DOCSLIB.ORG

Vizualizace Parciálních Atomových Náboj ˚U V Molekulách

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Vizualizace Parciálních Atomových Náboj ˚U V Molekulách MASARYKOVA UNIVERZITA F}w¡¢£¤¥¦§¨ AKULTA INFORMATIKY !"#$%&'()+,-./012345<yA| Vizualizace parciálních atomových náboj ˚uv molekulách BAKALÁRSKÁˇ PRÁCE Jakub Vá ˇna Brno, podzim 2010 Prohlášení Prohlašuji, že tato bakaláˇrskápráce je mým p ˚uvodnímautorským dílem, které jsem vypracoval samostatnˇe.Všechny zdroje, prameny a literaturu, které jsem pˇrivypracování používal nebo z nich ˇcerpal,v práci ˇrádnˇecituji s uvedením úplného odkazu na pˇríslušnýzdroj. Jakub Váˇna Vedoucí práce: RNDr. Radka Svobodová Vaˇreková,Ph.D. ii Podˇekování Rád bych podˇekovalpaní RNDr. Radce Svobodové Vaˇrekové,Ph.D. za vedení mé práce. Pˇre- devším bych rád vyzdvihl její peˇclivost,trpˇelivosta obˇetavost.Dále bych rád podˇekovalsvým rodiˇc˚umza d ˚uvˇeru a podporu ve studiu. iii Shrnutí V pˇrírodovˇednýchi dalších oborech je v posledních desetiletích experiment jako metoda ˇcasto doplnˇennebo nahrazen matematickými výpoˇcty, pˇrípadnˇesimulacemi. Klíˇcovýmobjektem v tˇechtovýpoˇctechje molekula, protože je nositelem chemických vlastností látek. Pro práci chemik ˚uˇcibiolog ˚ujsou rovnˇežvelmi d ˚uležitéinformace o parciálních nábojích na atomech v rámci molekuly. Tyto náboje jsou reálná ˇcísla,která popisují, jakou ˇcást elektron ˚uz molekuly (tzv. elektronové hustoty) si daný atom pˇritáhnuldo své blízkosti nebo naopak odevzdal jiným atom ˚um.Ideálním zp ˚usobem,jak zprostˇredkovatinformace o nábojích, je jejich vizualizace. Díky vizualizaci jsme napˇríkladschopni posoudit, kde je náboj na molekule koncentrován a která místa jsou nábojovˇeneutrální. Právˇetématem vizualizace parciálních náboj ˚use zabývá má bakaláˇrskápráce. V rámci této práce jsem se nejdˇríveseznámil se zp ˚usobemreprezetace molekuly v poˇcítaˇcia s formáty pro zápis struktury molekuly a jejích parciálních náboj ˚u.Dále jsem nastudoval modely pro vizu- alizaci molekuly a parciálních náboj ˚u.Všechny tyto informace jsem shrnul v textu své práce. Poté jsem vyhledal softwarové nástroje vhodné pro vizualizaci náboj ˚u– VMD, Jmol, Chem3D, DSV a Mol2mol. Využitelnost tˇechtonástroj ˚ujsem analyzoval na tˇrechr ˚uznýchtypech molekul (malá organická molekula, peptid a protein) a v práci popsal jejich silné a slabé stránky. iv Klíˇcováslova Parciální náboje na atomech, vizualizace náboj ˚u,molekuly, 3D struktury, MOL, MOL2, PDB, VMD, MOE, Jmol, Mol2mol, Chem3D, DSV v Obsah 1 Úvod ............................................... 1 2 Teoretická ˇcást .......................................... 2 2.1 Molekula v poˇcítaˇci .................................... 2 2.1.1 Poˇcítaˇcovýzápis molekul . 2 2.1.2 Grafické modely molekul . 2 2.1.3 Grafické modely povrchu molekul . 3 2.1.4 Zp ˚usobyvizualizace povrchu molekul . 5 2.2 Základní chemické pojmy ................................ 7 2.2.1 Parciální náboj . 7 2.3 Vizualizace náboj ˚u .................................... 8 2.3.1 Zabarvení atom ˚ua vazeb podle hodnoty parciálního náboje . 8 2.3.2 Velikost atom ˚upodle hodnoty parciálního náboje . 9 2.3.3 Zabarvení povrchu molekuly podle hodnoty parciálního náboje . 9 3 Metodická a implementaˇcníˇcást ............................... 10 3.1 Použité datové formáty .................................. 