Halogen Bonds of Halonium Ions
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And [Z–Hali]- Halogen Bonds: Electron Density Properties And
molecules Article Strength of the [Z–I···Hal]− and [Z–Hal···I]− Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy Maxim L. Kuznetsov 1,2 1 Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal; [email protected]; Tel.: +351-218-419-236 2 Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia Abstract: Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, Eint, us- ing relationships between Eint and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between Eint and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z–I···Hal]− and [Z–Hal···I]− types bearing halogen bonds and involving iodine as interact- ing atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06–4.76 kcal/mol. Keywords: bond critical point properties; interaction energy; bond energy; bond strength; den- sity functional theory; electron density; energy density; halogen bond; QTAIM Citation: Kuznetsov, M.L. Strength of the [Z–I···Hal]− and [Z–Hal···I]− Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy. 1. Introduction Molecules 2021, 26, 2083. https:// The halogen bond is one of the most important types of non-covalent interactions doi.org/10.3390/molecules26072083 being second only to hydrogen bonds in its significance. -
A New Way for Probing Bond Strength J
A New Way for Probing Bond Strength J. Klein, H. Khartabil, J.C. Boisson, J. Contreras-Garcia, Jean-Philip Piquemal, E. Henon To cite this version: J. Klein, H. Khartabil, J.C. Boisson, J. Contreras-Garcia, Jean-Philip Piquemal, et al.. A New Way for Probing Bond Strength. Journal of Physical Chemistry A, American Chemical Society, 2020, 124 (9), pp.1850-1860. 10.1021/acs.jpca.9b09845. hal-02377737 HAL Id: hal-02377737 https://hal.archives-ouvertes.fr/hal-02377737 Submitted on 27 Mar 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. A New Way for Probing Bond Strength Johanna Klein,y Hassan Khartabil,y Jean-Charles Boisson,z Julia Contreras-Garc´ıa,{ Jean-Philip Piquemal,{ and Eric H´enon∗,y yInstitut de Chimie Mol´eculaire de Reims UMR CNRS 7312, Universit´ede Reims Champagne-Ardenne, Moulin de la Housse 51687 Reims Cedex 02 BP39 (France) zCReSTIC EA 3804, Universit´ede Reims Champagne-Ardenne, Moulin de la Housse 51687 Reims Cedex 02 BP39 (France) {Sorbonne Universit´es,UPMC, Laboratoire de Chimie Th´eoriqueand UMR CNRS 7616, 4 Pl Jussieu, 75252 Paris Cedex 05(France) E-mail: [email protected] Phone: +33(3)26918497 1 Abstract The covalent chemical bond is intimately linked to electron sharing between atoms. -
Halogen Bonds in Biological Molecules
Halogen bonds in biological molecules Pascal Auffinger†‡, Franklin A. Hays§, Eric Westhof†, and P. Shing Ho‡§ †Institut de Biologie Mole´culaire et Cellulaire, Centre National de la Recherche Scientifique, Unite´Propre de Recherche 9002, Universite´Louis Pasteur, 15 Rue Rene´Descartes, F-67084 Strasbourg, France; and §Department of Biochemistry and Biophysics, Agriculture͞Life Sciences Building, Room 2011, Oregon State University, Corvallis, OR 97331-7305 Communicated by K. E. van Holde, Oregon State University, Corvallis, OR, October 13, 2004 (received for review August 17, 2004) Short oxygen–halogen interactions have been known in organic chemistry since the 1950s and recently have been exploited in the design of supramolecular assemblies. The present survey of protein and nucleic acid structures reveals similar halogen bonds as po- tentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding. A halogen bond in biomolecules can be defined as a short COX⅐⅐⅐OOY interaction (COX is a carbon-bonded chlorine, bromine, or iodine, and OOY is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X⅐⅐⅐O distance is less than or equal to the sums of the respective van der Waals radii (3.27 Å for Cl⅐⅐⅐O, 3.37Å for Br⅐⅐⅐O, and 3.50 Å for I⅐⅐⅐O) and can conform to the geometry seen in small molecules, with the COX⅐⅐⅐O angle Ϸ165° (consistent with a strong Fig. 1. Schematic of short halogen (X) interactions to various oxygen- directional polarization of the halogen) and the X⅐⅐⅐OOY angle containing functional groups (where OOY can be a carbonyl, hydroxyl, or Ϸ120°. -
