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Computational Organic Chemistry by Steven M. Bachrach
<html> <head> <title>Computational Organic Chemistry by Steven M. Bachrach</title> <link rel="stylesheet" href="style.css" type="text/css" media="screen" /> <link rel="shortcut icon" href="favicon.ico" type="image/x-icon" /> <meta name="author" content="Steven Bachrach" /> <meta name="copyright" content="© 2014 Steven Bachrach" /> <meta name="description" content="The supplemental website to Steven Bachrach's book Computational Organic Chemistry" /> <meta name="keywords" content="chemistry, organic, organic chemistry, computational chemistry, computational, book, wiley, steven bachrach, bachrach, steven m. bachrach, steven m bachrach" /> <meta http-equiv="content-type" content="text/html; charset=UTF-16" /> <meta name="google-site-verification" content="g1Myv4tUVAmqRbwZeBi7IPuSZpP64RWjVJ6itIoouCo" /> <script type="text/javascript"> function hideOrShow(idVal) { if(document.getElementById(idVal).style.display=='') document.getElementById(idVal).style.display = 'none'; else document.getElementById(idVal).style.display = ''; } function hideAll() { for(var i = 1; i <= 31; i++) { document.getElementById('ch'+i).style.display = "none"; } } function showAll() { for(var i = 1; i <= 31; i++) { document.getElementById('ch'+i).style.display = ""; } } </script> </head> <body> <div id="header"> <div id="header_img"></div> </div> <div id="sidebar_background"></div> <div id="wrapper1"> <div id="wrapper2"> <div id="maincol"> <div id="leftcol"> <a href="http://www.wiley.com/WileyCDA/WileyTitle/productCd-1118291921,subjectCd-CHD0.html"> <img src="COC2_cover.jpg" alt="Book Cover" /> <p>Buy the book now</p> </a> </div> <div id="rightcol"> <h3>About the Book</h3> <ul> <li>» <a href="/index.html">Home</a></li> <li>» <a href="/blog/">Read the blog</a></li> <li>» <a href="http://www.trinity.edu/sbachrac/">Steven M. Bachrach</a></li> <li>» <a href="http://www.trinity.edu/">Trinity University</a></li> <li>» <a href="http://www.wiley.com/">Published by Wiley</a></li> <li>» <a href="/indexFirst.html">First Edition Web Page</a></li> </ul> <h3>Citations</h3> <ul> <li>» <a href="CitationsSPref.htm">Preface</a></li> <li>» <a href="CitationsS1.htm">Chapter 1</a></li> <li>» <a href="CitationsS2.htm">Chapter 2</a></li> <li>» <a href="CitationsS3.htm">Chapter 3</a></li> <li>» <a href="CitationsS4.htm">Chapter 4</a></li> <li>» <a href="CitationsS5.htm">Chapter 5</a></li> <li>» <a href="CitationsS6.htm">Chapter 6</a></li> <li>» <a href="CitationsS7.htm">Chapter 7</a></li> <li>» <a href="CitationsS8.htm">Chapter 8</a></li> <li>» <a href="CitationsS9.htm">Chapter 9</a></li> </ul> <h3>Molecules</h3> <ul> <li>» Under Construction</li> </ul> </div> <div id="centercol"> <h2><center>Second Edition now available!</center></h2> <p>This web site serves as the companion to my book <em>Computational Organic Chemistry, Second Edition</em> published by Wiley. It provides access to supplementary materials for the book and to the ongoing blog.