (2), [mer -(dien)(NO)Ru(EthdH,2)]BPh4 (3), and [mer -(dien)(NO)Ru(Me-,- D -Ribf2,3H,2)]BPh4·5.5,H2O (4) have been synthesized in the form of light pink crystals by the reaction of [mer -(dien)(NO)RuCl2]X with the respective diol in aqueous sodium hydroxide solution (dien = diethylenetriamine, AnEryt = anhydroerythritol, Chxd = cyclohexane-1,2-diol, Ethd = ethanediol, Rib = ribose; X = BPh4 or PF6). The nitrosyl ligand exhibits a strong trans influence which causes the trans -bonded oxygen atom of the diolato ligand to form a shorter bond with the Ru centre. Mean values are 2.038 for cis and 1.946 Å for transO -binding. Back donation is strongly supported by the diolato ligand resulting in low energies for the N,O stretch which can be observed as low as 1805 cm,1. trans -Oxygen atoms do not act as hydrogen-bond acceptors in any of the cases. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source]

Direct-temperature mass spectrometric detection of volatile terpenoids and natural terpenoid polymersin fresh and artificially aged resins

JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 6 2003
Dominique Scalarone
Abstract Electron impact (EI) ionization and ammonia chemical ionization (NH3/CI) direct-temperature mass spectrometry (DTMS) was used to characterize five natural terpenoid resins: dammar, mastic, colophony, Manila copal and sandarac. Compositional differences were highlighted by the identification of low molecular mass compounds, ranging from di- to triterpenoids, and polymeric components, based on polycadinene and polycommunic acid. Photo-ageing processes occurring under accelerated indoor and outdoor exposure conditions were also investigated. NH3/CI and tetramethylammonium hydroxide EI were applied to increase the sensitivity towards highly oxidized molecules. Oxidation and cross-linking reactions were found to affect mostly triterpenoid resins and diterpenoid abietane and pimarane molecules. Oxidation proceeds through a radical mechanism, generally starting from conjugated double bonds. Oxygen atoms are incorporated in the terpenoid structures in the form of alcohols, ketones and carboxylic acids. Oxidized cadinene oligomers released by pyrolytic degradation of the polycadinene fraction of dammar were detected even in unaged samples. Evidence is given indicating the occurrence of cleavages in the cross-linked polycommunic structure of aged sandarac and Manila copal. Bond scissions produce oligomeric fragments based on the communic acid structure and sufficiently volatile to be desorbed at low temperature in DTMS measurements. Copyright © 2003 John Wiley & Sons, Ltd. [source]

Drug design: hiding in full view

DRUG DEVELOPMENT RESEARCH, Issue 1 2008
Norman S. Radin
Abstract Compounds that can produce potent biological effects in cells encompass a variety of structural motifs. Many of these compounds share a structural feature that has rarely been noted. It is an allylic cluster of atoms, a 3-carbon chain with a double bond between two of the atoms and an oxygen atom at the other end. The oxygen can be in a hydroxyl group, or in an ether or ketal or ester linkage, or simply a carbonyl form. In the latter case, the linkage is an allylic ketone (ene-one) structure. Nitrogen is often seen in equivalent forms. Inclusion of at least one allylic moiety appears to be able to turn a modestly active or inert compound into an effective drug or toxin. Some compounds lack the allylic moiety but develop one by enzymatic action, usually via cytochrome P-450 enzymes. These metabolites probably represent the active drug forms. The above concepts seem to be radically simplistic and improbable, but the evidence supporting them and the explanations for the biological activities are hidden "in plain view." Comparisons with the pleiotropic activities of the allylic sphingolipid, ceramide, indicate that many allylic drugs operate by controlling the state of protein phosphorylation, by activating proteases, by generating reactive oxygen species, by slowing mitochondrial electron transport, or by lowering cellular glutathione concentrations. Drug Dev Res 69:15,25, 2008 © 2008 Wiley-Liss, Inc. [source]

Synthesis and Characterization of 1-, 2-, and 3-Dimensional Bimetallic UO22+/Zn2+ Phosphonoacetates

