Chemistry as a Game of Molecular Construction

Sason S. Shaik, PhD, is a Professor and the Director of the Lise Meitner-Minerva Center for Computational Quantum Chemistry in the Hebrew University in Jerusalem. He has been a Fulbright Fellow (1974-1979) and became a Fellow of the AAAS in 2005. Among his awards are the Israel Chemical Society Medal for the Outstanding Young Chemist (1987), the Alexander von Humboldt Senior Award in 1996-1999, the 2001 Kolthoff Award, the 2001 Israel Chemical Society Prize, and the 2007 Schrödinger Medal of WATOC. His research interests are in the use of quantum chemistry to develop paradigms that can pattern data and lead to the generation and solution of new problems. From 1981-1992, the main focus of his research was on valence bond theory and its relationship to MO theory, and during that time, he developed a general model of reactivity based on a blend of VB and MO elements. In 1994, he entered the field of oxidation and bond activation by metal oxo catalysts and enzymes, an area where he has contributed several seminal ideas (e.g., two-state reactivity) that led to resolution of major controversies and new predictions.

• FOREWORD xvPREFACE xviiComments to the Teachers/Students xviiA Conversation on the Textbook and Its Intended Readers xxLECTURE 1 MOLECULAR BLUES 11.1 Conversation on Contents of Lecture 1 11.2 The Universal Aspect of Chemistry 21.3 Love, Addiction, Psychological Balance, etc. 21.4 The Chemical Mechanism of Neurotransmission 81.5 Molecules of Pleasure, Wellness, and Pair Bonding 101.6 More Chemical Control 131.7 The Chemical Matter 151.8 Molecular Architecture and Its Emergent Properties 181.8.1 Diamond, Graphite, and More 181.8.2 And There Was Light… 191.9 Chirality, and the Magic by Which Molecules Recognize Others in Nature 211.10 Our Genetic Code Is Chemical 231.11 Chemistry and Its Emergent Expressions 241.12 References and Notes 261.A Appendix 291.A.1 Proposed Demonstrations 291.A.2 References for Appendix 1.A 311.R Retouches 311.R.1 More Drugs Looking like PEA 311.R.2 The Atomic Hypothesis 321.R.3 The Uncertainty Principle, The Exclusion Rule, and Valence 321.R.4 Units of Size 331.R.5 References for Retouches 33LECTURE 2 THE CHEMICAL BOND AND THE LEGO PRINCIPLE 352.1 Conversation on Contents of Lecture 2 352.2 The Periodic Table: The Storehouse of Atoms 362.2.1 The Chemical Language 382.3 The LEGO Principle 402.3.1 The Covalent Bond in H2 412.4 The Bonding Capability of Atoms and The Law of Nirvana for Main Group Elements 442.4.1 The Valence Shell and Connectivity in a Family 452.4.2 The Octet and Duet Rules: The Law of Nirvana 462.5 Making Molecules Using the Available Atom Connectivity and The Law of Nirvana 482.5.1 Using the Table of Connectivity to Make Molecules That Attain Nirvana 502.5.2 Bonding in Atoms with Multiple Connectivity 532.6 The Principle of Conservation of the Number of Atoms in Chemical Reactions 562.7 Summary 572.8 References 592.A Appendix 592.R Retouches 602.R.1 Elements versus Atoms 602.R.2 Electron Pairing 612.R.3 Enzymes and Catalysis 612.R.4 Alchemy 622.R.5 References for Retouches 632.P Problem Set 63LECTURE 3 ELECTRON-DEFICIENT MOLECULES, GIANT MOLECULES, AND CONNECTIVITY OF LARGE FRAGMENTS 653.1 Conversation on Contents of Lecture 3 653.2 Electron-Deficient Molecules 663.2.1 Electron-Deficient Free Radicals 683.3 The Power of Multiple Connectivity: SiO2—A Giant Molecule 693.3.1 SiO2—A Giant Molecule 693.3.2 Definitions of Terms That Follow from the SiO2 Story: Stoichiometry and Polymers 713.4 SiO2 and Glass Making 733.5 Glass Making from Water Glass 743.6 Must We Work So Hard to Construct Large Molecules? 