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Author:   Chérif F. Matta (Dalhousie University, Halifax, Kanada) ,  Russell J. Boyd (Dalhousie University, Halifax, Kanada) ,  Axel Becke (Queen's University, Kingston, Canada)
Publisher:   Wiley-VCH Verlag GmbH
Imprint:   Blackwell Verlag GmbH
Dimensions:   Width: 17.80cm , Height: 3.30cm , Length: 24.40cm
Weight:   1.179kg
ISBN:  

9783527307487

ISBN 10:   3527307486
Pages:   567
Publication Date:   26 January 2007
Audience:   Professional and scholarly ,  Professional & Vocational
Format:   Hardback
Publisher's Status:   Active
Availability:   To order  
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Table of Contents

Foreword vii Preface xix List of Abbreviations Appearing in this Volume xxvii List of Contributors xxxiii 1 An Introduction to the Quantum Theory of Atoms in Molecules 1 Chérif F. Matta and Russell J. Boyd 1.1 Introduction 1 1.2 The Topology of the Electron Density 1 1.3 The Topology of the Electron Density Dictates the Form of Atoms in Molecules 5 1.4 The Bond and Virial Paths, and the Molecular and Virial Graphs 8 1.5 The Atomic Partitioning of Molecular Properties 9 1.6 The Nodal Surface in the Laplacian as the Reactive Surface of a Molecule 10 1.7 Bond Properties 10 1.7.1 The Electron Density at the BCP (pb) 11 1.7.2 The Bonded Radius of an Atom (rb), and the Bond Path Length 11 1.7.3 The Laplacian of the Electron Density at the BCP (∇2pb) 11 1.7.4 The Bond Ellipticity (є) 12 1.7.5 Energy Densities at the BCP 12 1.7.6 Electron Delocalization between Bonded Atoms: A Direct Measure of Bond Order 13 1.8 Atomic Properties 15 1.8.1 Atomic Electron Population [N(Ω)] and Charge [q(Ω)] 16 1.8.2 Atomic Volume [Vol.(Ω)] 16 1.8.3 Kinetic Energy [T(Ω)] 17 1.8.4 Laplacian [L(Ω)] 17 1.8.5 Total Atomic Energy [Ee(Ω)] 18 1.8.6 Atomic Dipolar Polarization [μ(Ω)] 20 1.8.7 Atomic Quadrupolar Polarization [Q(Ω)] 24 1.9 ‘‘Practical’’ Uses and Utility of QTAIM Bond and Atomic Properties 25 1.9.1 The Use of QTAIM Bond Critical Point Properties 25 1.9.2 The Use of QTAIM Atomic Properties 26 1.10 Steps of a Typical QTAIM Calculation 27 References 30 Part I Advances in Theory 35 2 The Lagrangian Approach to Chemistry 37 Richard F. W. Bader 2.1 Introduction 37 2.1.1 From Observation, to Physics, to QTAIM 37 2.2 The Lagrangian Approach 38 2.2.1 What is The Lagrangian Approach and What Does it Do? 38 2.2.2 The Lagrangian and the Action Principle – A Return to the Beginnings 39 2.2.3 Minimization of the Action 40 2.2.4 Steps in Minimizing the Action 41 2.3 The Action Principle in Quantum Mechanics 42 2.3.1 Schrödinger’s Appeal to the Action 42 2.3.2 Schrödinger’s Minimization 42 2.3.2.1 Two Ways of Expressing the Kinetic Energy 43 2.3.3 Obtaining an Atom from Schrödinger’s Variation 44 2.3.3.1 The Role of Laplacian in the Definition of an Atom 45 2.3.4 Getting Chemistry from δG(Ψ, ∇Ψ; Ω) 46 2.4 From Schrödinger to Schwinger 48 2.4.1 From Dirac to Feynman and Schwinger 48 2.4.2 From Schwinger to an Atom in a Molecule 49 2.5 Molecular Structure and Structural Stability 52 2.5.1 Definition of Molecular Structure 52 2.5.2 Prediction of Structural Stability 53 2.6 Reflections and the Future 53 2.6.1 Reflections 53 2.6.2 The Future 55 References 57 3 Atomic Response Properties 61 Todd A. Keith 3.1 Introduction 61 3.2 Apparent Origin-dependence of Some Atomic Response Properties 62 3.3 Bond Contributions to ‘‘Null’’ Molecular Properties 64 3.4 Bond Contributions to Atomic Charges in Neutral Molecules 70 3.5 Atomic Contributions to Electric Dipole Moments of Neutral Molecules 71 3.6 Atomic Contributions to Electric Polarizabilities 73 3.7 Atomic Contributions to Vibrational Infrared Absorption