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 8 2010
Karah E. Knope
Abstract Four bimetallic UO22+/Zn2+ phosphonoacetates have been prepared from hydrothermal reactions of uranyl nitrate, zinc nitrate, and triethyl phosphonoacetate. These compounds, (UO2)2(PPA)2(H2O)2·Zn(H2O)6·4H2O (1), (UO2)4(PPA)2(HPPA)2·Zn(H2O)6·5H2O·(2), (UO2)2(H2O)2(PPA)2Zn(H2O)4 (3), and (UO2)2(PPA)2(HPPA)Zn2(H2O)2·3(H2O) (4), adopt 1-, 2-, and 3-dimensional architectures wherein the UO22+ cation exhibits coordination preference for the phosphonate over the carboxylate oxygen atoms. The Zn2+ metal centers show an increased degree of ligand coordination with increasing reaction temperature. At 120 °C, compounds 1 and 2 are formed. These structures are 1- and 2-dimensional, respectively, and contain fully hydrated [Zn(H2O)6]2+ cations. At 150 °C and 180 °C, the HPPA ligand displaces H2O molecules from the inner Zn2+ hydration sphere and binds to the metal centers via a ,CO2H oxygen atom in 3 and both carboxylate and phosphonate oxygen atoms in 4. The overall Zn2+ reaction can be expressed by the equation Zn(H2O)62+ + HPPA [rlarr2] Zn(H2O)5(HPPA) + H2O. Presented here are the syntheses, structures, and characterization of these materials. [source]

One-Dimensional Coordination Polymers of MnII, CuII, and ZnII Supported by Carboxylate-Appended (2-Pyridyl)alkylamine Ligands , Structure and Magnetism

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 22 2009
Himanshu Arora
Abstract Four new complexes [MnII(L1OO)(H2O)][ClO4]·2H2O (1), [ZnII(L1OO)][ClO4]·2H2O (2), [CuII(L3OO)][CF3SO3]·H2O (3), and [ZnII(L3OO)][ClO4] (4) (L1OO, = 3-[(2-(pyridine-2-yl)ethyl){2-(pyridine-2-yl)methyl}amino]propionate; L3OO, = 3-[(2-(pyridine-2-yl)ethyl){(dimethylamino)ethyl}amino]propionate) have been synthesized and characterized by elemental analysis, IR, and UV/Vis spectroscopy. Structural analysis revealed that 1, 3, and 4 are one-dimensional chain-like coordination polymers. In 1 distorted octahedral MnN3O3 and in 3 square-pyramidal CuN3O2 coordination is satisfied by three nitrogen atoms and an appended carboxylate oxygen atom of the ligand, and an oxygen atom belonging to the carboxylate group of an adjacent molecule. In 4 trigonal bipyramidal ZnN3O2 coordination environment is provided by two nitrogen atoms and an appended carboxylate oxygen atom of the ligand in the equatorial plane, and the two axial positions are satisfied by a tertiary amine nitrogen and an oxygen atom belonging to the carboxylate group of an adjacent molecule. In 1 the MnII center is coordinated by an additional water molecule. In these complexes each monomeric unit is sequentially connected by syn - anti carboxylate bridges. Temperature-dependent magnetic susceptibilities for 1 and 3 are measured, revealing antiferromagnetic interactions through syn - anti carboxylate bridges between the MII centers. Analysis of the crystal packing diagram reveals that in 1 extensive ,,, stacking involving alternate pyridine rings of adjacent 1D chain exists, which eventually lead to the formation of a 2D network structure. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source]

Control of Intramolecular Ether-Oxygen Coordination in the Crystal Structure of Copper(II) Complexes With Dipicolylamine-Based Ligands

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 8 2007
Yuji Mikata
Abstract Thirteen crystal structures of copper(II) complexes with a series of dipicolylamine (DPA)-derived ligands, N -(2-methoxyethyl)- N,N -bis(2-pyridylmethyl)amine (L1), N -[2-(2-hydroxyethyloxy)ethyl]- N,N -bis(2-pyridylmethyl)amine (L2) and N -(3-methoxypropyl)- N,N -bis(2-pyridylmethyl)amine (L3), have been determined and the factors that control the coordination of the ether-oxygen atom of these ligands to the copper centre are discussed. Complexes that have +1 or +2 charges exhibit coordination of the ether-oxygen atom, whereas neutral complexes in which two anions are bound to the copper(II) centre tend to lose the oxygen coordination. Upon chelation of the oxygen atom, L3 forms a six-membered chelate ring with respect to the 3-aminopropyl ether moiety whereas L1 and L2 form a five-membered chelate. This difference, especially in the nitrate and bromide complexes, determines whether the ether-oxygen atom chelates to the metal centre to give a monocationic complex, or the second anion coordinates to the metal centre to form the ether-free, neutral complex. The terminal anchor hydroxy group of L2 facilitates the ether-oxygen coordination via a hydrogen bond interaction to the donor atom located trans to the aliphatic nitrogen atom in the basal plane. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]

