Modeling of Molecular Properties

Molecular modeling encompasses applied theoretical approaches and computational techniques to model structures and properties of molecular compounds and materials in order to predict and / or interpret their properties. The modeling covered in this book ranges from methods for small chemical to large biological molecules and materials. With its comprehensive coverage of important research fields in molecular and materials science, this is a must-have for all organic, inorganic and biochemists as well as materials scientists interested in applied theoretical and computational chemistry. The 28 chapters, written by an international group of experienced theoretically oriented chemists, are grouped into four parts: Theory and Concepts; Applications in Homogeneous Catalysis; Applications in Pharmaceutical and Biological Chemistry; and Applications in Main Group, Organic and Organometallic Chemistry. The various chapters include concept papers, tutorials, and research reports.

Table of Contents:
Preface XVII List of Contributors XIX Part One Theory and Concepts 1 1 Accurate Dispersion-Corrected Density Functionals for General Chemistry Applications 3 Lars Goerigk and Stefan Grimme 1.1 Introduction 3 1.2 Theoretical Background 4 1.3 Examples 8 1.4 Summary and Conclusions 12 References 14 2 Free-Energy Surfaces and Chemical Reaction Mechanisms and Kinetics 17 Jeremy N. Harvey 2.1 Introduction 17 2.2 Elementary Reactions 19 2.3 Two Consecutive Steps 20 2.4 Multiple Consecutive Steps 23 2.5 Competing Reactions 24 2.6 Catalysis 25 2.7 Conclusions 28 References 28 3 The Art of Choosing the Right Quantum Chemical Excited-State Method for Large Molecular Systems 29 Philipp H.P Harbach and Andreas Dreuw 3.1 Introduction 29 3.2 Existing Excited-State Methods for Medium-Sized and Large Molecules 30 3.3 Analysis of Electronic Transitions 34 3.4 Calculation of Static Absorption and Fluorescence Spectra 37 3.5 Dark States 40 3.6 Summary and Conclusions 44 References 45 4 Assigning and Understanding NMR Shifts of Paramagnetic Metal Complexes 49 Markus Enders 4.1 The Aim and Scope of the Chapter 49 4.2 Basic Theory of Paramagnetic NMR 50 4.3 Signal Assignments 58 4.4 Case Studies 60 References 63 5 Tracing Ultrafast Electron Dynamics by Modern Propagator Approaches 65 Markus Pernpointner, Alexander I. Kuleff, and Lorenz S. Cederbaum 5.1 Charge Migration Processes 65 5.2 Interatomic Coulombic Decay in Noble Gas Clusters 70 References 74 6 Natural Bond Orbitals and Lewis-Like Structures of Copper Blue Proteins 77 Clark R. Landis and Frank Weinhold 6.1 Introduction: Localized Bonding Concepts in Copper Chemistry 77 6.2 Localized Bonds and Molecular Geometries in Polyatomic Cu Complexes 83 6.3 Copper Blue Proteins and Localized Bonds 86 6.4 Summary 88 References 88 7 Predictive Modeling of Molecular Properties: Can We Go Beyond Interpretation? 91 Timothy Clark 7.1 Introduction 91 7.2 Models and Modeling 91 7.3 Parameterized Classical and Quantum Mechanical Theories 93 7.4 Predictive Energies and Structures 94 7.5 Other Gas-Phase Properties 94 7.6 Solvent Effects: The Major Problem 95 7.7 Reaction Selectivity 96 7.8 Biological and Pharmaceutical Modeling 97 7.9 Conclusions 100 References 102 8 Interpretation and Prediction of Properties of Transition Metal Coordination Compounds 107 Peter Comba 8.1 Introduction 107 8.2 Molecular Structure Optimization 108 8.3 Correlation of Molecular Structures and Properties 110 8.4 Computation of Molecular Properties 111 8.5 A Case Study: Electronic and Magnetic Properties of Cyano-Bridged Homodinuclear Copper(II) Complexes 112 8.6 Conclusions 116 References 117 9 How to Realize the Full Potential of DFT: Build a Force Field Out of It 123 Robert James Deeth 9.1 Introduction 123 9.2 Spin-Crossover in Fe(II) Complexes 124 9.3 Ligand Field Molecular Mechanics 126 9.4 Molecular Discovery for New SCO Complexes 129 9.5 Dynamic Behavior of SCO Complexes 