Modeling of Molecular Properties
, by Comba, Peter
- ISBN: 9783527330218 | 3527330216
- Cover: Hardcover
- Copyright: 10/17/2011
Most of the molecular modeling or computational chemistry books focus on one discipline or are introductory texts for students or beginners in the field. This book is comprehensive in coverage of topics in view of the most important research fields in chemistry and materials science and has the general topic of the various molecular properties as ordering concept.
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 Neuch?tel, 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.
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.
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 Müller, 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 Çelebi-Ölçüm, 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 Höltje
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 Gräter
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 Hüttinger, 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
Áron Pintér 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-Jörg 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 Bühler, 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
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