Syntheses, Spectroscopic Studies, and Crystal Structures of Chiral [Rh(aminocarboxylato)(,4 -cod)] and Chiral [Rh(amino alcohol)(,4 -cod)](acetate) Complexes with an Example of a Spontaneous Resolution of a Racemic Mixture into Homochiral Helix-Enantiomers

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 11 2006
Mohammed Enamullah
Abstract The dimeric complex acetato(,4 -cycloocta-1,5-diene)rhodium(I), [Rh(O2CMe)(,4 -cod)]2 (cod = cycloocta-1,5-diene), reacts with amino acids [HAA = L -alanine, (S)-2-amino-2-phenylacetic acid (L -phenylglycine), N -methylglycine, and N -phenylglycine] and with the amino alcohol (S)-2-amino-2-phenylethanol to afford the aminocarboxylato(,4 -cycloocta-1,5-diene)rhodium(I) complexes [Rh(AA)(,4 -cod)] (AA = deprotonated amino acid = aminocarboxylato ligand) and [(S)-2-amino-2-phenylethanol](,4 -cycloocta-1,5-diene)rhodium(I) acetate, [Rh{(S)-HOCH2,CH(Ph)-NH2}(,4 -cod)](O2CMe) (V). The complexes are characterized by IR, UV/Vis, 1H/13C NMR and mass spectroscopy. The achiral N -phenylglycine ligand gives a chiral N -phenylglycinato complex [Rh(O2C,CH2,NHPh)(,4 -cod)] (IV) with the amine nitrogen atom becoming the stereogenic center upon metal coordination. Complex IV crystallizes in the tetragonal, chiral space group P43 and the crystal structure reveals twofold spontaneous resolution of a racemic mixture into homochiral helix-enantiomers. The investigated crystal contained only one type of helix, namely (left-handed or M- ) 43 -helical chains. This is traced first to an intermolecular N,H···O hydrogen bonding from the stereogenic amino group to a neighboring unligated carboxyl oxygen atom that connects only molecules of the same (R)-configuration into (left-handed or M- ) 43 -helical chains. This intrachain homochirality is supplemented, secondly, by the interlocking of adjacent chains with their corrugated van der Waals surface to allow for an interchain transmission of the sense of helicity, building the single crystal from the same homochiral helix-enantiomer. The enantiomeric amino alcohol complex V crystallizes in the monoclinic, noncentrosymmetric (Sohncke) space group P21. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]

Oxidorhenium(V) Complexes of a Family of Bipyridine-Like Ligands Including Pyridyltriazines and Pyrazinyltriazine: Oxygen-Atom Transfer, Metal Redox and Correlations

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 11 2006
Samir Das
Abstract The title ligands (general abbreviation L) are bipyridine (bpy), its dimethyl (mbpy) and diphenyl (pbpy) derivatives, phenanthroline (phen), 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine (ppyt) and its dimethyl (mpyt) and pyrazinyl (ppzt) analogues. The concerned oxido complexes are [ReOCl3(L)],[ReOBr3(ppyt)] and [ReOBr3(ppzt)]. The chloro and bromo complexes of ppyt and ppzt were prepared by reacting these ligands with [ReOX3(AsPh3)2] (X = Cl, Br). The X-ray structures of [ReOCl3(ppyt)] and [ReOCl3(ppzt)] reveal that the ReCl3 fragment is meridionally disposed and that the L ligand is N,N -coordinated such that the pyridine/pyrazine nitrogen lies trans to the oxido oxygen atom. The Re,O lengths [1.656(10)/1.625(9) Å] correspond to approximate triple bonding. The rate of oxygen-atom transfer from [ReOX3(L)] to triphenylphosphane in solution follows second-order kinetics and is associated with a large and negative entropy of activation (approx. ,30 cal,K,1,mol,1). The initial attack is believed to involve the phosphane lone pair and Re,O ,*-orbitals. Electron withdrawal from the ReVO moiety by varying X or L facilitates oxygen-atom transfer. Thus, the rates follow the orders Br < Cl; mbpy < bpy < phen < pbpy << mpyt < ppyt < ppzt. The reduction potential of the quasireversible ReVIO/ReVO couple displays similar trends and the logarithmic rate constant of oxygen-atom transfer is found to correlate linearly with the reduction potential. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]

