Representation of Three-Center−Two-Electron Bonds in Covalent Molecules with Bridging Hydrogen Atoms Gerard Parkin*
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Fundamental Studies of Early Transition Metal-Ligand Multiple Bonds: Structure, Electronics, and Catalysis
Fundamental Studies of Early Transition Metal-Ligand Multiple Bonds: Structure, Electronics, and Catalysis Thesis by Ian Albert Tonks In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy CALIFORNIA INSTITUTE OF TECHNOLOGY Pasadena, California 2012 Defended December 6th 2011 ii 2012 Ian A Tonks All Rights Reserved iii ACKNOWLEDGEMENTS I am extremely fortunate to have been surrounded by enthusiastic, dedicated, and caring mentors, colleagues, and friends throughout my academic career. A Ph.D. thesis is by no means a singular achievement; I wish to extend my wholehearted thanks to everyone who has made this journey possible. First and foremost, I must thank my Ph.D. advisor, Prof. John Bercaw. I think more so than anything else, I respect John for his character, sense of fairness, and integrity. I also benefitted greatly from John’s laissez-faire approach to guiding our research group; I’ve always learned best when left alone to screw things up, although John also has an uncanny ability for sensing when I need direction or for something to work properly on the high-vac line. John also introduced me to hiking and climbing in the Eastern Sierras and Owens Valley, which remain amongst my favorite places on Earth. Thanks for always being willing to go to the Pizza Factory in Lone Pine before and after all the group hikes! While I never worked on any of the BP projects that were spearheaded by our co-PI Dr. Jay Labinger, I must also thank Jay for coming to all of my group meetings, teaching me an incredible amount while I was TAing Ch154, and for always being willing to talk chemistry and answer tough questions. -
The Chemistry of Alkynes
14_BRCLoudon_pgs4-2.qxd 11/26/08 9:04 AM Page 644 14 14 The Chemistry of Alkynes An alkyne is a hydrocarbon containing a carbon–carbon triple bond; the simplest member of this family is acetylene, H C'C H. The chemistry of the carbon–carbon triple bond is similar in many respects toL that ofL the carbon–carbon double bond; indeed, alkynes and alkenes undergo many of the same addition reactions. Alkynes also have some unique chem- istry, most of it associated with the bond between hydrogen and the triply bonded carbon, the 'C H bond. L 14.1 NOMENCLATURE OF ALKYNES In common nomenclature, simple alkynes are named as derivatives of the parent compound acetylene: H3CCC' H L L methylacetylene H3CCC' CH3 dimethylacetyleneL L CH3CH2 CC' CH3 ethylmethylacetyleneL L Certain compounds are named as derivatives of the propargyl group, HC'C CH2 , in the common system. The propargyl group is the triple-bond analog of the allyl group.L L HC' C CH2 Cl H2CA CH CH2 Cl L L LL propargyl chloride allyl chloride 644 14_BRCLoudon_pgs4-2.qxd 11/26/08 9:04 AM Page 645 14.1 NOMENCLATURE OF ALKYNES 645 We might expect the substitutive nomenclature of alkynes to be much like that of alkenes, and it is. The suffix ane in the name of the corresponding alkane is replaced by the suffix yne, and the triple bond is given the lowest possible number. H3CCC' H CH3CH2CH2CH2 CC' CH3 H3C CH2 C ' CH L L L L L L L propyne 2-heptyne 1-butyne H3C CH C ' C CH3 HC' C CH2 CH2 C' C CH3 L L L L 1,5-heptadiyneLL L "CH3 4-methyl-2-pentyne Substituent groups that contain a triple bond (called alkynyl groups) are named by replac- ing the final e in the name of the corresponding alkyne with the suffix yl. -
Chemical Bonding Valence Electrons Are the Outer Shell Electrons of an Atom
Chapter 8 Chemical Bonding Valence electrons are the outer shell electrons of an atom. The valence electrons are the electrons that participate in chemical bonding. Group e- configuration # of valence e- 1 ns1 1 2 ns2 2 13 ns2np1 3 14 ns2np2 4 15 ns2np3 5 16 ns2np4 6 17 ns2np5 7 Lewis Dot Symbols for the Representative Elements & Noble Gases Lewis dot symbol consists of the symbol of the element and one dot for each valence electron in an atom of each element The Ionic Bond Ionic bond = the electrostatic force that holds ions Li + F Li+ F - together in an 2 1 2 2 5 [He]2[Ne]2 2 6 ionic compound 1s 2s1s 2s 2p 1s1s 2s 2p Li Li+ + e- e- + F F - Lithium fluoride, LiF Li+ + F - Li+ F - Ionic Bonds 3Mg (s) + N2 (g) → Mg3N2 (s) .. .. 2 3 3 Mg2 N 3Mg 2: N : (Mg3N2 ) . .. Electrostatic (Lattice) Energy Lattice energy (E) is the energy required to completely separate one mole of a solid ionic compound into gaseous ions. Coulomb’s Law: the potential energy between 2 ions is directly proportional to the product of their charges and inversely proportional to the distance of separation between them Q+ is the charge on the cation Q Q E = k + - Q is the charge on the anion r - r is the distance between the ions cmpd lattice energy MgF2 2957 Q= +2,-1 Lattice energy (E) increases MgO 3938 Q= +2,-2 as Q increases and/or as r decreases. LiF 1036 r F- < r Cl- LiCl 853 Born-Haber Cycle for Determining Lattice Energy The Born-Haber cycle relates lattice energies of ionic compounds to ionization energies, electron affinities, and other atomic & molecular properties o o o o o o DHoverall = DH1 + DH2 + DH3 + DH4 + DH5 Born-Haber cycle for lithium fluoride 1. -
