RESONANCE and INDUCTION TUTORIAL Jack Deruiter The
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Inductive Effect
Dr Anju K. Gupta Associate Professor Department of Chemistry A.N. College, Patna Lecture note for B.Sc. (I) Subsidiary Inductive Effect If a covalent bond is formed between atoms having similar electronegativity, the bonding electrons will be shared equally between the two atoms. For example, in hydrogen molecule, the two hydrogen atoms have identical electronegativities. Therefore, the electron pair is shared equally between the two hydrogen atoms and so the molecular orbital (σ-bond) will be symmetrically distributed. Similarly, if we consider a chlorine molecule, the molecular orbital (σ- bond) formed between the two identical chlorine atoms is symmetrically distributed. This type of bond is called a non-polar covalent bond. However, if we consider a hydrogen chloride molecule, the electron pair is not equally shared between hydrogen and chlorine because chlorine has a greater electronegativity than hydrogen. Therefore, the electron pair shifts towards the more electronegative atom. This causes polarization in the bond in which the more electronegative atom chlorine acquires a partial positive charge. This type of bond in which unequal sharing of electron pair between two atoms of different electronegativities are involved is called a polar covalent bond. The atom which has a greater share of the paired electrons is given a symbol δ- and the atom with a smaller share is given a symbol δ+. Thus, a polar covalent bond can be represented as: 1 Dr Anju K. Gupta Associate Professor Department of Chemistry A.N. College, Patna Lecture note for B.Sc. (I) Subsidiary Consider a chain of carbon atoms such as C4—C3—C2—C1—X with an atom X at the terminal having higher electronegativity than carbon. -
Polar Covalent Bonds: Electronegativity
Polar Covalent Bonds: Electronegativity Covalent bonds can have ionic character These are polar covalent bonds Bonding electrons attracted more strongly by one atom than by the other Electron distribution between atoms is not symmetrical Bond Polarity and Electronegativity Symmetrical Covalent Bonds Polar Covalent Bonds C – C + - C – H C – O (non-polar) (polar) Electronegativity (EN): intrinsic ability of an atom to attract the shared electrons in a covalent bond Inductive Effect: shifting of sigma bonded electrons in resppygonse to nearby electronegative atom The Periodic Table and Electronegativity C – H C - Br and C - I (non-pol)lar) (po l)lar) Bond Polarity and Inductive Effect Nonpolar Covalent Bonds: atoms with similar EN Polar Covalent Bonds: Difference in EN of atoms < 2 Ionic Bonds: Difference in EN > 2 C–H bonds, relatively nonpolar C-O, C-X bonds (more electronegative elements) are polar Bonding electrons shift toward electronegative atom C acqqppuires partial positive char g,ge, + Electronegative atom acquires partial negative charge, - Inductive effect: shifting of electrons in a bond in response to EN of nearby atoms Electrostatic Potential Maps Electrostatic potential maps show calculated charge distributions Colors indicate electron- rich (red) and electron- poor (blue ) reg ions Arrows indicate direction of bond polarity Polar Covalent Bonds: Net Dipole Moments Molecules as a whole are often polar from vector summation of individual bond polarities and lone-pair contributions Strongly polar substances soluble in polar solvents like water; nonpolar substances are insoluble in water. Dipole moment ( ) - Net molecular polarity, due to difference in summed charges - magnitude of charge Q at end of molecular dipole times distance r between charges = Q r, in debyes (D), 1 D = 3.336 1030 coulomb meter length of an average covalent bond, the dipole moment would be 1.60 1029 Cm, or 4.80 D. -
Topological Model on the Inductive Effect in Alkyl Halides Using Local Quantum Similarity and Reactivity Descriptors in the Density Functional Theory
