Understanding Nonplanarity in Metallabenzene Complexes
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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. -
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. -
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). -
Interpretation of Both Electron Pushing and Electron Withdrawing Inductive Effect of Alkyl Groups in Terms of Mulliken–Jaffe’S Charge Coefficient Parameters (B)∗
GENERAL ARTICLE Interpretation of Both Electron Pushing and Electron Withdrawing Inductive Effect of Alkyl Groups in Terms of Mulliken–Jaffe’s Charge Coefficient Parameters (b)∗ Asim K Das Alkyl groups can delocalize both the negative and positive charges through ion (charge)-induced dipole interaction with the polarizable alkyl groups. This charge induced polariza- tion of the alkyl group to delocalize the charge is the origin of ‘inductive effect’ of the alkyl groups. The apparent less effi- ciency in negative charge delocalization compared to positive charge delocalization by a particular alkyl group is attributed Asim K Das is currently a to the less polarizing field strength of the anionic charge. senior Professor of Chemistry Department, Visva Bharati, a Central University, 1. Introduction Santiniketan. His research interest is in the field of ff thermodynamic and kinetic The concept of inductive e ect and its application are the impor- aspects of metal-ligand tant course components of organic chemistry taught at the high interactions. He has authored school and undergraduate level. Inductive effect actually delocal- some advanced level text izes the charge [1, 2]. Depending on the properties of the atoms books on inorganic chemistry, ff bioinorganic chemistry and or groups, they can show electron withdrawing (i.e. –I e ect) or environmental chemistry for electron pushing (i.e. +Ieffect) inductive effect [1, 2]. The +Ief- the undergraduate and fect delocalizes the positive charge while the −Ieffect delocalizes postgraduate students. the negative charge. By considering the inductive effect of the groups or atoms, many important aspects of organic chemistry like the relative stabilities of carbocations and carbanions, acid- base strength, reaction mechanism, etc., are explained [1, 2] in the classrooms, and these are also discussed in all organic textbooks. -
Measuring the Electronic Effect of Some Phosphines and Phosphites
Measuring the electronic effect of some phosphines and phosphites By Sanaa Moftah Ali Abushhewa A dissertation submitted to the University of Manchester for the degree of Master of Science by research in the Faculty of Engineering and Physical Sciences. School of Chemistry 2010 Contents page Abstract 6 Declaration 7 Acknowledgement 8 1. Introduction 9 1.1 History of Phosphorus 9 1.2 Phosphorus (III) compounds 10 1.3 Preparation and Properties of Phosphines 11 1.4 Preparation and Properties of Phosphites 12 1.5 Bonding of phosphorus (III) ligands 14 1.6 Measurement of Electronic and Steric Effects 15 1.7 Steric parameter 17 1.8 Electronic parameter 17 1.9 Effects of electronegative substituents 21 1.10 Phosphines and Phosphites ligand effects 21 2. Experimental section 24 General conditions 25 2.1- Preparation of phosphites 25 2.1.1- Synthesis of 2, 2’- Biphenyl Chlorophosphite 25 2.1.2- Synthesis of 1H,1H,2H,2H-perfluorodecyldiphenyl phosphinite 25 2 2.1.3- Synthesis of 3-fluorophenyldiphenyl phosphinite 26 2.1.4- Synthesis of 2-fluorophenyldiphenyl phosphinite 26 2.1.5- Synthesis of 2, 2-biphenyltrifluoroethyl phosphinite 27 2.1.6- Synthesis of 2, 2'-biphenylhexafluoroisopropyl phosphinite 27 2.1.7-Synthesis of 2, 2'-biphenylpropyl phosphite 28 2.2-Preparation of P(III) Selenides 28 2.2.1- Synthesis of triphenylphosphine selenide 28 2.2.2- Synthesis of triphenylphosphite selenide 29 2.2.3- Synthesis of tris(2,4,6-trimethylphenyl)phosphite selenide 29 2.2.4- Synthesis of diphenyl(o-tolyl) phosphine selenide 30 2.2.5- Synthesis of 2, 2’-biphenyl -
Hyperconjugation Article Type
Article Title: Hyperconjugation Article type: Advanced review Authors: Igor V Alabugin* 0000-0001-9289-3819, Florida State University, [email protected], this author declares no conflicts of interest Gabriel dos Passos Gomes 0000-0002-8235-5969, Florida State University, [email protected], this author declares no conflicts of interest Miguel A Abdo 0000-0002-2009-6340, Florida State University, [email protected], this author declares no conflicts of interest Keywords Bond theory, Hyperconjugation, Stereoelectronic effects, Delocalization, Orbital Graphical abstract This review outlines the role of hyperconjugative interactions in the structure and reactivity of organic molecules. After defining the common hyperconjugative patterns, we discuss the main factors controlling the magnitude of hyperconjugative effects, including orbital symmetry, energy gap, electronegativity, and polarizability. The danger of underestimating the contribution of hyperconjugative interactions are illustrated by a number of spectroscopic, conformational, and structural effects. The stereoelectronic nature of hyperconjugation offers useful ways for control of molecular stability and reactivity. New manifestations of hyperconjugative effects continue to be uncovered by theory and experiments. 1 Hyperconjugation, conjugation and σ-conjugation: The classic picture of covalent chemical bonding starts by creating the framework of two- center/two-electron bonds. These bonds are formed by sharing of electron pairs which is a quantum mechanical phenomenon based -