</p> <p>The book provides a survey of examples where computational chemistry served to explicate problems in organic chemistry. The second edition inlcudes updates to the subjects covered in the first edition, along with a number of new studies, including two entirely new chapters. Details on the new materials in the second edition can be found in these blog posts.</p> <h3>Table of Contents</h3> <ul> <li><strong><a href="" onclick="hideOrShow('ch1');return false;">Chapter 1. Quantum Mechanics for Organic Chemistry</a></strong> <ul id="ch1"> <li><a href="" onclick="hideOrShow('ch11');return false;">1.1 Approximations to the Schrödinger Equation — the Hartree Fock Method</a> <ul id="ch11"> <li>1.1.1 Non-Relativistic Mechanics</li> <li>1.1.2 The Born Oppenheimer Approximation</li> <li>1.1.3 The One-Electron Wavefunction and the Hartree-Fock Method</li> <li>1.1.4 Linear Combination of Atomic Orbitals (LCAO) Approximation</li> <li>1.1.5 Hartree-Fock-Roothaan Procedure</li> <li>1.1.6 Restricted vs. Unrestricted Wavefunctions</li> <li>1.1.7 The Variational Principle</li> <li><a href="" onclick="hideOrShow('ch111');return false;">1.1.8 Basis Sets</a> <ul id="ch111"> <li>Basis Set Superposition Error</li> </ul></li> </ul></li> <li><a href="" onclick="hideOrShow('ch12');return false;">1.2 Electron Correlation — Post-Hartree-Fock Methods</a> <ul id="ch12"> <li>1.2.1 Configuration Interaction (CI)</li> <li>1.2.2 Size Consistency</li> <li>1.2.3 Perturbation Theory</li> <li>1.2.4 Coupled-Cluster Theory</li> <li>1.2.5 Multi-Configuration SCF (MCSCF) Theory and Complete Active Space SCF (CASSCF) Theory</li> <li>1.2.6 Composite Energy Methods</li> </ul></li> <li><a href="" onclick="hideOrShow('ch13');return false;">1.3 Density Functional Theory (DFT)</a> <ul id="ch13"> <li><a href="" onclick="hideOrShow('ch131');return false;">1.3.1 The Exchange-Correlation Functionals: Climbing Jacob's Ladder</a> <ul id="ch131"> <li>1.3.1.1 Double Hybrid Functionals</li> </ul></li> <li>1.3.2 Dispersion-Corrected DFT</li> <li>1.3.3 Functional Selection</li> </ul></li> <li><a href="" onclick="hideOrShow('ch14');return false;">1.4 Computational Approaches to Solvation</a> <ul id="ch14"> <li>1.4.1 Microsolvation</li> <li>1.4.2 Implicit Solvation Models</li> <li>1.4.3 Hybrid Solvation Models</li> </ul></li> <li><a href="" onclick="hideOrShow('ch15');return false;">1.5 Hybrid QM/MM Methods</a> <ul id="ch15"> <li>1.5.1 Molecular Mechanics</li> <li>1.5.2 QM/MM Theory</li> <li>1.5.3 ONIOM</li> </ul></li> <li><a href="" onclick="hideOrShow('ch16');return false;">1.6 Potential Energy Surfaces</a> <ul id="ch16"> <li>1.6.1 Geometry Optimization</li> </ul></li> <li><a href="" onclick="hideOrShow('ch17');return false;">1.7 Population Analysis</a> <ul id="ch17"> <li>1.7.1 Orbital-based Population Methods</li> <li>1.7.2 Topological Electron Density Analysis</li> </ul></li> <li>1.8 Interview: Stefan Grimme</li> <li>1.9 References</li> </ul></li> <li><b><a href="" onclick="hideOrShow('ch2');return false;">Chapter 2. Computed Spectral Properties and Structure Identification</a></b> <ul id="ch2"> <li>2.1 Computed Bond Lengths and Angles</li> <li>2.2 IR Spectroscopy</li> <li><a href="" onclick="hideOrShow('ch23');return false;">2.3 Nuclear Magnetic Resonance</a> <ul id="ch23"> <li>2.3.1 General Considerations</li> <li>2.3.2 Scaling Chemical Shift