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.
Subjects:	Biochemistry. Chemistry, Inorganic. Chemistry, Organic. Molecules > Models. Electronic books.
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.

Modeling of Molecular Properties.

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