Intensities 78 3.8 Atomic Nuclear Virial Energies 82 3.9 Atomic Contributions to Induced Electronic Magnetic Dipole Moments 88 3.10 Atomic Contributions to Magnetizabilities of Closed-Shell Molecules 90 References 94 4 QTAIM Analysis of Raman Scattering Intensities: Insights into the Relationship Between Molecular Structure and Electronic Charge Flow 95 Kathleen M. Gough, Richard Dawes, Jason R. Dwyer, and Tammy L. Welshman 4.1 Introduction 95 4.2 Background to the Problem 96 4.2.1 Conceptual Approach to a Solution 97 4.2.1.1 Experimental Measurement of Raman Scattering Intensities 97 4.2.1.2 Theoretical Modeling of Raman Scattering Intensities: What We Did and Why 99 4.3 Methodology 100 4.3.1 Modeling α and ∂α/∂r 101 4.3.2 Recouping α From the Wavefunction, With QTAIM 102 4.3.3 Recovering ∂α/∂r From QTAIM 103 4.4 Specific Examples of the Use of AIM2000 Software to Analyze Raman Intensities 103 4.4.1 Modeling α in H2 104 4.4.1.1 Modeling ∆α/∆r in H2 106 4.4.2 Modeling α and ∆α/∆r in CH4 106 4.4.3 Additional Exercises for the Interested Reader 108 4.5 Patterns in α That Are Discovered Through QTAIM 109 4.6 Patterns in ∂α/∂rCH That Apply Across Different Structures, Conformations, Molecular Types: What is Transferable? 111 4.6.1 Patterns in ∆α/∆rCH Revealed by QTAIM 111 4.6.1.1 QTAIM Analysis of ∆α/∆rCH in Small Alkanes 111 4.6.1.2 What Did We Learn From QTAIM That Can be Transferred to the Other Molecules? 113 4.7 What Can We Deduce From Simple Inspection of ∂α/∂rCH and ∂α/∂rCC From Gaussian? 114 4.7.1 Variations in ∂α/∂rCH Among the Alkanes 114 4.7.2 ∆α/∆rCH in Cycloalkanes, Bicycloalkanes, and Hedranes 116 4.7.3 Patterns That Emerge in ∆α/∆rCC of Alkanes 116 4.7.4 Unsaturated Hydrocarbons and the Silanes: C-H, C=C, and Si-Si Derivatives 117 4.8 Conclusion 118 References 119 5 Topological Atom–Atom Partitioning of Molecular Exchange Energy and its Multipolar Convergence 121 Michel Rafat and Paul L. A. Popelier 5.1 Introduction 121 5.2 Theoretical Background 123 5.3 Details of Calculations 128 5.4 Results and Discussion 130 5.4.1 Convergence of the Exchange Energy 130 5.4.2 Convergence of the Exchange Force 136 5.4.3 Diagonalization of a Matrix of Exchange Moments 136 5.5 Conclusion 139 References 139 6 The ELF Topological Analysis Contribution to Conceptual Chemistry and Phenomenological Models 141 Bernard Silvi and Ronald J. Gillespie 6.1 Introduction 141 6.2 Why ELF and What is ELF? 142 6.3 Concepts from the ELF Topology 144 6.3.1 The Synaptic Order 145 6.3.2 The Localization Domains 145 6.3.3 ELF Population Analysis 147 6.4 VSEPR Electron Domains and the Volume of ELF Basins 149 6.5 Examples of the Correspondence Between ELF Basins and the Domains of the VSEPR Model 153 6.5.1 Octet Molecules 153 6.5.1.1 Hydrides (CH4, NH3, H2O) 153 6.5.1.2 AX4 (CH4, CF4, SiCl4) 154 6.5.1.3 AX3E and AX2E2 (NCl3, OCl2) 154 6.5.2 Hypervalent Molecules 155 6.5.2.1 PCl5 and SF6 155 6.5.2.2 SF4 and ClF3 155 6.5.2.3 AX7 and AX6E Molecules 155 6.5.3 Multiple Bonds 156 6.5.3.1 C2H4 and C2H2 156 6.5.3.2 Si2Me4 and Si2Me2 157 6.6 Conclusions 158 References 159 Part II Solid State and Surfaces 163 7 Solid State Applications of QTAIM and the Source Function – Molecular Crystals, Surfaces, Host–Guest Systems and Molecular Complexes 165 Carlo Gatti 7.1 Introduction 165 7.2 QTAIM Applied to Solids – the TOPOND Package 166 7.2.1 QTAIM Applied to Experimental Densities: TOPXD and XD Packages 168 7.3 QTAIM Applied to Molecular Crystals 170 7.3.1 Urea 171 7.3.1.1 Urea: Packing Effects 172 7.4 QTAIM Applied to Surfaces 179 7.4.1 Si(111)(1*1) Clean and Hydrogen-covered Surfaces 180 7.4.2 Si(111)(2*1) Reconstructed Surface 184 7.5 QTAIM Applied to Host–Guest Systems 186 7.5.1 Type