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. -
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. -
18- Electron Rule. 18 Electron Rule Cont’D Recall That for MAIN GROUP Elements the Octet Rule Is Used to Predict the Formulae of Covalent Compounds
18- Electron Rule. 18 Electron Rule cont’d Recall that for MAIN GROUP elements the octet rule is used to predict the formulae of covalent compounds. Example 1. This rule assumes that the central atom in a compound will make bonds such Oxidation state of Co? [Co(NH ) ]+3 that the total number of electrons around the central atom is 8. THIS IS THE 3 6 Electron configuration of Co? MAXIMUM CAPACITY OF THE s and p orbitals. Electrons from Ligands? Electrons from Co? This rule is only valid for Total electrons? Period 2 nonmetallic elements. Example 2. Oxidation state of Fe? The 18-electron Rule is based on a similar concept. Electron configuration of Fe? [Fe(CO) ] The central TM can accommodate electrons in the s, p, and d orbitals. 5 Electrons from Ligands? Electrons from Fe? s (2) , p (6) , and d (10) = maximum of 18 Total electrons? This means that a TM can add electrons from Lewis Bases (or ligands) in What can the EAN rule tell us about [Fe(CO)5]? addition to its valence electrons to a total of 18. It can’t occur…… 20-electron complex. This is also known Effective Atomic Number (EAN) Rule Note that it only applies to metals with low oxidation states. 1 2 Sandwich Compounds Obeying EAN EAN Summary 1. Works well only for d-block metals. It does not apply to f-block Let’s draw some structures and see some new ligands. metals. 2. Works best for compounds with TMs of low ox. state. Each of these ligands is π-bonded above and below the metal center. -
Aromaticity in Polyhydride Complexes of Ru, Ir, Os, and Pt† Cite This: DOI: 10.1039/C5cp04330a Elisa Jimenez-Izala and Anastassia N
PCCP View Article Online PAPER View Journal r-Aromaticity in polyhydride complexes of Ru, Ir, Os, and Pt† Cite this: DOI: 10.1039/c5cp04330a Elisa Jimenez-Izala and Anastassia N. Alexandrova*ab Transition-metal hydrides represent a unique class of compounds, which are essential for catalysis, organic i À i À synthesis, and hydrogen storage. In this work we study IrH5(PPh3)2,(RuH5(P Pr3)2) ,(OsH5(PPr3)2) ,and À OsH4(PPhMe2)3 polyhydride complexes, inspired by the recent discovery of the s-aromatic PtZnH5 cluster À anion. The distinctive feature of these molecules is that, like in the PtZnH5 cluster, the metal is five-fold Received 23rd July 2015, coordinated in-plane, and holds additional ligands attheaxialpositions.Thisworkshowsthattheunusual Accepted 17th September 2015 coordination in these compounds indeed can be explained by s-aromaticity in the pentagonal arrangement, DOI: 10.1039/c5cp04330a stabilized by the atomic orbitals on the metal. Based on this newly elucidated bonding principle, we additionally propose a new family of polyhydrides that display a uniquely high coordination. We also report the first www.rsc.org/pccp indications of how aromaticity may impact the reactivity of these molecules. 1 Introduction many catalytic cycles, where they have either been used as catalysts or invoked as key intermediates.15,16 Aromaticity in Aromaticity is a very important concept in the contemporary general is associated with high symmetry, stability, and specific chemistry: the particular electronic structure of aromatic reactivity. Therefore, the stability of transition-metal hydride systems, where electrons are delocalized, explains their large complexes might have an important repercussion in the kinetics energetic stabilization and low reactivity. -
Alkenes and Alkynes