Nitrosyl Ruthenium Diolato Complexes

Regioselectivity in the Addition of Grignard Reagents to Bis(2-benzothiazolyl) Ketone: C - vs.

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 29 2010
O -Alkylation Using Aryl Grignard Reagents
Abstract The reaction between bis(2-benzothiazolyl) ketone (1) and a series of ring-substituted phenyl Grignard reagents gives, in considerable amount, the unexpected O -alkylation product derived from the attack of the Grignard reagent to thecarbonyl oxygen atom, thus extending the range of rarely reported cases in which O -alkylation can occur. The expected classic 1,2-addition product and that derived from O -alkylation have been obtained in a relative molar ratio dependent on the substituent on the phenyl ring. Bis(2-benzothiazolyl) aryl carbinols, the classic 1,2-addition products to the carbonyl group of 1, were obtained in high yield through an alternative synthetic route that permitted the limit imposed by O - vs. C -alkylation competition to be overcome. [source]

Indium Triiodide Catalyzed Direct Hydroallylation of Esters

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 18 2010
Yoshihiro Nishimoto
Abstract The InI3 -catalyzed hydroallylation of esters by using hydro- and allysilanes under mild conditions has been accomplished. Many significant groups such as alkenyl, alkynyl, cyano, and nitro ones survive under these conditions. This reaction system provided routes to both homoallylic alcohols and ethers, in which either elimination of the alkoxy moiety or of the carbonyl oxygen atom could be freely selected by changing the substituents on the alkoxy moiety and on the hydrosilane. In addition, the hydroallylation of lactones took place without ring cleavage to produce the desired cyclic ethers in high yields. [source]

Pyrrolidino DNA with Bases Corresponding to the 2-Oxo Deletion Mutants of Thymine and Cytosine: Synthesis and Triplex-Forming Properties

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2007
Alain Mayer
Abstract The dual recognition properties of pyrrolidino DNA species as parallel triplex-forming oligonucleotides were previously found to be strongly dependent upon the nature of the pyrimidine bases. In the structure,activity study presented here we were able to exclude this differential binding being due to their 2-oxo function. We had previously reported on the incorporation of pyrrolidino C -nucleosides into triplex-forming 2,-deoxyoligonucleotides (TFOs). The basic nitrogen atom that replaces the 4,-oxygen atom of the 2,-deoxysugar in such modified units introduces a positive charge in the third strand, and this is able to produce favourable electrostatic interaction with the negatively charged DNA target duplex. A first series of pyrrolidino pseudonucleosides with the bases isocytosine and uracil proved successful for GC base-pair recognition, but was unsuccessful for AT base-pair recognition within the parallel triplex binding motif. Here we report on the synthesis of the two novel 2,-deoxypyrrolidino nucleosides carrying the bases pyridin-2-one and 2-aminopyridine, their phosphoramidite building blocks and theirincorporation into TFOs. Pyrrolidinylpyridin-2-one (dp2P) and -2-aminopyridine (dp2AP), prepared as part of a structure,activity profiling of pyrrolidino DNA in triplex binding, are deletion mutants of T and C, respectively. We found by Tm measurements that neither modification increased triplex binding efficiency relative to the iso-C- and -U-containing pyrrolidino TFOs. These experiments clearly show that the C4 carbonyl function, although important for triplex binding through indirect contributions in general, is not responsible for the differential binding of the latter two aminonucleosides and suggest that TFO conformation is more important. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]

Comparison between the Photophysical Properties of Pyrazolo- and Isoxazolo[60]fullerenes with Dual Donors (Ferrocene, Aniline and Alkoxyphenyl)

