Hydrogen Bond Versus Halogen Bond in Hxon (X = F, Cl, Br, and I) Complexes with Lewis Bases
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Thèse En Co-Tutelle
UNIVERSITÉ DE REIMS CHAMPAGNE-ARDENNE ÉCOLE DOCTORALE SCIENCES FONDAMENTALES - SANTÉ N619 FACULTÉ DES SCIENCES DE TUNIS (FST) ÉCOLE DOCTORALE MATHÉMATIQUES, INFORMATIQUE, SCIENCES ET TECHNOLOGIES DES MATÉRIAUX THÈSE EN CO-TUTELLE Pour obtenir le grade de Docteur de l’Université de Reims Champagne-Ardenne Discipline : Physique Spécialité : Physique moléculaire ET Docteur de la Faculté des Sciences de Tunis Discipline : Physique Présentée et soutenue publiquement par Olfa FERCHICHI Le 28 Septembre 2020 Étude des propriétés structurales et spectroscopiques de peroxydes aux niveaux DFT et ab initio JURY Manef ABDERRABBA Professeur à l’Université de Carthage Rapporteur Jean Christophe TREMBLAY Professeur à l’Université de Lorraine Rapporteur et Président du Jury Halima MOUHIB Maître de conférences à l’Université Gustave EiUel Examinatrice Hassen GHALILA Professeur à l’Université de Tunis El Manar Examinateur Alexander ALIJAH Professeur à l’Université de Reims Directeur de thèse Najoua DERBEL Professeur à la Faculté des Sciences de Bizerte Directrice de thèse Thibaud COURS Maître de conférences à l’Université de Reims Membre invité Dédicaces Je dédie cette thèse : À mes très chers parents Mohammed et Latifa, Loin de vous, votre soutien et votre encouragement m'ont toujours donné de la force pour persévérer et pour prospérer dans la vie. À mes sœurs et mon frère, Je vous remercie énormément pour tous les efforts que vous avez fait pour moi et les soutiens moraux dont j’ai pu bénéficier. À mon cher mari Johan TARAPEY Merci pour tes encouragements, tu as toujours su trouver les mots qui conviennent pour me remonter la morale dans les moments pénibles, grâce à toi j’ai pu surmonter toutes les difficultés. -
Group 17 (Halogens)
Sodium, Na Gallium, Ga CHEMISTRY 1000 Topic #2: The Chemical Alphabet Fall 2020 Dr. Susan Findlay See Exercises 11.1 to 11.4 Forms of Carbon The Halogens (Group 17) What is a halogen? Any element in Group 17 (the only group containing Cl2 solids, liquids and gases at room temperature) Exists as diatomic molecules ( , , , ) Melting Boiling 2State2 2 2Density Point Point (at 20 °C) (at 20 °C) Fluorine -220 °C -188 °C Gas 0.0017 g/cm3 Chlorine -101 °C -34 °C Gas 0.0032 g/cm3 Br2 Bromine -7.25 °C 58.8 °C Liquid 3.123 g/cm3 Iodine 114 °C 185 °C Solid 4.93 g/cm3 A nonmetal I2 Volatile (evaporates easily) with corrosive fumes Does not occur in nature as a pure element. Electronegative; , and are strong acids; is one of the stronger weak acids 2 The Halogens (Group 17) What is a halogen? Only forms one monoatomic anion (-1) and no free cations Has seven valence electrons (valence electron configuration . ) and a large electron affinity 2 5 A good oxidizing agent (good at gaining electrons so that other elements can be oxidized) First Ionization Electron Affinity Standard Reduction Energy (kJ/mol) Potential (kJ/mol) (V = J/C) Fluorine 1681 328.0 +2.866 Chlorine 1251 349.0 +1.358 Bromine 1140 324.6 +1.065 Iodine 1008 295.2 +0.535 3 The Halogens (Group 17) Fluorine, chlorine and bromine are strong enough oxidizing agents that they can oxidize the oxygen in water! When fluorine is bubbled through water, hydrogen fluoride and oxygen gas are produced. -
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. -
Periodic Trends in the Main Group Elements
Chemistry of The Main Group Elements 1. Hydrogen Hydrogen is the most abundant element in the universe, but it accounts for less than 1% (by mass) in the Earth’s crust. It is the third most abundant element in the living system. There are three naturally occurring isotopes of hydrogen: hydrogen (1H) - the most abundant isotope, deuterium (2H), and tritium 3 ( H) which is radioactive. Most of hydrogen occurs as H2O, hydrocarbon, and biological compounds. Hydrogen is a colorless gas with m.p. = -259oC (14 K) and b.p. = -253oC (20 K). Hydrogen is placed in Group 1A (1), together with alkali metals, because of its single electron in the valence shell and its common oxidation state of +1. However, it is physically and chemically different from any of the alkali metals. Hydrogen reacts with reactive metals (such as those of Group 1A and 2A) to for metal hydrides, where hydrogen is the anion with a “-1” charge. Because of this hydrogen may also be placed in Group 