131 9.6 Light-Induced Excited Spin-State Trapping 132 9.7 Summary and Future Prospects 135 References 136 Part Two Applications in Homogeneous Catalysis 137 10 Density Functional Theory for Transition Metal Chemistry: The Case of a Water-Splitting Ruthenium Cluster 139 Maren Podewitz, Thomas Weymuth, and Markus Reiher 10.1 Introduction 139 10.2 Shortcomings of Present-Day Density Functionals 139 10.3 Strategies for Constructing Density Functionals 142 10.4 A Practical Example: Catalytic Water Splitting 144 10.5 Conclusions 158 References 159 11 Rational and Efficient Development of a New Class of Highly Active Ring-Opening Metathesis Polymerization Catalysts 165 Martin August Otfried Volland, Thomas Schnetz, and Peter Hofmann 11.1 Introduction 165 11.2 A New Lead Structure: Introduction of Chelating, Bulky, Electron-Rich Bisphosphines with Small Bite Angles 168 11.3 ROMP Activity of the Neutral Systems 170 11.4 Cationic Carbene Complexes: Synthesis and Structure 170 11.5 Olefin Metathesis with Cationic Carbene Complexes: Mechanistic Considerations 175 11.6 ROMP Kinetics in Solution 183 11.7 Summary and Outlook 186 References 187 12 Effects of Substituents on the Regioselectivity of Palladium-Catalyzed Allylic Substitutions: A DFT Study 191 Jevgenij A. Raskatov and Guenter Helmchen 12.1 Introduction 191 12.2 Computational Details 195 12.3 Results and Discussion 195 12.4 Conclusions 203 References 204 13 Dicopper Catalysts for the Azide Alkyne Cycloaddition: A Mechanistic DFT Study 207 Bernd F. Straub, Michael Bessel, and Regina Berg 13.1 Introduction 207 13.2 Theoretical Methods 209 13.3 Discussion of the CuAAC Mechanism 209 13.4 Conclusion and Summary 212 References 214 From Dynamics to Kinetics: Investigation of Interconverting Stereoisomers and Catalyzed Reactions 215 Oliver Trapp 14.1 Investigation of Interconversions by Gas Chromatography 215 14.2 Evaluation Tools 216 14.3 Investigation of Catalyzed Reactions 218 14.4 Perspectives 224 References 225 15 Mechanistic Dichotomies in Coupling-Isomerization-Claisen Pericyclic Domino Reactions in Experiment and Theory 227 Thomas J.J Muller, Daniel M. D'Souza, and Bernhard Mayer 15.1 Introduction 227 15.2 Computation of the Concluding Intramolecular Diels-Alder Reaction in the Domino Formation of (Tetrahydroisobenzofuran) spiro-Benzofuranones or spiro-Indolones 230 15.3 Computation of the Pericyclic Dichotomies of Propargyl Tritylethers 231 15.4 Conclusions 238 References 239 Part Three Applications in Pharmaceutical and Biological Chemistry 241 16 Computational Design of New Protein Catalysts 243 Gert Kiss, Scott A. Johnson, Geoffrey Nosrati, Nihan Celebi-Olcum, Seonah Kim, Robert Paton, and Kendal N. Houk 16.1 Introduction 243 16.2 The Inside-Out Approach 244 16.3 Catalyst Selection and the Catalytic Unit 244 16.4 Theozymes 246 16.5 Scaffold Selection and Theozyme Incorporation 249 16.6 Design 252 16.7 Evaluating Matches and Designs 253 16.8 Experiments 257 16.9 Successful Enzyme Designs 257 16.10 Rational Redesign and Directed Evolution of Designed Enzymes with Low Activities 260 16.11 Summary 263 References 263 17 Computer- Assisted Drug Design 267 Hans-Dieter Holtje 17.1 Neuraminidase Inhibitors 267 17.2 Cyclooxygenase Inhibitors 273 17.3 Concluding Remarks 279 References 279 18 Statics of Biomacromolecules 281 Prakash C. Rathi, Christopher Pfleger, Simone Fulle, Doris L. Klein, and Holger Gohlke 18.1 Introduction 281 18.2 Rigidity Theory and Analysis 282 18.3 Application of Rigidity Analysis to Biomacromolecules 289 18.4 Conclusions 294 References 294 19 Strained Molecules: Insights from Force Distribution Analysis 301 Frauke Grater 19.1 Strain in Molecules 301 19.2 Force Distribution Analysis 303 19.3 Outlook 309 References 309 20 Mercury Detoxification by Bacteria: Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage 311 Hao-Bo Guo, Jerry M. Parks, Alexander Johs, and Jeremy C. Smith 20.1 Introduction 311 20.2 Transcription Activation