Principles of Organic Chemistry I for Chemistry’ Students, College of Science Pre-Requisites Course; Chem 101 Credit Hours; 2 (2+0)
2/10/2020 CHEM 240 PRINCIPLES OF ORGANIC CHEMISTRY I FOR CHEMISTRY’ STUDENTS, COLLEGE OF SCIENCE PRE-REQUISITES COURSE; CHEM 101 CREDIT HOURS; 2 (2+0) Prof. Mohamed El-Newehy Chemistry Department, College of Science, King Saud University http://fac.ksu.edu.sa/melnewehy/home 1 TOPICS TO BE COVERED o Introduction (Lectures; 4) Introduction (Carbon Compounds, Chemical Bonds (ionic, Covalent), Atomic and Molecular orbitals, Hybridization, Polarity and Inductive effect). o Alkanes and Cycloalkanes (Lectures; 4) (Alkyl groups, IUPAC nomenclature, Physical properties, Sources off, Synthesis. Reactions (Combustion, Halogenation, Ring opening). Configuration, cyclohexanes. o Stereochemistry (Lectures; 4) (Structural isomers and Stereoisomerism, Enantiomers, Diastereomers and Chirality, D and L, The R-S system, Resolution, Molecules with more than one chiral carbon, Reactions of chiral molecules: Inversion, Racemization). 1st Midterm Exam (Lectures; 1) 2 1 2/10/2020 TOPICS TO BE COVERED o Alkenes and Alkynes (Lectures 7) (IUPAC nomenclature, Physical properties, Synthesis (Dehydrohalogenation, from vicinal dihalides, Dehydration of alcohols). Reactions (Acidity of terminal alkynes, Addition reactions (Reduction, Halogenation, Addition of HX – Markovnikov rule, Carbonium ions and their stability, Reaction mechanism), Addition in the presence of peroxides, Hydration, Halohydrin formation), Oxidation of Alkenes (KMnO4, Peroxides and Ozonolysis). o Conjugated Dienes (Lectures 3) (Allyl radical and stability, Allyl cation, 1,3-Butadiene - electron delocalization, Resonance and the Stability of conjugated dienes, 1,4-Addition and 1,4-Cycloaddition reactions of diene). o Aromatic Compound (Lectures 6) (Aromaic character, Hukel rule, Nomenlature, Electrophilic substitution reactions (Alkylation, Acylation, Halogenatio, Sulphonation, Nitration; reaction mechanism), Side chain halogenation and oxidation, Reactivity and Orientation in substituted benzene, Polynuclear aromatics). -
Electronic Structure, Chemical Bonding, and Electronic Delocalization of Organic and Inorganic Systems with Three-Dimensional Or Excited State Aromaticity
ELECTRONIC STRUCTURE, CHEMICAL BONDING, AND ELECTRONIC DELOCALIZATION OF ORGANIC AND INORGANIC SYSTEMS WITH THREE-DIMENSIONAL OR EXCITED STATE AROMATICITY Ouissam El Bakouri El Farri Per citar o enllaçar aquest document: Para citar o enlazar este documento: Use this url to cite or link to this publication: http://hdl.handle.net/10803/565444 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art. -
Bond Insertion at Distorted Si(001) Subsurface Atoms
inorganics Article Bond Insertion at Distorted Si(001) Subsurface Atoms Lisa Pecher ID and Ralf Tonner * ID Faculty of Chemistry and Material Sciences Center, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-6421-282-5418 Received: 22 December 2017; Accepted: 17 January 2018; Published: 23 January 2018 Abstract: Using density functional theory (DFT) methods, we analyze the adsorption of acetylene and ethylene on the Si(001) surface in an unusual bond insertion mode. The insertion takes place at a saturated tetravalent silicon atom and the insight gained can thus be transferred to other saturated silicon compounds in molecular and surface chemistry. Molecular orbital analysis reveals that the distorted and symmetry-reduced coordination of the silicon atoms involved due to surface reconstruction raises the electrophilicity and, additionally, makes certain σ bond orbitals more accessible. The affinity towards bond insertion is, therefore, caused by the structural constraints of the surface. Additionally, periodic energy decomposition analysis (pEDA) is used to explain why the bond insertion structure is much more stable for acetylene than for ethylene. The increased acceptor abilities of acetylene due to the presence of two π*-orbitals (instead of one π*-orbital and a set of σ*(C–H) orbitals for ethylene), as well as the lower number of hydrogen atoms, which leads to reduced Pauli repulsion with the surface, are identified as the main causes. While our findings imply that this structure might be an intermediate in the adsorption of acetylene on Si(001), the predicted product distributions are in contradiction to the experimental findings. -
Electronic Effect: Introduction the Effect Which Appears Due to Electronic Distribution Is Called Electronic Effect
