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 larg...
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Format: | eBook |
Language: | English |
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Weinheim :
John Wiley & Sons, Incorporated,
2011.
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Edition: | 2nd ed. |
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Online Access: | Click to View |
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Table of Contents:
- Modeling of Molecular Properties
- Contents
- Preface
- List of Contributors
- Part One: Theory and Concepts
- 1 Accurate Dispersion-Corrected Density Functionals for General Chemistry Applications
- 1.1 Introduction
- 1.2 Theoretical Background
- 1.2.1 Double-Hybrid Density Functionals
- 1.2.2 London-Dispersion-Corrected DFT
- 1.3 Examples
- 1.3.1 GMTKN30
- 1.3.2 A Mechanistic Study with B2PLYP-D
- 1.3.3 Double-Hybrids for Excited States
- 1.4 Summary and Conclusions
- References
- 2 Free-Energy Surfaces and Chemical Reaction Mechanisms and Kinetics
- 2.1 Introduction
- 2.2 Elementary Reactions
- 2.3 Two Consecutive Steps
- 2.4 Multiple Consecutive Steps
- 2.5 Competing Reactions
- 2.6 Catalysis
- 2.7 Conclusions
- References
- 3 The Art of Choosing the Right Quantum Chemical Excited-State Method for Large Molecular Systems
- 3.1 Introduction
- 3.2 Existing Excited-State Methods for Medium-Sized and Large Molecules
- 3.2.1 Wavefunction-Based ab initio Methods
- 3.2.2 Density-Based Methods
- 3.3 Analysis of Electronic Transitions
- 3.4 Calculation of Static Absorption and Fluorescence Spectra
- 3.5 Dark States
- 3.5.1 Excited Electronic States with Large Double Excitation Character
- 3.5.2 Charge-Transfer Excited States
- 3.6 Summary and Conclusions
- References
- 4 Assigning and Understanding NMR Shifts of Paramagnetic Metal Complexes
- 4.1 The Aim and Scope of the Chapter
- 4.2 Basic Theory of Paramagnetic NMR
- 4.2.1 The Origin of the Hyper.ne Shift
- 4.2.1.1 The Contact Shift
- 4.2.1.2 The Pseudocontact Shift
- 4.2.2 Relaxation and Line Widths
- 4.2.2.1 Electronic Relaxation
- 4.2.2.2 Dipolar Relaxation
- 4.2.2.3 Contact Relaxation
- 4.2.2.4 Curie Relaxation
- 4.2.3 Advice for Recording Paramagnetic NMR Spectra
- 4.3 Signal Assignments
- 4.3.1 Comparison of Similar Compounds.
- 4.3.2 Separation of Contact and Pseudocontact Shift
- 4.3.3 Estimating the Dipolar Contributions
- 4.3.4 DFT-Calculation of Spin-Densities
- 4.4 Case Studies
- 4.4.1 Organochromium Complexes
- 4.4.2 Nickel Complexes
- References
- 5 Tracing Ultrafast Electron Dynamics by Modern Propagator Approaches
- 5.1 Charge Migration Processes
- 5.1.1 Theoretical Considerations of Charge Migration
- 5.2 Interatomic Coulombic Decay in Noble Gas Clusters
- 5.2.1 Theoretical Considerations of ICD
- References
- 6 Natural Bond Orbitals and Lewis-Like Structures of Copper Blue Proteins
- 6.1 Introduction: Localized Bonding Concepts in Copper Chemistry
- 6.2 Localized Bonds and Molecular Geometries in Polyatomic Cu Complexes
- 6.3 Copper Blue Proteins and Localized Bonds
- 6.4 Summary
- References
- 7 Predictive Modeling of Molecular Properties: Can We Go Beyond Interpretation?