Values</li> <li>2.3.3 Customized Density Functionals and Basis Sets</li> <li>2.3.4 Methods for Structure Prediction</li> <li>2.3.5 Statistical Approaches to Computed Chemical Shifts</li> <li>2.3.6 Computed Coupling Constants</li> <li><a href="" onclick="hideOrShow('ch237');return false;">2.3.7 Case Studies</a> <ul id="ch237"> <li>2.3.7.1 Hexcyclinol</li> <li>2.3.7.2 Maitotoxin</li> <li>2.3.7.3 Vannusal B</li> <li>2.3.7.4 Conicasterol F</li> <li>2.3.7.5 1-Adamantyl Cation</li> </ul></li> </ul></li> <li><a href="" onclick="hideOrShow('ch24');return false;">2.4 Optical Rotation, Optical Rotatory Dispersion, Electronic Circular Dichroism, and Vibrational Circular Dichroism</a> <ul id="ch24"> <li><a href="" onclick="hideOrShow('ch241');return false;">2.4.1 Case Studies</a> <ul id="ch241"> <li>2.4.1.1 Solvent Effect</li> <li>2.4.1.2 Chiral Solvent Imprinting</li> <li>2.4.1.3 Plumericin and Prismatomerin</li> <li>2.4.1.4 2,3-Hexadiene</li> <li>2.4.1.5 Multilayered Paracyclophane</li> <li>2.4.1.6 Optical Activity of an Octaphyrin</li> </ul></li> </ul></li> <li>2.5 Interview: Jonathan Goodman</li> <li>1.9 References</li> <li>1.9 References</li> <li>1.9 References</li> </ul></li> <li><strong><a href="" onclick="hideOrShow('ch3');return false;">Chapter 3. Fundamentals of Organic Chemistry</a></strong> <ul id="ch3"> <li><a href="" onclick="hideOrShow('ch31');return false;">3.1 Bond Dissociation Enthalpy</a> <ul id="ch31"> <li>3.1.1 Case Studies of BDE: Trends in the R-X BDE</li> </ul></li> <li><a href="" onclick="hideOrShow('ch32');return false;">3.2 Acidity</a> <ul id="ch32"> <li><a href="" onclick="hideOrShow('ch321');return false;">3.2.1 Case Studies of Acidity</a> <ul id="ch321"> <li>3.2.1.1 Carbon Acidity of Strained Hydrocarbons</li> <li>3.2.1.2 Origin of the Acidity of Carboxylic Acids</li> <li>3.2.1.3 Acidity of Amino Acids</li> </ul></li> </ul></li> <li><a href="" onclick="hideOrShow('ch33');return false;">3.3 Isomerism and Problems With DFT</a> <ul id="ch33"> <li>3.3.1 Conformational Isomerism</li> <li>3.3.2 Conformations of Amino Acids</li> <li><a href="" onclick="hideOrShow('ch333');return false;">3.3.3 Alkane Isomerism and DFT Errors</a> <ul id="ch333"> <li>3.3.3.1 Chemical Consequences of Dispersion</li> </ul></li> </ul></li> <li><a href="" onclick="hideOrShow('ch34');return false;">3.4 Ring Strain Energy</a> <ul id="ch34"> <li>3.4.1 RSE of Cyclopropane and Cylcobutane</li> </ul></li> <li><a href="" onclick="hideOrShow('ch35');return false;">3.5 Aromaticity</a> <ul id="ch35"> <li>3.5.1 Aromatic Stabilization Energy (ASE)</li> <li>3.5.2 Nucleus-Independent Chemical Shift (NICS)</li> <li><a href="" onclick="hideOrShow('ch353');return false;">3.5.3 Case Studies of Aromatic Compounds</a> <ul id="ch353"> <li>3.5.3.1 [n]Annulenes</li> <li>3.5.3.2 The Mills-Nixon Effect</li> <li>3.5.3.3 Aromaticity Versus Strain</li> </ul></li> <li>3.5.4 π-π Stacking</li> </ul></li> <li>3.6 Interview: Professor Paul Von Rague Schleyer</li> <li>3.7 References</li> </ul></li> <li><strong><a href="" onclick="hideOrShow('ch4');return false;">Chapter 4. Pericyclic Reactions</a></strong> <ul id="ch4"> <li><a href="" onclick="hideOrShow('ch41');return false;">4.1 The