Automated Structure Generation for First-Principles Transition-Metal
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CHEM 250 (4 Credits): Reactions of Nucleophiles and Electrophiles (Reactivity 1)
CHEM 250 (4 credits): Reactions of Nucleophiles and Electrophiles (Reactivity 1): Description: This course investigates fundamental carbonyl reactivity (addition and substitution) in understanding organic, inorganic and biochemical processes. Some emphasis is placed on enthalpy, entropy and free energy as a basis of understanding reactivity. An understanding of chemical reactivity is based on principles of Lewis acidity and basicity. The formation, stability and reactivity of coordination complexes are included. Together, these topics lead to an understanding of biochemical pathways such as glycolysis. Enzyme regulation and inhibition is discussed in the context of thermodynamics and mechanisms. Various applications of modern multi-disciplinary research will be explored. Prerequisite: CHEM 125. Course Goals and Objectives: 1. Students will gain a qualitative understanding of thermodynamics. A. Students will develop a qualitative understanding of enthalpy and entropy. B. Students will predict the sign of an entropy change for chemical or physical processes. C. Students will understand entropy effects such as the chelate effect on chemical reactions. D. Students will use bond enthalpies or pKas to determine the enthalpy change for a reaction. E. Students will draw or interpret a reaction progress diagram. F. Students will apply the Principle of Microscopic Reversibility to understand reaction mechanisms. G. Students will use Gibbs free energy to relate enthalpy and entropy changes. H. Students will develop a qualitative understanding of progress toward equilibrium under physiological conditions (the difference between G and Go.) I. Students will understand coupled reactions and how this can be used to drive a non- spontaneous reaction toward products. J. Students will apply LeChatelier’s Principle to affect the position of anequilibrium by adding or removing reactants or products. -
An Earlier Collection of These Notes in One PDF File
UNIVERSITY OF THE WEST INDIES MONA, JAMAICA Chemistry of the First Row Transition Metal Complexes C21J Inorganic Chemistry http://wwwchem.uwimona.edu.jm/courses/index.html Prof. R. J. Lancashire September 2005 Chemistry of the First Row Transition Metal Complexes. C21J Inorganic Chemistry 24 Lectures 2005/2006 1. Review of Crystal Field Theory. Crystal Field Stabilisation Energies: origin and effects on structures and thermodynamic properties. Introduction to Absorption Spectroscopy and Magnetism. The d1 case. Ligand Field Theory and evidence for the interaction of ligand orbitals with metal orbitals. 2. Spectroscopic properties of first row transition metal complexes. a) Electronic states of partly filled quantum levels. l, ml and s quantum numbers. Selection rules for electronic transitions. b) Splitting of the free ion energy levels in Octahedral and Tetrahedral complexes. Orgel and Tanabe-Sugano diagrams. c) Spectra of aquated metal ions. Factors affecting positions, intensities and shapes of absorption bands. 3. Magnetic Susceptibilities of first row transition metal complexes. a) Effect of orbital contributions arising from ground and excited states. b) Deviation from the spin-only approximation. c) Experimental determination of magnetic moments. Interpretation of data. 4. General properties (physical and chemical) of the 3d transition metals as a consequence of their electronic configuration. Periodic trends in stabilities of common oxidation states. Contrast between first-row elements and their heavier congeners. 5. A survey of the chemistry of some of the elements Ti....Cu, which will include the following topics: a) Occurrence, extraction, biological significance, reactions and uses b) Redox reactions, effects of pH on the simple aqua ions c) Simple oxides, halides and other simple binary compounds. -
Photoacoustic Measurements of Porphyrin Triplet-State Quantum Yields and Singlet-Oxygen Efficiencies
FULL PAPER Photoacoustic Measurements of Porphyrin Triplet-State Quantum Yields and Singlet-Oxygen Efficiencies Marta Pineiro, Ana L. Carvalho, Mariette M. Pereira, A. M. dA. Rocha Gonsalves, Luís G. Arnaut,* and SebastiaÄo J. Formosinho Abstract: Photoacoustic calorimetry was used to measure the quantum yields of singlet molecular oxygen production by the triplet states of tetraphenylporphyrin (TPP), ZnTPP and CuTPP in toluene, yielding values of 0.67 Æ 0.14, 0.68 Æ 0.19 Keywords: metalloporphyrins ´ and 0.03 Æ 0.01, respectively. We show that a novel dichlorophenyl derivative of photoacoustic calorimetry ´ por- ZnTPP is capable of singlet-oxygen production with a 0.90 Æ 0.07 quantum yield. phyrinoids ´ singlet oxygen ´ sensi- The synthesis and characterisation of a new photostable chlorin with high absorptivity tizers in the red that is capable of singlet-oxygen production with 0.54 Æ 0.06 quantum yield is described. Our results suggest that chlorinated chlorins may be interesting new sensitisers for photodynamic therapy. Introduction Type II photooxygenation process in cells.