7A (17) together with the halogens. Like other nonmetals, hydrogen has a relatively high ionization energy (I.E. = 1311 kJ/mol), and its electronegativity is 2.1 (twice as high as those of alkali metals). Reactions of Hydrogen with Reactive Metals to form Salt like Hydrides Hydrogen reacts with reactive metals to form ionic (salt like) hydrides: 2Li(s) + H2(g) 2LiH(s); Ca(s) + H2(g) CaH2(s); The hydrides are very reactive and act as a strong base. It reacts violently with water to produce hydrogen gas: NaH(s) + H2O(l) NaOH(aq) + H2(g); It is also a strong reducing agent and is used to reduce TiCl4 to titanium metal: TiCl4(l) + 4LiH(s) Ti(s) + 4LiCl(s) + 2H2(g) Reactions of Hydrogen with Nonmetals Hydrogen reacts with nonmetals to form covalent compounds such as HF, HCl, HBr, HI, H2O, H2S, NH3, CH4, and other organic and biological compounds. -
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. -
P – Block Elements SYJC
P – Block Elements Introduction The p-block elements are placed in groups 13 – 18 . The general electronic configuration is ns 2 np1 – 6. The groups included in the syllabus are 15, 16, 17 and 18. Group 15 Elements Nitrogen family: configuration is ns2np3. The elements of group 15 – nitrogen (N), phosphorus (P), arsenic (As), antimony (Sb) bismuth (Bi) All Group 15 Elements tend to follow the general periodic trends: Periodic properties Trends Electronegativity:(the atom's ability of Decreases down the group attracting electrons) Ionization Enthalpy (the amount of decreases energy required to remove an electron from the atom in it's gaseous phase) Atomic Radii (the radius of the atom) increases Electron Affinity (ability of the atom to decreases accept an electron) Melting Point (amount of energy increases going down the required to break bonds to change a group solid phase substance to a liquid phase) Boiling Point (amount of energy increases going down the required to break bonds to change a group liquid phase substance to a gas) Chemical properties Action of air;(high temp arc) N2 + O2 2NO Action oxidizing agents: P4 +20HNO3 4H3PO4 + 20 NO2+4 H20 As4 + 20 HNO3 4H3AsO4 + 20 NO2+4 H20 Action of hot conc H2SO4 P4 +10 H2SO4 4H3PO4 + 10 SO2+4 H20 As4 +10 H2SO4 4H3AsO4 + 4 Sb + 6 H2SO4 Sb2(SO4)3 + 3 Hydrides All form hydrides with formula EH3 ( E = N, P, As, Sb , Bi) oxidation state = – 3 Hydrogen bonding in NH3 The stability of hydrides decrease down the group due to decrease in bond Hydrides comparison Anomalous behaviour of -
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. -
Kinetics and Mechanism of Oxidation of Glycine and Alanine by Oxone R
http://dx.doi.org/10.5935/0103-5053.20140139 J. Braz. Chem. Soc., Vol. 25, No. 9, 1545-1551, 2014. Printed in Brazil - ©2014 Sociedade Brasileira de Química Article 0103 - 5053 $6.00+0.00 A Kinetics and Mechanism of Oxidation of Glycine and Alanine by Oxone® Catalyzed by Bromide Ion Malharrao R. Thombare and Gavisiddappa S. Gokavi* Kinetics and Catalysis Laboratory, Department of Chemistry, Shivaji University, 416004 Kolhapur, India A oxidação da glicina e alanina por Oxone®, catalisada por íons brometo foi estudada em meio ácido. A reação é iniciada pela oxidação do brometo ao bromo, que reage com o aminoácido. A formação de bromo é comprovada pelo exame espectrofotométrico da mistura reacional. O intermediário proposto envolve a formação de um complexo entre o bromo e o ânion do aminoácido. A taxa de reação é inibida por um aumento na concentração do íon hidrogênio devido ao equilíbrio de protonação dos aminoácidos. Um mecanismo é proposto e a lei da razão derivada foi verificada graficamente. O efeito da permissividade relativa, força iônica e temperatura também foram acompanhados e esses efeitos também dão suporte ao mecanismo proposto. Oxidation of glycine and alanine by Oxone® catalysed by bromide ions has been studied in acidic medium. The reaction is initiated by the oxidation of bromide to bromine, which then reacts with the amino acid. The formation of bromine is supported by the spectrophotometric examination of the reaction mixture. The proposed intermediate involves a complex formation between bromine and the anion of the amino acid. The rate of the reaction is inhibited by an increase in the hydrogen ion concentration due to the protonation equilibria of the amino acids. -
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. -
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.