Diels-Alder Reaction</a> <ul id="ch41"> <li>4.1.1 The Concerted Reaction of 1,3-Butadiene with Ethylene</li> <li>4.1.2 The Non-Concerted Reaction of 1,3-Butadiene with Ethylene</li> <li>4.1.3 Kinetic Isotope Effects and the Nature of the Diels-Alder Transition State</li> <li>4.1.4 Transition State Distortion Energy</li> </ul></li> <li><a href="" onclick="hideOrShow('ch42');return false;">4.2 The Cope Rearrangement</a> <ul id="ch42"> <li>4.2.1 Theoretical Considerations</li> <li>4.2.2 Computational Results</li> <li>4.2.3 Chameleons and Centaurs</li> </ul></li> <li><a href="" onclick="hideOrShow('ch43');return false;">4.3 The Bergman Cyclization</a> <ul id="ch43"> <li>4.3.1 Theoretical Considerations</li> <li>4.3.2 Activation and Reaction Energies of the Parent Bergman Cyclization</li> <li>4.3.3 The cd Criteria and Cyclic Enediynes</li> <li>4.3.4 Mayers-Saito and Schmittel Cyclization</li> </ul></li> <li>4.4 Bispericyclic Reactions</li> <li>4.5 Pseudopericyclic Reactions</li> <li>4.6 Torquoselectivity</li> <li>4.7 Interview: Professor Weston Thatcher Borden</li> <li>4.8 References</li> </ul></li> <li><strong><a href="" onclick="hideOrShow('ch5');return false;">Chapter 5. Diradicals and Carbenes</a></strong> <ul id="ch5"> <li><a href="" onclick="hideOrShow('ch51');return false;">5.1 Methylene</a> <ul id="ch51"> <li>5.1.1 Theoretical Considerations of Methylene</li> <li>5.1.2 The H-C-H Angle in Triplet Methylene</li> <li>5.1.3 The Methylene Singlet-Triplet Energy Gap</li> </ul></li> <li><a href="" onclick="hideOrShow('ch52');return false;">5.2 Phenylnitrene and Phenylcarbene</a> <ul id="ch52"> <li>5.2.1 The Low-Lying States of Phenylnitrene and Phenylcarbene</li> <li>5.2.2 Ring Expansion of Phenylnitrene and Phenylcarbene</li> <li>5.2.3 Substituent Effects on the Rearrangement of Phenylnitrene</li> </ul></li> <li><a href="" onclick="hideOrShow('ch53');return false;">5.3 Tetramethyleneethane</a> <ul id="ch53"> <li>5.3.1 Theoretical Considerations of Tetramethyleneethane</li> <li>5.3.2 Is TME a Ground-State Singlet or Triplet?</li> </ul></li> <li>5.4 Oxyallyl Diradical</li> <li><a href="" onclick="hideOrShow('ch55');return false;">5.5 Benzynes</a> <ul id="ch55"> <li>5.5.1 Theoretical Considerations of Benzyne</li> <li>5.5.2 Relative Energies of the Benzynes</li> <li>5.5.3 Structure of m-Benzyne</li> <li>5.5.4 The Singlet-Triplet Gap and Reactivity of the Benzynes</li> </ul></li> <li><a href="" onclick="hideOrShow('ch56');return false;">5.6 Tunneling of Carbenes</a> <ul id="ch56"> <li>5.6.1 Tunneling control</li> </ul></li> <li>5.7 Interview: Professor Henry "Fritz" Schaefer</li> <li>5.8 Interview: Professor Peter R. Schreiner</li> <li>5.9 References</li> </ul></li> <li><strong><a href="" onclick="hideOrShow('ch6');return false;">Chapter 6. Organic Reactions of Anions</a></strong> <ul id="ch6"> <li><a href="" onclick="hideOrShow('ch61');return false;">6.1 Substitution Reactions</a> <ul id="ch61"> <li>6.1.1 The Gas Phase S<sub>N</sub>2 Reaction</li> <li>6.1.2 Effect of Solvent on S<sub>N</sub>2 Reactions</li> </ul></li> <li>6.2 Asymmetric Induction via 1,2-Addition to Carbonyl Compounds</li> <li><a href="" onclick="hideOrShow('ch63');return false;">6.3 