10 3.1.1 Formát PDB . 10 3.1.2 Formát PDBQ . 11 3.1.3 Formát MOL . 11 3.1.4 Formát MOL2 . 12 3.1.5 Formát Gaussian . 13 3.2 Použité softwarové nástroje ............................... 14 3.2.1 Open Babel . 14 3.2.2 VMD . 15 3.2.3 Jmol . 17 3.2.4 MOE . 19 3.2.5 Chem3D . 21 3.2.6 DSV . 24 3.2.7 Mol2mol . 27 3.2.8 Software bez možnosti vizualizace náboje . 28 3.3 Implementace programu Import charges ........................ 29 3.3.1 Programovací jazyk . 29 3.3.2 Funkcionalita . 29 3.3.3 Vstup a výstup . 29 3.3.4 Volání . 30 4 Výsledky a diskuse ....................................... 31 4.1 Ukázka výpoˇctunáboj ˚u ................................. 31 4.2 Vizualizace molekul ................................... 32 4.2.1 Vizualizace malé molekuly . 33 4.2.2 Vizualizace stˇrednímolekuly . 35 4.2.3 Vizualizace velké molekuly . 37 4.3 Pˇrehleda srovnání vlastností softwarových nástroj ˚u . 38 4.3.1 Komentáˇrek jednotlivým program ˚um. 38 4.3.2 Pˇrehledvlastností nástroj ˚u . 40 5 Závˇer ............................................... 41 6 Pˇrílohy .............................................. 43 6.1 Obsah pˇriloženéhoDVD ................................. 43 vi 6.2 Skript Jmol ......................................... 44 6.3 Dodateˇcnévizualizace vytvoˇrenév rámci práce .................... 44 6.4 Vizualizace extra velké molekuly ............................ 46 6.5 RasMol ........................................... 47 6.6 Formát POV ........................................ 48 vii 1 Úvod V pˇrírodovˇednýchi dalších oborech je v posledních desetiletích experiment jako metoda ˇcasto doplnˇennebo nahrazen matematickými výpoˇcty, pˇrípadnˇesimulacemi. Takto vznikly nové vˇedníobory, jako tˇrebapoˇcítaˇcováchemie, bioinformatika, chemoinformatika nebo systémová biologie. Klíˇcovýmobjektem v tˇechtovˇedníchdisciplínách je molekula, protože je nositelem chemických vlastností látek. Pro práci chemik ˚uˇcibiolog ˚ujsou velmi d ˚uležitéinformace o par- ciálních nábojích [1] na atomech v rámci molekuly. Tyto náboje jsou reálná ˇcísla,která popisují, jakou ˇcástelektron ˚uz molekuly (tzv. elektronové hustoty) si daný atom pˇritáhnuldo své blíz- kosti nebo naopak odevzdal jiným atom ˚um.Parciální náboje ukazují místa s vysokým a nízkým výskytem elektron ˚uneboli místa, v nichž nejpravdˇepodobnˇejidochází k chemickým reakcím. Navíc jsou náboje také významnými veliˇcinamipro výpoˇctyrealizované bˇehempoˇcítaˇcovˇe chemických simulací [1, 2] a v chemoinformatických modelech [3, 4]. V souˇcasnédobˇeje dostupné velké množství informací o struktuˇreorganických molekul a biomolekul a také máme k dispozici vysoce výkonné poˇcítaˇcea nové softwarové nástroje pro výpoˇcetnáboj ˚u.Proto jsou náboje stále populárnˇejšímicharakteristikami pro popis chemického chování molekuly. Ideálním zp ˚usobem,jak chemik ˚uma biolog ˚umzprostˇredkovatinformaci o nábojích, je tyto náboje vizualizovat. Díky vizualizaci jsme schopni posoudit, kde je náboj na molekule koncentrován a která místa jsou nábojovˇeneutrální. Takto získáme celkový pˇrehledo distribuci náboj ˚uv rámci molekuly pˇrípadnˇejejí studované ˇcásti.Tématem vizualizace náboj ˚u se zabývá má bakaláˇrskápráce. Konkrétní cíle práce jsou: • Seznámit se se zp ˚usobemreprezentace molekuly v poˇcítaˇcia s formáty pro zápis struk- tury molekuly a náboj ˚ujejích atom ˚u. • Nastudovat a popsat r ˚uznézp ˚usobyzobrazování náboj ˚u. • Vyhledat softwarové nástroje pro vizualizaci náboj ˚u. • Analyzovat využitelnost tohoto softwaru a popsat jeho silné a slabé stránky. • Ukázat využití vybraného softwaru pro vizualizaci r ˚uzných typ ˚umolekul (malé orga- nické molekuly, biomolekuly, . ). 