Status of Inorganic Chemistry Research in India
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Quantum Chemical Cluster Modeling of Enzymatic Reactions Rong-Zhen
Quantum Chemical Cluster Modeling of Enzymatic Reactions Rong-Zhen Liao 1 Rong-Zhen Liao, Stockholm, 2010 ISBN 978-91-7447-129-8 Printed in Sweden by US-AB, Stockholm 2010 Distributor: Department of Organic Chemistry, Stockholm University 2 3 4 Abstract The Quantum chemical cluster approach has been shown to be quite powerful and efficient in the modeling of enzyme active sites and reaction mechanisms. In this thesis, the reaction mechanisms of several enzymes have been investigated using the hybrid density functional B3LYP. The enzymes studied include four dinuclear zinc enzymes, namely dihydroorotase, N-acyl-homoserine lactone hydrolase, RNase Z, and human renal dipeptidase, two trinuclear zinc enzymes, namely phospholipase C and nuclease P1, two tungstoenzymes, namely formaldehyde ferredoxin oxidoreductase and acetylene hydratase, aspartate α-decarboxylase, and mycolic acid cyclopropane synthase. The potential energy profiles for various mechanistic scenarios have been calculated and analyzed. The role of the metal ions as well as important active site residues has been discussed. In the cluster approach, the effects of the parts of the enzyme that are not explicitly included in the model are taken into account using implicit solvation methods. With aspartate α-decarboxylase as an example, systematic evaluation of the solvation effects with the increase of the model size has been performed. At a model size of 150-200 atoms, the solvation effects almost vanish and the choice of the dielectric constant becomes rather insignificant. For all six zinc-dependent enzymes studied, the di-zinc bridging hydroxide has been shown to be capable of performing nucleophilic attack on the substrate. In addition, one, two, or even all three zinc ions participate in the stabilization of the negative charge in the transition states and intermediates, thereby lowering the barriers. -
UNIVERSITY of EMBU EDWARD NDERITU KARANJA Phd 2020
UNIVERSITY OF EMBU EDWARD NDERITU KARANJA PhD 2020 MICROBIAL COMMUNITY DIVERSITY AND STRUCTURE WITHIN ORGANIC AND CONVENTIONAL FARMING SYSTEMS IN CENTRAL HIGHLANDS OF KENYA EDWARD NDERITU KARANJA (MSc) A THESIS SUBMITTED IN PARTIAL FULFILLMENT FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN APPLIED MICROBIOLOGY IN THE UNIVERSITY OF EMBU NOVEMBER, 2020 DECLARATION This thesis is my original work and has not been presented for a degree in any other University Signature……………………………. Date………….……….. Edward Nderitu Karanja Department of Biological Science B801/147/2015 This thesis has been submitted for examination with our approval as the University Supervisors Signature……………………………. Date………….………. Prof. Romano Mwirichia Department of Biological science University of Embu (UoEm), Kenya Signature………. …………………………. Date………….…………. Dr. Andreas Fliessbach Department of Soil Science Research Institute of Organic Agriculture - FIBL, Switzerland i DEDICATION I dedicated to my family; my wife Anne Kelly Kambura, my children; Shawn Karanja, Melissa Wangithi, Joseph Munyuithia, Shayne Koome and Ann Wanjiku, my parents; Mr. Samuel Karanja and Mrs. Agnes Wangithi, my siblings, Ruth Wairimu, Juliet Muthoni, Alex Ngochi, James Karuma and Nelly Njoki. I appreciate the support you have accorded me during my studies. Your inspiration and backing in this journey made it easier to manage all challenges encountered. ii ACKNOWLEDGEMENT I express gratitude toward Almighty God for his mercies from the beginning of this long and thought-provoking journey. This was conducted in the framework of long-term systems comparison program, with financial support from Biovision Foundation, Coop Sustainability Fund, Liechtenstein Development Service (LED) and the Swiss Agency for Development and Cooperation (SDC). I acknowledge icipe core funding for the kind contribution provided by UK-Aid from UK Government, Swedish International Development Cooperation Agency, Swiss Agency for Development and Cooperation, Federal Democratic Republic of Ethiopia and the Kenyan Government. -