of MerOP by MerR upon Hg(II)-Binding 312 20.3 Hg-C Bond Cleavage Catalyzed by the MerB 318 20.4 Summary and Conclusions 322 References 323 21 Elucidation of the Conformational Freedom of Ferrocene Amino Acid (Bio)Conjugates: A Complementary Theoretical and Experimental Approach 325 Katja Heinze, Kristina Huttinger, and Daniel Siebler 21.1 Introduction 325 21.2 Simple Ferrocene Amino Acid (Bio)Conjugates 328 21.3 Systems with Amide-Bridged Fca Units 336 21.4 Modeling Responses to External Stimuli 341 21.5 Conclusions 344 References 345 Part Four Applications in Main Group, Organic, and Organometallic Chemistry 347 22 Theoretical Investigation of the 13C NMR Chemical Shift-NCN Angle Correlation in N-Heterocyclic Carbenes 349 Michael Nonnenmacher and Doris Kunz 22.1 Introduction 349 22.2 Method Validation 350 22.3 13C-NMR Chemical Shift -N-C-N Angle Correlation Within Various Carbene Types 351 22.4 N-C-N Angle-Shielding Tensor Correlations: Carbene A 353 22.5 Correlation Between N-C-N Angle and HOMO-LUMO Gap DE: Carbene A 356 22.6 Correlations in N-Heterocyclic Carbenes 359 References 362 23 Structures of Azole-Containing Macrocyclic Peptides 365 Aron Pinter and Gebhard Haberhauer 23.1 Azoles in Nature and Civilization 365 23.2 Azole-Containing Macrocyclic Peptides in Nature: Opening New Boundaries in Science 366 23.3 Achiral Applications of Lissoclinum-Related Macrocyclic Peptides 386 23.4 Applications of Lissoclinum-Related Macrocyclic Peptides as Chiral Tools 387 References 393 24 Modeling of Complex Polyketides: Stereochemical Determination by a Combination of Computational and NMR Methods 397 Dirk Menche and Sandra Dreisigacker 24.1 Myxobacterial Polyketides 397 24.2 Development of Computational and NMR Methods for Stereochemical Determination: Case Studies with the Archazolids 399 24.3 Selected Applications of Combined Computational and NMR Methods for Stereochemical Determination 406 24.4 Conclusion and Perspectives 410 References 410 25 Quantifying Building Principles of Borane Clusters 413 Matthias Hofmann 25.1 Introduction 413 25.2 Structural Features and Energy Penalties 414 25.3 Macropolyhedral Boranes 419 25.4 Conclusions 423 References 423 26 Hydrogenation and Dehydrogenation of Dinuclear Boron- and Gallium Hydrides: Quantum Chemical Calculations and Experiments 425 Hans-Jorg Himmel 26.1 Dihydrogen Activation with Main-Group Element Compounds 425 26.2 Preliminary Quantum Chemical Calculations 426 26.3 Experimental Studies in Concert with Quantum Chemical Calculations 430 References 452 27 Cages and Clusters of Indium: Spherical Aromaticity? 455 Gerald Linti, Martina Buhler, Kirill Monakhov, and Thomas Zessin 27.1 Introduction 455 27.2 Synthesis of Polyhedral Indium Clusters 456 27.3 Quantum Chemical Calculations 459 27.4 Summery 462 References 466 28 Lipophilic Anions 469 Bernd F. Straub and Michael Wrede References 472 Index 473

About the Author :
Peter Comba is Professor of Inorganic Chemistry at the University of Heidelberg, Germany. He obtained his diploma in chemistry from ETH and his PhD in 1981 from the University of Neuchatel, Switzerland. After postdoctoral positions at the Australian National University (ANU) and the University of Lausanne and the habilitation at the University of Basel, he moved in 1992 to Heidelberg. He received the Humboldt South Africa Research Award in 2000 and had visiting professorships at the universities of Leiden, ANU, Pretoria, Brisbane and Osaka. His research includes theory and experiments in transition metal coordination and bioinorganic chemistry - molecular modeling, spectroscopy, thermodynamics, magnetochemistry, kinetics and mechanisms, synthesis and catalysis.

Review :
“This volume will certainly find its place in the libraries of universities and research institutions, but it will be most useful in the hands of graduate students, researchers and collaborators of molecular modelers.”  (Appl. Organometal.Chem, 1 September 2013)