I Inorganic Clathrates A8Ga16Ge30 (A=Sr, Ba) 186 7.5.2 Sodium Electrosodalite 190 7.6 The Source Function: Theory 192 7.6.1 The Source Function and Chemical Transferability 194 7.6.2 Chemical Information from the Source Function: Long and Short-range Bonding Effects in Molecular Complexes 196 7.6.3 The Source Function: Latest Developments 201 References 202 8 Topology and Properties of the Electron Density in Solids 207 Víctor Luaña, Miguel A. Blanco, Aurora Costales, Paula Mori-Sánchez, and Angel Martín Penda´s 8.1 Introduction 207 8.2 The Electron Density Topology and the Atomic Basin Shape 209 8.3 Crystalline Isostructural Families and Topological Polymorphism 213 8.4 Topological Classification of Crystals 215 8.5 Bond Properties – Continuity from the Molecular to the Crystalline Regime 217 8.6 Basin Partition of the Thermodynamic Properties 219 8.7 Obtaining the Electron Density of Crystals 222 References 227 9 Atoms in Molecules Theory for Exploring the Nature of the Active Sites on Surfaces 231 Yosslen Aray, Jesus Rodríguez, and David Vega 9.1 Introduction 231 9.2 Implementing the Determination of the Topological Properties of p(r) from a Three-dimensional Grid 231 9.3 An Application to Nanocatalyts – Exploring the Structure of the Hydrodesulfurization MoS2 Catalysts 236 9.3.1 Catalyst Models 237 9.3.2 The Full p(r) Topology of the MoS2 Bulk 241 9.3.3 The p(r) Topology of the MoS2 Edges 245 References 254 Part III Experimental Electron Densities and Biological Molecules 257 10 Interpretation of Experimental Electron Densities by Combination of the QTAMC and DFT 259 Vladimir G. Tsirelson 10.1 Introduction 259 10.2 Specificity of the Experimental Electron Density 261 10.3 Approximate Electronic Energy Densities 262 10.3.1 Kinetic and Potential Energy Densities 262 10.3.2 Exchange and Correlation Energy Densities 271 10.4 The Integrated Energy Quantities 275 10.5 Concluding Remarks 276 References 278 11 Topological Analysis of Proteins as Derived from Medium and Highresolution Electron Density: Applications to Electrostatic Properties 285 Laurence Leherte, Benoȋt Guillot, Daniel P. Vercauteren, Virginie Pichon-Pesme, Christian Jelsch, Angélique Lagoutte, and Claude Lecomte 11.1 Introduction 285 11.2 Methodology and Technical Details 287 11.2.1 Ultra-high X-ray Resolution Approach 287 11.2.2 Medium-resolution Approach 289 11.2.2.1 Promolecular Electron Density Distribution Calculated from Structure Factors 289 11.2.2.2 Promolecular Electron Density Distribution Calculated from Atoms 290 11.2.3 A Test System – Human Aldose Reductase 291 11.3 Topological Properties of Multipolar Electron Density Database 294 11.4 Analysis of Local Maxima in Experimental and Promolecular Mediumresolution Electron Density Distributions 298 11.4.1 Experimental and Promolecular Electron Density Distributions Calculated from Structure Factors 299 11.4.2 Promolecular Electron Density Distributions Calculated from Atoms (PASA Model) 301 11.5 Calculation of Electrostatic Properties from Atomic and Fragment Representations of Human Aldose Reductase 305 11.5.1 Medium- and High-resolution Approaches of Electrostatic Potential Computations 307 11.5.2 Electrostatic Potential Comparisons 309 11.5.3 Electrostatic Interaction Energies 312 11.6 Conclusions and Perspectives 312 References 314 12 Fragment Transferability Studied Theoretically and Experimentally with QTAIM – Implications for Electron Density and Invariom Modeling 317 Peter Luger and Birger Dittrich 12.1 Introduction 317 12.2 Experimental Electron-density Studies 318 12.2.1 Experimental Requirements 318 12.2.2 Recent Experimental Advances 319 12.2.2.1 Synchrotron Radiation Compared with Laboratory Sources 319 