- 7.1 Introduction
- 7.2 Models and Modeling
- 7.3 Parameterized Classical and Quantum Mechanical Theories
- 7.4 Predictive Energies and Structures
- 7.5 Other Gas-Phase Properties
- 7.6 Solvent Effects: The Major Problem
- 7.7 Reaction Selectivity
- 7.8 Biological and Pharmaceutical Modeling
- 7.8.1 SAR Modeling
- 7.8.2 Force Fields, Docking, and Scoring
- 7.9 Conclusions
- References
- 8 Interpretation and Prediction of Properties of Transition Metal Coordination Compounds
- 8.1 Introduction
- 8.2 Molecular Structure Optimization
- 8.3 Correlation of Molecular Structures and Properties
- 8.4 Computation of Molecular Properties
- 8.5 A Case Study: Electronic and Magnetic Properties of Cyano-Bridged Homodinuclear Copper(II) Complexes
- 8.6 Conclusions
- References
- 9 How to Realize the Full Potential of DFT: Build a Force Field Out of It
- 9.1 Introduction
- 9.2 Spin-Crossover in Fe(II) Complexes
- 9.3 Ligand Field Molecular Mechanics.
- 9.3.1 Training Data: Fe(II)-Amine Complexes
- 9.3.2 LFMM Parameter Fitting
- 9.4 Molecular Discovery for New SCO Complexes
- 9.5 Dynamic Behavior of SCO Complexes
- 9.6 Light-Induced Excited Spin-State Trapping
- 9.7 Summary and Future Prospects
- References
- Part Two: Applications in Homogeneous Catalysis
- 10 Density Functional Theory for Transition Metal Chemistry: The Case of a Water-Splitting Ruthenium Cluster
- 10.1 Introduction
- 10.2 Shortcomings of Present-Day Density Functionals
- 10.2.1 Delocalization Error/Self-Interaction Error
- 10.2.2 Spin-Polarization/Static-Correlation Error
- 10.3 Strategies for Constructing Density Functionals
- 10.4 A Practical Example: Catalytic Water Splitting
- 10.4.1 A Binuclear Ruthenium Water-Splitting Catalyst
- 10.4.2 Comparison of Different Density Functionals
- 10.4.3 Comparison with Experimental Data
- 10.4.4 The Oxo and the Superoxo Structure of the Reactive [Ru2O2]3+ Species
- 10.4.5 Interaction with the Environment: Explicit Solvation of [Ru2O2]3+
- 10.4.6 Formation and Structure of the [Ru2(OH2)O2]3+ Intermediate
- 10.5 Conclusions
- References
- 11 Rational and Efficient Development of a New Class of Highly Active Ring-Opening Metathesis Polymerization Catalysts
- 11.1 Introduction
- 11.2 A New Lead Structure: Introduction of Chelating, Bulky, Electron-Rich Bisphosphines with Small Bite Angles
- 11.3 ROMP Activity of the Neutral Systems
- 11.4 Cationic Carbene Complexes: Synthesis and Structure
- 11.4.1 A Comparison of Carbene versus Carbyne Hydride Isomers: L2ClRu=CH+2 versus L2Cl(H)Ru≡CH+
- 11.4.2 DFT Calculations
- 11.5 Olefin Metathesis with Cationic Carbene Complexes: Mechanistic Considerations
- 11.5.1 A Gas-Phase Study of Cationic Carbene Complexes
- 11.5.2 Screening Results
- 11.5.3 Mechanistic Results
- 11.5.3.1 Isotope Effects.
