Molecular Modeling Experiment
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Organometallic Chemistry from the Interacting Quantum Atoms Approach
CORSO DI DOTTORATO DI RICERCA IN SCIENZE CHIMICHE CICLO XXIII TESI DI DOTTORATO DI RICERCA ORGANOMETALLIC CHEMISTRY FROM THE INTERACTING QUANTUM ATOMS APPROACH sigla del settore scientifico disciplinare CHIM03 NOME DEL TUTOR NOME DEL DOTTORANDO Prof: Angelo Sironi Davide Tiana NOME DEL COORDINATORE DEL DOTTORATO Prof. Silvia Ardizzone ANNO ACCADEMICO 2009/2010 1 2 Index Introduction ............................................................................................................................................................................ 5 The ligand field theory (LFT) .................................................................................................................................... 5 The chemistry from a real space point of view ................................................................................................. 9 Chapter 1: The quantum theory of atoms in molecules (QTAM) ............................................................... 12 Topological analysis of electron charge density ........................................................................................... 12 Analysis of the electronic charge density Laplacian ................................................................................... 16 Other properties ........................................................................................................................................................... 18 Chapter 2: The interacting quantum atoms theory (IQA) ............................................................................ -
Chemical Bonding II: Molecular Shapes, Valence Bond Theory, and Molecular Orbital Theory Review Questions
Chemical Bonding II: Molecular Shapes, Valence Bond Theory, and Molecular Orbital Theory Review Questions 10.1 J The properties of molecules are directly related to their shape. The sensation of taste, immune response, the sense of smell, and many types of drug action all depend on shape-specific interactions between molecules and proteins. According to VSEPR theory, the repulsion between electron groups on interior atoms of a molecule determines the geometry of the molecule. The five basic electron geometries are (1) Linear, which has two electron groups. (2) Trigonal planar, which has three electron groups. (3) Tetrahedral, which has four electron groups. (4) Trigonal bipyramid, which has five electron groups. (5) Octahedral, which has six electron groups. An electron group is defined as a lone pair of electrons, a single bond, a multiple bond, or even a single electron. H—C—H 109.5= ijj^^jl (a) Linear geometry \ \ (b) Trigonal planar geometry I Tetrahedral geometry I Equatorial chlorine Axial chlorine "P—Cl: \ Trigonal bipyramidal geometry 1 I Octahedral geometry I 369 370 Chapter 10 Chemical Bonding II The electron geometry is the geometrical arrangement of the electron groups around the central atom. The molecular geometry is the geometrical arrangement of the atoms around the central atom. The electron geometry and the molecular geometry are the same when every electron group bonds two atoms together. The presence of unbonded lone-pair electrons gives a different molecular geometry and electron geometry. (a) Four electron groups give tetrahedral electron geometry, while three bonding groups and one lone pair give a trigonal pyramidal molecular geometry. -
Pauling's Defence of Bent-Equivalent Bonds
Pauling’s Defence of Bent-Equivalent Bonds: A View of Evolving Explanatory Demands in Modern Chemistry Summary Linus Pauling played a key role in creating valence-bond theory, one of two competing theories of the chemical bond that appeared in the first half of the 20th century. While the chemical community preferred his theory over molecular-orbital theory for a number of years, valence-bond theory began to fall into disuse during the 1950s. This shift in the chemical community’s perception of Pauling’s theory motivated Pauling to defend the theory, and he did so in a peculiar way. Rather than publishing a defence of the full theory in leading journals of the day, Pauling published a defence of a particular model of the double bond predicted by the theory in a revised edition of his famous textbook, The Nature of the Chemical Bond. This paper explores that peculiar choice by considering both the circumstances that brought about the defence and the mathematical apparatus Pauling employed, using new discoveries from the Ava Helen and Linus Pauling Papers archive. Keywords: Linus Pauling, Chemical Bond, Double Bond, Chemistry, Valence, Resonance, Explanation, Chemical Education Contents 1. Introduction………………………………………………………….. 