12.2.2.2 Data Collection at Ultra-low Temperatures (10–20 K) 321 12.3 Studying Transferability with QTAIM – Atomic and Bond Topological Properties of Amino Acids and Oligopeptides 323 12.4 Invariom Modeling 328 12.4.1 Invariom Notation, Choice of Model Compounds, and Practical Considerations 330 12.4.2 Support for Pseudoatom Fragments from QTAIM 331 12.5 Applications of Aspherical Invariom Scattering Factors 334 12.5.1 Molecular Geometry and Anisotropic Displacement Properties 334 12.5.2 Using the Enhanced Multipole Model Anomalous Dispersion Signal 335 12.5.3 Modeling the Electron Density of Oligopeptide and Protein Molecules 336 12.6 Conclusion 338 References 339 Part IV Chemical Bonding and Reactivity 343 13 Interactions Involving Metals – From ‘‘Chemical Categories’’ to QTAIM, and Backwards 345 Piero Macchi and Angelo Sironi 13.1 Introduction 345 13.2 The Electron Density in Isolated Metal Atoms – Hints of Anomalies 345 13.3 Two-center Bonding 349 13.3.1 The Dative Bond 350 13.3.1.1 Metal Carbonyls 351 13.3.1.2 Donor–Acceptor Interactions of Heavy Elements 352 13.3.2 Direct Metal–Metal Bonding 352 13.4 Three-center Bonding 356 13.4.1 π-Complexes 357 13.4.2 σ-Complexes 363 13.4.2.1 Dihydrogen and Dihydride Coordination 364 13.4.2.2 Agostic Interactions 364 13.4.2.3 Hydride Bridges 367 13.4.3 Carbonyl-supported Metal–Metal Interactions 370 13.5 Concluding Remarks 371 References 372 14 Applications of the Quantum Theory of Atoms in Molecules in Organic Chemistry – Charge Distribution, Conformational Analysis and Molecular Interactions 375 Jesús Hernández-Trujillo, Fernando Cortés-Guzmn, and Gabriel Cuevas 14.1 Introduction 375 14.2 Electron Delocalization 375 14.2.1 The Pair-density 375 14.2.2 3JHH Coupling Constants and Electron Delocalization 378 14.3 Conformational Equilibria 380 14.3.1 Rotational barriers 380 14.3.1.1 Rotational Barrier of Ethane 380 14.3.1.2 Rotational Barrier of 1,2-Disubstituted Ethanes 382 14.3.2 Anomeric Effect on Heterocyclohexanes 386 14.4 Aromatic Molecules 391 14.4.1 Electronic Structure of Polybenzenoid Hydrocarbons 391 14.5 Conclusions 395 References 396 15 Aromaticity Analysis by Means of the Quantum Theory of Atoms in Molecules 399 Eduard Matito, Jordi Poater, and Miquel Solà 15.1 Introduction 399 15.2 The Fermi Hole and the Delocalization Index 401 15.3 Electron Delocalization in Aromatic Systems 403 15.4 Aromaticity Electronic Criteria Based on QTAIM 404 15.4.1 The para-Delocalization Index (PDI) 404 15.4.2 The Aromatic Fluctuation Index (FLU) 406 15.4.3 The π-Fluctuation Aromatic Index (FLUπ) 407 15.5 Applications of QTAIM to Aromaticity Analysis 409 15.5.1 Aromaticity of Buckybowls and Fullerenes 409 15.5.2 Effect of Substituents on Aromaticity 412 15.5.3 Assessment of Clar’s Aromatic π-Sextet Rule 416 15.5.4 Aromaticity Along the Diels–Alder Reaction. The Failure of Some Aromaticity Indexes 418 15.6 Conclusions 419 References 421 16 Topological Properties of the Electron Distribution in Hydrogen-bonded Systems 425 Ignasi Mata, Ibon Alkorta, Enrique Espinosa, Elies Molins, and José Elguero 16.1 Introduction 425 16.2 Topological Properties of the Hydrogen Bond 426 16.2.1 Topological Properties at the Bond Critical Point (BCP) 426 16.2.2 Integrated Properties 429 16.3 Energy Properties at the Bond Critical Point (BCP) 431 16.4 Topological Properties and Interaction Energy 435 16.5 Electron Localization Function, n(r) 438 16.6 Complete Interaction Range 440 16.6.1 Dependence of Topological and Energy Properties on the Interaction Distance 440 16.6.2 Perturbed Systems 448 16.7 Concluding Remarks 450 References 450 17 Relationships between QTAIM and the Decomposition of the Interaction Energy – Comparison of