- 11.5.3.2 Olefin π-Complex Pre-Equilibrium
- 11.5.3.3 Backbiting
- 11.5.4 Direct Comparison of Active Species
- 11.6 ROMP Kinetics in Solution
- 11.6.1 Bite Angle Influence on ROMP Activity
- 11.6.2 ROMP Activity: A comparison with First- and Second-Generation Grubbs Systems in Solution
- 11.7 Summary and Outlook
- References
- 12 Effects of Substituents on the Regioselectivity of Palladium-Catalyzed Allylic Substitutions: A DFT Study
- 12.1 Introduction
- 12.2 Computational Details
- 12.3 Results and Discussion
- 12.3.1 Calculations of the π-Allyl Complexes
- 12.3.1.1 Geometries of the π-Allyl Complexes
- 12.3.1.2 Charge Analysis of the π-Allyl Complexes
- 12.3.1.3 Frontier Orbital Analysis
- 12.3.2 Calculations of Transition States and Product Olefin Complexes
- 12.3.3 Transition State Analysis
- 12.3.4 Olefin Complexes
- 12.4 Conclusions
- References
- 13 Dicopper Catalysts for the Azide Alkyne Cycloaddition: A Mechanistic DFT Study
- 13.1 Introduction
- 13.2 Theoretical Methods
- 13.3 Discussion of the CuAAC Mechanism
- 13.4 Conclusion and Summary
- References
- 14 From Dynamics to Kinetics: Investigation of Interconverting Stereoisomers and Catalyzed Reactions
- 14.1 Investigation of Interconversions by Gas Chromatography
- 14.2 Evaluation Tools
- 14.3 Investigation of Catalyzed Reactions
- 14.3.1 Catalytic Studies with On-Column Reaction Chromatography
- 14.4 Perspectives
- References
- 15 Mechanistic Dichotomies in Coupling-Isomerization-Claisen Pericyclic Domino Reactions in Experiment and Theory
- 15.1 Introduction
- 15.2 Computation of the Concluding Intramolecular Diels-Alder Reaction in the Domino Formation of (Tetrahydroisobenzofuran) spiro-Benzofuranones or spiro-Indolones
- 15.3 Computation of the Pericyclic Dichotomies of Propargyl Tritylethers
- 15.4 Conclusions
- References.
- Part Three: Applications in Pharmaceutical and Biological Chemistry
- 16 Computational Design of New Protein Catalysts
- 16.1 Introduction
- 16.2 The Inside-Out Approach
- 16.3 Catalyst Selection and the Catalytic Unit
- 16.4 Theozymes
- 16.4.1 Background
- 16.4.2 Definition
- 16.4.3 Selection of Catalytic Groups
- 16.4.4 Theozyme Diversity
- 16.4.5 Applications of Theozymes
- 16.5 Scaffold Selection and Theozyme Incorporation
- 16.5.1 Overview and Background
- 16.5.2 RosettaMatch
- 16.5.3 Gess
- 16.6 Design
- 16.6.1 Overview
- 16.6.2 RosettaDesign
- 16.7 Evaluating Matches and Designs
- 16.7.1 Filtering and Ranking Matches
- 16.7.1.1 EDGE
- 16.7.1.2 SASA
- 16.7.2 Ranking and Evaluating Designs
- 16.7.2.1 Empirical Criteria
- 16.7.2.2 Reverting Unnecessary Mutations
- 16.7.2.3 Molecular Dynamics Evaluation
- 16.8 Experiments
- 16.9 Successful Enzyme Designs
- 16.9.1 Retro-Aldol Reaction
- 16.9.2 Kemp Elimination
- 16.9.3 Diels-Alder Cycloaddition
- 16.10 Rational Redesign and Directed Evolution of Designed Enzymes with Low Activities
- 16.10.1 Iterative Approach to de novo Enzyme Design: Rational Redesign
- 16.10.2 Directed Evolution of KE70
- 16.11 Summary
- References
- 17 Computer- Assisted Drug Design
- 17.1 Neuraminidase Inhibitors
- 17.1.1 Physiological Function of Neuraminidase
- 17.1.2 The Substrate: Sialic Acid
- 17.1.3 The Development of Zanamivir
- 17.1.4 Development of the Orally Active Agent Oseltamivir
- 17.2 Cyclooxygenase Inhibitors
- 17.2.1 Cyclooxygenase (Cox)
- 17.2.1.1 Physiological Functions of Cox-1 and Cox-2
- 17.2.1.2 Structural Comparison of Cox-1 and Cox-2
- 17.2.2 Molecular Structures of Typical Cox-1 Selective Inhibitors
- 17.2.3 Molecular Structure of Typical Cox-2 Selective Inhibitors
- 17.3 Concluding Remarks
- References
- 18 Statics of Biomacromolecules.
- 18.1 Introduction.