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 13 2007
Laura Perez
Abstract Two series of new pyrazolo- and isoxazolo[60]fullerenes covalently linked to vinylenephenylene bearing ferrocene, dibutylaniline or dodecyloxyphenyl electron-donor groups attached in the periphery have been synthesized. The photophysical properties of these newly synthesized dual-donor,C60 derivatives have been investigated and compared by applying time-resolved fluorescence and nanosecond transient techniques in both polar and nonpolar solvents. Charge separation via the excited singlet state of C60 is more efficient in the pyrazolo-C60 triads than in the isoxazolo-C60 triads. It was found that the pyrazoline ring mediates charge separation as a result of the stronger electron-donating character of the nitrogen atom of the pyrazoline ring compared with the oxygen atom of the isoxazoline ring. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]

Lewis Acid Induced [2+2] Cycloadditions of Silyl Enol Ethers with ,,,-Unsaturated Esters: A DFT Analysis

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 18 2005
Manuel Arnó
Abstract The Lewis acid (LA) induced cycloaddition of trimethysilyl vinyl ether with methyl acrylate has been studied by DFT methods at the B3LYP/6-31G* level. In the absence of an LA, a [4+2] cycloaddition between the silyl enol ether and methyl acrylate in the s-cis conformation takes place through an asynchronous, concerted bond-formation process. This cycloaddition presents a large activation enthalpy of 21.1 kcal,mol,1. Coordination of the LA AlCl3 to the carbonyl oxygen atom of methyl acrylate yields a change of molecular mechanism from a concerted to a two-step mechanism and produces a drastic reduction of the activation energy. This stepwise mechanism is initialized by the nucleophilic attack of the enol ether at the ,-position of methyl acrylate in a Michael-type addition. The very low activation energy (7.1 kcal,mol,1)associated with this nucleophilic attack can be related to the increase of the electrophilicity of the LA-coordinated ,,,-unsaturated ester, which favors the cycloaddition through a polar process. The subsequent ring-closure allows the formation of the corresponding [2+2] and [4+2] cycloadducts. While the [4+2] cycloadduct is formed by kinetic control, the [2+2] cycloadducts are formed by thermodynamic control. The energetic results provide an explanation for the conversion of [4+2] cycloadducts into the thermodynamically more stable [2+2] ones. The cis/trans ratio found for the catalytic [2+2] process is in agreement with the experimental outcome. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source]

Ring-Expansion of MCPs in the Presence of DIAD or DEAD and Lewis Acids

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 2 2004
Li-Xiong Shao
Abstract Treatment of methylenecyclopropanes (MCPs) with DIAD or DEAD in MeCN under mild conditions in the presence of Lewis acid Zr(OTf)4 gave the cyclobutanone ring-expansion products in good to high yields based on the employed DIAD or DEAD. From a deuterium labeling experiment, the oxygen atom is derived from ambient water. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source]

Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis

FEBS JOURNAL, Issue 3 2002
Evert Bokma
Hevamine is a chitinase from the rubber tree Hevea brasiliensis. Its active site contains Asp125, Glu127, and Tyr183, which interact with the ,1 sugar residue of the substrate. To investigate their role in catalysis, we have successfully expressed wild-type enzyme and mutants of these residues as inclusion bodies in Escherichia coli. After refolding and purification they were characterized by both structural and enzyme kinetic studies. Mutation of Tyr183 to phenylalanine produced an enzyme with a lower kcat and a slightly higher Km than the wild-type enzyme. Mutating Asp125 and Glu127 to alanine gave mutants with ,,2% residual activity. In contrast, the Asp125Asn mutant retained substantial activity, with an approximately twofold lower kcat and an approximately twofold higher Km than the wild-type enzyme. More interestingly, it showed activity to higher pH values than the other variants. The X-ray structure of the Asp125Ala/Glu127Ala double mutant soaked with chitotetraose shows that, compared with wild-type hevamine, the carbonyl oxygen atom of the N -acetyl group of the ,1 sugar residue has rotated away from the C1 atom of that residue. The combined structural and kinetic data show that Asp125,and Tyr183 contribute to catalysis by positioning the,carbonyl oxygen of the N -acetyl group near to the C1 atom. This allows the stabilization of a positively charged transient intermediate, in agreement with a previous proposal that the enzyme makes use of substrate-assisted catalysis. [source]