Asymmetric Organocatalysis of Aldol Reactions</a> <ul id="ch63"> <li>6.3.1 Mechanism of Amine-Catalyzed Intermolecular Aldol Reactions</li> <li>6.3.2 Mechanism of Proline-Catalyzed Intramolecular Aldol Reactions</li> <li>6.3.3 Comparison with the Mannich Reaction</li> <li>6.3.4 Catalysis of the Aldol Reaction in Water</li> <li>6.3.5 Another Organocatalysis Example: The Claisen Rearrangement</li> </ul></li> <li>6.4 Interview - Professor Kendall N. Houk</li> <li>6.5 References</li> </ul></li> <li><strong><a href="" onclick="hideOrShow('ch7');return false;">Chapter 7. Solution-Phase Organic Chemistry</a></strong> <ul id="ch7"> <li>7.1 Aqueous Diels-Alder Reactions</li> <li><a href="" onclick="hideOrShow('ch72');return false;">7.2 Glucose</a> <ul id="ch72"> <li><a href="" onclick="hideOrShow('ch721');return false;">7.2.1 Models Compounds: Ethylene Glycol and Glycerol</a> <ul id="ch721"> <li>7.2.1.1 Ethylene Glycol</li> <li>7.2.1.2 Glycerol</li> </ul></li> <li>7.2.2 Solvation Studies of Glucose</li> </ul></li> <li><a href="" onclick="hideOrShow('ch73');return false;">7.3 Nucleic Acids</a> <ul id="ch73"> <li><a href="" onclick="hideOrShow('ch731');return false;">7.3.1 Nucleic Acid Bases</a> <ul id="ch731"> <li>7.3.1.1 Cytosine</li> <li>7.3.1.2 Guanine</li> <li>7.3.1.3 Adenine</li> <li>7.3.1.4 Uracil and Thymine</li> </ul></li> <li>7.3.2 Base Pairs</li> </ul></li> <li>7.4 Amino Acids</li> <li>7.5 Interview: Professor Christopher J. Cramer</li> <li>7.6 References</li> </ul></li> <li><strong><a href="" onclick="hideOrShow('ch8');return false;">Chapter 8. Organic Reaction Dynamics</a></strong> <ul id="ch8"> <li><a href="" onclick="hideOrShow('ch81');return false;">8.1 A Brief Introduction to Molecular Dynamics Trajectory Computations</a> <ul id="ch81"> <li>8.1.1 Integrating the Equations of Motion</li> <li>8.1.2 Selecting the PES</li> <li>8.1.3 Initial Conditions</li> </ul></li> <li>8.2 Statistical Kinetic Theories</li> <li><a href="" onclick="hideOrShow('ch83');return false;">8.3 Examples of Organic Reactions with Non-Statistical Dynamics</a> <ul id="ch83"> <li>8.3.1 [1,3]-Sigmatropic rearrangement of bicyclo[3.2.0]hex-2-ene</li> <li><a href="" onclick="hideOrShow('ch832');return false;">8.3.2 Life in the Caldera: Concerted vs. Diradical Mechanisms</a> <ul id="832"> <li>8.3.2.1 Rearrangement of Vinylcyclopropane to Cyclopentane</li> <li>8.3.2.2 Bicyclo[3.1.0]hex-2-ene</li> <li>8.3.2.3 Cyclopropane Stereomutation</li> </ul></li> <li><a href="" onclick="hideOrShow('ch833');return false;">8.3.3 Entrance into Intermediates from Above</a> <ul id="ch833"> <li>8.3.3.1 Deazetization of 2,3-Diazabicyclo[2.2.1]hept-2-ene</li> </ul></li> <li><a href="" onclick="hideOrShow('ch834');return false;">8.3.4 Avoiding Local Minima</a> <ul id="ch834"> <li>8.3.4.1 Methyl Loss from Acetone Radical Cation</a> <li>8.3.4.2 Cope Rearrangement of 1,2,6-Heptatriene</a> <li>8.3.4.3 The S<sub>N</sub>2 Reaction: HO<sup>-</sup> + CH<sub>3</sub>F</li> <li>8.3.4.4 Reaction of Fluoride with Formic Acid</li> </ul></li> <li><a href="" onclick="hideOrShow('ch835');return false;">8.3.5 Bifurcating Surfaces: One TS, Two Products</a> <ul id="ch835"> <li>8.3.5.1 C<sub>2</sub>-C<sub>6</sub> Enyne