Low Bandgap Coplanar Conjugated Molecules Featuring Dynamic Intramolecular Lewis Acid-Base Coordination
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Aromaticity Sem- Ii
AROMATICITY SEM- II In 1931, German chemist and physicist Sir Erich Hückel proposed a theory to help determine if a planar ring molecule would have aromatic properties .This is a very popular and useful rule to identify aromaticity in monocyclic conjugated compound. According to which a planar monocyclic conjugated system having ( 4n +2) delocalised (where, n = 0, 1, 2, .....) electrons are known as aromatic compound . For example: Benzene, Naphthalene, Furan, Pyrrole etc. Criteria for Aromaticity 1) The molecule is cyclic (a ring of atoms) 2) The molecule is planar (all atoms in the molecule lie in the same plane) 3) The molecule is fully conjugated (p orbitals at every atom in the ring) 4) The molecule has 4n+2 π electrons (n=0 or any positive integer Why 4n+2π Electrons? According to Hückel's Molecular Orbital Theory, a compound is particularly stable if all of its bonding molecular orbitals are filled with paired electrons. - This is true of aromatic compounds, meaning they are quite stable. - With aromatic compounds, 2 electrons fill the lowest energy molecular orbital, and 4 electrons fill each subsequent energy level (the number of subsequent energy levels is denoted by n), leaving all bonding orbitals filled and no anti-bonding orbitals occupied. This gives a total of 4n+2π electrons. - As for example: Benzene has 6π electrons. Its first 2π electrons fill the lowest energy orbital, and it has 4π electrons remaining. These 4 fill in the orbitals of the succeeding energy level. The criteria for Antiaromaticity are as follows: 1) The molecule must be cyclic and completely conjugated 2) The molecule must be planar. -
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. -
AROMATIC COMPOUNDS Aromaticity
AROMATICITY AROMATIC COMPOUNDS Aromaticity Benzene - C6H6 H H H H H H H H H H H H Kekulé and the Structure of Benzene Kekule benzene: two forms are in rapid equilibrium 154 pm 134 pm • All bonds are 140 pm (intermediate between C-C and C=C) • C–C–C bond angles are 120° • Structure is planar, hexagonal A Resonance Picture of Bonding in Benzene resonance hybrid 6 -electron delocalized over 6 carbon atoms The Stability of Benzene Aromaticity: cyclic conjugated organic compounds such as benzene, exhibit special stability due to resonance delocalization of -electrons. Heats of hydrogenation + H2 + 120 KJ/mol + 2 H2 + 230 KJ/mol calc'd value= 240 KJ/mol 10 KJ/mol added stability + 3 H 2 + 208 KJ/mol calc'd value= 360 KJ/mol 152 KJ/mol added stability + 3 H2 + 337 KJ/mol 1,3,5-Hexatriene - conjugated but not cyclic Resonance energy of benzene is 129 - 152 KJ/mol An Orbital Hybridization View of Bonding in Benzene • Benzene is a planar, hexagonal cyclic hydrocarbon • The C–C–C bond angles are 120° = sp2 hybridized • Each carbon possesses an unhybridized p-orbital, which makes up the conjugated -system. • The six -electrons are delocalized through the -system The Molecular Orbitals of Benzene - the aromatic system of benzene consists of six p-orbitals (atomic orbitals). Benzene must have six molecular orbitals. Y6 Y4 Y5 six p-orbitals Y2 Y3 Y1 Degenerate orbitals: Y : zero nodes orbitals that have the 1 Bonding same energy Y2 and Y3: one node Y and Y : two nodes 4 5 Anti-bonding Y6: three node Substituted Derivatives of Benzene and Their Nomenclature -
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. -
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. -
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. -
Sc-Homoaromaticity
This is a repository copy of Modern Valence-Bond Description of Homoaromaticity. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/106288/ Version: Accepted Version Article: Karadakov, Peter Borislavov orcid.org/0000-0002-2673-6804 and Cooper, David L. (2016) Modern Valence-Bond Description of Homoaromaticity. Journal of Physical Chemistry A. pp. 8769-8779. ISSN 1089-5639 https://doi.org/10.1021/acs.jpca.6b09426 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Modern Valence-Bond Description of Homoaromaticity Peter B. Karadakov; and David L. Cooper; Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K. Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K. Abstract Spin-coupled (SC) theory is used to obtain modern valence-bond (VB) descriptions of the electronic structures of local minimum and transition state geometries of three species that have been con- C sidered to exhibit homoconjugation and homoaromaticity: the homotropenylium ion, C8H9 , the C cycloheptatriene neutral ring, C7H8, and the 1,3-bishomotropenylium ion, C9H11. -
