Electron Counting Organometallic Compounds
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Organic Ligand Complexation Reactions On
Organic ligand complexation reactions on aluminium-bearing mineral surfaces studied via in-situ Multiple Internal Reflection Infrared Spectroscopy, adsorption experiments, and surface complexation modelling A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Engineering and Physical Sciences 2010 Charalambos Assos School of Earth, Atmospheric and Environmental Sciences Table of Contents LIST OF FIGURES ......................................................................................................4 LIST OF TABLES ........................................................................................................8 ABSTRACT.................................................................................................................10 DECLARATION.........................................................................................................11 COPYRIGHT STATEMENT....................................................................................12 CHAPTER 1 INTRODUCTION ...............................................................................13 AIMS AND OBJECTIVES .................................................................................................38 CHAPTER 2 THE USE OF IR SPECTROSCOPY IN THE STUDY OF ORGANIC LIGAND SURFACE COMPLEXATION............................................40 INTRODUCTION.............................................................................................................40 METHODOLOGY ...........................................................................................................44 -
Crystal Field Theory (CFT)
Crystal Field Theory (CFT) The bonding of transition metal complexes can be explained by two approaches: crystal field theory and molecular orbital theory. Molecular orbital theory takes a covalent approach, and considers the overlap of d-orbitals with orbitals on the ligands to form molecular orbitals; this is not covered on this site. Crystal field theory takes the ionic approach and considers the ligands as point charges around a central metal positive ion, ignoring any covalent interactions. The negative charge on the ligands is repelled by electrons in the d-orbitals of the metal. The orientation of the d orbitals with respect to the ligands around the central metal ion is important, and can be used to explain why the five d-orbitals are not degenerate (= at the same energy). Whether the d orbitals point along or in between the cartesian axes determines how the orbitals are split into groups of different energies. Why is it required? The valence bond approach could not explain the Electronic spectra, Magnetic moments, Reaction mechanisms of the complexes. Assumptions of CFT: 1. The central Metal cation is surrounded by ligand which contain one or more lone pair of electrons. 2. The ionic ligand (F-, Cl- etc.) are regarded as point charges and neutral molecules (H2O, NH3 etc.) as point dipoles. 3. The electrons of ligand does not enter metal orbital. Thus there is no orbital overlap takes place. 4. The bonding between metal and ligand is purely electrostatic i.e. only ionic interaction. The approach taken uses classical potential energy equations that take into account the attractive and repulsive interactions between charged particles (that is, Coulomb's Law interactions). -
1 5. Chemical Bonding
5. Chemical Bonding: The Covalent Bond Model 5.1 The Covalent Bond Model Almost all chemical substances are found as aggregates of atoms in the form of molecules and ions produced through the reactions of various atoms of elements except the noble-gas elements which are stable mono-atomic gases. Chemical bond is a term that describes the attractive force that is holding the atoms of the same or different kind of atoms in forming a molecule or ionic solid that has more stability than the individual atoms. Depending on the kinds of atoms participating in the interaction there seem to be three types of bonding: Gaining or Losing Electrons: Ionic bonding: Formed between many ions formed by metal and nonmetallic elements. Sharing Electrons: Covalent bonding: sharing of electrons between two atoms of non-metals. Metallic Bonding: sharing of electrons between many atoms of metals. Ionic Compounds Covalent Compounds Metallic Compounds 1. Metal and non-meal Non-metal and non-meal Metal of one type or, element combinations. elements combinations. combinations of two or metal elements combinations. 2. High melting brittle Gases, liquids, or waxy, low Conducting, high melting, crystalline solids. melting soft solids. malleable, ductile crystalline solids. 3. Do not conduct as a solid Do not conduct electricity at Conduct electricity at solid but conducts electricity any state. and molten states. when molten. 4. Dissolved in water produce Most are soluble in non-polar Insoluble in any type of conducting solutions solvents and few in water. solvents. (electrolytes) and few These solutions are non- are soluble in non-polar conducting (non- solvents. -