753.6.1 Creating Larger Modular Building Blocks 753.6.2 Making New Molecules from the New Modular Fragments 753.7 Summary 803.8 References 813.A Appendix 813.A.1 Proposed Demonstrations 813.A.2 References for Appendix 3.A 823.R Retouches 823.R.1 Formal Charges 823.R.2 Multiple Bonds to Silicon 833.R.3 The Lone-Pair Bond Weakening Effect 833.R.4 The O2 Molecule and Its Magnetism 843.R.5 References for Retouches 863.P Problem Set 86LECTURE 4 CONSTRUCTING MOLECULAR WORLDS OF CARBON–HYDROGEN FROM LARGE LEGO FRAGMENTS 874.1 Conversation on Contents of Lecture 4 874.2 Molecular Chains Involving Only C and H 894.2.1 Extended Chains 894.2.2 Branched Chains and Isomerism 914.2.3 Isomers of Octane (C8H18) 934.2.4 Some Applications of Alkanes 944.3 Molecular Rings and Cages Made From CH2 and CH Fragments 964.3.1 Molecular Rings Made of CH2 Fragments 964.3.2 Molecular Cages Made of CH Fragments 974.4 Molecular Planes and Cages Made from C Fragments 1004.5 Isomers of Rings and Cages 1054.6 Infinity of Molecular Worlds Made from C and H 1064.7 Summary 1084.8 References 1084.R Retouches 1084.R.1 Atomic Weight, Isotopes, Atomic Mass Unit, and Molecular Weights 1084.R.2 Avogadro’s Number 1094.R.3 The Mole Concept 1104.R.4 Calculation of CO2 Emission by a Car 1114.R.5 The Molecule Benzene, Kekul´e’s Dream, and Resonance Theory 1124.R.6 Resonance Theory and Collective Bonding 1144.R.7 References for Retouches 1154.P Problem Set 115LECTURE 5 CONSTRUCTING MOLECULAR WORLDS OF LIFE FROM LARGE LEGO FRAGMENTS 1175.1 Conversation on Contents of Lecture 5 1175.2 Alcohols, Aldehydes, Ketones, Ethers, and Amines 1205.2.1 Alcohols 1205.2.2 Ethers 1225.2.3 Amines 1245.2.4 Biogenic Amines: Our Neurotransmitters 1245.2.5 Aldehydes, Ketones, Acids, and Esters 1285.2.6 Fats (Lipids): Fatty Acids, Prostaglandins, Triglycerides, Cholesterol, Cortisone, etc. 1305.2.7 Amino Acids, Peptides, Proteins, and Enzymes 1365.3 Summary 1455.4 References 1455.A Appendix 1465.A.1 The Natural Amino Acids (NAAs) 1465.R Retouches 1465.R.1 P450 Enzymes and Grapefruit Juice 1465.R.2 The Discovery of O2 1465.R.3 References for Retouches 1505.P Problem Set 150LECTURE 6 ELECTRON RICHNESS, DNA AND RNA MOLECULES, AND SYNTHETIC POLYMERS 1536.1 Conversation on Contents of Lecture 6 1536.2 Electron Richness: A Different State of Nirvana 1556.2.1 “Who Is Who in Electron Richness” 1556.2.2 Examples of Electron-Rich Molecules 1566.2.3 Phosphoric and Sulfuric Acids 1576.3 DNA and RNA Strands 1596.3.1 Formation of DNA and RNA Strands 1616.3.2 DNA and RNA Nucleotide-Based Drugs 1616.4 Synthetic Polymers 1646.4.1 Constructing Polymers Using the LEGO Principles 1656.4.2 Polymers and Additives 1716.5 Summary 1726.6 References and Notes 1736.A Appendix 1746.A.1 Proposed Demonstrations 1746.A.2 References for Appendix 6.A 1756.R Retouches 1756.R.1 To Be or Not to Be in Octet? This Is the Question 1756.P Problem Set 177LECTURE 7 THE 3D STRUCTURE OF MOLECULES, ELECTRONEGATIVITY, HYDROGEN BONDS, AND MOLECULAR ARCHITECTURE 1797.1 Conversation on Contents of Lecture 7 1797.2 3D Structures of Molecules 1867.2.1 Selection Rules of 3D Molecular Structures 1867.2.2 Lone Pairs Count in 3D Structure Determination 1897.2.3 A Multiple Bond Counts as a Single Space Unit 1917.2.4 Isomerism in Double-Bonded Molecules 1927.2.5 Nature’s Usage of Cis and Trans Isomers 1947.3 Handedness (Chirality) and Isomerism 1957.3.1 Handedness (Chirality) in Nature 1977.4 Extension of the 3D Rules to Conformations 2007.5 The Architecture of Matter and Its Origins 2027.5.1 The Electronegativity of Atoms 2037.5.2 Polarity Trends in Bonds 2047.5.3 Molecular Polarity 2057.5.4 Intermolecular Interactions and the Hydrogen Bond 2067.5.5 Properties of Water 2077.5.6 H-Bonds in Proteins 2087.6 H-Bonding and Our Genetic Code 2097.7 Summary 2137.8 References and Note 2147.A Appendix 2157.A.1 The Periodic Table of Electronegativity Values 2157.A.2 Proposed Demonstrations for Lecture 7 2157.A.3 References for Appendix 7.A 2187.R Retouches 2187.R.1 Electron Pair Repulsion 2187.R.2 Pictorial Description of Lone Pairs 2187.R.3 The Nature of the Double Bond 2197.R.4 Conformations of C2H6 2197.R.5 Other Intermolecular Forces 2207.R.6 More on DNA 2217.R.7 References for Retouches 2257.P Problem Set 225LECTURE 8 THE IONIC BOND AND IONIC MATTER 2278.1 Conversation on Contents of Lecture 8 2278.2 Ionic Bonds versus Covalent Bonds 2328.2.1 The Formation of Ionic Bonds. How and When? 2328.2.2 Construction of Ionic Bonds by “Click-Clack” 2358.2.3 Ionic Molecules Containing Complex Ions 2368.2.4 Why Are Ionic Materials Generally Solids? 