Conjugated Molecules
Conjugated Molecules - Conjugated molecules have alternating single and multiple (i.e. double or triple) bonds. Example 1: Nomenclature: 2,6-dimethylhepta-2,5-diene This molecule is not conjugated because it does not have alternating single and multiple bonds (the arrangement of the bonds starting from C2 is double, single, single and double). Between the two double bonds, there is a saturated center (C4) and two intersecting single bonds. Example 2: Nomenclature: 2,5-dimethylhexa-2,4-diene This molecule is conjugated because the arrangement of the bonds starting at C2 is double, single, and double. They are alternated. Example 3: Nomenclature: (2E)-hept-2-en-5-yne note: (2E) is a stereochemical identifier. The letter “E” indicates the arrangement of the double bond (where E usually refers to trans and Z refers to cis). The number “2” indicates the position of the double bond. This molecule is not conjugated because the single and multiple bonds are not alternated. Example 4: Nomenclature: (2Z)-hex-2-en-4-yne This molecule is conjugated because there is an alternation of multiple and single bonds (double, single, and triple starting from C2). More examples: note: the term conjugation refers to parts of the molecule. If you can find one conjugated system within the molecule, that molecule is said to be conjugated. Example: In this molecule, the double bond A is not conjugated. However, since double bond B is conjugated with double bond C, the molecule is said to be conjugated. Special Nomenclature: The Letter "S" stands for “single” and indicates that we are talking about the conjugated double bonds. -
Organic and Biological Chemistry
CHAPTER 23 Organic and Biological Chemistry CONTENTS HO H 23.1 ▶ Organic Molecules and Their C Structures: Alkanes H H C 23.2 ▶ Families of Organic Compounds: HO O O C C Functional Groups 23.3 ▶ Naming Organic Compounds H CC 23.4 ▶ Carbohydrates:HO A Biological Example HO OH of Isomers H 23.5 ▶ Valence Bond TCheory and Orbital OverlapH Pictures H C 23.6 ▶ Lipids:HO A Biological EOxample ofO Cis–Trans IsomerismC C 23.7 ▶ Formal Charge and Resonance in Organic CompoundsH CC 23.8 ▶ Conjugated SystemsHO OH 23.9 ▶ Proteins: A Biological Example of Conjugation 23.10 ▶ Aromatic Compounds and Molecular Ascorbic acid, also known as vitamin C, is an essential nutrient in the human diet Orbital Theory because it is not synthesized in our body. We can eat citrus fruits or take pills that contain vitamin C to maintain health. 23.11 ▶ Nucleic Acids: A Biological Example of Aromaticity ? Which Is Better, Natural or Synthetic? The answer to this question can be found in the INQUIRY ▶▶▶ on page 1021. STUDY GUIDE M23_MCMU3170_07_SE_C23.indd 978 27/11/14 2:11 AM f the ultimate goal of chemistry is to understand the world around us on a molecular level, then a knowledge of biochemistry—the chemistry of living organisms—is a central part Iof that goal. Biochemistry, in turn, is a branch of organic chemistry, a term originally used to mean the study of compounds from living organisms while inorganic chemistry was used for the study of compounds from nonliving sources. Today, however, we know that there are no fundamental differences between organic and inorganic compounds; the same principles apply to both. -
Principles of Drug Action 1, Spring 2005, Resonance and Induction
Principles Of Drug Action 1, Spring 2005, Resonance and Induction RESONANCE AND INDUCTION TUTORIAL Jack DeRuiter The terms "resonance" and "induction" refer to the electronic effects that atoms or functional groups may have within a compound. These effects are defined below and are dependent on the valence, bonding order and electronegativity of atoms, as well as the molecular geometry. Thus it is important that you understand these concepts prior to reviewing this tutorial. I. INDUCTION Induction or the inductive effect of an atom or functional group is a function of that groups 1). electronegativity, 2). bonding order and charge and 3). position within a structure. Inductive effects refer to those electronic effects of an