Hindawi Publishing Corporation Journal of Quantum Chemistry Volume 2014, Article ID 850163, 12 pages http://dx.doi.org/10.1155/2014/850163 Research Article Topological Model on the Inductive Effect in Alkyl Halides Using Local Quantum Similarity and Reactivity Descriptors in the Density Functional Theory Alejandro Morales-Bayuelo1,2 and Ricardo Vivas-Reyes1 1 Grupo de Qu´ımica Cuantica´ y Teorica,´ Universidad de Cartagena, Programa de Qu´ımica, Facultad de Ciencias Exactas y Naturales, Cartagena de Indias, Colombia 2 Departamento de Ciencias Qu´ımicas, Universidad Nacional Andres Bello, Republica 275, Santiago, Chile Correspondence should be addressed to Alejandro Morales-Bayuelo; [email protected] and Ricardo Vivas-Reyes; [email protected] Received 19 September 2013; Revised 16 December 2013; Accepted 16 December 2013; Published 19 February 2014 Academic Editor: Daniel Glossman-Mitnik Copyright © 2014 A. Morales-Bayuelo and R. Vivas-Reyes. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. We present a topological analysis to the inductive effect through steric and electrostatic scales of quantitative convergence. Using the molecular similarity field based in the local guantum similarity (LQS) with the Topo-Geometrical Superposition Algorithm (TGSA) alignment method and the chemical reactivity in the density function theory (DFT) context, all calculations were carried out with Amsterdam Density Functional (ADF) code, using the gradient generalized approximation (GGA) and local exchange correlations PW91, in order to characterize the electronic effect by atomic size in the halogens group using a standard Slater-type- orbital basis set. -
Heterocycles 2 Daniel Palleros
Heterocycles 2 Daniel Palleros Heterocycles 1. Structures 2. Aromaticity and Basicity 2.1 Pyrrole 2.2 Imidazole 2.3 Pyridine 2.4 Pyrimidine 2.5 Purine 3. Π-excessive and Π-deficient Heterocycles 4. Electrophilic Aromatic Substitution 5. Oxidation-Reduction 6. DNA and RNA Bases 7. Tautomers 8. H-bond Formation 9. Absorption of UV Radiation 10. Reactions and Mutations Heterocycles 3 Daniel Palleros Heterocycles Heterocycles are cyclic compounds in which one or more atoms of the ring are heteroatoms: O, N, S, P, etc. They are present in many biologically important molecules such as amino acids, nucleic acids and hormones. They are also indispensable components of pharmaceuticals and therapeutic drugs. Caffeine, sildenafil (the active ingredient in Viagra), acyclovir (an antiviral agent), clopidogrel (an antiplatelet agent) and nicotine, they all have heterocyclic systems. O CH3 N HN O O N O CH 3 N H3C N N HN N OH O S O H N N N 2 N O N N O CH3 N CH3 caffeine sildenafil acyclovir Cl S N CH3 N N H COOCH3 nicotine (S)-clopidogrel Here we will discuss the chemistry of this important group of compounds beginning with the simplest rings and continuing to more complex systems such as those present in nucleic acids. Heterocycles 4 Daniel Palleros 1. Structures Some of the most important heterocycles are shown below. Note that they have five or six-membered rings such as pyrrole and pyridine or polycyclic ring systems such as quinoline and purine. Imidazole, pyrimidine and purine play a very important role in the chemistry of nucleic acids and are highlighted. -
Understanding Nonplanarity in Metallabenzene Complexes
1986 Organometallics 2007, 26, 1986-1995 Understanding Nonplanarity in Metallabenzene Complexes Jun Zhu, Guochen Jia,* and Zhenyang Lin* Department of Chemistry, The Hong Kong UniVersity of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China ReceiVed February 11, 2007 The nonplanarity found in metallabenzene complexes has been investigated theoretically via density functional theory (DFT) calculations. A metallabenzene has four occupied π molecular orbitals (8 π electrons) instead of three that benzene has. Our electronic structure analyses show that the extra occupied π molecular orbital, which is the highest occupied molecular orbital (HOMO) in many metallabenzenes, has antibonding interactions between the metal center and the metal-bonded ring-carbon atoms, providing the electronic driving force toward nonplanarity. Calculations indicate that the electronic driving force toward nonplanarity, however, is relatively small. Therefore, other factors such as steric effects also play important roles in determining the planarity of these metallabenzene complexes. In this paper, how the various electronic and steric factors interplay has been discussed. Introduction benzene complexes. For example, the formation mechanism and chemical reactivity of