General Organic Chemistry-I Electronic effect: Introduction The effect which appears due to electronic distribution is called electronic effect. Classification: Section (A): Inductive effect Th1: Inductive effect The normal C–C bond has no polarity as two atoms of same electronegativity (EN) value are connected to each other. Hence the bond is nonpolar. Consider a carbon chain in 1-Chloro butane, here due to more EN of Cl atom C–Cl bond pair is slightly displaced towards Cl atom hence creating partial negative (–) charge over Cl atom and partial positive (+) charge over C1 atom. Now since C1 is slightly positive, it will also cause shifting of C1–C2 bond pair electrons towards itself causing C2 to acquire small positive charge. Similarly C3 acquires slightly positive charge creating an induction of charge in carbon chain. Such an effect is called inductive effect. Diagram showing I effect. The arrow shows electron withdrawing nature of –Cl group. D1: Thus inductive effect may be defined as a permanent displacement of bond pair electrons due to a dipole. (Polar bond) Some important points are: (a) It can also be defined as polarisation of one bond caused by polarisation of adjacent bond. (b) It is also called transmission effect. (c) It causes permanent polarisation in molecule, hence it is a permanent effect. (d) The displacement of electrons takes place due to difference in electronegativity of the two atoms involved in the covalent bond. (e) The electrons never leave their original atomic orbital. (f) Its magnitude decreases with distance and it is almost negligible after 3rd carbon atom. -
Understanding the Molecular Aspects of Tetrahydrocannabinol and Cannabidiol As Antioxidants
Molecules 2013, 18, 12663-12674; doi:10.3390/molecules181012663 OPEN ACCESS molecules ISSN 1420-3049 www.mdpi.com/journal/molecules Article Understanding the Molecular Aspects of Tetrahydrocannabinol and Cannabidiol as Antioxidants Rosivaldo S. Borges 1,*, João Batista Jr. 1, Rommel B. Viana 2, Ana C. Baetas 1, Ednilsom Orestes 2, Marcieni A. Andrade 1, Káthia M. Honório 3 and Albérico B. F. da Silva 2 1 Institute of Health Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; E-Mails: [email protected] (J.B.J.); [email protected] (A.C.B.); [email protected] (M.A.A.) 2 Institute of Chemistry of São Carlos, University of São Paulo, São Carlos 13560-970, SP, Brazil; E-Mails: [email protected] (R.B.V.); [email protected] (E.O.); [email protected] (A.B.F.S.) 3 School of Arts, Sciences and Humanities, University of São Paulo, São Carlos 03828-000, SP, Brazil; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +55-91-3271-7202; Fax: +55-91-3271-7201. Received: 4 October 2013; in revised form: 4 October 2013 / Accepted: 10 October 2013 / Published: 14 October 2013 Abstract: An antioxidant mechanism of tetrahydrocannabinol (THC) and cannabidiol (CBD) were compared with a simplified model of α-tocopherol, butylhydroxytoluene and hydroxytoluene in order to understand the antioxidant nature of THC and CBD molecules using DFT. The following electronic properties were evaluated: frontier orbitals nature, ionization potential, O-H bond dissociation energy (BDEOH), stabilization energy, and spin density distribution. An important factor that shows an influence in the antioxidant property of THC is the electron abstraction at the phenol position. -
Block – 2: Organic Reaction Mechanism Lecture-3
Programme Code- MSCCH-17/18/19 Course Code-CHE- 502 Block – 2: Organic reaction mechanism Lecture-3 Presented by - Dr. Charu C. Pant Department of Chemistry Uttarakhand Open University, Haldwani LEARNING OUTCOMES After studying this Chapter, you shall be able to: To know about electronic effect and its types inductive effects Classify a group into +I or –I group Understand mesomeric or resonance effect Applications of Electronic Effects To Know about aromaticity Be familiar with the terms aromatic and anti-aromatic Classify any organic compound into aromatic, anti-aromatic and aliphatic (or non- aromatic) To know about Resonance, Conjugation and Cross Conjugation INTRODUCTION: You are already familiar with various electronic effects. But to understand the properties of organic molecules, like acidity, basicity, stability of various species, and to understand the organic reactions and their mechanism, it is very important that we revisit the electronic effects operating especially with a detailed study of conjugated chemical bonding. During most of the organic reactions, reagents either undergo heterolysis to give rise to electrophiles and/ or nucleophiles; or they undergo homolysis to give rise to free radicals. Electrophiles being electron deficient search for electron rich site in the organic substrate to attack and form the bond. But, if there are more than one electron rich sites in the organic substrate, the electrophile obviously would prefer to attack on the most electron rich site. On the other hand, nucleophiles being electron rich, search for electron deficient sites in the organic substrate. Types of Electronic Effects: There are four types of electronic effects mainly, viz. inductive effect, mesomeric (or resonance) effect, electromeric effect and hyperconjugative effect.