INTRODUCTORY ORGANIC CHEMISTRY AND HYDROCARBONS A Physical Chemistry Approach Caio Lima Firme Organic Chemistry Professor Chemistry Institute Federal University of Rio Grande do Norte Natal, Rio Grande do Norte Brazil Cover credit: Part of the illustrations on the cover are reproduced from the article by the author published in Open Access article in Hindawi, Journal of Chemistry, Volume 2019, Article ID 2365915, 13 pages https://doi.org/10.1155/2019/2365915 CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2020 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed on acid-free paper Version Date: 20190705 International Standard Book Number-13: 978-0-8153-8357-4 (Hardback) This book contains information obtained from authentic and highly regarded sources. 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Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com To my beloved daughter Ananda França Firme Preface This book has several differentiating features from most, if not all, chemistry books: much of the information and most figures were obtained from the author’s own Quantum mechanical calculations (the vast majority published in papers or to be published shortly). They were obtained using several methods and theories which are not well known by the average audience, such as quantum chemistry calculations using quantum theory of atoms in molecules (QTAIM), spin-coupled valence bond (SCVB), generalized valence bond (GVB), non-covalent interaction (NCI), intrinsic reaction coordinate (IRC), and molecular dynamics (MD). The book begins with a brief description of the wave function and the antisymmetric wave function, which is the starting point to differentiate the molecular orbital (MO) and valence bond (VB) theories. The latter is widely used in this book (in its modern version: GVB and SCVB) to describe the electronic nature of several types of chemical bonds. Another important theory (based on the electronic density – the square of the wave function) is presented- the QTAIM, which is very important to describe the intermolecular interactions and chemical bonds. In addition, a very important model used in this book is the electrostatic force and its relation to energy. Both concepts (force and energy) are used to understand the bond strength and relative stability of localized and delocalized systems besides all types of intermolecular interactions with the help of QTAIM analysis as well. The concept of energy is expanded with the presentation of the electronic energy and the thermodynamic properties of enthalpy, internal energy, and Gibbs free energy (all four types of molecular energy). They are essential to discuss the stability of molecules by means of specific reactions. We also show that it is possible to obtain their absolute values theoretically and to compare to experimental values of the corresponding reaction by means of the concepts of statistical thermodynamics which are also explored in this book. From the theoretical data of the statistical thermodynamics, it is possible to understand the concepts of internal energy and entropy microscopically in each molecular entity, which is not possible in the classical thermodynamics. The second part of the book deals with the introductory organic chemistry, where firstly the concepts of atomic radius and electronegative are presented as key points to understand the bond length and bond/molecular polarity/atomic charge, vi Introductory Organic Chemistry and Hydrocarbons respectively. Afterwards, the resonance theory for delocalized systems is discussed with the help of electrostatic force model and its relation to energy to rationalize the stability of these systems with respect to the localized systems. The MO theory is also used to understand the relation between the increasing delocalization and decreasing HOMO-LUMO gap. The historical relation between matrix mechanics and valence bond theory, plus its consequent onset of the concepts of the chemical bond and hybridization, are established and constructed in four chapters. Then, a comprehensive view of the concepts associated with the chemical bond is presented in a historical and mathematical approach. Hereafter, the second part of the book deals with the geometric parameters of a molecule and the practical procedure of its optimization and the importance of this process for obtaining all theoretical properties of the molecule of interest. In addition, it advances to a thorough understanding of the transition state as a critical point of the potential energy surface. From this point on, the mechanistic aspects of a reaction and its relation to the potential energy surface, PES, are discussed. In a subsequent chapter, a comprehensive analysis of the transition state theory (from classical and statistical standpoints) is done as a key point to understand the kinetics of a chemical reaction, which is also important to understand the mechanism of the reaction. Also, in the second part of the book, the models for representing the organic molecules and their specific applications are also presented as important tools to interpret the molecule in different perspectives. In the third part of the book, a thorough analysis