Interplay Between Gating and Block of Ligand-Gated Ion Channels
brain sciences Review Interplay between Gating and Block of Ligand-Gated Ion Channels Matthew B. Phillips 1,2, Aparna Nigam 1 and Jon W. Johnson 1,2,* 1 Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA; [email protected] (M.B.P.); [email protected] (A.N.) 2 Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA * Correspondence: [email protected]; Tel.: +1-(412)-624-4295 Received: 27 October 2020; Accepted: 26 November 2020; Published: 1 December 2020 Abstract: Drugs that inhibit ion channel function by binding in the channel and preventing current flow, known as channel blockers, can be used as powerful tools for analysis of channel properties. Channel blockers are used to probe both the sophisticated structure and basic biophysical properties of ion channels. Gating, the mechanism that controls the opening and closing of ion channels, can be profoundly influenced by channel blocking drugs. Channel block and gating are reciprocally connected; gating controls access of channel blockers to their binding sites, and channel-blocking drugs can have profound and diverse effects on the rates of gating transitions and on the stability of channel open and closed states. This review synthesizes knowledge of the inherent intertwining of block and gating of excitatory ligand-gated ion channels, with a focus on the utility of channel blockers as analytic probes of ionotropic glutamate receptor channel function. Keywords: ligand-gated ion channel; channel block; channel gating; nicotinic acetylcholine receptor; ionotropic glutamate receptor; AMPA receptor; kainate receptor; NMDA receptor 1. Introduction Neuronal information processing depends on the distribution and properties of the ion channels found in neuronal membranes. -
Chemical Forces Understanding the Relative Melting/Boiling Points of Two
Chapter 8 – Chemical Forces Understanding the relative melting/boiling points of two substances requires an understanding of the forces acting between molecules of those substances. These intermolecular forces are important for many additional reasons. For example, solubility and vapor pressure are governed by intermolecular forces. The same factors that give rise to intermolecular forces (e.g. bond polarity) can also have a profound impact on chemical reactivity. Chemical Forces Internuclear Distances and Atomic Radii There are four general methods of discussing interatomic distances: van der Waal’s, ionic, covalent, and metallic radii. We will discuss the first three in this section. Each has a unique perspective of the nature of the interaction between interacting atoms/ions. Van der Waal's Radii - half the distance between two nuclei of the same element in the solid state not chemically bonded together (e.g. solid noble gases). In general, the distance of separation between adjacent atoms (not bound together) in the solid state should be the sum of their van der Waal’s radii. F F van der Waal's radii F F Ionic Radii – Ionic radii were discussed in Chapter 4 and you should go back and review that now. One further thing is worth mentioning here. Evidence that bonding really exists and is attractive can be seen in ionic radii. For all simple ionic compounds, the ions attain noble gas configurations (e.g. in NaCl the Na+ ion is isoelectronic to neon and the Cl- ion is isoelectronic to argon). For the sodium chloride example just given, van der Waal’s radii would predict (Table 8.1, p. -
Chapter 21 D-Metal Organometalloc Chemistry
Chapter 21 d-metal organometalloc chemistry Bonding Ligands Compounds Reactions Chapter 13 Organometallic Chemistry 13-1 Historical Background 13-2 Organic Ligands and Nomenclature 13-3 The 18-Electron Rule 13-4 Ligands in Organometallic Chemistry 13-5 Bonding Between Metal Atoms and Organic π Systems 13-6 Complexes Containing M-C, M=C, and M≡C Bonds 13-7 Spectral Analysis and Characterization of Organometallic Complexes “Inorganic Chemistry” Third Ed. Gary L. Miessler, Donald A. Tarr, 2004, Pearson Prentice Hall http://en.wikipedia.org/wiki/Expedia 13-1 Historical Background Sandwich compounds Cluster compounds 13-1 Historical Background Other examples of organometallic compounds 13-1 Historical Background Organometallic Compound Organometallic chemistry is the study of chemical compounds containing bonds between carbon and a metal. Organometallic chemistry combines aspects of inorganic chemistry and organic chemistry. Organometallic compounds find practical use in stoichiometric and catalytically active compounds. Electron counting is key in understanding organometallic chemistry. The 18-electron rule is helpful in predicting the stabilities of organometallic compounds. Organometallic compounds which have 18 electrons (filled s, p, and d orbitals) are relatively stable. This suggests the compound is isolable, but it can result in the compound being inert. 13-1 Historical Background In attempt to synthesize fulvalene Produced an orange solid (ferrocene) Discovery of ferrocene began the era of modern organometallic chemistry. Staggered -
Chapter Eleven: Chemical Bonding