Allene Cyclization</li> <li>8.3.5.2 Cycloadditions Involving Ketenes</li> <li>8.3.5.3 Diels-Alder Reactions: Steps toward Predicting Dynamic Effects on Bifurcating Surfaces</li> </ul></li> <li><a href="" onclick="hideOrShow('ch836');return false;">8.3.6 Stepwise Reaction on a Concerted Surface</a> <ul id="ch836"> <li>8.3.6.1 Rearrangement of Protonated Pinacolyl Alcohol</li> </ul></li> <li>8.3.7 Roaming Mechanism</li> <li>8.3.8 A Roundabout SN2 reaction</li> <li>8.3.9 Hydroboration: Dynamical or Statistical?</li> <li>8.3.10 A Look at the Wolff Rearrangement</li> </ul></li> <li>8.4 Conclusions</li> <li>8.5 Interview: Professor Daniel Singleton</li> <li>8.6 References</li> </ul></li> <li><strong><a href="" onclick="hideOrShow('ch9');return false;">Chapter 9. Computational Approaches to Understanding Enzymes</a></strong> <ul id="ch9"> <li>9.1 Models for Enzymatic Activity</li> <li><a href="" onclick="hideOrShow('ch92');return false;">9.2 Strategy for Computational Enzymology</a> <ul id="ch92"> <li>9.2.1 High Level QM/MM Computations of Enzymes</li> <li>9.2.2 Chorismate Mutase</li> <li>9.2.3 Catechol-O-Methyltransferase (COMT)</li> </ul></li> <li>9.3 De Novo Design of Enzymes</li> <li>9.4 References</li> </ul></li> </ul> <script type="text/javascript">hideAll();</script> <p>Any book that hopes to capture the status of a dynamic field like computational chemistry is destined to become out-of-date. Even between the time the manuscript is completed and the book is printed and distributed, research continues on, and the book is by definition incomplete. This blog serves as a mechanism to update the book, providing brief posts commenting on recent articles that touch on or expand upon the subjects discussed in the printed book.</p> <p>The book's auxiliary web site and blog extend the printed version into Web 2.0 space. On this auxiliary site, I have included all of the citations with links (using the <a href="http://doi.org/">DOI</a>) to the cited articles, where electronic versions of those articles exist. Please keep in mind that most of these articles are not open-access and it is up to the reader to secure proper access rights to these articles. Also, most of the figures of 3-D molecules are reproduced along with their 3-D coordinates (as xyz files). These coordinates can be downloaded into your favorite molecular visualization tool for manipulation and re-use. All figures of 3-D molecules that have a border are actually links to the 3-D coordinates that will automatically load up into a <a href="http://jmol.sourceforge.net/">Jmol</a> applet, allowing you to manipulate the structure on-screen, in real time, within the blog window. Simply click on the figure to get this to work!</p> <p>In addition, the blog provides an avenue for feedback from the readers. I welcome readers to comment on the book and the blog posts. I am particularly interested in correcting any errors that may be present in the book (or the blog).</p> <p>Steven Bachrach<br /> <i>Trinity University</i></p> </div> </div> <div id="footer"> <p>© 2014 Steven Bachrach. Site designed by <a href="http://www.dbachrach.com">Dustin Bachrach</a>.</p> </div> </div> </div> </body> </html>