Fermentation of Acetylene by an Obligate Anaerobe, Pelobacter Acetylenicus Sp
Archives of Arch Microbiol (1985) 142: 295- 301 Microbiology Springer-Verlag 1985 Fermentation of acetylene by an obligate anaerobe, Pelobacter acetylenicus sp. nov. * Bernhard Schink Fakult/it ffir Biologie, Universit/it Konstanz, Postfach 5560, D-7750 Konstanz, Federal Republic of Germany Abstract. Four strains of strictly anaerobic Gram-negative tion reactions (Schink 1985a). No significant anaerobic rod-shaped non-sporeforming bacteria were enriched and degradation could be observed with ethylene (ethene), the isolated from marine and freshwater sediments with acety- most simple unsaturated hydrocarbon (Schink 1985 a, b). lene (ethine) as sole source of carbon and energy. Acetylene, It was reported recently that also acetylene can be metab- acetoin, ethanolamine, choline, 1,2-propanediol, and glyc- olized in the absence of molecular oxygen (Watanabe and erol were the only substrates utilized for growth, the latter de Guzman 1980). Enrichment cultures with acetylene as two only in the presence of small amounts of acetate. Sub- sole carbon source were obtained in mineral media with strates were fermented by disproportionation to acetate and sulfate as electron acceptor, and acetate could be identified ethanol or the respective higher acids and alcohols. No as an intermediary metabolite (Culbertson et al. 1981). How- cytochromes were detectable; the guanine plus cytosine ever, these enrichment cultures were difficult to maintain, content of the DNA was 57.1 _+ 0.2 tool%. Alcohol dehy- and the acetylene-degrading bacteria could not be identified drogenase, aldehyde dehydrogenase, phosphate acetyl- (C. W. Culbertson and R. S. Oremland, Abstr. 3rd Int. transferase, and acetate kinase were found in high activities Syrup. -
ATP-Dependent Substrate Reduction at an [Fe8s9] Double-Cubane Cluster
ATP-dependent substrate reduction at an [Fe8S9] double-cubane cluster Jae-Hun Jeounga and Holger Dobbeka,1 aInstitut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany Edited by Amy C. Rosenzweig, Northwestern University, Evanston, IL, and approved February 2, 2018 (received for review November 23, 2017) Chemically demanding reductive conversions in biology, such as the We have characterized the two components of a widespread reduction of dinitrogen to ammonia or the Birch-type reduction of system of the third type and find that the electron-accepting – aromatic compounds, depend on Fe/S-cluster containing ATPases. component features a double-cubane [Fe8S9]-cluster. This [Fe8S9]- These reductions are typically catalyzed by two-component systems, cluster, so far unknown to biology, catalyzes reductive reactions in which an Fe/S-cluster–containing ATPase energizes an electron to otherwise associated only with the complex iron–sulfur clusters reduce a metal site on the acceptor protein that drives the reductive of nitrogenases. Our results reveal several parallels between the reaction. Here, we show a two-component system featuring a double-cubane cluster-containing enzymes and nitrogenases μ double-cubane [Fe8S9]-cluster [{Fe4S4(SCys)3}2( 2-S)]. The double- and suggest that an unexplored biochemical reactivity space cubane–cluster-containing enzyme is capable of reducing small mol- may be hidden among the diverse ATP-dependent two-component − ecules, such as acetylene (C2H2), azide (N3 ), and hydrazine (N2H4). enzymes. We thus present a class of metalloenzymes akin in fold, metal clus- ters, and reactivity to nitrogenases. Results Distribution of Double-Cubane Cluster Protein-Like Proteins. -