© Adrian Dingle’s Chemistry Pages 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012. All rights reserved. These materials may NOT be copied or redistributed in any way, except for individual class instruction. Revised August 2011 AP TOPIC 8: Chemical Bonding Introduction In the study of bonding we will consider several different types of chemical bond and some of the theories associated with them. TYPES OF BONDING INTRA INTER (Within (inside) compounds) (Interactions between the STRONG molecules of a compound) WEAK Ionic Covalent Hydrogen Bonding Dipole-Dipole London Dispersion (Metal + Non-metal) (Non-metals) (H attached to N, O or F) (Polar molecules) Forces Giant lattice of ions Discrete molecules Strong, permanent dipole Permanent dipoles (Non-polar molecules) Induced dipoles Dative or (Co-ordinate) (Electron deficient species) Discrete molecules To help distinguish the difference in strength of intra and inter bonds consider the process of boiling of water. When water boils the product is steam (gaseous water). The products are not hydrogen and oxygen. This is because the weak inter molecular forces are broken not the much stronger intra molecular forces. C:\Documents and Settings\AdrianD\My Documents\Dropbox\ADCP\apnotes08.doc Page 1 of 26 © Adrian Dingle’s Chemistry Pages 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012. All rights reserved. These materials may NOT be copied or redistributed in any way, except for individual class instruction. Revised August 2011 Intra Bonding Ionic (the transfer of electrons between atoms to form ions that form giant ionic lattices) Atoms have equal numbers of protons and electrons and consequently have no overall charge. -
Basic Concepts of Chemical Bonding
Basic Concepts of Chemical Bonding Cover 8.1 to 8.7 EXCEPT 1. Omit Energetics of Ionic Bond Formation Omit Born-Haber Cycle 2. Omit Dipole Moments ELEMENTS & COMPOUNDS • Why do elements react to form compounds ? • What are the forces that hold atoms together in molecules ? and ions in ionic compounds ? Electron configuration predict reactivity Element Electron configurations Mg (12e) 1S 2 2S 2 2P 6 3S 2 Reactive Mg 2+ (10e) [Ne] Stable Cl(17e) 1S 2 2S 2 2P 6 3S 2 3P 5 Reactive Cl - (18e) [Ar] Stable CHEMICAL BONDSBONDS attractive force holding atoms together Single Bond : involves an electron pair e.g. H 2 Double Bond : involves two electron pairs e.g. O 2 Triple Bond : involves three electron pairs e.g. N 2 TYPES OF CHEMICAL BONDSBONDS Ionic Polar Covalent Two Extremes Covalent The Two Extremes IONIC BOND results from the transfer of electrons from a metal to a nonmetal. COVALENT BOND results from the sharing of electrons between the atoms. Usually found between nonmetals. The POLAR COVALENT bond is In-between • the IONIC BOND [ transfer of electrons ] and • the COVALENT BOND [ shared electrons] The pair of electrons in a polar covalent bond are not shared equally . DISCRIPTION OF ELECTRONS 1. How Many Electrons ? 2. Electron Configuration 3. Orbital Diagram 4. Quantum Numbers 5. LEWISLEWIS SYMBOLSSYMBOLS LEWISLEWIS SYMBOLSSYMBOLS 1. Electrons are represented as DOTS 2. Only VALENCE electrons are used Atomic Hydrogen is H • Atomic Lithium is Li • Atomic Sodium is Na • All of Group 1 has only one dot The Octet Rule Atoms gain, lose, or share electrons until they are surrounded by 8 valence electrons (s2 p6 ) All noble gases [EXCEPT HE] have s2 p6 configuration. -
Organometrallic Chemistry
CHE 425: ORGANOMETALLIC CHEMISTRY SOURCE: OPEN ACCESS FROM INTERNET; Striver and Atkins Inorganic Chemistry Lecturer: Prof. O. G. Adeyemi ORGANOMETALLIC CHEMISTRY Definitions: Organometallic compounds are compounds that possess one or more metal-carbon bond. The bond must be “ionic or covalent, localized or delocalized between one or more carbon atoms of an organic group or molecule and a transition, lanthanide, actinide, or main group metal atom.” Organometallic chemistry is often described as a bridge between organic and inorganic chemistry. Organometallic compounds are very important in the chemical industry, as a number of them are used as industrial catalysts and as a route to synthesizing drugs that would not have been possible using purely organic synthetic routes. Coordinative unsaturation is a term used to describe a complex that has one or more open coordination sites where another ligand can be accommodated. Coordinative unsaturation is a very important concept in organotrasition metal chemistry. Hapticity of a ligand is the number of atoms that are directly bonded to the metal centre. Hapticity is denoted with a Greek letter η (eta) and the number of bonds a ligand has with a metal centre is indicated as a superscript, thus η1, η2, η3, ηn for hapticity 1, 2, 3, and n respectively. Bridging ligands are normally preceded by μ, with a subscript to indicate the number of metal centres it bridges, e.g. μ2–CO for a CO that bridges two metal centres. Ambidentate ligands are polydentate ligands that can coordinate to the metal centre through one or more atoms. – – – For example CN can coordinate via C or N; SCN via S or N; NO2 via N or N. -
Bond Distances and Bond Orders in Binuclear Metal Complexes of the First Row Transition Metals Titanium Through Zinc