Different Kinds of Hydrogen Bond 453 Sławomir J. Grabowski 17.1 Introduction 453 17.2 Diversity of Hydrogen-bonding Interactions 456 17.3 The Decomposition of the Interaction Energy 459 17.4 Relationships between the Topological and Energy Properties of Hydrogen Bonds 460 17.5 Various Other Interactions Related to Hydrogen Bonds 464 17.5.1 H+…π Interactions 464 17.5.2 Hydride Bonds 466 17.6 Summary 467 References 468 Part V Application to Biological Sciences and Drug Design 471 18 QTAIM in Drug Discovery and Protein Modeling 473 Nagamani Sukumar and Curt M. Breneman 18.1 QSAR and Drug Discovery 473 18.2 Electron Density as the Basic Variable 474 18.3 Atom Typing Scheme and Generation of the Transferable Atom Equivalent (TAE) Library 476 18.4 TAE Reconstruction and Descriptor Generation 478 18.5 QTAIM-based Descriptors 480 18.5.1 TAE Descriptors 482 18.5.2 RECON Autocorrelation Descriptors 485 18.5.3 PEST Shape–Property Hybrid Descriptors 485 18.5.4 Electron Density-based Molecular Similarity Analysis 487 18.6 Sample Applications 489 18.6.1 QSAR/QSPR with TAE Descriptors 489 18.6.2 Protein Modeling with TAE Descriptors 491 18.7 Conclusions 492 References 494 19 Fleshing-out Pharmacophores with Volume Rendering of the Laplacian of the Charge Density and Hyperwall Visualization Technology 499 Preston J. MacDougall and Christopher E. Henze 19.1 Introduction 499 19.2 Computational and Visualization Methods 501 19.2.1 Computational Details 501 19.2.2 Volume Rendering of the Laplacian of the Charge Density 501 19.2.3 The Hyperwall 505 19.2.4 Hyper-interactive Molecular Visualization 505 19.3 Subatomic Pharmacophore Insights 507 19.3.1 Hydrogen-bonding Donor Sites 507 19.3.2 Inner-valence Shell Charge Concentration (i-VSCC) Features in Transition-metal Atoms 509 19.3.3 Misdirected Valence in the Ligand Sphere of Transition-metal Complexes 511 19.4 Conclusion 513 References 514 Index 515

Reviews

...a handsome text that serves to create a one-stop reference point exploring the quantum theory of atoms and molecules in complete detail. (Electric Review, May 2007)

Author Information

Chérif F. Matta is an assistant professor of chemistry at Mount Saint Vincent University and an adjunct professor of chemistry at Dalhousie University, both in Halifax, Canada. He obtained his BSc from Alexandria University, Egypt, in 1987 and gained his PhD in theoretical chemistry from McMaster University, Hamilton, Canada in 2002. He was then a postdoctoral fellow at the University of Toronto, Canada, before being awarded an I. W. Killam Fellowship at Dalhousie University. Professor Matta has held the J. C. Polanyi Prize in Chemistry, two BioVision Next Fellowships, and a Chemistry Teaching Award, and has more than 40 papers and book chapters and two software programs to his credit. His research is in theoretical and computational chemistry with a focus on QTAIM and its applications. Russell Boyd graduated from the University of British Columbia in chemistry in 1967, receiving his PhD in theoretical chemistry from McGill University in 1971. He subsequently went to Oxford University, UK, as a postdoctoral fellow, before returning to British Columbia with a Killam Postdoctoral Fellowship at the Department of Chemistry from 1973 to 1975. He then joined Dalhousie University, Halifax, where he held the Chair of Chemistry from 1992 to 2005 and became McLeod Chair in 2001. Professor Boyd has published about 200 papers in computational and theoretical chemistry. His current interests include the effects of radiation on DNA and proteins, the mechanism by which a leading anti-tumor drug cleaves DNA, and the design of catalysts.

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