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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Main Author: Comba, Peter.
Format: eBook
Language:English
Published: Weinheim : John Wiley & Sons, Incorporated, 2011.
Edition:2nd ed.
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245 1 0 |a Modeling of Molecular Properties. 
250 |a 2nd ed. 
264 1 |a Weinheim :  |b John Wiley & Sons, Incorporated,  |c 2011. 
264 4 |c ©2011. 
300 |a 1 online resource (513 pages) 
336 |a text  |b txt  |2 rdacontent 
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505 0 |a 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. 
505 8 |a 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. 
505 8 |a 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. 
505 8 |a 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. 
505 8 |a 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. 
505 8 |a 18.1 Introduction. 
520 |a 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. 
588 |a Description based on publisher supplied metadata and other sources. 
590 |a Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2021. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.  
650 0 |a Biochemistry. 
650 0 |a Chemistry, Inorganic. 
650 0 |a Chemistry, Organic. 
650 0 |a Molecules -- Models. 
655 4 |a Electronic books. 
776 0 8 |i Print version:  |a Comba, Peter  |t Modeling of Molecular Properties  |d Weinheim : John Wiley & Sons, Incorporated,c2011  |z 9783527330218 
797 2 |a ProQuest (Firm) 
856 4 0 |u https://ebookcentral.proquest.com/lib/suleyman-ebooks/detail.action?docID=822720  |z Click to View