Computational organic chemistry / Steven M. Bachrach.

Format:

Book

Author/Creator:

Bachrach, Steven M., 1959- author.

Language:

English

Subjects (All):

Chemistry, Organic--Mathematics.

Chemistry, Organic.

Chemistry, Organic--Mathematical models.

Physical Description:

1 online resource (640 p.)

Edition:

Second edition.

Place of Publication:

Hoboken, New Jersey : Wiley, 2014.

Language Note:

English

Summary:

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.

Contents:

Cover

Title Page

Contents

Preface

Acknowledgments

Chapter 1 Quantum Mechanics for Organic Chemistry

1.1 Approximations to the Schrodinger Equation

-The Hartree

Fock Method

1.1.1 Nonrelativistic Mechanics

1.1.2 The Born

Oppenheimer Approximation

1.1.3 The One-Electron Wavefunction and the Hartree

1.1.4 Linear Combination of Atomic Orbitals (LCAO) Approximation

1.1.5 Hartree

Fock

Roothaan Procedure

1.1.6 Restricted Versus Unrestricted Wavefunctions

1.1.7 The Variational Principle

1.1.8 Basis Sets

1.1.8.1 Basis Set Superposition Error

1.2 Electron Correlation

-Post-Hartree

Fock Methods

1.2.1 Configuration Interaction (CI)

1.2.2 Size Consistency

1.2.3 Perturbation Theory

1.2.4 Coupled-Cluster Theory

1.2.5 Multiconfiguration SCF (MCSCF) Theory and Complete Active Space SCF (CASSCF) Theory

1.2.6 Composite Energy Methods

1.3 Density Functional Theory (DFT)

1.3.1 The Exchange-Correlation Functionals: Climbing Jacob's Ladder

1.3.1.1 Double Hybrid Functionals

1.3.2 Dispersion-Corrected DFT

1.3.3 Functional Selection

1.4 Computational Approaches to Solvation

1.4.1 Microsolvation

1.4.2 Implicit Solvent Models

1.4.3 Hybrid Solvation Models

1.5 Hybrid QM/MM Methods

1.5.1 Molecular Mechanics

1.5.2 QM/MM Theory

1.5.3 ONIOM

1.6 Potential Energy Surfaces

1.6.1 Geometry Optimization

1.7 Population Analysis

1.7.1 Orbital-Based Population Methods

1.7.2 Topological Electron Density Analysis

1.8 Interview: Stefan Grimme

References

Chapter 2 Computed Spectral Properties and Structure Identification

2.1 Computed Bond Lengths and Angles

2.2 IR Spectroscopy

2.3 Nuclear Magnetic Resonance

2.3.1 General Considerations

2.3.2 Scaling Chemical Shift Values

2.3.3 Customized Density Functionals and Basis Sets.

2.3.4 Methods for Structure Prediction

2.3.5 Statistical Approaches to Computed Chemical Shifts

2.3.6 Computed Coupling Constants

2.3.7 Case Studies

2.3.7.1 Hexacyclinol

2.3.7.2 Maitotoxin

2.3.7.3 Vannusal B

2.3.7.4 Conicasterol F

2.3.7.5 1-Adamantyl Cation

2.4 Optical Rotation, Optical Rotatory Dispersion, Electronic Circular Dichroism, and Vibrational Circular Dichroism

2.4.1 Case Studies

2.4.1.1 Solvent Effect

2.4.1.2 Chiral Solvent Imprinting

2.4.1.3 Plumericin and Prismatomerin

2.4.1.4 2,3-Hexadiene

2.4.1.5 Multilayered Paracyclophane

2.4.1.6 Optical Activity of an Octaphyrin

2.5 Interview: Jonathan Goodman

Chapter 3 Fundamentals of Organic Chemistry

3.1 Bond Dissociation Enthalpy

3.1.1 Case Study of BDE: Trends in the R

X BDE

3.2 Acidity

3.2.1 Case Studies of Acidity

3.2.1.1 Carbon Acidity of Strained Hydrocarbons

3.2.1.2 Origin of the Acidity of Carboxylic Acids

3.2.1.3 Acidity of the Amino Acids

3.3 Isomerism and Problems With DFT

3.3.1 Conformational Isomerism

3.3.2 Conformations of Amino Acids

3.3.3 Alkane Isomerism and DFT Errors

3.3.3.1 Chemical Consequences of Dispersion

3.4 Ring Strain Energy

3.4.1 RSE of Cyclopropane (28) and Cylcobutane (29)

3.5 Aromaticity

3.5.1 Aromatic Stabilization Energy (ASE)

3.5.2 Nucleus-Independent Chemical Shift (NICS)

3.5.3 Case Studies of Aromatic Compounds

3.5.3.1 [n]Annulenes

3.5.3.2 The Mills

Nixon Effect

3.5.3.3 Aromaticity Versus Strain

3.5.4 π

π Stacking

3.6 Interview: Professor Paul Von Rague Schleyer

Chapter 4 Pericyclic Reactions

4.1 The Diels

Alder Reaction

4.1.1 The Concerted Reaction of 1,3-Butadiene with Ethylene

4.1.2 The Nonconcerted Reaction of 1,3-Butadiene with Ethylene.

4.1.3 Kinetic Isotope Effects and the Nature of the Diels

Alder Transition State

4.1.4 Transition State Distortion Energy

4.2 The Cope Rearrangement

4.2.1 Theoretical Considerations

4.2.2 Computational Results

4.2.3 Chameleons and Centaurs

4.3 The Bergman Cyclization

4.3.1 Theoretical Considerations