2 2. Using Valence Bonds and Molecular Orbitals to Explain the Double Bond………………………………………………………................. 3 3. Textbook Explanations……………………………………………… 5 4. The Origins of Bent-Equivalent Bonds ……………………..……… 7 4.1 An Early Defence …………………………………………….. 8 5. Catalysing the Mature Defence……………………………………… 9 5.1 Soviet Suppression and Pedagogical Disfavour ………………. 11 5.2 Wilson…………………………………………………………. 12 5.3 Kekulé…………………………………………………………. 14 6. Concentrating Bond Orbitals into a Defence………………………… 15 7. Conclusions………………………………………………………….. 17 Word Count: 8658 (9936 with footnotes) Pauling’s Defence of Bent-Equivalent Bonds Page 2 of 19 1. -
Chemical Applications of X-Ray Charge-Density Analysis
Chem. Rev. 2001, 101, 1583−1627 1583 Chemical Applications of X-ray Charge-Density Analysis Tibor S. Koritsanszky† Department of Chemistry, University of the Witwatersrand, WITS 2050, Johannesburg, South Africa Philip Coppens* Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000 Received October 18, 2000 Contents VII. Physical Properties from the Experimental 1617 Density I. Charge Densities from X-ray Diffraction 1583 A. Net Atomic and Molecular Charges 1617 II. Elements of Electron Density Determination 1585 B. Solid-State Dipole and Higher Moments and 1618 A. Expressions 1585 Nonlinear Optical Properties 1. Electron Density 1585 C. Electric Field Gradient at the Nuclear 1621 2. Structure Factor and Difference Densities 1585 Positions 3. Aspherical-Atom Formalism 1586 D. Electrostatic Potential 1621 4. Electrostatic Properties from the Charge 1586 E. Quantitative Evaluation of Electrostatic 1623 Density Interactions from the X-ray Charge Density B. Experiment and Analysis 1587 VIII. Concluding Remarks 1624 1. Experimental Conditions 1587 IX. Glossary of Abbreviations 1624 2. Data Analysis 1588 X. Acknowledgments 1624 III. Chemistry from the Electron Density 1590 XI. References 1625 A. Use of the Deformation Density 1590 B. Theory of Atoms in Molecules 1591 I. Charge Densities from X-ray Diffraction 1. Topological Atom 1591 As X-ray scattering by electrons is much stronger 2. Topological Structure of Molecules 1591 than that of the nuclei, intensities of scattered X-rays 3. Topological Classification of Atomic 1591 are almost exclusively determined by the distribution Interactions of the electrons. Thus, X-ray diffraction is a priori a 4. Laplacian of the Electron Density 1592 tool for the determination of electron distribution in 5. -
Cyclopentane Synthesis
Cyclopentane Synthesis Dan O’Malley Baran Group Meeting Cyclopentane Synthesis Group Meeting O'Malley 2/9/2005 This presentation is broken down into the following catagories. Some reactions either fit more than one Students of organic chemistry are taught a number of reactions for the synthesis of category or do not fit easily into any of them. Efforts have been made to place all such reactions in the cyclohexanes at a very early stage of their careers. Techniques for the creation of cyclopentanes, most appropriate category. however, are generally taught at a much later stage and are rarely given the same detailed treatment. This may be the result of the fact that there are no equivalents of reactions such as the Diels-Alder and I. General Information Robinson Annulation in terms of generality, extent of use, and historical importance. This may, in turn, II. Ionic Reactions be caused by the fact that the cyclopentane is an inherintly "umpoled" functionality, as illustrated below. III. Metal Mediated Reactions IV. Radical Reactions FG V. Pericyclic and Pseudo-pericyclic Reactions VI. Ring Expansion and Contraction Reactions I. General Information This situation is further exacerbated by the general lack of cheaply available cyclopentane compounds Baldwin's rules in the chiral pool; wheras a number of cyclohexane terpenes are readily available for elaboration, there Baldwin has divided ring closure reactions into those that are "favored" and those that are "disfavored". are no analogous cylcopentane natural products. Cyclopentanes are however, present in many Those that are disfavored are not always impossible, but are frequently much more difficult to effect. -
