Table Of ContentINTRODUCTORY
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
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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