02/21/2019 CHAPTER FOUR Alkenes and Alkynes H N O I Cl C O C O Cl F3C C Cl C Cl Efavirenz Haloprogin (antiviral, AIDS therapeutic) (antifungal, antiseptic) Chapter 4 Table of Content * Unsaturated Hydrocarbons * Introduction and hybridization * Alkenes and Alkynes * Benzene and Phenyl groups * Structure of Alkenes, cis‐trans Isomerism * Nomenclature of Alkenes and Alkynes * Configuration cis/trans, and cis/trans Isomerism * Configuration E/Z * Physical Properties of Hydrocarbons * Acid‐Base Reactions of Hydrocarbons * pka and Hybridizations 1 02/21/2019 Unsaturated Hydrocarbons • Unsaturated Hydrocarbon: A hydrocarbon that contains one or more carbon‐carbon double or triple bonds or benzene‐like rings. – Alkene: contains a carbon‐carbon double bond and has the general formula CnH2n. – Alkyne: contains a carbon‐carbon triple bond and has the general formula CnH2n‐2. Introduction Alkenes ● Hydrocarbons containing C=C ● Old name: olefins • Steroids • Hormones • Biochemical regulators 2 02/21/2019 • Alkynes – Hydrocarbons containing C≡C – Common name: acetylenes Unsaturated Hydrocarbons • Arene: benzene and its derivatives (Ch 9) 3 02/21/2019 Benzene and Phenyl Groups • We do not study benzene and its derivatives until Chapter 9. – However, we show structural formulas of compounds containing a phenyl group before that time. – The phenyl group is not reactive under any of the conditions we describe in chapters 5‐8. Structure of Alkenes • The two carbon atoms of a double bond and the four atoms bonded to them lie in a plane, with bond angles of approximately 120°. 4 02/21/2019 Structure of Alkenes • Figure 4.1 According to the orbital overlap model, a double bond consists of one bond formed by overlap of sp2 hybrid orbitals and one bond formed by overlap of parallel 2p orbitals. -
Bsc Chemistry
Subject Chemistry Paper No and Title Paper 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No and Module 3: Hyper-Conjugation Title Module Tag CHE_P1_M3 CHEMISTRY PAPER No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 3: Hyper-Conjugation TABLE OF CONTENT 1. Learning outcomes 2. Introduction 3. Hyperconjugation 4. Requirements for Hyperconjugation 5. Consequences and Applications of Hyperconjugation 6. Reverse Hyperconjugation 7. Summary CHEMISTRY PAPER No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 3: Hyper-Conjugation 1. Learning Outcomes After studying this module you shall be able to: Understand the concept of hyperconjugation. Know about the structural requirements in a molecule to show hyperconjugation. Learn about the important consequences and applications of hyperconjugation. Comprehend the concept of reverse hyperconjugation. 2. Introduction In conjugation, we have studied that the electrons move from one p orbital to other which are aligned in parallel planes. Is it possible for electron to jump from p orbital to sp3 orbital that are not parallelly aligned with one another? The answer is yes. This type of conjugation is not normal, it is extra-ordinary. Hence, the name hyper-conjugation. It is also know as no-bond resonance. Let us study more about it. 3. Hyperconjugation The normal electron releasing inductive effect (+I effect) of alkyl groups is in the following order: But it was observed by Baker and Nathan that in conjugated system, the attachment of alkyl groups reverse their capability of electron releasing. They suggested that alkyl groups are capable of releasing electrons by some process other than inductive. -
Chemical Bonding Chemical Bonding Chemical Bonding
Chemical Bonding • Petrucci, Harwood and Herring: Chapters 10 and 11 • Aims: – To look at bonding and possible shapes of molecules • We will mainly do this through Lewis structures – To look at ionic and covalent bonds – Use valence shell electronic structure to predict shapes of molecules CHEM 1000 3.0 Chemical Bonding I 1 Chemical Bonding • The most important concepts here are: – Electrons, particularly valence electrons play a fundamental role in chemical bonding. – When elements combine to produce compounds they are attempting to achieve a valence shell like a noble gas CHEM 1000 3.0 Chemical Bonding I 2 Chemical Bonding • The driving force for the production of chemical bonds is the need for an atom to complete a valence shell (usually 8 electrons) – Often electrons can be transferred from one atom to another to make ions. The atoms are then held together by coulombic forces in an ionic bond – More often the only way an atom can gain electrons is by sharing. This sharing produces a covalent bond CHEM 1000 3.0 Chemical Bonding I 3 •1 Lewis Symbols • This is a way of representing the valence electrons in an element – It does not include the inner shell electrons – It does not include the spin of an electron – e.g. Si ([Ne]3s 23p 2) Si – N ([He]2s 22p 3) N CHEM 1000 3.0 Chemical Bonding I 4 Lewis Structures • These are the combination of Lewis symbols that represents the sharing or transfer of electrons in a molecule – Examples – Ionic bond Na x + Cl [Na] + [ x Cl ] - – Covalent bond Hx + Cl H x Cl CHEM 1000 3.0 Chemical Bonding I 5 Ionic Compounds • We don’t usually see isolated ionic compounds – Normally they are in crystals where one anion (negative) is attached to several cations (positive) and vice versa.