1 2 Teoretická ˇcást 2.1 Molekula v poˇcítaˇci 2.1.1 Poˇcítaˇcovýzápis molekul Molekuly mohou být zapsány v poˇcítaˇcimnoha zp ˚usoby[3], ale základ bývá vˇetšinoustejný. Soubor s informacemi o molekule by mˇelobsahovat alespoˇnnásledující údaje o každém atomu molekuly: • ID atomu, tj. jeho unikátní identifikátor • chemickou znaˇckuatomu • kartézské souˇradniceatomu • informace o vazbách daného atomu s ostatními atomy Soubory popisující molekuly mohou pˇrípadnˇeobsahovat další informace, záleží na definici for- mátu použitého pro zápis molekuly. Mohou to být napˇríkladinformace o sekundárních struk- turách, hodnotách parciálního náboje, typech atomových vazeb a jiné. 2.1.2 Grafické modely molekul V poˇcítaˇcovéchemii a dalších souvisejících oborech mohou být molekuly vizualizovány r ˚uz- nými zp ˚usoby[1]. Zde si krátce popíšeme nˇekterénejˇcastˇejipoužívané grafické modely. Ukázky tˇechtomodel ˚unaleznete na obrázku 2.1. Drátový model (wire-frame): V drátovém modelu jsou atomy zmenšeny do velikosti ma- lých bod ˚ua vazby jsou zobrazeny jako tenké ˇcáryspojující tyto body. Velikosti ˇcarjsou ne- mˇenné. Tyˇcinkovýmodel (sticks): Obdobné jako drátový model, ale místo ˇcarjsou použity tyˇcinky o r ˚uznémpolomˇeru. Atomy opˇetnejsou viditelné. Tyˇcinkya kuliˇcky(ball & sticks): V modelu "tyˇcinkya kuliˇcky"jsou atomy reprezentovány jako malé koule a vazby jako tyˇcinkyspojující tyto kuliˇcky. Velikosti kuliˇceka tyˇcinek se mohou lišit v závislosti na nastavení. Kalotový model (CPK, spacefill): CPK model je pojmenován po chemicích Robertu Co- reym, Linusi Paulingovi a Walteru Koltunovi. Model vyobrazuje pouze atomy jako velké koule bez propojení, jejichž velikosti atom ˚uodpovídají polovinˇevan der Waalsova polomˇeru. Tento polomˇerje roven vzdálenosti, na kterou se k atomu m ˚užepˇriblížitdruhý atom stejného prvku. OznaˇceníCPK se zároveˇnpoužívá i jako oznaˇcenípro barevné schéma [5]. Šedá barva pro uhlík, ˇcervenákyslík, bílá vodík, oranžová fosfor apod. Toto barevné schéma bylo použito na obrázku 2.1. 2 2. TEORETICKÁ CÁSTˇ (a) Ukázka drátového modelu (b) Ukázka tyˇcinkovéhomodelu (c) Ukázka modelu tyˇcinkya kuliˇcky (d) Ukázka kalotového modelu Obrázek 2.1: Ukázka model ˚umolekul 2.1.3 Grafické modely povrchu molekul Pˇrivizualizaci molekul je velmi d ˚uležitýmtématem vizualizace jejich povrchu. Povrch mo- lekuly lze vyjádˇritrovnˇežpomocí r ˚uznýchgrafických model ˚u.Nejˇcastˇejipoužívané modely povrchu molekuly jsou popsány níže: Van der Waals ˚uvpovrch [6]: Tento povrch (dále jen vdW povrch) je spojením sférických povrch ˚uatom ˚udefinovaných van der Waalsovým polomˇerem urˇcenýmpro každý atom mole- kuly. Obrázek 2.2: Ukázka vdW povrchu pro molekulu cilengitidu 3 2. TEORETICKÁ CÁSTˇ 3D izopovrch [7]: Znaˇcípovrch reprezentující
Load more

Recommended publications
  • Open Babel Documentation Release 2.3.1
    Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options .................................................