[7, 8] Adequate sensitisers have specific biological and photochemical proper- The ubiquitous tetrapyrrolic macrocycles play highly diverse ties. The desired biological features of the sensitiser are: roles in biological systems.[1±5] The natural roles of these 1) little or no dark toxicity structures stimulated the search for new applications, exploit- 2) selective accumulation and prolonged retention in tumour ing in particular the use of new synthetic porphyrins.[6] One of tissues the more recent and promising applications of porphyrin 3) controlled photofading to reduce the unwanted skin chemistry in medicine is in the detection and cure of photosensitivity side effects and increase light penetration tumours,[7, 8] referred to as photodynamic therapy (PDT). -
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). -
Carbon Dioxide Adsorption by Metal Organic Frameworks (Synthesis, Testing and Modeling)
Western University Scholarship@Western Electronic Thesis and Dissertation Repository 8-8-2013 12:00 AM Carbon Dioxide Adsorption by Metal Organic Frameworks (Synthesis, Testing and Modeling) Rana Sabouni The University of Western Ontario Supervisor Prof. Sohrab Rohani The University of Western Ontario Graduate Program in Chemical and Biochemical Engineering A thesis submitted in partial fulfillment of the equirr ements for the degree in Doctor of Philosophy © Rana Sabouni 2013 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Other Chemical Engineering Commons Recommended Citation Sabouni, Rana, "Carbon Dioxide Adsorption by Metal Organic Frameworks (Synthesis, Testing and Modeling)" (2013). Electronic Thesis and Dissertation Repository. 1472. https://ir.lib.uwo.ca/etd/1472 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. i CARBON DIOXIDE ADSORPTION BY METAL ORGANIC FRAMEWORKS (SYNTHESIS, TESTING AND MODELING) (Thesis format: Integrated Article) by Rana Sabouni Graduate Program in Chemical and Biochemical Engineering A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy The School of Graduate and Postdoctoral Studies The University of Western Ontario London, Ontario, Canada Rana Sabouni 2013 ABSTRACT It is essential to capture carbon dioxide from flue gas because it is considered one of the main causes of global warming. Several materials and various methods have been reported for the CO2 capturing including adsorption onto zeolites, porous membranes, and absorption in amine solutions. -
CESMIX: Center for the Exascale Simulation of Materials in Extreme Environments
CESMIX: Center for the Exascale Simulation of Materials in Extreme Environments Project Overview Youssef Marzouk MIT PSAAP-3 Team 18 August 2020 The CESMIX team • Our team integrates expertise in quantum chemistry, atomistic simulation, materials science; hypersonic flow; validation & uncertainty quantification; numerical algorithms; parallel computing, programming languages, compilers, and software performance engineering 1 Project objectives • Exascale simulation of materials in extreme environments • In particular: ultrahigh temperature ceramics in hypersonic flows – Complex materials, e.g., metal diborides – Extreme aerothermal and chemical loading – Predict materials degradation and damage (oxidation, melting, ablation), capturing the central role of surfaces and interfaces • New predictive simulation paradigms and new CS tools for the exascale 2 Broad relevance • Intense current interest in reentry vehicles and hypersonic flight – A national priority! – Materials technologies are a key limiting factor • Material properties are of cross-cutting importance: – Oxidation rates – Thermo-mechanical properties: thermal expansion, creep, fracture – Melting and ablation – Void formation • New systems being proposed and fabricated (e.g., metallic high-entropy alloys) • May have relevance to materials aging • Yet extreme environments are largely inaccessible in the laboratory – Predictive simulation is an essential path… 3 Demonstration problem: specifics • Aerosurfaces of a hypersonic vehicle… • Hafnium diboride (HfB2) promises necessary temperature -
Nobel Lecture, 8 December 1981 by ROALD HOFFMANN Department of Chemistry, Cornell University, Ithaca, N.Y