Stereoselective biosynthesis of chloroarylpropane diols by the basidiomycete Bjerkandera adusta: exploring the roles of amino acids, pyruvate, glycerol and phenyl acetyl carbinol

FEMS MICROBIOLOGY LETTERS, Issue 1 2003
Peter James Silk
Abstract Bjerkandera adusta produces many chlorometabolites including chlorinated anisyl metabolites (CAMs) and 1-arylpropane-1,2-diols (1, 2, 3, 4) as idiophasic metabolic products of l -phenylalanine. These diols are stereoselectively biosynthesized from a C7 -unit (benzylic, from l -phenylalanine) and a C2 -unit, of unknown origin, as predominantly erythro (1R,2S) enantiomers. Of the labeled amino acids tested as possible C2 -units, at the 4,10 mM level, none were found to efficiently label the 2,3-propane carbons of the diols. However, glycine (2- 13C), l -serine (2,3,3-d3) and l -methionine (methyl-d3) entered the biomethylation pathway. Neither pyruvate (2,3- 13C2), acetate (1,2- 13C2), acetaldehyde (d4) nor ethanol (ethyl-d5) labeled the 2,3-propane carbons of the diols at the 4,10 mM level. Pyruvate (2,3- 13C2) and l -serine (2,3,3-d3) (which also entered the biomethylation pathway) did, however, effectively label the 2,3-propane carbons of the ,-ketols and diols at the 40 mM level as evidenced by mass spectrometry. Glycerol (1,1,2,3,3-d5) also appeared to label one of the 2,3-propane carbons (ca. 5% as 2H2 in the C3 side chain) as suggested by mass spectrometric data and also entered the biomethylation pathway, likely via amino acid synthesis. Glycerol (through pyruvate), therefore, likely supplies C2 and C3 of the propane side chain with arylpropane diol biosynthesis. Incubation of B. adusta with synthetic [2- 2H1,2- 18O]-glycerol showed that neither 2H nor 18O were incorporated in the ,-ketols or diols. The oxygen atom on the C2 of the ketols/diols, therefore, does not appear to come from the oxygen atom on the C2 of glycerol. Glycerol, however, can readily form l -serine (which can then form pyruvate via PLP/serine dehydratase and involve transamination washing out the 18O label and providing the oxygen from water), and can then go on to label the C2 -unit. Labeled ,-ketol, phenyl acetyl carbinol (5) (PAC; ring-d5, 2,3- 13C2 propane) cultured with B. adusta leads to stereospecific reduction to the (1R,2S)-diol (6) (ring-d5 and 2,3- 13C2); in all other metabolites produced, the 2,3- 13C2 label is washed out. Incubation of the fungus with 4-fluorobenzaldehyde (13) produces a pooling of predominantly erythro (1R,2S) 1-(4,-fluorophenyl)-1,2-propane diol (18 as diacetate) (through the corresponding ,-ketols 16, 17). Blocking the para-position with fluorine thus appears to prevent ring oxygenation and also chlorination, forcing the conclusion that para-ring oxygenation precedes meta-chlorination. [source]

Enhanced reactivity in the ammonolysis of phenyl thiolacetates in aqueous medium

INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 1 2002
D. Rajarathnam
The ammonolysis of several substituted phenyl thiolacetates is kinetically studied in aqueous medium, 18°C, ionic strength 0.1 M (KCl). By following the leaving groups spectrophotometrically (,max = 260,410 nm), under excess free ammonia, pseudo-first-order rate coefficients (kobs) are obtained. The plots of (kobs , kH) against free ammonia concentration are linear at constant pH. The macroscopic nucleophilic substitution rate coefficients (kN) are obtained as the slopes of these plots and found to be pH-independent for all the thiolesters. The Brönsted-type plot (log kN against pKa of leaving groups) and the Hammett plot (log kN against , values of substituents) obtained for the title reactions of thiolesters are linear with slope values of ,lg = ,0.34 and , = 0.74 respectively. From the magnitude of these values, experimental data, the kinetic law, and the analysis of products, it is deduced that the ammonolysis of thiolesters proceeds through a simple bimolecular nucleophilic substitution pathway with a zwitterionic tetrahedral addition intermediate (T±), whereby its formation is rate-determining (k1 step). Comparison of this reaction of thiolesters with a similar reaction of analogue oxyesters shows a mechanistic difference. Further, for thiolesters there is a rate enhancement with larger kN values. The change in mechanism and enhanced reactivity observed by substitution of the oxygen atom by sulphur atom on the phenyl moiety are discussed in detail. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 34: 18,26, 2002 [source]