Reactions of Aromatic Compounds Just Like an Alkene, Benzene Has Clouds of Electrons Above and Below Its Sigma Bond Framework
Reactions of Aromatic Compounds Just like an alkene, benzene has clouds of electrons above and below its sigma bond framework. Although the electrons are in a stable aromatic system, they are still available for reaction with strong electrophiles. This generates a carbocation which is resonance stabilized (but not aromatic). This cation is called a sigma complex because the electrophile is joined to the benzene ring through a new sigma bond. The sigma complex (also called an arenium ion) is not aromatic since it contains an sp3 carbon (which disrupts the required loop of p orbitals). Ch17 Reactions of Aromatic Compounds (landscape).docx Page1 The loss of aromaticity required to form the sigma complex explains the highly endothermic nature of the first step. (That is why we require strong electrophiles for reaction). The sigma complex wishes to regain its aromaticity, and it may do so by either a reversal of the first step (i.e. regenerate the starting material) or by loss of the proton on the sp3 carbon (leading to a substitution product). When a reaction proceeds this way, it is electrophilic aromatic substitution. There are a wide variety of electrophiles that can be introduced into a benzene ring in this way, and so electrophilic aromatic substitution is a very important method for the synthesis of substituted aromatic compounds. Ch17 Reactions of Aromatic Compounds (landscape).docx Page2 Bromination of Benzene Bromination follows the same general mechanism for the electrophilic aromatic substitution (EAS). Bromine itself is not electrophilic enough to react with benzene. But the addition of a strong Lewis acid (electron pair acceptor), such as FeBr3, catalyses the reaction, and leads to the substitution product. -
Binuclear Copper(I) Borohydride Complex Containing Bridging Bis
crystals Article Binuclear Copper(I) Borohydride Complex Containing Bridging Bis(diphenylphosphino) Methane Ligands: Polymorphic Structures of 2 [(µ2-dppm)2Cu2(η -BH4)2] Dichloromethane Solvate Natalia V. Belkova 1 ID , Igor E. Golub 1,2 ID , Evgenii I. Gutsul 1, Konstantin A. Lyssenko 1, Alexander S. Peregudov 1, Viktor D. Makhaev 3, Oleg A. Filippov 1 ID , Lina M. Epstein 1, Andrea Rossin 4 ID , Maurizio Peruzzini 4 and Elena S. Shubina 1,* ID 1 A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 119991 Moscow, Russia; [email protected] (N.V.B.); [email protected] (I.E.G.); [email protected] (E.I.G.); [email protected] (K.A.L.); [email protected] (A.S.P.); [email protected] (O.A.F.); [email protected] (L.M.E.) 2 Inorganic Chemistry Department, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia 3 Institute of Problems of Chemical Physics, Russian Academy of Sciences (IPCP RAS), 142432 Moscow, Russia; [email protected] 4 Istituto di Chimica dei Composti Organometallici Consiglio Nazionale delle Ricerche (ICCOM CNR), 50019 Sesto Fiorentino, Italy; [email protected] (A.R.); [email protected] (M.P.) * Correspondence: [email protected]; Tel.: +7-495-135-5085 Academic Editor: Sławomir J. Grabowski Received: 18 September 2017; Accepted: 17 October 2017; Published: 20 October 2017 Abstract: Bis(diphenylphosphino)methane copper(I) tetrahydroborate was synthesized by ligands exchange in bis(triphenylphosphine) copper(I) tetrahydroborate, and characterized by XRD, FTIR, NMR spectroscopy. According to XRD the title compound has dimeric structure, [(µ2-dppm)2Cu2(η2-BH4)2], and crystallizes as CH2Cl2 solvate in two polymorphic forms (orthorhombic, 1, and monoclinic, 2) The details of molecular geometry and the crystal-packing pattern in polymorphs were studied. -
Reactions of Alkenes and Alkynes