metallabenzene complexes have been Metallabenzenes, organometallic compounds formed by extensively studied.17 formal replacement of a CH group in benzene by an isolobal In the studies of metallabenzene complexes, a central issue transition metal fragment, were first considered theoretically by concerns the π-conjugation of the six-membered metal-contain- Hoffman et al. in 1979.1 Since the isolation of the first stable 2 ing ring. Indeed, it is true that metallabenzene complexes are osmabenzenes by Roper’s group in 1982, metallabenzene highly conjugated in view of the fact that the single-double complexes have attracted considerable interest over the last bond alternation is insignificant in the six-membered metal- quarter century. -
PS 6 Answers, Spring 2003, Prof
Chem 332, PS 6 answers, Spring 2003, Prof. Fox 1. Which of the following are aromatic. Draw "Frost Circles" that support your answers 2– 2+ 2+ + all bonding MO's although all electrons all bonding MO's this is an interesting case: this is are in bonding orbitals, are filled are filled a 4n+2 molecule, and it is flat-- two bonding MO's are aromatic aromatic characteristic of aromatic only half-filled molecules. However, it has four anti-aromatic electrons in non-bonding orbitals, so we might have considered this to be non-aromatic. So it comes down to how you define aromaticity. For now we will call it aromatic with a question mark. 2. Which of the following are aromatic. Use the Huckel rule to support your answer 2– P H B 14 electrons, aromatic H 6 electrons 10 electrons 2 6 electrons sp3 center (filled sp on aromatic (empty sp2 on not conjugated phosphorus) boron) and not aromatic aromatic aromatic 3. Compound 1 has an unusually large dipole moment for an organic hydrocarbon. Explain why (consider resonance structures for the central double bond) We need to remember that for any double bond compound, we can draw two polar resonance structure. Normally, these resonance structures are unimportant unimportant unimportant However, for 1 the story is different because there is a polar resonance form that has two aromatic components. In other words, 'breaking' the double bond gives rise to aromaticity, and therefore the polar resonance structure is important and leads to the observed dipole. dipole 1 8 e– 4 e– 6 e– 6 e– anti- anti- aromatic aromatic aromatic aromatic important resonance unimportant resonance structure structure 5. -
Rational Design of Small Molecule Fluorescent Probes for Biological Applications
Organic & Biomolecular Chemistry Rational Design of Small Molecule Fluorescent Probes for Biological Applications Journal: Organic & Biomolecular Chemistry Manuscript ID OB-REV-06-2020-001131.R1 Article Type: Review Article Date Submitted by the 13-Jul-2020 Author: Complete List of Authors: Jun, Joomyung; University of Pennsylvania, Chemistry; Massachusetts Institute of Technology, Chemistry Chenoweth, David; University of Pennsylvania, Department of Chemistry Petersson, E.; University of Pennsylvania, Chemistry Page 1 of 16 Organic & Biomolecular Chemistry ARTICLE Rational Design of Small Molecule Fluorescent Probes for Biological Applications a,b a a,c Received 00th January 20xx, Joomyung V. Jun, David M. Chenoweth* and E. James Petersson* Accepted 00th January 20xx Fluorescent small molecules are powerful tools for visualizing biological events, embodying an essential facet of chemical DOI: 10.1039/x0xx00000x biology. Since the discovery of the first organic fluorophore, quinine, in 1845, both synthetic and theoretical efforts have endeavored to “modulate” fluorescent compounds. An advantage of synthetic dyes is the ability to employ modern organic chemistry strategies to tailor chemical structures and thereby rationally tune photophysical properties and functionality of the fluorophore. This review explores general factors affecting fluorophore excitation and emission spectra, molar absorption, Stokes shift, and quantum efficiency; and provides guidelines for chemist to create novel probes. Structure- property relationships concerning the substituents are discussed in detail with examples for several dye families. Then, we present a survey of functional probes based on PeT, FRET, and environmental or photo-sensitivity, focusing on representative recent work in each category. We believe that a full understanding of dyes with diverse chemical moieties enables the rational design of probes for the precise interrogation of biochemical and biological phenomena. -