    [Show full text]
  • Chemical File Format Conversion Tools : a N Overview
    International Journal of Engineering Research & Technology (IJERT) ISSN: 2278-0181 Vol. 3 Issue 2, February - 2014 Chemical File Format Conversion Tools : A n Overview Kavitha C. R Dr. T Mahalekshmi Research Scholar, Bharathiyar University Principal Dept of Computer Applications Sree Narayana Institute of Technology SNGIST Kollam, India Cochin, India Abstract— There are a lot of chemical data stored in large different chemical file formats. Three types of file format databases, repositories and other resources. These data are used conversion tools are discussed in section III. And the by different researchers in different applications in various areas conclusion is given in section IV followed by the references. of chemistry. Since these data are stored in several standard chemical file formats, there is a need for the inter-conversion of II. CHEMICAL FILE FORMATS chemical structures between different formats because all the formats are not supported by various software and tools used by A chemical is a collection of atoms bonded together the researchers. Therefore it becomes essential to convert one file in space. The structure of a chemical makes it unique and format to another. This paper reviews some of the chemical file gives it its physical and biological characteristics. This formats and also presents a few inter-conversion tools such as structure is represented in a variety of chemical file formats. Open Babel [1], Mol converter [2] and CncTranslate [3]. These formats are used to represent chemical structure records and its associated data fields. Some of the file Keywords— File format Conversion, Open Babel, mol formats are CML (Chemical Markup Language), SDF converter, CncTranslate, inter- conversion tools.
    [Show full text]
  • Titelei 1..30
    Johann Gasteiger, Thomas Engel (Eds.) Chemoinformatics Chemoinformatics: A Textbook. Edited by Johann Gasteiger and Thomas Engel Copyright 2003 Wiley-VCH Verlag GmbH & Co. KGaA. ISBN: 3-527-30681-1 Related Titles from WILEY-VCH Hans-Dieter HoÈltje, Wolfgang Sippl, Didier Rognan, Gerd Folkers Molecular Modeling 2003 ISBN 3-527-30589-0 Helmut GuÈnzler, Hans-Ulrich Gremlich IR Spectroscopy An Introduction 2002 ISBN 3-527-28896-1 Jure Zupan, Johann Gasteiger Neural Networks in Chemistry and Drug Design An Introduction 1999 ISBN 3-527-29778-2 (HC) ISBN 3-527-29779-0 (SC) Siegmar Braun, Hans-Otto Kalinowski, Stefan Berger 150 and More Basic NMR Experiments A Practical Course 1998 ISBN 3-527-29512-7 Johann Gasteiger, Thomas Engel (Eds.) Chemoinformatics A Textbook Editors: This book was carefully produced. Never- theless, editors, authors and publisher do Prof. Dr. Johann Gasteiger not warrant the information contained Computer-Chemie-Centrum and Institute therein to be free of errors. Readers are ofOrganic Chemistry advised to keep in mind that statements, University ofErlangen-NuÈrnberg data, illustrations, procedural details or NaÈgelsbachstraûe 25 other items may inadvertently be inaccurate. 91052 Erlangen Germany Library of Congress Card No.: applied for A catalogue record for this book is available from the British Library. Dr. Thomas Engel Computer-Chemie-Centrum and Institute Bibliographic information published by ofOrganic Chemistry Die Deutsche Bibliothek University ofErlangen-NuÈrnberg Die Deutsche Bibliothek lists this publica- NaÈgelsbachstraûe 25 tion in the Deutsche Nationalbibliografie; 91052 Erlangen detailed bibliographic data is available in the Germany Internet at http://dnb.ddb.de ISBN 3-527-30681-1 c 2003 WILEY-VCH Verlag GmbH & Co.