05 Reactions of Alkenes and Alkynes Polyethylene is the most widely used plastic, making up items such as packing foam, plastic bottles, and plastic utensils (top: © Jon Larson/iStockphoto; middle: GNL Media/Digital Vision/Getty Images, Inc.; bottom: © Lakhesis/iStockphoto). Inset: A model of ethylene. KEY QUESTIONS 5.1 What Are the Characteristic Reactions of Alkenes? 5.8 How Can Alkynes Be Reduced to Alkenes and 5.2 What Is a Reaction Mechanism? Alkanes? 5.3 What Are the Mechanisms of Electrophilic Additions HOW TO to Alkenes? 5.1 How to Draw Mechanisms 5.4 What Are Carbocation Rearrangements? 5.5 What Is Hydroboration–Oxidation of an Alkene? CHEMICAL CONNECTIONS 5.6 How Can an Alkene Be Reduced to an Alkane? 5A Catalytic Cracking and the Importance of Alkenes 5.7 How Can an Acetylide Anion Be Used to Create a New Carbon–Carbon Bond? IN THIS CHAPTER, we begin our systematic study of organic reactions and their mecha- nisms. Reaction mechanisms are step-by-step descriptions of how reactions proceed and are one of the most important unifying concepts in organic chemistry. We use the reactions of alkenes as the vehicle to introduce this concept. 129 130 CHAPTER 5 Reactions of Alkenes and Alkynes 5.1 What Are the Characteristic Reactions of Alkenes? The most characteristic reaction of alkenes is addition to the carbon–carbon double bond in such a way that the pi bond is broken and, in its place, sigma bonds are formed to two new atoms or groups of atoms. Several examples of reactions at the carbon–carbon double bond are shown in Table 5.1, along with the descriptive name(s) associated with each. -
Aromatic Substitution Reactions: an Overview
Review Article Published: 03 Feb, 2020 SF Journal of Pharmaceutical and Analytical Chemistry Aromatic Substitution Reactions: An Overview Kapoor Y1 and Kumar K1,2* 1School of Pharmaceutical Sciences, Apeejay Stya University, Sohna-Palwal Road, Sohna, Gurgaon, Haryana, India 2School of Pharmacy and Technology Management, SVKM’s NMIMS University, Hyderabad, Telangana, India Abstract The introduction or replacement of substituent’s on aromatic rings by substitution reactions is one of the most fundamental transformations in organic chemistry. On the basis of the reaction mechanism, these substitution reactions can be divided into electrophilic, nucleophilic, radical, and transition metal catalyzed. This article also focuses on electrophilic and nucleophilic substitution mechanisms. Introduction The replacement of an atom, generally hydrogen, or a group attached to the carbon from the benzene ring by another group is known as aromatic substitution. The regioselectivity of these reactions depends upon the nature of the existing substituent and can be ortho, Meta or Para selective. Electrophilic Aromatic Substitution (EAS) reactions are important for synthetic purposes and are also among the most thoroughly studied classes of organic reactions from a mechanistic point of view. A wide variety of electrophiles can effect aromatic substitution. Usually, it is a substitution of some other group for hydrogen that is of interest, but this is not always the case. For example, both silicon and mercury substituent’s can be replaced by electrophiles. The reactivity of a particular electrophile determines which aromatic compounds can be successfully substituted. Despite the wide range of electrophilic species and aromatic ring systems that can undergo substitution, a single broad mechanistic picture encompasses most EAS reactions. -
Advices for Studying Organic Chemistry
Table of Contents Partial table of contents: Carbon Compounds and Chemical Bonds. Representative Carbon Compounds. An Introduction to Organic Reactions: Acids and Bases. Alkanes and Cycloalkanes: Conformations of Molecules. Stereochemistry: Chiral Molecules. Alkenes and Alkynes I: Properties and Synthesis. Alkenes and Alkynes II: Addition Reactions. Radical Reactions. Alcohols and Ethers. Conjugated Unsaturated Systems. Aromatic Compounds. Reactions of Aromatic Compounds. Aldehydes and Ketones I: Nucleophilic Additions to the Carbonyl Group. Aldehydes and Ketones II: Aldol Reactions. Carboxylic Acids and Their Derivatives: Nucleophilic Substitution at the Acyl Carbon. Amines. Carbohydrates. Lipids. Answers to Selected Problems. Glossary. Index. Solomons/Advices ADVICES FOR STUDYING ORGANIC CHEMISTRY 1. Keep up with your studying day to day –– never let yourself get behind, or better yet, be a little ahead of your instructor. Organic chemistry is a course in which one idea almost always builds on another that has gone before. 2. Study materials in small units, and be sure that you understand each new section before you go on to the next. Because of the cumulative nature of organic chemistry, your studying will be much more effective if you take each new idea as it comes and try to understand it completely before you move onto the nest concept. 3. Work all of the in-chapter and assigned problems. 4. Write when you study. Write the reactions, mechanisms, structures, and so on, over and over again. You need to know the material so thoroughly that you can explain it to someone else. This level of understanding comes to most of us (those of us without photographic memories) through writing. -