atom or functional group can contribute through single bonds such as saturated (sp3) carbon atoms! This is very different from resonance effects discussed later in this section. The contribution of electronegativity, bonding order and position toward induction is as follows: Electronegativity: Atoms or functional groups that are electronegative relative to hydrogen such as the halogens, oxygen, nitrogen, etc. may have a negative inductive effect (-I), depending on their bonding order (see the Table below). Thus these atoms withdraw electron density through the single bond structure of a compound and can assist in the stabilization of negative charge that may form in reactions. One such reaction where -I groups can have a stabilizing (enhancing) effect is the ionization of acids. Consider the case of acetic acid, chloroacetic acid and trichloroacetic acid shown below. All three of these compounds can ionize (loss of proton from the carboxyl OH). -
Chapter 12 Arenes and Aromaticity
CH. 12 Chapter 12 Arenes and Aromaticity Arenes Arenes are hydrocarbon derivatives of benzene. They are called aromatic systems due to their special stability (not due to their aroma!). The special stability results from the highly conjugated system with the electrons delocalized all the way around the ring. The name benzene comes from the Arabic luban jawi or “incense from Java” since it is isolated as a degradation product of gum benzoin. This is a balsam obtained from a tree that grows in Java and Sumatra. This degradation product is benzoic acid, which can be decarboxylated by heating with calcium oxide, CaO. O C OH CaO + CO2 heat benzoic acid benzene And tolu balsam from the South American tolu tree, when distilled, produces toluene or methylbenzene. The term aliphatic hydrocarbons, given to alkanes, alkenes, alkynes and benzene derivatives, comes from the Greek word aleiphar which means oil or unguent. Benzene Benzene has three double bonds that are conjugated and in a circular arrangement. Due to this conjugation and circular arrangement, the double bonds are much less reactive than normal, isolated alkenes. For example, benzene will not react with bromine or hydrogen gas in the presence of a metal catalyst, reactions that alkenes undergo readily. Br H Br2 CH3 CH CH CH3 CH3 C C CH3 rt H Br Br2 No Reaction rt 1 CH. 12 H2, Pd CH3 CH CH CH3 CH3CH2CH2CH3 rt H , Pd 2 No Reaction rt If we examine the structure of benzene we do not see a series of alternating double and single bonds as we would expect from the Lewis structure. -
Unit 2- Organic Chemistry Unit 2 - Organic Chemistry
CfE Advanced Higher Unit 2- Organic Chemistry Unit 2 - Organic Chemistry 2.1 Molecular Structure Molecular Orbitals Molecular Structure Colour Stereoisomerism * p4 * p3 Energy p2 p1 400 nm 750 nm 650 nm Pupil Notes 430 nm Learning Outcomes 460 nm 580 nm Questions& Answers 490 nm 560 nm 525 nm KHS Chemistry Nov 2015 page 1 Molecular Structure CfE Advanced Higher Unit 2- Organic Chemistry 2.1 Organic Molecular Structure 2.1.1 Atomic Orbitals and Molecular Orbitals Revisited As early 1923, Louis de Broglie suggested that the properties of electrons in atoms are better explained by treating the electrons as waves rather than as particles. An electron in an atomic orbital is like a stationary, bound vibration: a standing wave, similar to the wave pattern of a guitar string when it is plucked. For a split-second the guitar string is displaced upward. For an instant the wave function, is positive A split-second흍, later the string is displaced downwards. An instant later the wave function, is negative 흍, The wave function, is the mathematical description of the shape of the wave as it vibrates. We are normally more interested in the electron density which is determined by 2 and, therefore, regardless of the sign of the wave흍, function, an identical orbital shape will be produced. 흍 As we've seen before, a plot of electron density for an s-orbital results in a spherical shape and most of the time it has been 'irrelevant' that the original wave function alternates between a positive and a negative value. KHS Chemistry Nov 2015 page 2 Molecular Structure CfE Advanced Higher Unit 2- Organic Chemistry However, when atomic orbitals overlap to form molecular orbitals, the different possible signs on the wave function become more significant and explain whymultiple molecular orbitals will be formed.