of nearly all types of intermolecular interactions and carbocations is done by means of QTAIM and NCI, besides the electrostatic force model as important auxiliary tools for rationalizing their geometric parameters, chemical bonds, interaction/bond strength, and stability. The third part of the book also deals with stereoisomerism (molecular symmetry, enantiomerism, diastereomerism, meso isomer, nomenclature, etc.) and its physical properties. In the first three parts of the book, all prerequisites to a comprehensive understanding of the organic chemistry in a more profound perspective, supported by quantum chemistry, classical/statistical thermodynamics, and kinetics, are presented in an easy-to-understand mathematical/historical approach. The fourth part of the book deals with the hydrocarbon chemistry itself in a physical chemistry approach using quantum chemistry to obtain: (i) optimized geometries; (ii) electronic nature of the chemical bonds and intermolecular interactions; (iii) the stability trend; (iv) the reactivity; (v) the regioselectivity; (vi) the potential energy surface and the structures of its critical points; (vii) deep insights on the mechanisms; (viii) thermodynamic data, etc. The main target audience is made up of the undergraduate students from Chemistry, Chemical Engineering, and other related courses, plus graduate students of organic chemistry and physical chemistry. Caio Lima Firme Advice for Students Students should bear in mind that an appropriate learning of organic chemistry depends on the basic concepts of general chemistry (for instance, electronegativity, polarizability, dipole moment, inter/intra-molecular interactions, nucleophilicity, acid-base reactions, formal charge, chemical bond, and hybridization) and some basic equations (see below). Some general chemistry formulas to bear in mind: FC = Z – Ne i i i µ = Q.r Some basic physical chemistry formulas to bear in mind: DG=DH -TDS DG=-RTlnK ’[product]k K = ’[reagent]n Q.q F =K elect r2 ratee=k’[reagent]v RdS All these formulas will be properly discussed in due time. Note About the Next Volume The title of the second book that succeeds this one is: “Introductory Organic Chemistry Continued and Beyond Hydrocarbons – a Physical Chemistry Approach”. In this second book there are topics such as acidity/basicity, solubility, nucleophicility/ electrophilicity, leaving groups, oxidation and reduction reactions, organometallic compounds, stereoselectivity, acid/base catalysis, properties and reactions of alcohols, amines, ethers and carbonyl compounds, and so on…following the same methodology of the present book. viii Introductory Organic Chemistry and Hydrocarbons Note About the Illustrations and Calculations All illustrations of this book were done by the author. Drawings not derived from quantum chemistry calculations were mostly done using Accelrys Draw software an older version of Biovia Draw (Dessault Systèmes BIOVIA). All other illustrations were obtained from quantum chemistry calculations that were graphically generated by ChemCraft (Zhurko and Zhurko), AIM2000 (Biegler- König et al. 2002), or VMD (Humphrey et al. 1996), or Gausview v.5. Geometry optimization, frequency calculations, along with thermodynamic data used in this book were done in Gaussian09 (Frisch et al. 2009). Intrinsic reaction coordinate, IRC, calculations were based on HPC algorithm (Hratchian and Schlegel 2005). Subsequent calculations of the optimized molecules for QTAIM, NCI (Contreras- García et al. 2011), and GVB/SCVB calculations were done using AIM2000, MultiWFN (Lu and Chen2012), and VB2000 (Li et al. 2009), respectively. RefeRences cited Biegler-König, F., Schönbohm, J. and Bayles, D. 2001. AIM2000 - A program to analyze and visualize atoms in molecules. J. Comp. Chem. 22: 545-559 ChemCraft: graphical software for visualization of quantum chemistry computations. http:// www.chemcraftprog.com Contreras-Garcia, J., Johnson, E.R., Keinan, S., Chaudret, R., Piquemal, J.-P., Beratan, D.N. and Yang, W. 2011. NCIPLOT: A program for plotting non-covalent interactions. J. Chem. Theory Comput. 7: 625-632. Dassault Systèmes BIOVIA, Biovia Draw, San Diego: Dassault Systèmes. Older version used: Accelrys Draw: Accelrys Draw 4.1 - Accelrys Inc. Hratchian, N.H.P. and Schlegel, H.B. 2005. Using hessian updating to increase the efficiency of a hessian based predictor-corrector reaction path following method. J. Chem. Theory Comput. 1: 61–69. Humphrey, W., Dalke, A. and Schulten, K. 1996. VMD: visual molecular dynamics. J. Mol. Graph 14: 33-38. Li, J., Duke, B. and McWeeny, R. 2009. VB2000 v.2.1. SciNet Technologies, San Diego, CA. Lu, T. and Chen, F. 2012. Quantitative analysis of molecular surface based on improved Marching Tetrahedra algorithm. J. Mol. Graph. Model. 38: 314-323. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J.A., Jr., Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Advice for Students ix Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, Ö., Foresman, J.B., Ortiz, J.V., Cioslowski, J., Fox, D.J. 2009. Gaussian 09. Revision B.01. Gaussian, Inc., Wallingford CT. Zhurko, G.A. and Zhurko, D.A., Chemcraft. Version 1.8 (Build 538). www.chemcraftprogram. com