Metal-Metal (MM) Bond Distances and Bond Orders in Binuclear Metal Complexes of the First Row Transition Metals Titanium Through Zinc Richard H. Duncan Lyngdoh*,a, Henry F. Schaefer III*,b and R. Bruce King*,b a Department of Chemistry, North-Eastern Hill University, Shillong 793022, India B Centre for Computational Quantum Chemistry, University of Georgia, Athens GA 30602 ABSTRACT: This survey of metal-metal (MM) bond distances in binuclear complexes of the first row 3d-block elements reviews experimental and computational research on a wide range of such systems. The metals surveyed are titanium, vanadium, chromium, manganese, iron, cobalt, nickel, copper, and zinc, representing the only comprehensive presentation of such results to date. Factors impacting MM bond lengths that are discussed here include (a) n+ the formal MM bond order, (b) size of the metal ion present in the bimetallic core (M2) , (c) the metal oxidation state, (d) effects of ligand basicity, coordination mode and number, and (e) steric effects of bulky ligands. Correlations between experimental and computational findings are examined wherever possible, often yielding good agreement for MM bond lengths. The formal bond order provides a key basis for assessing experimental and computationally derived MM bond lengths. The effects of change in the metal upon MM bond length ranges in binuclear complexes suggest trends for single, double, triple, and quadruple MM bonds which are related to the available information on metal atomic radii. It emerges that while specific factors for a limited range of complexes are found to have their expected impact in many cases, the assessment of the net effect of these factors is challenging. -
Searching Coordination Compounds
CAS ONLINEB Available on STN Internationalm The Scientific & Technical Information Network SEARCHING COORDINATION COMPOUNDS December 1986 Chemical Abstracts Service A Division of the American Chemical Society 2540 Olentangy River Road P.O. Box 3012 Columbus, OH 43210 Copyright O 1986 American Chemical Society Quoting or copying of material from this publication for educational purposes is encouraged. providing acknowledgment is made of the source of such material. SEARCHING COORDINATION COMPOUNDS prepared by Adrienne W. Kozlowski Professor of Chemistry Central Connecticut State University while on sabbatical leave as a Visiting Educator, Chemical Abstracts Service Table of Contents Topic PKEFACE ............................s.~........................ 1 CHAPTER 1: INTRODUCTION TO SEARCHING IN CAS ONLINE ............... 1 What is Substructure Searching? ............................... 1 The Basic Commands .............................................. 2 CHAPTEK 2: INTKOOUCTION TO COORDINATION COPPOUNDS ................ 5 Definitions and Terminology ..................................... 5 Ligand Characteristics.......................................... 6 Metal Characteristics .................................... ... 8 CHAPTEK 3: STKUCTUKING AND REGISTKATION POLICIES FOR COORDINATION COMPOUNDS .............................................11 Policies for Structuring Coordination Compounds ................. Ligands .................................................... Ligand Structures........................................... Metal-Ligand -
Understanding the Invisible Hands of Sample Preparation for Cryo-EM
FOCUS | REVIEW ARTICLE FOCUS | REVIEWhttps://doi.org/10.1038/s41592-021-01130-6 ARTICLE Understanding the invisible hands of sample preparation for cryo-EM Giulia Weissenberger1,2,3, Rene J. M. Henderikx1,2,3 and Peter J. Peters 2 ✉ Cryo-electron microscopy (cryo-EM) is rapidly becoming an attractive method in the field of structural biology. With the exploding popularity of cryo-EM, sample preparation must evolve to prevent congestion in the workflow. The dire need for improved microscopy samples has led to a diversification of methods. This Review aims to categorize and explain the principles behind various techniques in the preparation of vitrified samples for the electron microscope. Various aspects and challenges in the workflow are discussed, from sample optimization and carriers to deposition and vitrification. Reliable and versatile specimen preparation remains a challenge, and we hope to give guidelines and posit future directions for improvement. ryo-EM is providing macromolecular structures with the optimum biochemical state of the sample. Grid preparation up to atomic resolution at an unprecedented rate. In this describes the steps needed to make a sample suitable for analysis Ctechnique, electron microscopy images of biomolecules in the microscope. These steps involve chemical or plasma treat- embedded in vitreous, glass-like ice are combined to generate ment of the grid, sample deposition and vitrification. The first three-dimensional (3D) reconstructions. The detailed structural breakthroughs came about from a manual blot-and-plunge method models obtained from these reconstructions grant insight into the developed in the 1980s15 that is still being applied to achieve formi- function of macromole cules and their role in biological processes.