2388.2.5 Ionic Liquids? 2408.2.6 Solubility and Insolubility of Ionic Materials 2408.3 The Use of Ionic Matter in Living Organisms 2428.3.1 Soluble Ionic Material Takes Care of Biological Communication 2428.3.2 The Insoluble Ionic Material Makes Our Skeleton and Teeth 2438.4 Covalent Molecules that Form Ions in Solution: Acids and Bases 2448.4.1 Acids in Water: A Proton Transfer Reaction from the Acid to Water 2448.4.2 Bases in Water: A Proton Transfer Reaction from Water to the Base 2488.4.3 A Proton Transfer Reaction from Acids to Bases 2498.4.4 A Few Facts About Our Acids and Bases 2508.5 Summary 2518.6 References and Notes 2528.A Appendix 2538.A.1 Proposed Demonstrations for Lecture 8 2538.A.2 References for Appendix 8.A 2548.R Retouches 2558.R.1 Energetic Aspects of Ionic Bonding 2558.R.2 Energy Units and Bond Energy Calculation for Ionic Bonds 2578.R.3 Dissolution of Ionic Solids in Water 2598.R.4 Concentration, the pH Scale, and Indicators 2608.R.5 Symbolic Representations of Chemical Reactions Using Curved Arrows 2628.R.6 References for Retouches 2648.P Problem Set 264LECTURE 9 BONDING IN TRANSITION METALS, SPECTROSCOPY, AND MOLECULAR DIMENSIONS 2659.1 Conversation on Contents of Lecture 9 2659.2 The 18-Electron Rule for Transition Metal Bonding 2759.2.1 An Example of a Transition Metal Complex That Obeys the 18e Rule 2769.2.2 Electron Counts of Ligand Contributions 2779.3 Construction of Transition Metal Complexes That Obey the 18e Rule 2799.4 Transition Metal Complexes with 14–16e 2809.4.1 Comments on TM-Based Catalysts 2829.5 3D Shapes of Transition Metal Complexes 2839.6 Bridging Transition Metal and Organic Molecules: Bonding Capabilities of Fragments of Transition Metal Complexes 2859.7 Summary of Transition Metal Complexes 2889.8 Spectroscopy or How Do Chemists “Listen to Molecules”? 2889.8.1 The Electromagnetic Radiation Spectrum 2889.8.2 Energy Levels of Molecules as the Basis of Spectroscopy 2919.8.3 X-Ray Crystallography and 3D Molecular Information 2949.9 Summary of Spectroscopic Methods 2979.10 References and Notes 2979.A Appendix 2989.A.1 Radii Values for Transition Metals in Covalent and Ionic Bonds 2989.A.2 Bond Dissociation Energies and Their Usage as Building Blocks 2989.A.3 Proposed Demonstrations for Lecture 9 3009.A.4 References for Appendix 9.A 3029.R Retouches 3029.R.1 Why the 18e Rule, and Why Are Many TM Complexes Colored? 3029.R.2 High-Spin Complexes 3049.R.3 The Active Species of CYP 450 3059.R.4 The “Life” of a Catalyst: The Catalytic Cycle 3059.R.5 The Relation Between the Energy of the Photon and the Frequency of the Light 3089.R.6 References for Retouches 3089.P Problem Set 308LECTURE 10 CHEMISTRY, THE TWO-FACED JANUS—THE DAMAGE IT CAUSES VERSUS ITS IMMENSE CONTRIBUTION TO MANKIND 31110.1 Conversation on Contents of Lecture 10 31110.2 Types of Potential Chemical Damage 31610.2.1 The Ozone Hole 31610.2.2 The Montreal Protocol 31910.2.3 Climate Change 31910.2.4 Acid Rain 32110.2.5 More Evils and the Other Side of the Chemical Janus 32210.3 Summary 32410.4 References and Notes 32410.R Retouches 32510.R.1 The Electronic Structure of Ozone 32510.R.2 Reference for Retouches 32510.P Problem Set 326LECTURE 11 CHEMISTRY IS EVERYTHING AND EVERYTHING IS CHEMISTRY 32711.1 Conversation on Contents of Lecture 11 32711.2 The Birth of Chemistry Is the Nascence of Mankind 32811.3 Chemistry Is Everything 33111.4 The Magic of Chemistry and Pathological Science 33411.5 The Love of Chemistry 33711.6 Summary 33911.7 References and Notes 34011.A Appendix 34011.A.1 Proposed Demonstrations for Lecture 11 34011.A.2 References for Appendix 11.A 342EPILOGUE 343ANSWERS TO PROBLEM SETS 345INDEX 377