    [Show full text]
  • Multitarget Molecular Hybrids of Cinnamic Acids
    Molecules 2014, 19, 20197-20226; doi:10.3390/molecules191220197 OPEN ACCESS molecules ISSN 1420-3049 www.mdpi.com/journal/molecules Article Multitarget Molecular Hybrids of Cinnamic Acids Aikaterini Peperidou 1, Dorothea Kapoukranidou 2, Christos Kontogiorgis 3 and Dimitra Hadjipavlou-Litina 1,* 1 Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; E-Mail: [email protected] 2 Department of Physiology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; E-Mail: [email protected] 3 Laboratory of Hygiene and Environmental Protection, Medical School, Democritus University of Thrace, Dragana (Campus), Alexandroupolis 68100, Greece; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +30-231-099-7627; Fax: +30-231-099-7679. External Editor: Derek J. McPhee Received: 27 October 2014; in revised form: 14 November 2014 / Accepted: 25 November 2014 / Published: 2 December 2014 Abstract: In an attempt to synthesize potential new multitarget agents, 11 novel hybrids incorporating cinnamic acids and paracetamol, 4-/7-hydroxycoumarin, benzocaine, p-aminophenol and m-aminophenol were synthesized. Three hybrids—2e, 2a, 2g—and 3b were found to be multifunctional agents. The hybrid 2e derived from the phenoxyphenyl cinnamic acid and m-acetamidophenol showed the highest lipoxygenase (LOX) inhibition and analgesic activity (IC50 = 0.34 μΜ and 98.1%, whereas the hybrid 3b of bromobenzyloxycinnamic acid and hymechromone exhibited simultaneously good LOX inhibitory activity (IC50 = 50 μΜ) and the highest anti-proteolytic activity (IC50= 5 μΜ). The hybrid 2a of phenyloxyphenyl acid with paracetamol showed a high analgesic activity (91%) and appears to be a promising agent for treating peripheral nerve injuries.
    [Show full text]
  • Titelei 1..30
    Johann Gasteiger, Thomas Engel (Eds.) Chemoinformatics Chemoinformatics: A Textbook. Edited by Johann Gasteiger and Thomas Engel Copyright 2003 Wiley-VCH Verlag GmbH & Co. KGaA. ISBN: 3-527-30681-1 Related Titles from WILEY-VCH Hans-Dieter HoÈltje, Wolfgang Sippl, Didier Rognan, Gerd Folkers Molecular Modeling 2003 ISBN 3-527-30589-0 Helmut GuÈnzler, Hans-Ulrich Gremlich IR Spectroscopy An Introduction 2002 ISBN 3-527-28896-1 Jure Zupan, Johann Gasteiger Neural Networks in Chemistry and Drug Design An Introduction 1999 ISBN 3-527-29778-2 (HC) ISBN 3-527-29779-0 (SC) Siegmar Braun, Hans-Otto Kalinowski, Stefan Berger 150 and More Basic NMR Experiments A Practical Course 1998 ISBN 3-527-29512-7 Johann Gasteiger, Thomas Engel (Eds.) Chemoinformatics A Textbook Editors: This book was carefully produced. Never- theless, editors, authors and publisher do Prof. Dr. Johann Gasteiger not warrant the information contained Computer-Chemie-Centrum and Institute therein to be free of errors. Readers are ofOrganic Chemistry advised to keep in mind that statements, University ofErlangen-NuÈrnberg data, illustrations, procedural details or NaÈgelsbachstraûe 25 other items may inadvertently be inaccurate. 91052 Erlangen Germany Library of Congress Card No.: applied for A catalogue record for this book is available from the British Library. Dr. Thomas Engel Computer-Chemie-Centrum and Institute Bibliographic information published by ofOrganic Chemistry Die Deutsche Bibliothek University ofErlangen-NuÈrnberg Die Deutsche Bibliothek lists this publica- NaÈgelsbachstraûe 25 tion in the Deutsche Nationalbibliografie; 91052 Erlangen detailed bibliographic data is available in the Germany Internet at http://dnb.ddb.de ISBN 3-527-30681-1 c 2003 WILEY-VCH Verlag GmbH & Co.
    [Show full text]
  • Open Babel Documentation
    Open Babel Documentation Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) Mar 26, 2021 Contents 1 Introduction 3 1.1 Goals of the Open Babel project.....................................3 1.2 Frequently Asked Questions.......................................4 1.3 Thanks..................................................7 2 Install Open Babel 11 2.1 Install a binary package......................................... 11 2.2 Compiling Open Babel.......................................... 11 3 obabel - Convert, Filter and Manipulate Chemical Data 19 3.1 Synopsis................................................. 19 3.2 Options.................................................. 19 3.3 Examples................................................. 22 3.4 Format Options.............................................. 24 3.5 Append property values to the title.................................... 24 3.6 Generating conformers for structures.................................. 24 3.7 Filtering molecules from a multimolecule file.............................. 25 3.8 Substructure and similarity searching.................................. 28 3.9 Sorting molecules............................................ 28 3.10 Remove duplicate molecules....................................... 28 3.11 Aliases for chemical groups....................................... 29 3.12 Forcefield energy and minimization................................... 30 3.13 Aligning molecules or substructures..................................
    [Show full text]
  • S.A. Raja Pharmacy College Vadakkangulam-627 116
    S.A. RAJA PHARMACY COLLEGE VADAKKANGULAM-627 116 MEDICINAL CHEMISTRY -III VI SEMESTER B. PHARM PRACTICAL MANUAL CONTENT S.No Experiment Name Page No. 1. Synthesis of Sulphanilamide 01 2. Synthesis of 7- Hydroxy -4- methyl coumarin 03 3. Synthesis of Chlorbutanol 05 4. Synthesis of Tolbutamide 07 5. Synthesis of Hexamine 09 6. Assay of Isonicotinic acid hydrazide 11 7. Assay of Metronidazole 13 8. Assay of Dapsone 16 9. Assay of Chlorpheniramine Maleate 18 10. Assay of Benzyl Penicillin 20 11. Synthesis of Phenytoin from Benzil by Microwave 23 Irradiation 12. Synthesis of Aspirin Assisted by Microwave Oven 26 13. Drawing structure and Reaction using Chemsketch 28 MEDICINAL CHEMISTRY- III Experiment No: 01 Synthesis of Sulphanilamide Aim: To synthesis and submit sulphanilamide from p-acetamido benzene sulphanilamide and calculate its percentage yield. Principle: Sulphanilamide can be prepared by the reaction of P-acetamido benzene sulphanilamide with Hydrochloric acid or ammonium carbonate. The acetamido groups are easily undergo acid catalysed hydrolysis reaction to form p-amino benzene sulphonamide. Reaction: O HN H2N HCl O S O O S O NH NH2 2 4 Acetamidobenzene sulphonamide p Amino benzene sulphonamide Chemical Required: Resorcinol - 1.2 g Ethyl acetoacetate - 2.4 ml Conc. Sulphuric acid - 7.5 ml Procedure: 1.5 gm of 4- acetamido benzene sulphonamide is treated with a mixture of 1 ml of conc. Sulphuric acid diluted with 2 ml water. This mixture is gently heated under reflux for 1 hour. Then 3ml of water is added and the solution is boiled again, with the addition of a small quantity of activated charcoal.
    [Show full text]
  • Ab Initio Methods 268, 303, 304, 320, 327–333, 335–337 Ab
    555 Index a allosteric 315, 382 ab initio methods 268, 303, 304, 320, AMBER 280, 281, 283, 284, 286, 288, 327–333, 335–337 293–295, 303, 304, 311, 312, 315, ab initio molecular dynamics (MD) 316 303, 304 AM1 326, 327 absorption band 168 analytical chemistry 214, 399, 423, 434 acidity 128, 130, 336 angle bending 283–284, 289, 295 activity cliffs 458, 468, 470 antimalarial 479, 480 addition reaction 141 antioxidation 369 adjacency matrix 18–21, 367 applicability domain (AD) 158, 346, ADME (absorption, distribution, 434, 450, 466, 468, 475–478 metabolism and excretion) 384, application programming interface 466 (API) 71, 222 advanced interatomic potentials Arabidopsis Information Resource 207 290–291 arithmetic mean 288, 402, 414, 433 adverse drug reactions (ADRs) 479 aromaticity 29, 48, 79, 109, 110, 144, agglomerative HCA 420 193 ALADDIN 362 aromatization 469, 484, 486 algorithms artificial intelligence (AI) 166, 168, 453 backtracking 83, 236–239, 251, 258 brute force 237 artificial neural network (ANN) 345, complexity 232 346, 438, 442–451, 467 deep learning 453 asphericity 378 depth-first search 238 association coefficients 247, 248 dynamic programming 256–258 atom-by-atom 163, 164, 237, 243 efficiency 232 atomic mean force potentials 517 hash 49 atomic orbitals (AOs) 321–325, heuristic 415 327–329 leapfrog 304 atom pairs (AP) 249, 283, 287, 288, learning 380, 453, 458, 529 303, 304, 352, 359–362 alignment atom surface assignments (ASA) 381 global 256 atropisomers 32 local 258 attenuation models 271–277, 384 pair-wise 254 augmented annealing 445 target-template 516 augmented atoms (AA) 249 Chemoinformatics: Basic Concepts and Methods, First Edition.
