Computational Organic Chemistry

Steven M. Bachrach

• Publisher: Wiley
• Year: 2014
• ISBN:
  9781118671221
• Edition: 2
• Topic: Naturwissenschaften
• Subtopic: Organische Chemie

The Second Edition demonstrates how computational chemistry continues to shed new light on organic chemistry

The Second Edition of author Steven Bachrach's highly acclaimed Computational Organic Chemistry reflects the tremendous advances in computational methods since the publication of the First Edition, explaining how these advances have shaped our current understanding of organic chemistry. Readers familiar with the First Edition will discover new and revised material in all chapters, including new case studies and examples. There's also a new chapter dedicated to computational enzymology that demonstrates how principles of quantum mechanics applied to organic reactions can be extended to biological systems.

Computational Organic Chemistry covers a broad range of problems and challenges in organic chemistry where computational chemistry has played a significant role in developing new theories or where it has provided additional evidence to support experimentally derived insights. Readers do not have to be experts in quantum mechanics. The first chapter of the book introduces all of the major theoretical concepts and definitions of quantum mechanics followed by a chapter dedicated to computed spectral properties and structure identification. Next, the book covers:

• Fundamentals of organic chemistry
• Pericyclic reactions
• Diradicals and carbenes
• Organic reactions of anions
• Solution-phase organic chemistry
• Organic reaction dynamics

The final chapter offers new computational approaches to understand enzymes. The book features interviews with preeminent computational chemists, underscoring the role of collaboration in developing new science. Three of these interviews are new to this edition.

Readers interested in exploring individual topics in greater depth should turn to the book's ancillary website www.comporgchem.com, which offers updates and supporting information. Plus, every cited article that is available in electronic form is listed with a link to the article.

Chapter 1
Quantum Mechanics for Organic Chemistry

Computational chemistry, as explored in this book, will be restricted to quantum mechanical descriptions of the molecules of interest. This should not be taken as a slight upon alternate approaches. Rather, the aim of this book is to demonstrate the power of high level quantum computations in offering insight toward understanding the nature of organic molecules—their structures, properties, and reactions—and to show their successes and point out the potential pitfalls. Furthermore, this book will address the applications of traditional ab initio and density functional theory (DFT) methods to organic chemistry, with little mention of semiempirical methods. Again, this is not to slight the very important contributions made from the application of complete neglect of differential overlap (CNDO) and its progenitors. However, with the ever-improving speed of computers and algorithms, ever-larger molecules are amenable to ab initio treatment, making the semiempirical and other approximate methods for treatment of the quantum mechanics (QM) of molecular systems simply less necessary. This book is therefore designed to encourage the broader use of the more exact treatments of the physics of organic molecules by demonstrating the range of molecules and reactions already successfully treated by quantum chemical computation. We will highlight some of the most important contributions that this discipline has presented to the broader chemical community toward understanding of organic chemistry.

We begin with a brief and mathematically light-handed treatment of the fundamentals of QM necessary to describe organic molecules. This presentation is meant to acquaint those unfamiliar with the field of computational chemistry with a general understanding of the major methods, concepts, and acronyms. Sufficient depth will be provided so that one can understand why certain methods work well while others may fail when applied to various chemical problems, allowing the casual reader to be able to understand most of any applied computational chemistry paper in the literature. Those seeking more depth and details, particularly more derivations and a fuller mathematical treatment, should consult any of the three outstanding texts: Essentials of Computational Chemistry by Cramer,¹ Introduction to Computational Chemistry by Jensen,² and Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory by Szabo and Ostlund.³

Quantum chemistry requires the solution of the time-independent Schrödinger equation,

1.1

where

is the Hamiltonian operator,

is the wavefunction for all of the nuclei and electrons, and E is the energy associated with this wavefunction. The Hamiltonian contains all the operators that describe the kinetic and potential energies of the molecule at hand. The wavefunction is a function of the nuclear positions R and the electron positions r. For molecular systems of interest to organic chemists, the Schrödinger equation cannot be solved exactly and so a number of approximations are required to make the mathematics tractable.

1.1 Approximations to the Schrödinger Equation—The Hartree–Fock Method

1.1.1 Nonrelativistic Mechanics

Dirac⁴ achieved the combination of QM and relativity. Relativistic corrections are necessary when particles approach the speed of light. Electrons near heavy nuclei will achieve such velocities, and for these atoms, relativistic quantum treatments are necessary for accurate description of the electron density. However, for typical organic molecules, which contain only first- and second-row elements, a relativistic treatment is unnecessary. Solving the Dirac relativistic equation is much more difficult than for nonrelativistic computations. A common approximation is to utilize an effective field for the nuclei associated with heavy atoms, which corrects for the relativistic effect. This approximation is beyond the scope of this book, especially since it is unnecessary for the vast majority of organic chemistry.

The complete nonrelativistic Hamiltonian for a molecule c...

Table of contents

• Cover
• Title Page
• Copyright
• Dedication
• Preface
• Acknowledgments
• Chapter 1: Quantum Mechanics for Organic Chemistry
• Chapter 2: Computed Spectral Properties and Structure Identification
• Chapter 3: Fundamentals of Organic Chemistry
• Chapter 4: Pericyclic Reactions
• Chapter 5: Diradicals and Carbenes
• Chapter 6: Organic Reactions of Anions
• Chapter 7: Solution-Phase Organic Chemistry
• Chapter 8: Organic Reaction Dynamics
• Chapter 9: Computational Approaches to Understanding Enzymes
• Index