4.3.2 Activation and Reaction Energies of the Parent Bergman Cyclization

4.3.3 The cd Criteria and Cyclic Enediynes

4.3.4 Myers

Saito and Schmittel Cyclization

4.4 Bispericyclic Reactions

4.5 Pseudopericyclic Reactions

4.6 Torquoselectivity

4.7 Interview: Professor Weston Thatcher Borden

Chapter 5 Diradicals and Carbenes

5.1 Methylene

5.1.1 Theoretical Considerations of Methylene

5.1.2 The H

C

H Angle in Triplet Methylene

5.1.3 The Methylene and Dichloromethylene Singlet

Triplet Energy Gap

5.2 Phenylnitrene and Phenylcarbene

5.2.1 The Low Lying States of Phenylnitrene and Phenylcarbene

5.2.2 Ring Expansion of Phenylnitrene and Phenylcarbene

5.2.3 Substituent Effects on the Rearrangement of Phenylnitrene

5.3 Tetramethyleneethane

5.3.1 Theoretical Considerations of Tetramethyleneethane

5.3.2 Is TME a Ground-State Singlet or Triplet?

5.4 Oxyallyl Diradical

5.5 Benzynes

5.5.1 Theoretical Considerations of Benzyne

5.5.2 Relative Energies of the Benzynes

5.5.3 Structure of m-Benzyne

5.5.4 The Singlet

Triplet Gap and Reactivity of the Benzynes

5.6 Tunneling of Carbenes

5.6.1 Tunneling control

5.7 Interview: Professor Henry ``Fritz'' Schaefer

5.8 Interview: Professor Peter R. Schreiner

Chapter 6 Organic Reactions of Anions

6.1 Substitution Reactions

6.1.1 The Gas Phase SN2 Reaction

6.1.2 Effects of Solvent on SN2 Reactions

6.2 Asymmetric Induction Via 1,2-Addition to Carbonyl Compounds.

6.3 Asymmetric Organocatalysis of Aldol Reactions

6.3.1 Mechanism of Amine-Catalyzed Intermolecular Aldol Reactions

6.3.2 Mechanism of Proline-Catalyzed Intramolecular Aldol Reactions

6.3.3 Comparison with the Mannich Reaction

6.3.4 Catalysis of the Aldol Reaction in Water

6.3.5 Another Organocatalysis Example

-The Claisen Rearrangement

6.4 Interview: Professor Kendall N. Houk

Chapter 7 Solution-Phase Organic Chemistry

7.1 Aqueous Diels

Alder Reactions

7.2 Glucose

7.2.1 Models Compounds: Ethylene Glycol and Glycerol

7.2.1.1 Ethylene Glycol

7.2.1.2 Glycerol

7.2.2 Solvation Studies of Glucose

7.3 Nucleic Acids

7.3.1 Nucleic Acid Bases

7.3.1.1 Cytosine

7.3.1.2 Guanine

7.3.1.3 Adenine

7.3.1.4 Uracil and Thymine

7.3.2 Base Pairs

7.4 Amino Acids

7.5 Interview: Professor Christopher J. Cramer

Chapter 8 Organic Reaction Dynamics

8.1 A Brief Introduction To Molecular Dynamics Trajectory Computations

8.1.1 Integrating the Equations of Motion

8.1.2 Selecting the PES

8.1.3 Initial Conditions

8.2 Statistical Kinetic Theories

8.3 Examples of Organic Reactions With Non-Statistical Dynamics

8.3.1 [1,3]-Sigmatropic Rearrangement of Bicyclo[3.2.0]hex-2-ene

8.3.2 Life in the Caldera: Concerted versus Diradical Mechanisms

8.3.2.1 Rearrangement of Vinylcyclopropane to Cyclopentene

8.3.2.2 Bicyclo[3.1.0]hex-2-ene 20

8.3.2.3 Cyclopropane Stereomutation

8.3.3 Entrance into Intermediates from Above

8.3.3.1 Deazetization of 2,3-Diazabicyclo[2.2.1]hept-2-ene 31

8.3.4 Avoiding Local Minima

8.3.4.1 Methyl Loss from Acetone Radical Cation

8.3.4.2 Cope Rearrangement of 1,2,6-Heptatriene

8.3.4.3 The SN2 Reaction: HO-+CH3F

8.3.4.4 Reaction of Fluoride with Methyl Hydroperoxide

8.3.5 Bifurcating Surfaces: One TS, Two Products.

8.3.5.1 C2

C6 Enyne Allene Cyclization

8.3.5.2 Cycloadditions Involving Ketenes

8.3.5.3 Diels

Alder Reactions: Steps toward Predicting Dynamic Effects on Bifurcating Surfaces

8.3.6 Stepwise Reaction on a Concerted Surface

8.3.6.1 Rearrangement of Protonated Pinacolyl Alcohol

8.3.7 Roaming Mechanism

8.3.8 A Roundabout SN2 reaction

8.3.9 Hydroboration: Dynamical or Statistical?

8.3.10 A Look at the Wolff Rearrangement

8.4 Conclusions

8.5 Interview: Professor Daniel Singleton

Chapter 9 Computational Approaches to Understanding Enzymes

9.1 Models for Enzymatic Activity

9.2 Strategy for Computational Enzymology

9.2.1 High Level QM/MM Computations of Enzymes

9.2.2 Chorismate Mutase

9.2.3 Catechol-O-Methyltransferase (COMT)

9.3 De Novo Design of Enzymes

Index

Supplemental Images.

Notes:

Bibliographic Level Mode of Issuance: Monograph

Includes bibliographical references at the end of each chapters and index.

Description based on print version record.

ISBN:

9781118671191

1118671198

9781118671221

1118671228

9781118671139

1118671139

OCLC:

854761804