1 Introduction
Phosphine-catalysed reductive coupling of Dihalophosphanes Jan-Erik Siewert,[a] André Schumann[a] and Christian Hering-Junghans*[a] [a] M.Sc. Jan-Erik Siewert, Dr. André Schumann, Dr. Chirstian Hering-Junghans Leibniz Institute of Catalysis e.V. Rostock (LIKAT) Albert-Einstein-Straße 29a, 18059 Rostock, Germany E-Mail: [email protected] Abstract Classically, tetraorgano diphosphanes have been synthesized through Wurtz-type reductive coupling of halophosphanes R2PX or more recently, through the dehydrocoupling of phosphines R2PH. Catalytic variants of the dehydrocoupling reaction have been reported but are limited to R2PH compounds. Using PEt3 as a catalyst, we now show that TipPBr2 (Tip = 2,4,6-iPr3C6H2) is selectively coupled to give the dibromodiphosphane (TipPBr)2 (1), a compound not accessible using classic Mg reduction. Surprisingly, when using DipPBr2 (Dip = 2,6-iPr3C6H3) in the PEt3-catalysed reductive coupling the diphosphene (PDip) 2 (2) with a P=P double was formed selectively. In benzene solutions (PDip)2 has a half life-time of ca. 28 days and can be utilized with NHCs to access NHC-phosphinidene adducts. Control experiments show that [BrPEt3]Br is a potential oxidation product in the catalytic cycle, which can be then debrominated by using Zn dust as sacrificial reductant. 1 Introduction The formation of element-element bonds in main group chemistry is still dominated by classic stoichiometric salt metathesis and reductive coupling reactions. Only in S1 recent years, catalytic protocols for the dehydrocoupling of main group (p-block) substrates to species with homonuclear (E−E) or heteronuclear (E−E’) bonds have emerged.1-3 Catalysis with earth-abundant metals, in particular Zr, Fe and Ni,4 has been shown to be a viable alternative to using rather expensive systems based on Rh,5-7 Ir7- 10 and Ru.11 Using main-group species to facilitate the homo- or heterocoupling of p- block elements has also been in the focus of current research. -
Substratstereochemie Und Untersuchungen Zum Mechanismus Der 4-Hydroxybutyryl-Coa-Dehydratase Aus Clostridium Aminobutyricum
Substratstereochemie und Untersuchungen zum Mechanismus der 4-Hydroxybutyryl-CoA-Dehydratase aus Clostridium aminobutyricum Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Biologie der Philipps-Universität Marburg vorgelegt von Peter Friedrich aus Marburg/Lahn Marburg/Lahn 2008 Die Untersuchungen zur vorliegenden Arbeit wurden von November 2003 bis November 2008 am Fachbereich Biologie der Philipps-Universität Marburg unter der Leitung von Herrn Prof. Dr. W. Buckel durchgeführt. Vom Fachbereich Biologie der Philipps-Universität Marburg als Dissertation am angenommen. Erstgutachter: Prof. Dr. W. Buckel Zweitgutachter: Prof. Dr. R. Thauer Tag der mündlichen Prüfung: 18.12.2008 für meine Familie für Christine Die Ergebnisse dieser Dissertation sind in folgenden Publikationen veröffentlicht: Friedrich P, Darley DJ, Golding BT, Buckel W (2008) The complete stereochemistry of the enzymatic dehydration of 4-hydroxybutyryl coenzyme A to crotonyl coenzyme A. Angew. Chem. Int. Ed. Engl. 47:3254-3257. Der stereochemische Verlauf der enzymatischen Wassereliminierung von 4-Hydroxybutyryl-Coenzym A zu Crotonyl- Coenzym A. Angew. Chem. 120:3298-3301 Martins BM, Messerschmidt A, Friedrich P, Zhang J, Buckel W (2007) 4-Hydroxybutyryl- CoA dehydratase. In: Messerschmidt A (ed) Handbook of Metalloproteins Online Edition. John Wiley & Sons Ltd., Sussex, UK. Publisched online Dez 2007 weitere Veröffentlichungen: Scott R, Näser U, Friedrich P, Selmer T, Buckel W, Golding BT (2004) Stereochemistry of hydrogen -
Catalysis Science & Technology