Theoretical Study on the Noncovalent Interactions Involving Triplet Diphenylcarbene
Theoretical Study on the Noncovalent Interactions Involving Triplet Diphenylcarbene Chunhong Zhao Hebei Normal University Huihua College Hui Lin Hebei Normal University Aiting Shan Hebei Normal University Shaofu Guo Hebei Normal University Huihua College Xiaoyan Li Hebei Normal University Xueying Zhang ( [email protected] ) Hebei Normal University https://orcid.org/0000-0003-1598-8501 Research Article Keywords: triplet diphenylcarbene, noncovalent interaction, electron density shift, electron spin density Posted Date: May 19th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-445417/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Journal of Molecular Modeling on July 9th, 2021. See the published version at https://doi.org/10.1007/s00894-021-04838-6. Page 1/21 Abstract The properties of some types of noncovalent interactions formed by triplet diphenylcarbene (DPC3) have been investigated by means of density functional theory (DFT) calculations and quantum theory of 3 atoms in molecules (QTAIM) studies. The DPC ···LA (LA = AlF3, SiF4, PF5, SF2, ClF) complexes have been analyzed from their equilibrium geometries, binding energies, charge transfer and properties of electron 3 density. The triel bond in the DPC ···AlF3 complex exhibits a partially covalent nature, with the binding energy − 65.7kJ/mol. The tetrel bond, pnicogen bond, chalcogen bond and halogen bond in the DPC3···LA (LA = SiF4, PF5, SF2, ClF) complexes show the character of a weak closed-shell noncovalent interaction. Polarization plays an important role in the formation of the studied complexes. -
The Halogen Bond in the Design of Functional Supramolecular Materials
The Halogen Bond in the Design of Functional Supramolecular Materials: Recent Advances † ‡ ARRI PRIIMAGI,*, GABRIELLA CAVALLO, ‡ ‡ PIERANGELO METRANGOLO,*, ,§ AND GIUSEPPE RESNATI*, † Department of Applied Physics, Aalto University, P.O. Box 13500, FI-00076 ‡ Aalto, Finland, NFMLab-DCMIC “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, IT-20131 Milano, Italy, and §VTT-Technical Research Centre of Finland, Tietotie 2, Espoo, FI-02044 VTT, Finland RECEIVED ON APRIL 9, 2013 CONSPECTUS alogen bonding is an emerging noncovalent interaction for constructing supramolecular assemblies. Though similar to the H more familiar hydrogen bonding, four primary differences between these two interactions make halogen bonding a unique tool for molecular recognition and the design of functional materials. First, halogen bonds tend to be much more directional than (single) hydrogen bonds. Second, the interaction strength scales with the polarizability of the bond-donor atom, a feature that researchers can tune through single-atom mutation. In addition, halogen bonds are hydrophobic whereas hydrogen bonds are hydrophilic. Lastly, the size of the bond-donor atom (halogen) is significantly larger than hydrogen. As a result, halogen bonding provides supramolecular chemists with design tools that cannot be easily met with other types of noncovalent interactions and opens up unprecedented possibilities in the design of smart functional materials. This Account highlights the recent advances in the design of halogen-bond-based functional materials. Each of the unique features of halogen bonding, directionality, tunable interaction strength, hydrophobicity, and large donor atom size, makes a difference. Taking advantage of the hydrophobicity, researchers have designed small-size ion transporters. The large halogen atom size provided a platform for constructing all-organic light-emitting crystals that efficiently generate triplet electrons and have a high phosphorescence quantum yield. -
