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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Bibliographic Details
Main Author: Comba, Peter.
Format: eBook
Language:English
Published: Weinheim : John Wiley & Sons, Incorporated, 2011.
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.