Catalysis Science & Technology Accepted Manuscript This is an Accepted Manuscript, which has been through the Royal Society of Chemistry peer review process and has been accepted for publication. Accepted Manuscripts are published online shortly after acceptance, before technical editing, formatting and proof reading. Using this free service, authors can make their results available to the community, in citable form, before we publish the edited article. We will replace this Accepted Manuscript with the edited and formatted Advance Article as soon as it is available. You can find more information about Accepted Manuscripts in the Information for Authors. Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal’s standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains. www.rsc.org/catalysis Page 1 of 34 Catalysis Science & Technology The selective addition of water Verena Resch a,b and Ulf Hanefeld* a a Gebouw voor Scheikunde, Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Manuscript Julianalaan 136, 2628BL Delft, Nederland. bOrganische und Bioorganische Chemie, Institut für Chemie, Karl-Franzens-Universität Graz, Heinrichstrasse 28, 8010 Graz, Österreich. Abstract: Water is omnipresent and essential. Yet at the same time it is a rather unreactive Accepted molecule. The direct addition of water to C=C double bonds is therefore a challenge not answered convincingly. In this perspective we critically evaluate the selectivity and the applicability of the different catalytic approaches for water addition reactions, homogeneous, heterogeneous and bio- catalytic. -
Mechanism of Tungsten-Dependent Acetylene Hydratase from Quantum Chemical Calculations
Mechanism of tungsten-dependent acetylene hydratase from quantum chemical calculations Rong-Zhen Liaoa,b, Jian-Guo Yub, and Fahmi Himoa,1 aDepartment of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden; and bCollege of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China Edited* by Arieh Warshel, University of Southern California, Los Angeles, CA, and approved November 12, 2010 (received for review September 20, 2010) Acetylene hydratase is a tungsten-dependent enzyme that cata- lyzes the nonredox hydration of acetylene to acetaldehyde. Density functional theory calculations are used to elucidate the reaction mechanism of this enzyme with a large model of the active site devised on the basis of the native X-ray crystal structure. Based Scheme 1. Reaction catalyzed by AH. on the calculations, we propose a new mechanism in which the acetylene substrate first displaces the W-coordinated water mole- The catalytic mechanism of AH is presently poorly under- cule, and then undergoes a nucleophilic attack by the water mole- stood. The mechanistic proposals can be divided into two groups, cule assisted by an ionized Asp13 residue at the active site. This is first- and second-shell mechanisms. Based on the crystal struc- followed by proton transfer from Asp13 to the newly formed vinyl ture, Seiffert et al. proposed a second-shell mechanism in which anion intermediate. In the subsequent isomerization, Asp13 shut- the W-bound water functions as an electrophile to deliver a pro- tles a proton from the hydroxyl group of the vinyl alcohol to the ton to the acetylene substrate (9). -
SUPERCLUSTERS a Search for Novel Structures and Functions Of
ytSolZo 0o )H(* SUPERCLUSTERS A search for novel structures and functions of biological iron-sulfur clusters A.F. Arendsen 5^2-C^ ~Y^8 Promotoren: DrC .Veeger , Emeritus hoogleraar ind eBiochemi e Landbouwuniversiteit te Wageningen DrW.R .Hagen , Hoogleraar ind eFysisch eChemi e KatholiekeUniversitei t Nijmegen (U <MO27.O! . £i<f£> A.F. Arendsen SUPERCLUSTERS Asearc hfo rnove lstructure san d functions ofbiologica liron-sulfu r clusters Proefschrift ter verkrijging van de graad van doctor opgeza g van derecto r magnificus, DrCM .Karsse n in het openbaar te verdedigen op 1oktobe r 1996 desnamiddag st evie r uuri nd eAul a van de Landbouwuniversiteit te Wageningen W-YAV-Z7 <r- r) »to. - » IWO ISBN 90-5485-595-9 The research described in this thesis was financially supported by the Netherlands Organization of Scientific Research (NWO) under the auspices of the Netherlands Foundation for Chemical Research (SON) 1. Het afbeelden van de natuur als een levende, uitvoerende instantie is een vorm van wetenschappelijk animisme. J.J.P. Frausto da Silva & RJ.P. Williams (1991) in The Biological Chemistry of the Elements, Oxford University Press, Oxford. 