BUILDING BRIDGES BETWEEN INORGANIC AND ORGANIC CHEMISTRY Nobel lecture, 8 December 1981 by ROALD HOFFMANN Department of Chemistry, Cornell University, Ithaca, N.Y. 14853 R. B. Woodward, a supreme patterner of chaos, was one of my teachers. I dedicate this lecture to him, for it is our collaboration on orbital symmetry conservation, the electronic factors which govern the course of chemical reac- tions, which is recognized by half of the 1981 Nobel Prize in Chemistry. From Woodward I learned much: the significance of the experimental stimulus to theory, the craft of constructing explanations, the importance of aesthetics in science. I will try to show you how these characteristics of chemical theory may be applied to the construction of conceptual bridges between inorganic and organic chemistry. FRAGMENTS Chains, rings, substituents - those are the building blocks of the marvelous edifice of modern organic chemistry. Any hydrocarbon may be constructed on paper from methyl groups, CH 3, methylenes, CH 2, methynes, CH, and carbon atoms, C. By substitution and the introduction of heteroatoms all of the skeletons and functional groupings imaginable, from ethane to tetrodotoxin, may be obtained. The last thirty years have witnessed a remarkable renaissance of inorganic chemistry, and the particular flowering of the field of transition metal organo- metallic chemistry. Scheme 1 shows a selection of some of the simpler creations of the laboratory in this rich and ever-growing field. Structures l-3 illustrate at a glance one remarkable feature of transition metal fragments. Here are three iron tricarbonyl complexes of organic moie- ties - cyclobutadiene, trimethylenemethane, an enol, hydroxybutadiene - which on their own would have little kinetic or thermodynamic stability. -
Popular GPU-Accelerated Applications
LIFE & MATERIALS SCIENCES GPU-ACCELERATED APPLICATIONS | CATALOG | AUG 12 LIFE & MATERIALS SCIENCES APPLICATIONS CATALOG Application Description Supported Features Expected Multi-GPU Release Status Speed Up* Support Bioinformatics BarraCUDA Sequence mapping software Alignment of short sequencing 6-10x Yes Available now reads Version 0.6.2 CUDASW++ Open source software for Smith-Waterman Parallel search of Smith- 10-50x Yes Available now protein database searches on GPUs Waterman database Version 2.0.8 CUSHAW Parallelized short read aligner Parallel, accurate long read 10x Yes Available now aligner - gapped alignments to Version 1.0.40 large genomes CATALOG GPU-BLAST Local search with fast k-tuple heuristic Protein alignment according to 3-4x Single Only Available now blastp, multi cpu threads Version 2.2.26 GPU-HMMER Parallelized local and global search with Parallel local and global search 60-100x Yes Available now profile Hidden Markov models of Hidden Markov Models Version 2.3.2 mCUDA-MEME Ultrafast scalable motif discovery algorithm Scalable motif discovery 4-10x Yes Available now based on MEME algorithm based on MEME Version 3.0.12 MUMmerGPU A high-throughput DNA sequence alignment Aligns multiple query sequences 3-10x Yes Available now LIFE & MATERIALS& LIFE SCIENCES APPLICATIONS program against reference sequence in Version 2 parallel SeqNFind A GPU Accelerated Sequence Analysis Toolset HW & SW for reference 400x Yes Available now assembly, blast, SW, HMM, de novo assembly UGENE Opensource Smith-Waterman for SSE/CUDA, Fast short -
Electronic Spectroscopy of Free Base Porphyrins and Metalloporphyrins
Absorption and Fluorescence Spectroscopy of Tetraphenylporphyrin§ and Metallo-Tetraphenylporphyrin Introduction The word porphyrin is derived from the Greek porphura meaning purple, and all porphyrins are intensely coloured1. Porphyrins comprise an important class of molecules that serve nature in a variety of ways. The Metalloporphyrin ring is found in a variety of important biological system where it is the active component of the system or in some ways intimately connected with the activity of the system. Many of these porphyrins synthesized are the basic structure of biological porphyrins which are the active sites of numerous proteins, whose functions range from oxygen transfer and storage (hemoglobin and myoglobin) to electron transfer (cytochrome c, cytochrome oxidase) to energy conversion (chlorophyll). They also have been proven to be efficient sensitizers and catalyst in a number of chemical and photochemical processes especially photodynamic therapy (PDT). The diversity of their functions is due in part to the variety of metals that bind in the “pocket” of the porphyrin ring system (Fig. 1). Figure 1. Metallated Tetraphenylporphyrin Upon metalation the porphyrin ring system deprotonates, forming a dianionic ligand (Fig. 2). The metal ions behave as Lewis acids, accepting lone pairs of electrons ________________________________ § We all need to thank Jay Stephens for synthesizing the H2TPP 2 from the dianionic porphyrin ligand. Unlike most transition metal complexes, their color is due to absorption(s) within the porphyrin ligand involving the excitation of electrons from π to π* porphyrin ring orbitals. Figure 2. Synthesis of Zn(TPP) The electronic absorption spectrum of a typical porphyrin consists of a strong transition to the second excited state (S0 S2) at about 400 nm (the Soret or B band) and a weak transition to the first excited state (S0 S1) at about 550 nm (the Q band). -
Copyrighted Material
1 INTRODUCTION 1.1 WHY STUDY ORGANOMETALLIC CHEMISTRY? Organometallic chemists try to understand how organic molecules or groups interact with compounds of the inorganic elements, chiefl y metals. These elements can be divided into the main group, consisting of the s and p blocks of the periodic table, and the transition elements of the d and f blocks. Main-group organometallics, such as n -BuLi and PhB(OH)2 , have proved so useful for organic synthesis that their leading characteristics are usually extensively covered in organic chemistry courses. Here, we look instead at the transition metals because their chemistry involves the intervention of d and f orbitals that bring into play reaction pathways not readily accessible elsewhere in the periodic table. While main-group organometallics are typically stoichiometric reagents, many of their transition metal analogs are most effective when they act as catalysts. Indeed, the expanding range of applications of catalysis is a COPYRIGHTEDmajor reason for the continued MATERIAL rising interest in organo- metallics. As late as 1975, the majority of organic syntheses had no recourse to transition metals at any stage; in contrast, they now very often appear, almost always as catalysts. Catalysis is also a central prin- ciple of Green Chemistry 1 because it helps avoid the waste formation, The Organometallic Chemistry of the Transition Metals, Sixth Edition. Robert H. Crabtree. © 2014 John Wiley & Sons, Inc. Published 2014 by John Wiley & Sons, Inc. 1 2 INTRODUCTION for example, of Mg salts from Grignard reactions, that tends to accom- pany the use of stoichiometric reagents. The fi eld thus occupies the borderland between organic and inorganic chemistry. -
Werner-Type Complexes of Uranium(III) and (IV) Judith Riedhammer, J
pubs.acs.org/IC Article Werner-Type Complexes of Uranium(III) and (IV) Judith Riedhammer, J. Rolando Aguilar-Calderon,́ Matthias Miehlich, Dominik P. Halter, Dominik Munz, Frank W. Heinemann, Skye Fortier, Karsten Meyer,* and Daniel J. Mindiola* Cite This: Inorg. Chem. 2020, 59, 2443−2449 Read Online ACCESS Metrics & More Article Recommendations *sı Supporting Information ABSTRACT: Transmetalation of the β-diketiminate salt [M]- Me Ph + Me Ph− − [ nacnac ](M =NaorK; nacnac = {PhNC(CH3)}2CH ) with UI3(THF)4 resulted in the formation of the homoleptic, Me Ph octahedral complex [U( nacnac )3](1). Green colored 1 was fully characterized by a solid-state X-ray diffraction analysis and a combination of UV/vis/NIR, NMR, and EPR spectroscopic studies as well as solid-state SQUID magnetization studies and density functional theory calculations. Electrochemical studies of 1 revealed this species to possess two anodic waves for the U(III/IV) and U(IV/V) redox couples, with the former being chemically accessible. Using mild oxidants, such as [CoCp2][PF6]or [FeCp ][Al{OC(CF ) } ], yields the discrete salts [1][A] (A = − 2 3 −3 4 PF6 , Al{OC(CF3)3}4 ), whereas the anion exchange of [1][PF6] with NaBPh4 yields [1][BPh4]. Me Dipp μ 12 ■ INTRODUCTION UCl3(THF)] and [{( nacnac )UCl}2( 2-Cl)3]Cl. In Me Dipp− ’ some cases, disubstitution of nacnac generates the Alfred Werner s disapproval of the complex ion-chain theory Me Dipp η3 Me Dipp 13 proposed by Jørgensen and Blomstrand,1 via the introduction rearranged species [( nacnac )( - nacnac )UI], of coordination complexes and the concept of Nebenvalenz,1,2 where one ligand has changed hapticity, most likely due to fi steric constraints. -
The Royal Society of Chemistry Turns Its Focus on Researchers with Better Search and Measurement Tools
The Royal Society of Chemistry turns its focus on researchers with better search and measurement tools The Royal Society of Chemistry offers a publishing platform providing access to over a million chemical science articles, book chapters and abstracts. Like many publishers of high quality peer-reviewed content, they are under pressure from their community to innovate quickly and harness digital technology in new ways that add value, simplicity and easier access to the research workflow. About Will Russell is responsible for some of the new technical developments • pubs.rsc.org at the Royal Society of Chemistry. “Although we do a lot of in-house • rsc.org development, we need to understand where developments can be • Location: Cambridge UK with improved by working with partners,” he says. “I really believe in the additional editorial teams in Beijing, benefit of strategic technology partnerships with an external partner. China, Bangalore India and There is the speed of getting a key utility to the market and this offers Washington D.C. USA us a tremendous business advantage.” • Scientific publisher of high-impact journals and books “We have journals going back to 1841,” he says. “We started migrating People print content online in the late 1990s. Our biggest challenge now is how • Will Russell we will deliver content in the future in the most useful way for the Business Relationship Manager researcher.” Goals Will pinpoints a way forward. “There are new opportunities presented • Embrace new technology to remain by open science and alternative metrics, and increasing importance competitive against innovative attached to data and open data,” he says.