Transmembrane Anion Transport Mediated by Halogen-Bond Donors
Article Transmembrane anion transport mediated by halogen-bond donors VARGAS JENTZSCH, Rodrigo Andreas, et al. Abstract In biology and chemistry, the transport of anions across lipid bilayer membranes is usually achieved by sophisticated supramolecular architectures. Significant size reduction of transporters is hampered by the intrinsically hydrophilic nature of typical anion-binding functionalities, hydrogen-bond donors or cations. To maximize the atom efficiency of anion transport, the hydrophobic nature, directionality, and strength of halogen bonds seem promising. Unlike the ubiquitous, structurally similar hydrogen bonds, halogen bonds have not been explored for anion transport. Here we report that transport across lipid bilayers can be achieved with small perfluorinated molecules that are equipped with strong halogen-bond donors. Transport is observed with trifluoroiodomethane (boiling point=−22 °C); that is, it acts as a 'single-carbon' transporter. Contrary to the destructive action of small-molecule detergents, transport with halogen bonds is leakage-free, cooperative, non-ohmic and highly selective, with anion/cation permeability ratios Reference VARGAS JENTZSCH, Rodrigo Andreas, et al. Transmembrane anion transport mediated by halogen-bond donors. Nature Communications, 2012, vol. 3 DOI : 10.1038/ncomms1902 Available at: http://archive-ouverte.unige.ch/unige:21674 Disclaimer: layout of this document may differ from the published version. 1 / 1 Transmembrane anion transport mediated by halogen bonds Andreas Vargas Jentzsch1, Daniel Emery1, Jiri Mareda1, Susanta K. Nayak2, Pierangelo Metrangolo2, Giuseppe Resnati2, Naomi Sakai1 & SteFan Matile1 1Department of Organic Chemistry, University of Geneva, Geneva, Switzerland. 2NFMLab, Department of Chemistry, Materials and Chemical Engineering EGiulio NattaG, Politecnico di Milano and Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, Politecnico di Milano, Milan, Italy. -
Copyright © 2010 by Shauna M. Paradine ASYMMETRIC HALOFUNCTIONALIZATION of OLEFINS Reported by Shauna M. Paradine April 12
ASYMMETRIC HALOFUNCTIONALIZATION OF OLEFINS Reported by Shauna M. Paradine April 12, 2010 INTRODUCTION The functionalization of olefins is a commonly employed strategy for the rapid construction of molecular complexity in organic synthesis. Since the hybridization change from sp2 to sp3 at the reactive carbon atoms creates new stereocenters, performing these reactions in a well-controlled and highly asymmetric manner is ideal. Development of highly enantioselective olefin functionalization reactions has been a major focus of organic methodology for the past thirty years, and a number of useful and general methods have emerged for the asymmetric epoxidation, dioxygenation, aminooxygenation, hydrogenation, and hydroboration of olefins.1 Although halogen functionality is not as ubiquitous as oxygen and nitrogen in natural products, halogenated natural products still represent a pharmacologically important subclass2 and halogens themselves can be useful for further functionalization.3 The asymmetric addition of halogen functionality onto a carbon framework, therefore, has been of recent interest in synthetic methodology development. Synthetically useful asymmetric methods for the α–halogenation of carbonyls have been developed in response to this challenge,4 but general methods for the highly enantioselective halofunctionalization of olefins has thus far eluded organic chemists. Over the past few years, a number of research groups have developed methods seeking to fill this clear gap in asymmetric synthesis. This recent progress will be presented here. MECHANISTIC AND STEREOCHEMICAL CONSIDERATIONS The electrophilic halogenation of olefins is one of the oldest and most basic transformations in organic synthesis. In fact, “olefin”, which means “oil-forming”, was a term used to describe compounds, typically low molecular weight gaseous alkenes, that became oily liquids upon chlorination.