Theoretical study of the gas-phase SN2 reactions of X, with CH3OY (X, Y = Cl, Br, I)

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2007
Jing-Gang Gai
Abstract The gas-phase nucleophilic substitution reactions at saturated oxygen X, + CH3OY (X, Y = Cl, Br, I) have been investigated at the level of CCSD(T)/6-311+G(2df,p)//B3LYP/6-311+G(2df,p). The calculated results indicate that X, preferably attacks oxygen atom of CH3OY via a SN2 pathway. The central barriers and overall barriers are respectively in good agreement with both the predictions of Marcus equation and its modification, respectively. Central barrier heights (,H and ,H) correlate well with the charges (Q) of the leaving groups (Y), Wiberg bond orders (BO) and the elongation of the bonds (OY and OX) in the transition structures. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]

Relative energies of conformations and sulfinyl oxygen-induced pentacoordination at silicon in 4-bromo- and 4,4-dibromo-4-silathiacyclohexane 1-oxide: A computational study

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2005
Fillmore Freeman
Abstract The equilibrium geometries and relative energies of the chair, twist, and boat conformations of cis - and trans -4-bromo-4-silathiacyclohexane 1-oxide and 4,4-dibromo-4-silathiacyclohexane 1-oxide have been calculated at the B3LYP/6-311G(d,p) and MP2/6-311+G(d,p) theoretical levels. The axial (SO) chair conformers of the sulfoxides are of lower energy than the chair conformers of the corresponding equatorial (SO) sulfoxides. The chair conformer of the axial (SO) trans -4-bromo-4-silathiacyclohexane 1-oxide is only 0.10 kcal/mol more stable than the corresponding 1,4-boat conformer which is stabilized by a transannular coordination of the sulfinyl oxygen with silicon that results in trigonal bipyramidal geometry at silicon. The 1,4-boat structure of equatorial (SO) trans -4-bromo-4-silathiacyclohexane 1-oxide is a transition state and is 5.77 kcal/mol higher in energy than the respective chair conformer. The 1,4-boat conformer of axial (SO) 4,4-dibromo-4-silathiacyclohexane 1-oxide is also stabilized by transannular coordination of the sulfinyl oxygen and silicon, but it is 4.31 kcal/mol higher in energy than the corresponding chair conformer. The relatively lower stability of the 1,4-boat conformer of 4,4-dibromo-4-silathiacyclohexane 1-oxide may be due to repulsive interactions of the axial halogen and sulfinyl oxygen atom. The relative energies of the conformers and transition states are discussed in terms of hyperconjugative interactions, orbital interactions, nonbonded interactions, and transannular sulfinyl oxygen-silicon coordination. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source]

Hydrogen-bonding effects on electronic g -tensors of semiquinone anion radicals: Relativistic density functional investigation

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2002
Konstantin M. Neyman
Abstract We report results of systematic g -tensor calculations of hydrogen-bonded complexes of two benchmark semiquinone anion radicals, 1,4 -benzoquinone and tetramethyl- 1,4 -benzoquinone (duroquinone), with water and methanol molecules. The calculations have been carried out with the help of a recently developed g -tensor module that is based on a relativistic density functional method that takes spin,orbit interaction self-consistently into account. We demonstrate the applicability of this new computational scheme to describe quantitatively delicate effects of hydrogen bonding on electronic g -tensor values. Also, we explored general trends of how g -tensors depend on the structure and stoichiometry of hydrogen-bonded semiquinone complexes. Complexes exhibiting one hydrogen bond per oxygen atom of the quinones with a linear arrangement of the CO , H moieties were shown to feature g-shifts induced by these hydrogen bonds that are in close agreement with measured electron paramagnetic resonance data. Based on deviations of calculated and measured g-components, we classify all other model complexes studied as less probable under the experimental conditions. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source]

