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Modeling of Molecular Properties

Modeling of Molecular Properties

Peter Comba (Editor)

ISBN: 978-3-527-63641-9

Oct 2011

510 pages

$157.99

Description

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.
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

“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)