Photoremovable Protecting Groups in Chemistry and Biology: Reaction Mechanisms and Efficacy Petr Klan,́*,†,‡ Tomaś̌solomek,̌ †,‡ Christian G
Review pubs.acs.org/CR Photoremovable Protecting Groups in Chemistry and Biology: Reaction Mechanisms and Efficacy Petr Klan,́*,†,‡ Tomaś̌Solomek,̌ †,‡ Christian G. Bochet,§ Aurelień Blanc,∥ Richard Givens,⊥ Marina Rubina,⊥ Vladimir Popik,# Alexey Kostikov,# and Jakob Wirz∇ † Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ‡ Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic § Department of Chemistry, University of Fribourg, Chemin du Museé 9, CH-1700 Fribourg, Switzerland ∥ Institut de Chimie, University of Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France ⊥ Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, 5010 Malott Hall, Lawrence, Kansas 66045, United States # Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States ∇ Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland 7.3. Arylsulfonyl Group 160 7.4. Ketones: 1,5- and 1,6-Hydrogen Abstraction 160 7.5. Carbanion-Mediated Groups 160 7.6. Sisyl and Other Silicon-Based Groups 161 7.7. 2-Hydroxycinnamyl Groups 161 7.8. α-Keto Amides, α,β-Unsaturated Anilides, CONTENTS and Methyl(phenyl)thiocarbamic Acid 162 7.9. Thiochromone S,S-Dioxide 162 1. Introduction 119 7.10. 2-Pyrrolidino-1,4-Benzoquinone Group 162 2. Arylcarbonylmethyl Groups 121 7.11. Triazine and Arylmethyleneimino Groups 162 2.1. Phenacyl and Other Related Arylcarbonyl- 7.12. Xanthene and Pyronin Groups 163 methyl Groups 121 o 7.13. Retro-Cycloaddition Reactions 163 2.2. -Alkylphenacyl Groups 123 8. Sensitized Release 163 2.3. p-Hydroxyphenacyl Groups 125 p 8.1. -
Screening Values for Non-Carcinogenic Hanford Waste Tank Vapor Chemicals That Lack Established Occupational Exposure Limits
PNNL-15640 Screening Values for Non-Carcinogenic Hanford Waste Tank Vapor Chemicals that Lack Established Occupational Exposure Limits TS Poet TJ Mast JL Huckaby February 2006 Prepared for the U.S. Department of Energy under Contract DE-AC05-76RL01830 DISCLAIMER This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor Battelle Memorial Institute, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. PACIFIC NORTHWEST NATIONAL LABORATORY operated by BATTELLE for the UNITED STATES DEPARTMENT OF ENERGY under Contract DE-AC05-76RL01830 Printed in the United States of America Available to DOE and DOE contractors from the Office of Scientific and Technical Information, P.O. Box 62, Oak Ridge, TN 37831-0062; ph: (865) 576-8401 fax: (865) 576-5728 email: [email protected] Available to the public from the National Technical Information Service, U.S. Department of Commerce, 5285 Port Royal Rd., Springfield, VA 22161 ph: (800) 553-6847 fax: (703) 605-6900 email: [email protected] online ordering: http://www.ntis.gov/ordering.htm This document was printed on recycled paper. -
Carboxylic Acids and Their Derivatives
8 CARBOXY A lmost all of the basic types of reactions now have been covered: addition, elimination, substitution, and rearrangement by polar, radical, and concerted mechanisms. Indeed, if you have been looking for similarities, you will have seen that most of the reactions discussed in the preceding three chapters are variations on basic types we have discussed earlier. Furthermore, most of the basic structural effects that determine chemical reactivity also have been covered in previous chapters: bond energies, steric hindrance, electronega- tivity, electron delocalization, hydrogen bonding, solvation, and conforma- tional influences. You might well ask what is left. The answer is, a great deal- but now we will be concerned mostly with putting concepts together, moving from the simple to the complex. For example, in this chapter we will be trying to under- stand the ways that carboxylic acids, which possess the -c' functional \ group, are similar to and different from alcohols, which have the OH group, and aldehydes and ketones, which have C=O bonds. Subsequently we will look at acids that also possess OH or NH, sub- stituent groups (or both) and develop a rationale for the behavior of these combinations in terms of effects we already have discussed. Insofar as pos- sible, you should try to do this yourself whenever you encounter a substance with a new set of combinations of functional groups on its molecules. You often will be in error (as many experts will be), because even if you take Carboxylic Acids and Their Derivatives 789 account of all of the structural effects, as well as the possible reactions or inter- actions, the overall result of these frequently is very difficult to judge in advance. -
Aldehydes, Ketones and Carboxylic Acids
1212Unit Objectives AldehydesAldehydesAldehydesAldehydes,,,,,, KKKKKKeeeeeetonestonestonestonestonestones After studying this Unit, you will be able to andandandandandand CarboxylicCarboxylicCarboxylicCarboxylicCarboxylicCarboxylic • write the common and IUPAC names of aldehydes, ketones and carboxylic acids; AAAAAAcidscidscidscidscidscids • write the structures of the compounds containing functional groups namely carbonyl and carboxyl groups; Carbonyl compounds are of utmost importance to organic chemistry. They are constituents of fabrics, flavourings, plastics • describe the important methods and drugs. of preparation and reactions of these classes of compounds; In the previous Unit, you have studied organic • correlate physical properties and compounds with functional groups containing carbon- chemical reactions of aldehydes, oxygen single bond. In this Unit, we will study about the ketones and carboxylic acids, organic compounds containing carbon-oxygen double with their structures; bond (>C=O) called carbonyl group, which is one of the • explain the mechanism of a few most important functional groups in organic chemistry. selected reactions of aldehydes and ketones; In aldehydes, the carbonyl group is bonded to a carbon and hydrogen while in the ketones, it is bonded • understand various factors to two carbon atoms. The carbonyl compounds in which affecting the acidity of carboxylic carbon of carbonyl group is bonded to carbon or acids and their reactions; hydrogen and oxygen of hydroxyl moiety (-OH) are • describe the uses of aldehydes, known as carboxylic acids, while in compounds where ketones and carboxylic acids. carbon is attached to carbon or hydrogen and nitrogen of -NH2 moiety or to halogens are called amides and acyl halides respectively. Esters and anhydrides are derivatives of carboxylic acids. The general formulas of these classes of compounds are given below: 2021–22 Aldehydes, ketones and carboxylic acids are widespread in plants and animal kingdom. -
ABSTRACT JANG, YUJIN. Synthesis of 1-Sulfonylcyclopropanols and Their Application in New Chemical Transformations As Powerful Cy
ABSTRACT JANG, YUJIN. Synthesis of 1-Sulfonylcyclopropanols and Their Application in New Chemical Transformations as Powerful Cyclopropanone Equivalents. (Under the direction of Dr. Vincent Lindsay). Cyclopropanone, a notoriously strained cycloalkanone (Baeyer strain ca. 49 kcal/mol), is a promising three carbon building block in organic synthesis where all three C–C bonds are labile, and can be readily involved in ring-opening or ring-expansion. Despite its tremendous potential as a strained reagent, the difficulties associated with its handling and storage have precluded its widespread use in organic synthesis. For these reasons, a majority of cyclopropanone chemistry in the literature involves the use of equivalents such as hemiketals that can equilibrate to the parent ketone in situ via base-induced α-elimination. Although the classical hemiketals are suitable in some reactions, a number of potential transformations are still inaccessible, as harsh conditions are often required to generate cyclopropanone due to the poor leaving group ability of alkoxides and the immense strain generated in the process. In order to elevate the chemistry of cyclopropanones as common building blocks in synthesis, well-behaved cyclopropanone precursors are highly demanded. Here, we describe the efficient and convenient synthesis and application of unsubstituted 1-sulfonylcyclopropanols as powerful cyclopropanone equivalents. By tuning the electronic and steric nature of leaving group, a variety 1-sulfonylcyclopropanols were furnished, and the relative propensity of their equilibration to cyclopropanone was investigated in a novel pyrazole substitution reaction. With this well-behaved class of surrogates, we explored the C–C bond activation of this strained cycloalkanone in the presence of transition metals and organocatalysts. -
Nucleophilic Addition to the Carbonyl Group 6
Nucleophilic addition to the carbonyl group 6 Connections Building on Arriving at Looking forward to • Functional groups, especially the C=O • How and why the C=O group reacts • Additions of organometallic group ch2 with nucleophiles reagents ch9 • Identifying the functional groups in a • Explaining the reactivity of the C=O • Substitution reactions of the C=O molecule spectroscopically ch3 group using molecular orbitals and curly group’s oxygen atom ch11 • How molecular orbitals explain arrows • How the C=O group in derivatives of molecular shapes and functional • What sorts of molecules can be made by carboxylic acids promotes substitution groups ch4 reactions of C=O groups reactions ch10 • How, and why, molecules react together • How acid or base catalysts improve the • C=O groups with an adjacent double and using curly arrows to describe reactivity of the C=O group bond ch22 reactions ch5 Molecular orbitals explain the reactivity of the carbonyl group We are now going to leave to one side most of the reactions you met in the last chapter—we will come back to them all again later in the book. In this chapter we are going to concentrate on just one of them—probably the simplest of all organic reactions—the addition of a nucleo- phile to a carbonyl group. The carbonyl group, as found in aldehydes, ketones, and many other compounds, is without doubt the most important functional group in organic chemis- try, and that is another reason why we have chosen it as our fi rst topic for more detailed study. You met nucleophilic addition to a carbonyl group on pp. -
Theory of Three-Electron Bond in the Four Works with Brief Comments
ry: C ist urr m en e t Dmytrovych, Organic Chem Curr Res 2017, 6:2 h R C e c s i DOI: 10.4172/2161-0401.1000182 e n a a r Organic Chemistry c g r h O ISSN: 2161-0401 Current Research ResearchResearch Article Article Open Accesss Theory of Three-Electron Bond in the Four Works with Brief Comments Bezverkhniy Volodymyr Dmytrovych* Street Chernivtsi 6, Village Nedoboevtsi, Chernivtsi Region, Khotyn District, Ukraine Abstract Using the concept of three-electron bond we can represent the actual electron structure of benzene and other molecules, explain specificity of the aromatic bond and calculate the delocalization energy. Gives theoretical justification and experimental confirmation of existence of the three-electron bond. It was shown, that functional relation y=a+b/x+c/ x2 fully describes dependence of energy and multiplicity of chemical bond from bond distance. Keywords: Benzene; Three-electron bond; Semi-virtual particle; Structure of the Benzene Molecule on the Basis of the Fermion; Entangled quantum state; Interfering universe Three-Electron Bond Introduction Results and Discussion Chemical bond has been always a basis of chemistry. Advancement Supposing that the chemical bond between two atoms can be of chemical science can be considered as evolution, development of established by means of three electrons with oppositely oriented spins concepts about chemical bond. Aromatic bond is fundamental basis ( ) the structure of the benzene molecule can be expressed as follows of organic chemistry. Concept of three-electron bond in benzene (Figures 2 and 3). molecule enables to explain specificity of aromatic bond. It also becomes ↑↓↑ It is interesting to point out that spins of central electrons on opposite apparent, why planar molecules with 6, 10 etc.