Adsorption of water in mordenite,An ab initio study

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2001
Th. Demuth
Abstract The adsorption of water in mordenite has been investigated using density functional theory using gradient corrections to the exchange,correlation functional. In the neutral complex water is strongly physisorbed through two different hydrogen bonds, the stronger between the acid site and the water oxygen atom, the weaker between a hydrogen atom of the adsorbed molecule and a framework oxygen atom. Strong polarizations and structural distortions of both the acid site and the molecule have been observed. To elucidate the question if a chemisorbed complex (creation of a hydroxonium ion) is possible, ab initio molecular dynamics have been performed, indicating that a protonation of water occurs even for the low coverage of one water molecule per unit cell. However, this ionic configuration cannot be stabilized by the electrostatic field of the zeolite framework and is therefore not a minimum of the potential energy surface. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 110,116, 2001 [source]

The Direct, Enantioselective, One-Pot, Three-Component, Cross-Mannich Reaction of Aldehydes: The Reason for the Higher Reactivity of Aldimine versus Aldehyde in Proline-Mediated Mannich and Aldol Reactions

ADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 11-13 2005
Yujiro Hayashi
Abstract In the proline-mediated Mannich and aldol reactions of propanal as a nucleophile, the aldimine prepared from benzaldehyde and p -anisidine is about 7 times more reactive than the corresponding aldehyde, benzaldehyde, as an electrophile. This higher reactivity of aldimine over aldehyde is attributed to the carboxylic acid of proline protonating the basic nitrogen atom of the aldimine more effectively than the oxygen atom of the aldehyde, an explanation which has been both experimentally and theoretically verified. [source]

Force-field parameters of the , and , around glycosidic bonds to oxygen and sulfur atoms

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2009
Minoru Saito
Abstract The , and , torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for , and , torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the , or , torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the , or , torsion angle. The , and , energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the , and , angles. The remaining energy component curves of , and , were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of , and , for the model glycosides by adopting the , and , force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for , and , well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our , and , force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009 [source]

A comprehensive theoretical study on the hydrolysis of carbonyl sulfide in the neutral water

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2008
Chao Deng
Abstract The detailed hydration mechanism of carbonyl sulfide (COS) in the presence of up to five water molecules has been investigated at the level of HF and MP2 with the basis set of 6-311++G(d, p). The nucleophilic addition of water molecule occurs in a concerted way across the CS bond of COS rather than across the CO bond. This preferential reaction mechanism could be rationalized in terms of Fukui functions for the both nucleophilic and electrophilic attacks. The activation barriers, ,H, for the rate-determining steps of one up to five-water hydrolyses of COS across the CS bond are 199.4, 144.4, 123.0, 115.5, and 107.9 kJ/mol in the gas phase, respectively. The most favorable hydrolysis path of COS involves a sort of eight-membered ring transition structure and other two water molecules near to the nonreactive oxygen atom but not involved in the proton transfer, suggesting that the hydrolysis of COS can be significantly mediated by the water molecule(s) and the cooperative effects of the water molecule(s) in the nonreactive region. The catalytic effect of water molecule(s) due to the alleviation of ring strain in the proton transfer process may result from the synergistic effects of rehybridization and charge reorganization from the precoordination complex to the rate-determining transition state structure induced by water molecule. The studies on the effect of temperature on the hydrolysis of COS show that the higher temperature is unfavorable for the hydrolysis of COS. PCM solvation models almost do not modify the calculated energy barriers in a significant way. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source]

Ab initio QM/MM dynamics of H3O+ in water

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2006
Pathumwadee Intharathep
Abstract A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6,8 water molecules. It is treated at the Hartree-Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O) structure. Besides the three nearest-neighbor water molecules directly hydrogen-bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ion's hydration shell indicate that such next-nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [source]

Synthesis of trisubstituted thiophenes designed as progesterone receptor modulator

JOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 5 2006
Weiqin Jiang
When a known 2-[4-morpholino]-3-aryl-5-substituted thiophene, which showed moderate activity as a progesterone antagonist, was superimposed with a potent steroidal progesterone antagonist Org-33628, it showed a fair alignment in most parts of the molecules. According to the molecular modelling, displacement of the morpholine oxygen atom in the thiophene derivative with a carbonyl group would provide a better alignment with the C-3 carbonyl in Org-33628. Thus, a series of novel trisubstituted thiophenes bearing a cyclic ketone moiety was synthesized. Although these compounds only showed weak activities as progesterone receptor antagonists, all target compounds are novel and are fully characterized. [source]