Structure of Benzene, Orbital Picture, Resonance in Benzene, Aromatic Characters, Huckel’S Rule B
Dr.Mrityunjay Banerjee, IPT, Salipur B PHARM 3rd SEMESTER BP301T PHARMACEUTICAL ORGANIC CHEMISTRY –II UNIT I UNIT I Benzene and its derivatives 10 Hours A. Analytical, synthetic and other evidences in the derivation of structure of benzene, Orbital picture, resonance in benzene, aromatic characters, Huckel’s rule B. Reactions of benzene - nitration, sulphonation, halogenationreactivity, Friedelcrafts alkylation- reactivity, limitations, Friedelcrafts acylation. C. Substituents, effect of substituents on reactivity and orientation of mono substituted benzene compounds towards electrophilic substitution reaction D. Structure and uses of DDT, Saccharin, BHC and Chloramine Benzene and its Derivatives Chemists have found it useful to divide all organic compounds into two broad classes: aliphatic compounds and aromatic compounds. The original meanings of the words "aliphatic" (fatty) and "aromatic" (fragrant/ pleasant smell). Aromatic compounds are benzene and compounds that resemble benzene in chemical behavior. Aromatic properties are those properties of benzene that distinguish it from aliphatic hydrocarbons. Benzene: A liquid that smells like gasoline Boils at 80°C & Freezes at 5.5°C It was formerly used to decaffeinate coffee and component of many consumer products, such as paint strippers, rubber cements, and home dry-cleaning spot removers. A precursor in the production of plastics (such as Styrofoam and nylon), drugs, detergents, synthetic rubber, pesticides, and dyes. It is used as a solvent in cleaning and maintaining printing equipment and for adhesives such as those used to attach soles to shoes. Benzene is a natural constituent of petroleum products, but because it is a known carcinogen, its use as an additive in gasoline is now limited. In 1970s it was associated with leukemia deaths. -
Resonance 1. Lone Pair Next to Empty 2P Orbital
1 Lecture 5 Resonance 1. Lone pair next to empty 2p orbital electron pair acceptors - lack of electrons C C CC sp2 R+ is more common sp R+ is less common R+ needs electrons, has to overlap with a. an adjacent 2p lone pair with electrons b. an adjacent pi bond a. an adjacent 2p lone pair with electrons on a neutral atom (+ overall, delocalization of positive charge) R R X = neutral atom with lone pair R R C C R X 2D resonance R X C C R X R X R R R R C R C R CX CX R N R N R 3D resonance R R R R R R R C R C R CX R O CX 3D resonance R O R R R R C better, more bonds, full octets C R F R F b. an adjacent 2p lone pair with electrons on a negative atom (neutral overall, delocalization of electrons) R R X =anion with lone pair R R C C R X 2D resonance R X C C R X R X R R R R C R C R CX CX R C R C R 3D resonance R R R R R R R C R C R CX R N CX 3D resonance R N R R R R C C better, more bonds, full octets R O R O 2 Lecture 5 Problem 1 – All of the following examples demonstrate delocalization of a lone pair of electrons into an empty 2p orbital. Usually in organic chemistry this is a carbocation site, but not always. -
Physics of Resonating Valence Bond Spin Liquids Julia Saskia Wildeboer Washington University in St
Washington University in St. Louis Washington University Open Scholarship All Theses and Dissertations (ETDs) Summer 8-13-2013 Physics of Resonating Valence Bond Spin Liquids Julia Saskia Wildeboer Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/etd Recommended Citation Wildeboer, Julia Saskia, "Physics of Resonating Valence Bond Spin Liquids" (2013). All Theses and Dissertations (ETDs). 1163. https://openscholarship.wustl.edu/etd/1163 This Dissertation is brought to you for free and open access by Washington University Open Scholarship. It has been accepted for inclusion in All Theses and Dissertations (ETDs) by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Department of Physics Dissertation Examination Committee: Alexander Seidel, Chair Zohar Nussinov Michael C. Ogilvie Jung-Tsung Shen Xiang Tang Li Yang Physics of Resonating Valence Bond Spin Liquids by Julia Saskia Wildeboer A dissertation presented to the Graduate School of Arts and Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy August 2013 St. Louis, Missouri TABLE OF CONTENTS Page LIST OF FIGURES ................................ v ACKNOWLEDGMENTS ............................. ix DEDICATION ................................... ix ABSTRACT .................................... xi 1 Introduction .................................. 1 1.1 Landau’s principle of symmetry breaking and topological order .... 2 1.2 From quantum dimer models to spin models .............. 5 1.2.1 The Rokhsar-Kivelson (RK) point ................ 12 1.3 QDM phase diagrams ........................... 14 1.4 Z2 quantum spin liquid and other topological phases .......... 15 1.4.1 Z2 RVB liquid ........................... 16 1.4.2 U(1) critical RVB liquid .................... -
Physical Organic Chemistry
PHYSICAL ORGANIC CHEMISTRY Yu-Tai Tao (陶雨台) Tel: (02)27898580 E-mail: [email protected] Website:http://www.sinica.edu.tw/~ytt Textbook: “Perspective on Structure and Mechanism in Organic Chemistry” by F. A. Corroll, 1998, Brooks/Cole Publishing Company References: 1. “Modern Physical Organic Chemistry” by E. V. Anslyn and D. A. Dougherty, 2005, University Science Books. Grading: One midterm (45%) one final exam (45%) and 4 quizzes (10%) homeworks Chap.1 Review of Concepts in Organic Chemistry § Quantum number and atomic orbitals Atomic orbital wavefunctions are associated with four quantum numbers: principle q. n. (n=1,2,3), azimuthal q.n. (m= 0,1,2,3 or s,p,d,f,..magnetic q. n. (for p, -1, 0, 1; for d, -2, -1, 0, 1, 2. electron spin q. n. =1/2, -1/2. § Molecular dimensions Atomic radius ionic radius, ri:size of electron cloud around an ion. covalent radius, rc:half of the distance between two atoms of same element bond to each other. van der Waal radius, rvdw:the effective size of atomic cloud around a covalently bonded atoms. - Cl Cl2 CH3Cl Bond length measures the distance between nucleus (or the local centers of electron density). Bond angle measures the angle between lines connecting different nucleus. Molecular volume and surface area can be the sum of atomic volume (or group volume) and surface area. Principle of additivity (group increment) Physical basis of additivity law: the forces between atoms in the same molecule or different molecules are very “short range”. Theoretical determination of molecular size:depending on the boundary condition. -
CONCISE STUDY NOTES for BG 4Th Semester (UNIT: Amines and Heterocyclic Compounds)
CONCISE STUDY NOTES FOR BG 4th Semester (UNIT: Amines and Heterocyclic Compounds) Syllabus Amines: Classification and factors affecting basicity of amines. Mechanistic details (wherever applicable) of methods of formation of alkyl and arylamines through reduction of nitro compounds and nitriles. Gabriel-Phthalamide reaction and Hofmann rearrangement. Mechanisms involved in the formation and reactions of arenediazonium salts including Azo coupling. Heterocyclic compounds bearing one nitrogen atom: Stuctural features of pyrrole, pyrrolidine, pyridine and piperidine and comparative account of their basic strength. Aromaticity and electrophilic substitution reactions of pyrrole and their comparison with those of furan and thiophene.Mechanisms involved in the preparations of Indole and quinoline using Fischer-Indole and Bishlier-Napierlaski syntheses. Amines: Their classification Alkyl, aryl and ar-alkyl derivatives of ammonia are known as amines General formula is RNH2, R2NH, R3NH, where R can be any alkyl, aryl or aralkyl group. Amines are classified in to primary, secondary and tertiary amines depending upon the number of Hydrogen atoms in ammonia replaced by alkyl or aryl group. If one of hydrogen atom in NH3 is replaced by alkyl or aryl group, the derivative of ammonia so obtained is known as primary amine, if two hydrogen atoms in ammonia are replaced by alkyl, aryl or ar-alkyl groups, the derivative obtained is known as secondary amine, while as if all H atoms in ammonia are replaced by alkyl aryl or aralkyl groups, a tertiaty amine is obtained as shown below: The R groups can be alkyl, aryl or aralkyl groups. Further a secondary or tertiary amine may contain same or different R groups.