2. Het ferredoxine uit Desulfovibrio vulgaris (Hildenborough) is mogelijkerwijs een ferreguline. Dit proefschrift, hoofdstuk 5 3. De hoge redoxpotentiaal van de wolfraam in het aldehyde oxidoreductase uit Pyrococcus furiosus doet geen lampje opgaan over de biologische functie van dit metaal. Dit proefschrift, hoofdstuk 6 4. Het veelvuldig citeren uit overzichtsartikelen betekent een onderwaardering van het oorspronkelijke, experimentele werk, leidt gemakkelijk tot verspreiding van onjuist gei'nterpreteerde of foutief overgenomen gegevens, en dient om deze redenen vermeden te worden. -
Nomenclature of Inorganic Chemistry (IUPAC Recommendations 2005)
NOMENCLATURE OF INORGANIC CHEMISTRY IUPAC Recommendations 2005 IUPAC Periodic Table of the Elements 118 1 2 21314151617 H He 3 4 5 6 7 8 9 10 Li Be B C N O F Ne 11 12 13 14 15 16 17 18 3456 78910 11 12 Na Mg Al Si P S Cl Ar 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe 55 56 * 57− 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Cs Ba lanthanoids Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn 87 88 ‡ 89− 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 Fr Ra actinoids Rf Db Sg Bh Hs Mt Ds Rg Uub Uut Uuq Uup Uuh Uus Uuo * 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu ‡ 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr International Union of Pure and Applied Chemistry Nomenclature of Inorganic Chemistry IUPAC RECOMMENDATIONS 2005 Issued by the Division of Chemical Nomenclature and Structure Representation in collaboration with the Division of Inorganic Chemistry Prepared for publication by Neil G. -
On the Michael Addition of Water to C = C Bonds
ON THE MICHAEL ADDITION OF WATER TO C = C BONDS ON THE MICHAEL ADDITION OF WATER TO C = C BONDS Proefschrift ter verkrijging van de graad van doctor aan de Technische Universiteit Delft, op gezag van de RectorMagnificus Prof. ir. K. C. A. M. Luyben, voorzitter van het College voor Promoties, in het openbaar te verdedigen op dinsdag 01 September 2015 om 10:00 uur door Bishuang CHEN Master in Organic Chemistry, Xiamen University, Xiamen, China geboren te Putian, Fujian Province, China Dit proefschrift is goedgekeurd door de promotoren: Prof. dr. Ulf Hanefeld Samenstelling promotiecommissie: Rector Magnificus, voorzitter Prof. dr. Ulf Hanefeld, Technische Universiteit Delft, promotor Prof. dr. W.R. Hagen, Technische Universiteit Delft Dr. ir. F. Hollmann Technische Universiteit Delft Prof. dr. W.J.H. van Berkel Wageningen University Prof. dr. J.G. Roelfes University of Groningen Prof. dr. H. Gröger Bielefeld University, Duitsland Dr. V.A. Resch University of Graz, Graz Prof. dr. I.W.C.E. Arends Technische Universiteit Delft, reserved water, Michael hydratase, ene-reductase, Rhodococcus, Keywords: -hydroxy carbonyl compound Printed by: Ipskamp Drukkers biocatalysis, lipase, β Cover by: Huayang Cai ISBN: 978-94-6259-773-0 Copyright © 2015 Bishuang CHEN An electronic version of this dissertation is available at http://repository.tudelft.nl/ All rights reserved. No parts of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photo-copying, recording, or otherwise, without the prior written permission of the author. To my parents Contents 1 Stereochemistry of enzymatic water addition to C=C bonds .................. -
All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA