Synthesis and Characterization of Metal Complexes Containing
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The Application of Semiempirical Methods in Drug Design
THE APPLICATION OF SEMIEMPIRICAL METHODS IN DRUG DESIGN By MARTIN B. PETERS A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2007 1 c 2007 Martin B. Peters 2 For Jane 3 ACKNOWLEDGMENTS Words cannot describe my Jane. She is everything I can could ask for. She has stood by me even when I left Ireland to pursue my dream of getting my PhD. Thank you honey for your love, support and the sacrifices you have made for us. I thank my mother for always giving me tremendous support and for her words of wisdom and encouragement. I would also like to thank my two brothers, Patrick and Francis, and my two sisters, Marian and Deirdre, for all their encouragement and support. Kennie thank you for giving me the opportunity to work with you; I have truly enjoyed the experience. I would like to express my gratitude to all Merz group members especially Kaushik, Andrew, Ken, Kevin, and Duane for their support and friendship. Also I would like to acknowledge the effort of Mike Weaver who helped by editing this dissertation. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS ................................. 4 LIST OF TABLES ..................................... 8 LIST OF FIGURES .................................... 11 LIST OF ABBREVIATIONS ............................... 15 ABSTRACT ........................................ 19 CHAPTER 1 INTRODUCTION .................................. 21 2 THEORY AND METHODS ............................. 25 2.1 Receptor-Ligand Binding Free Energy ..................... 28 2.2 Computational Drug Design .......................... 30 2.3 Molecular Mechanics .............................. 32 2.4 Quantum Mechanics .............................. 33 2.5 Ligand Based Drug Design .......................... -
Non-Empirical Calculations on the Electronic Structure of Olefins and Aromatics
NON-EMPIRICAL CALCULATIONS ON THE ELECTRONIC STRUCTURE OF OLEFINS AND AROMATICS by Robert H. Findlay, B.Sc. Thesis presented for the Degree of Doctor of philosophy University of Edinburgh December 1973 U N /),, cb CIV 3 ACKNOWLEDGEMENTS I Wish to express my gratitude to Dr. M.H. Palmer for his advice and encouragement during this period of study. I should also like to thank Professor J.I.G. Cadogan and Professor N. Campbell for the provision of facilities, and the Carnegie Institute for the Universities of Scotland for a Research Scholarship. SUMMARY Non-empirical, self-consistent field, molecular orbital calculations, with the atomic orbitals represented by linear combinations of Gaussian-type functions have been carried out on the ground state electronic structures of some nitrogen-, oxygen-, sulphur- and phosphorus-containing heterocycles. Some olefins and olefin derivatives have also been studied. Calculated values of properties have been compared with the appropriate experimental quantities, and in most cases the agreement is good, with linear relationships being established; these are found to have very small standard deviations. Extensions to molecules for which there is no experimental data have been made. In many cases it has been iôtrnd possible to relate the molecular orbitals to the simplest member of a series, or to the hydrocarbon analogue. Predictions of the preferred geometry of selected molecules have been made; these have been used to predict inversion barriers and reaction mechanisms. / / The extent of d-orbital participation in molecules containing second row atoms has been investigated and found to be of trivial importance except in molecules containing high valence states of the second row atoms. -
Synthetic Advances in the C‐H Activation of Rigid Scaffold Molecules
Synthesis Review Synthetic Advances in the C‐H Activation of Rigid Scaffold Molecules Nitika Grovera Mathias O. Senge*a a School of Chemistry, Trinity College Dublin, The University of Dublin, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Dublin 2, Ireland [email protected] Dedicated to Prof. Dr. Henning Hopf Received: only recall the epic endeavors involved in Eaton’s cubane Accepted: Published online: synthesis,3 Parquette’s preparation of dodecahedrane, DOI: Prinzbach’s pagodane route thereto, or Maier’s synthesis of Abstract The remarkable structural and electronic properties of rigid non‐ tetra-tert-butyltetrahedrane.4 conjugated hydrocarbons afford attractive opportunities to design molecular building blocks for both medicinal and material applications. The bridgehead positions provide the possibility to append diverse functional groups at specific angles and in specific orientations. The current review summarizes the synthetic development in CH functionalization of the three rigid scaffolds namely: (a) cubane, (b) bicyclo[1.1.1]pentane (BCP), (c) adamantane. 1 Introduction 2 Cubane 2.1 Cubane Synthesis 2.2 Cubane Functionalization 3 BCP 3.1 BCP Synthesis 3.2 BCP Functionalization 4 Adamantane 4.1 Adamantane Synthesis 4.2 Adamantane Functionalization 5 Conclusion and Outlook Key words Cubane, bicyclo[1.1.1]pentane, adamantane, rigid scaffolds, CH‐ functionalization. Figure 1 The structures of cubane, BCP and adamantane and the five platonic hydrocarbon systems. The fascinating architecture of these systems significantly 1 Introduction differs from scaffolds realized in natural compounds. Hence, they attracted considerable attention from synthetic and The practice of synthetic organic chemistry of non-natural physical organic chemists to investigate their properties and to compounds with rigid organic skeletons provides a deep establish possible uses.3,5 Significantly, over the past twenty understanding of bonding and reactivity. -
Isocyclicc Com- Poundscompounds
The Chemistry of Heterocycles Structure, Reactions, Syntheses, and Applications Mohammad Jafarzadeh Faculty of Chemistry, Razi University The Chemistry of Heterocycles, (Second Edition). By Theophil Eicher and Siegfried Hauptmann, Wiley-VCH Veriag GmbH, 2003 1 1 The Structure of Heterocyclic Compounds 1. The Structure of Heterocyclic Compounds • Molecules are defined by the type and number of atoms as well as by the covalent bonding within Mosthemt chemica. Therel arecompoundtwo mains consistypes tof ostructuref molecules: . The classification of such chemical compounds is base— Thed onatoms the structurform ae chainof thes-ealiphatic molecules(acyclic), whichcompounds is defined by the type and number of atoms as well as b—y thThee covalenatomst formbondina ringg withi- cyclicn themcompounds. There are two main types of structure: — The a t o m s form a chain - aliphatic (acyclic) compounds — The a t o m s form a ring - cyclic compounds CycliCyclicc compoundcompoundss iinn whicwhichh ththee rinringg isis madmadee upup ofof atomatomss ofof ononee elemenelementt onlonlyy areare callecalledd isocycliisocyclicc com- poundscompounds. If th.eIf rintheg consistring consistss of C-atomof C-atomss only,only, then thenwe speawe speakk of a carbocycliof a carbocyclicc compoundcompound,, e.g.: e.g.: NMe? O (4 - dimethylaminophenyl) pentazole cyclopenta -1,3 - diene isocyclic isocyclic und carbocyclic 2 Cyclic compounds with at least two different atoms in the ring (as ring atoms or members of the ring) are known as heterocyclic compounds. The ring itself is called a heterocycle. If the ring contains no C-atom, then we speak of an inorganic heterocycle, e.g.: MeO 2,4 - bis (4 - methoxyphenyl) - 1,3 - dithiadiphosphetan -2,4 - disulfide borazine (Lawesson - Reagent) If at least one ring atom is a C-atom, then the molecule is an organic heterocyclic compound. -
Octanitrocubane - the Most Powerful Explosive of All?
Octanitrocubane - The most powerful explosive of all? Since the invention of gunpowder in 9th in the international edition of "Angewandte century China[1] and its subsequent distribution Chemie" in Jan. 2000[6]. over Europe and Arabia, humanity has since strived for new and better forms of explosives, What finally culminated in Eaton's and especially after the military relevance of such Zhang's successful synthesis had been a long compounds became obvious. It took, however, and tedious journey: For over 10 years several centuries until notable progress was synthetic chemists had worked on adding nitrate groups to cubane, one by one, until made, aside from improving the already [5] known gunpowder: In the middle of the 19th octanitrocubane was finally created . It is no century Nitroglycerine became one of the first wonder, that the final synthesis is not only very complex, but also difficult: No less than practical explosives not derived from [5] gunpowder thanks to the ongoing 40 steps were required to get to the final product, while only yielding it in sparse advancements in science and technology [4] (mainly in chemistry).[2] Since then the quantities . diversity of explosives has steadily increased. Now only one question stays unanswered: It is no wonder, that at some point, after the Can the "real" octanitrocubane stand up to its very elementary principles of explosives had "theoretical" twin? Does it exhibit the finally been discovered, scientists started to predicted properties? Well, yes and no: theorize, which compound might be the most While it is insensitive to shock and friction as powerful of all explosives. -
Complexes of CO2 with the Azoles: Tetrel Bonds, Hydrogen Bonds and Other Secondary Interactions
molecules Article Complexes of CO2 with the Azoles: Tetrel Bonds, Hydrogen Bonds and Other Secondary Interactions Janet E. Del Bene 1,* ID , José Elguero 2 and Ibon Alkorta 2,* ID 1 Department of Chemistry, Youngstown State University, Youngstown, OH 44555, USA 2 Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain; [email protected] * Correspondence: [email protected] (J.E.D.B.); [email protected] (I.A.); Tel.: +1-330-609-5593 (J.E.D.B.); +34-91-562-29-00 (I.A.) Academic Editor: Steve Scheiner Received: 31 March 2018; Accepted: 11 April 2018; Published: 14 April 2018 Abstract: Ab initio MP2/aug’-cc-pVTZ calculations have been performed to investigate the complexes of CO2 with the azoles pyrrole, pyrazole, imidazole, 1,2,3- and 1,2,4-triazole, tetrazole and pentazole. Three types of complexes have been found on the CO2:azole potential surfaces. These include ten complexes stabilized by tetrel bonds that have the azole molecule in the symmetry plane of the complex; seven tetrel-bonded complexes in which the CO2 molecule is perpendicular to the symmetry plane; and four hydrogen-bonded complexes. Eight of the planar complexes are stabilized by Nx···C tetrel bonds and by a secondary interaction involving an adjacent Ny-H bond and an O atom of CO2. The seven perpendicular CO2:azole complexes form between CO2 and two adjacent N atoms of the ring, both of which are electron-pair donors. In three of the four hydrogen-bonded complexes, the proton-donor Nz-H bond of the ring is bonded to two C-H bonds, thereby precluding the planar and perpendicular complexes. -
Forensic Analysis of Explosives
Forensic analysis of explosives Youngeun Choi, Dario Remmler, Maximilian Ries, Felix Rösicke, Radwan Sarhan, Felix Stete, Zhiyang Zhang Detecting and identifying explosives is of great importance ●Airport and airline security ●Demining Picture: Wo st 01/Wikipedia ●Removal of unexploded ordnance Picture: MatthiasKabel/Wikipedia ●Forensic analysis Picture: Tom Oates/Wikipedia Picture: Mark A. Moore/Wikipedia Outline ● Forensic analysis ● Common explosives ■ Inorganic explosives ● examples and sample preparation ● selected analytical techniques ■ Organic explosives containing Nitro-moieties ● Principle of detection ● selected analytical techniques ■ Other important explosives Forensic analysis After an incident with an explosion: Where was the source of the explosion? Which explosive was used? Where did the explosive come from? Commonly used explosives Inorganic explosives: Explosives with containing Nitro- Others: moieties: K++ + S + C Black powder Trinitrotoluene (TNT) Triacetone triperoxide (TATP) Dust of flammable materials Ammonium nitrate Nitroglycerin (NG) Inorganic Explosives Pure compounds Type Decomposition mechanism Characteristic ions − + Ammonium nitrate 2 NH4NO3 → 4 H2O + 2 N2 + O2 NO3 , NH4 − - + Ammonium perchlorate 2 NH4ClO4 → Cl2 + 2 O2 + N2 + 4 H2O NO3 , ClO4 , NH4 Ignition needed! Inorganic Explosives Pure compounds Mixtures Type Composition Characteristic ions − + + ANFO NH4NO3, fuel oil NO3 , NH4 , MeNH3 (Ammonium nitrate fuel oil) (long chain hydrocarbons) − 2- 2− Black powder Nitrates, sulfur, charcoal NO3 , SO4 , -
Enhanced Performance from Insensitive Explosives
Calhoun: The NPS Institutional Archive Faculty and Researcher Publications Faculty and Researcher Publications Collection 2013 Enhanced performance from insensitive explosives Brown, Ronald Monterey, California. Naval Postgraduate School 2013 Insensitive Munitions and Energetic Materials Technology SymposiumPaper 16169 http://hdl.handle.net/10945/47519 Approved for Public Release ENHANCED PERFORMANCE FROM INSENSITIVE EXPLOSIVES Ronald Brown, John Gamble, Dave Amondson, Ronald Williams, Paul Murch, and Joshua Lusk Physics Department Naval Postgraduate School, Monterey, CA 93943 Contact: [email protected] 2013 Insensitive Munitions and Energetic Materials Technology Symposium Paper 16169 Approved for Public Release Acknowledgement Dr. Kevin Vandersall Lawrence Livermore National Laboratory Technical Staff ANSYS-AUTODYN Berkeley, CA 2013 Insensitive Munitions and Energetic Materials Technology Symposium Paper 16169 Approved for Public Release Projected 14 Demonstrated Levels of Increase 12 “ONC” = Octanitrocubane “N8” = Octaazacubane > - e Overview of s c a e 10 e s r / c > - Achievements n m I e k s , a y e t i Relative to 8 r c c o n l I e V n o 6 i t Explosives a n o t Chronology e D 4 2 0 TNT RDX HMX CL-20 ONC N8 IMX HPX HPX+ 2013 Insensitive Munitions and Energetic Materials Technology Symposium Paper 16169 Approved for Public Release OUTLINE • Objective • Background • Modeling & Validations • Effect of Detonation Convergence on Energy Partitioning • Coaxial Initiation Limitations • Results of Novel Dynamic Compression • Conclusions 2013 Insensitive Munitions and Energetic Materials Technology Symposium Paper 16169 Approved for Public Release Develop means for enhancing directed energy from explosive weapon systems by exploiting the effects of overdriven detonation. Explore means for overcoming the limitations of coaxial charges. -
Local Minima Then Are Used As Starting Points for the Third Step of the Procedure
LA-I142-MSI CiC-14REPO”RTCollection -- c. 3 REPRODUCTION ‘“” COPY ~ -.;,. .1.! Los Alamos Nal,onal Laboratory IS operated by the Unwersity of Cal,fornla for the Umted States Department of Energy under conlracl W.7405.ENG.36. 1 -——.Procedqre for Estima ting the Crystal SN- ,-:~.-.....—.-:”.–:,--- ~~~=m --:.”-”..... ... Densities of Organzc ~xploswes ““”P. ~-. -. .. ...- .. ‘= - - -- .- — . Los Alamos National Laboratory ~O~~l~~~~LOSA,amOSN.WM~x,Co,,,,, 9 This work was supported by the U.S. Department of Energyand the Naval Surface Weapons Center, Silver Spring, Maryland. DISCLAIMER This repon waspreparedasanaeeount of worksponsoredbyan ageneyofthe UnitedStatesGovernment. Neithcrthe UnitedStatesGovernment noranyagcney thereof,noranyoftheiremployecs, makesany warmnty,expressor implied,or assumesany legalliabilityor responsibilityfor theaccuracy, completeness, or usefulnessof any information,apparatus.product, or prmessdiselosed,or representsthat its usewould not infringeprivatelyownedrighls.Referencehereinto any specificcommercial product, process,or service bytradersame, trademark,manufacturer,or otherwise,does not necessarilyconstituteor implyits endorsemermrecommendation,or favoringby~heUnitedStatesGovemmenl or any agencythereof.The viewsandopinionsof authorsexpressedhereindo not necessarilystateor reflect!hoseof the Uni~edStates Govemmermorany ageniy thereof. LA-11142-MS UC-45 Issued: November 1987 A Procedure for Estimatingthe Crystal Densities of Organic Explosives Don T. Cromer Herman L. Ammon’ James R. Holden** . -- , “. .—.-—. ,..—,.-- -
Glossary of the Key Notions in Bionics and Beyond
Glossary of the key notions in Bionics and beyond Created by XMLmind XSL-FO Converter. Glossary of the key notions in Bionics and beyond Publication date PPKE ITK, Budapest, 2011 Copyright © 2011 Pázmány Péter Catholic University Created by XMLmind XSL-FO Converter. Table of Contents A. Glossary of the key notions in Bionics and beyond ....................................................................... 1 Preface ................................................................................................................................................ ii 1. Resources ........................................................................................................................................ 4 2. Glossary .......................................................................................................................................... 5 1. 1 ............................................................................................................................................ 5 2. 2 ............................................................................................................................................ 5 3. 6 ............................................................................................................................................ 5 4. A ............................................................................................................................................ 5 5. B ......................................................................................................................................... -
Synthesis of Polyheteroatomic Heterocycles: Relevance of Microwave-Assisted Reactions
Synthesis of polyheteroatomic heterocycles: relevance of microwave-assisted reactions Daniele Canestrari Dissertação para obtenção do Grau de Mestre em Química Orientadores: Prof. Pedro Paulo de Lacerda e Oliveira Santos Prof. Enrico Marcantoni Júri Presidente: Profª. Maria Matilde Soares Duarte Marques Vogais: Prof. Pedro Paulo de Lacerda e Oliveira Santos Prof. Corrado Bacchiochi Doutora Alexandra Maria Moita Antunes Maio de 2014 Abstract Heterocyclic structures, components of a large number of molecules, have been studied since the mid- 1800s due to their wide occurrence in nature, such as in the Heme and Chlorophyll A, and the discovery of their usefulness in organic chemistry, creating an interesting new branch, which continues today. From the first applications of simple heterocycles in main fields of research, such as in medicine, pharmaceutical, agrochemical and energy materials, polyheteroatomic heterocycles have achieved a remarkable position in the development of new products for clinical use with most advantageous features that allow different interactions with the biological target, not always possible with a simple heterocyclic ring. And this is the real aim of this thesis, based on a new research project on particular polyheteroatomic heterocyclic systems, namely 1,2,5-oxadiazoles, also called furazans, five-membered rings likely to be useful for the architectural structure of new drugs. Furthermore, this work wants to propose possible innovative methods to synthesize furazans from acyclic substrates in order to obtain specific heterocycles with particular substituents on the ring. Even more importantly, our attention has focused on the possibility to exploit microwave-assisted organic synthesis (MAOS) for its ability to optimize strategies both from the point of view of the time and of the yield. -
Design and Synthesis of Explosives: Polynitrocubanes and High Nitrogen Content Heterocycles Reported by Andrew L
Design and Synthesis of Explosives: Polynitrocubanes and High Nitrogen Content Heterocycles Reported by Andrew L. LaFrate March 17th, 2005 Introduction In the ninth century, Chinese alchemists discovered black powder, a mixture of sulfur, charcoal, 1 and saltpeter (KNO3), while trying to invent a formula for immortality. Since then humans have been fascinated by explosives and have strived to develop more powerful formulations. In 1846, the Italian chemist Ascanio Sobrero, prepared nitroglycerine (1) by adding glycerine to concentrated HNO3 and H2SO4. Nitroglycerine was not used as an explosive until 1863 when Alfred Nobel stabilized it by adding a nitrocellulose binder, a mixture he termed “dynamite” (from Greek: dynamis meaning power).2 Dynamite and 2,4,6-trinitrotoluene (2) were the explosives of choice until the advent of the nitramine explosives RDX (3) and HMX (4) prior to the second World War. More than 60 years later, HMX (and its formulations) is still O N CH3 2 ONO the workhorse for most 2 O N NO NO N NO 2 2 2 N 2 N military and heavy duty ONO2 N O2N N N N civilian applications. ONO2 NO2 O2N NO2 NO2 Nitroglycerine (1) TNT (2) RDX (3) HMX (4) Background The two most common methods used to quantitate the performance of explosives are the velocity of detonation (VOD) and the detonation pressure (PD). VOD is the rate at which the chemical reaction propagates through the solid explosive or the velocity of the shockwave produced by an explosion. PD is a measure of the increase in pressure followed by detonation of an explosive.3 Despite the development of high explosives such as HMX, active efforts have continued within the military and scientific communities to produce better explosives to complement emerging weapons and space technologies.