    [Show full text]
  • Open Babel Documentation Release 2.3.1
    Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) February 28, 2012 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Generating conformers for structures .................................. 22 3.8 Filtering molecules from a multimolecule file .............................. 23 3.9 Substructure and similarity searching .................................. 25 3.10 Sorting molecules ............................................ 26 3.11 Remove duplicate molecules ....................................... 26 3.12 Aliases for chemical groups ....................................... 27 4 The Open Babel GUI 29 4.1
    [Show full text]
  • Open Babel: an Open Chemical Toolbox Noel M O’Boyle1, Michael Banck2, Craig a James3, Chris Morley4, Tim Vandermeersch4 and Geoffrey R Hutchison5*
    O’Boyle et al. Journal of Cheminformatics 2011, 3:33 http://www.jcheminf.com/content/3/1/33 SOFTWARE Open Access Open Babel: An open chemical toolbox Noel M O’Boyle1, Michael Banck2, Craig A James3, Chris Morley4, Tim Vandermeersch4 and Geoffrey R Hutchison5* Abstract Background: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor- neutral formats. Results: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching.
    [Show full text]
  • Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances
    Send Orders for Reprints to [email protected] Current Topics in Medicinal Chemistry, 2014, 14, 1923-1938 1923 Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances Evanthia Lionta, George Spyrou, Demetrios K. Vassilatis and Zoe Cournia* Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece Abstract: Structure-based drug discovery (SBDD) is becoming an essential tool in assisting fast and cost-efficient lead discovery and optimization. The application of rational, structure-based drug design is proven to be more efficient than the traditional way of drug discovery since it aims to understand the molecular basis of a disease and utilizes the knowledge of the three-dimensional structure of the biological target in the process. In this review, we focus on the principles and ap- plications of Virtual Screening (VS) within the context of SBDD and examine different procedures ranging from the ini- tial stages of the process that include receptor and library pre-processing, to docking, scoring and post-processing of top- scoring hits. Recent improvements in structure-based virtual screening (SBVS) efficiency through ensemble docking, in- duced fit and consensus docking are also discussed. The review highlights advances in the field within the framework of several success studies that have led to nM inhibition directly from VS and provides recent trends in library design as well as discusses limitations of the method. Applications of SBVS in the design of substrates for engineered proteins that en- able the discovery of new metabolic and signal transduction pathways and the design of inhibitors of multifunctional pro- teins are also reviewed.
    [Show full text]
  • Excellence in an Overlapping Culture
    EXCELLENCE IN AN OVERLAPPING CULTURE ii Excellence In An Overlapping Culture EXCELLENCE IN AN OVERLAPPING CULTURE The Big History of India’s National Chemical Laboratory L. K. Doraiswamy Anson Marston Distinguished Professor of Engineering Emeritus Department of Chemical and Biological Engineering Iowa State University, Ames, Iowa, USA and Former Director, National Chemical Laboratory, Pune, India Council of Scientifi c and Industrial Research LONDON NEW YORK NEW DELHI First published 2011 in India by Routledge 912–915 Tolstoy House, 15–17 Tolstoy Marg, Connaught Place, New Delhi 110 001 Routledge is an imprint of the Taylor & Francis Group, an informa business © 2011 National Chemical Laboratory (CSIR) This material is the property of the Director, National Chemical Laboratory (CSIR). It is not to be sold, repoduced or distributed without the prior written permission of the owner. Typeset by Star Compugraphics Private Limited D–156, Second Floor Sector 7, Noida 201 301 Printed and bound in India by All rights reserved. This material is the property of National Chemical Laboratory (CSIR), Pune. No part of this book may be reproduced, sold, distributed or utilized in any form or by any electronic, mechanical or other means, now known or hereafter invented, including photocopying and recording, or in any information storage and retrieval system without permission in writing from the National Chemical Laboratory (CSIR), Pune. ISBN 978-81-89643-00-3 Dedication Indian science and technology as the country rapidly moves forward to global eminence. Council of Scientifi c and Industrial Research (CSIR), that ubiquitous stairway to technological dominance, for taking science in India from concept to commerce.
    [Show full text]