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.

Table of Contents:
Preface PART I: Theory and Concepts ACCURATE DISPERSION-CORRECTED DENSITY FUNCTIONALS FOR GENERAL CHEMISTRY APPLICATIONS Introduction Theoretical Background Examples Summary and Conclusions FREE-ENERGY SURFACES AND CHEMICAL REACTION MECHANISMS AND KINETICS Introduction Elementary Reactions Two Consecutive Steps Multiple Consecutive Steps Competing Reactions Catalysis Conclusions THE ART OF CHOOSING THE RIGHT QUANTUM CHEMICAL EXCITED-STATE METHOD FOR LARGE MOLECULAR SYSTEMS Introduction Existing Excited-State Methods for Medium-Sized and Large Molecules Basic Theory of Paramagnetic NMR Signal Assignments Case Studies TRACING ULTRAFAST ELECTRON DYNAMICS BY MODERN PROPAGATOR APPROACHES Charge Migration Processes Interatomic Coulombic Decay in Noble Gas Clusters NATURAL BOND ORBITALS AND LEWIS-LIKE STRUCTURES OF COPPER BLUE PROTEINS Introduction: Localized Bonding Concepts in Copper Chemistry Localized Bonds and Molecular Geometries in Polytomic Cu Complexes Copper Blue Proteins and Localized Bonds Summary PREDICTIVE MODELING OF MOLECULAR PROPERTIES: CAN WE GO BEYOND INTERPRETATION? Introduction Models and Modeling Parameterized Classical and Quantum Mechanical Theories Predictive Energies and Structures Other Gas-Phase Properties Solvent Effects: The Major Problem Reaction Selectivity Biological and Parmaceutical Modeling Conclusions INTERPRETATION AND PREDICTION OF PROPERTIES OF TRANSITION METAL COORDINATION COMPOUNDS Introduction Molecular Structure Optimization Correlation of Molecular Structures and Properties Computation of Molecular Properties A Case Study: Electronic and Magnetic Properties of Cyano-Bridged Homodinuclear Copper(II) Complexes Conclusions HOW TO REALIZE THE FULL POTENTIAL OF DFT: BUILD A FORCE FIELD OUT OF IT Introduction Spin-Crossover in Fe(II) Complexes Ligand Field Molecular Mechanics Molecular Discovery for New SCO Complexes Dynamic Behavior of SCO Complexes Light-Induced Excited Spin-State Trapping Summary and Future Prospects PART II: Applications in Homogeneous Catalysis DENSITY FUNCTIONAL THEORY FOR TRANSITION METAL CHEMISTRY: THE CASE OF A WATER-SPLITTING RUTHENIUM CLUSTER Introduction Shortcomings of Present-Day Density Functionals Strategies for Constructing Density Functionals A Practical Example: Catalytic Water Splitting Conclusions RATIONAL END EFFICIENT DEVELOPMENT OF A NEW CLASS OF HIGHLY ACTIVE RING-OPENING METATHESIS POLYMERIZATION CATALYSTS Introduction A New Lead Structure: Introduction of Chelating, Bulky, Electron-Rich Bisphosphines with Small Bite Angles ROMP Activity of the Neutral Systems Cationic Carbene Complexes: Synthesis and Structure Olefin Metathesis with Cationic Carbene Complexes: Mechanistic Considerations ROMP Kinetics in Solution Summary and Outlook EFFECTS OF SUBSTITUENTS ON THE REGIOSELECTIVITY OF PALLADIUM-CATALYZED ALLYLIC SUBSTITUTIONS: A DFT STUDY Introduction Computational Details Results and Discussion Conclusions DICOPPER CATALYSTS FOR THE AZIDE ALKYNE CYCLOADDITION: A MECHANISTIC DFT STUDY Introduction Theoretical Methods Discussion of the CuAAC Mechanism Conclusion and Summary FROM DYNAMICS TO KINETICS: INVESTIGATION OF INTERCONVERTING STEREOISOMERS AND CATALYZED REACTIONS Investigation of Interconversions by Gas Chromatography Evaluation Tools Investigation of Catalyzed Reactions Perspectives MECHANISTIC DICHOTOMIES IN COUPLING-ISOMERIZATION-CLAISEN PERICYCLIC DOMINO REACTIONS IN EXPERIMENT AND THEORY Introduction Computation of the Concluding Intramolecular Diels-Alder Reaction in the Domino Formation of (Tetrahydroisobenzofuran) spiro-Benzofuranones or spiro-Indolones Computation of the Pericyclic Dichotomies of Propargyl Tritylethers Conclusions PART III: Applications in Pharmaceutical and Biological Chemistry COMPUTATIONAL DESIGN OF NEW PROTEIN CATALYSTS Introduction The Inside-Out Approach Catalyst Selection and the Catalytic Unit Theozymes Scaffold Selection and Theozyme Incorporation Design Evaluating Matches and Designs Experiments Successful Enzyme Designs Rational Redesign and Directed Evolution of Designed Enzymes with Low Activities Summary COMPUTER-ASSISTED DRUG DESIGN Neuraminidase Inhibitors Cyclooxygenase Inhibitors Concluding Remarks STATICS OF BIOMACROMOLECULES Introduction Rigidity Theory and Analysis Application of Regidity Analysis to Biomacromolecules Conclusions STRAINED MOLECULES: INSIGHTS FROM FORCE DISTRIBUTION ANALYSIS Strain in Molecules Frce Distribution Analysis Outlook MERCURY DETOXIFICATION BY BACTERIA: SIMULATIONS OF TRANSCRIPTION ACTIVATION AND MERCURY-CARBON BOND CLEAVAGE Introduction Transcription Activation of MerOP by MerR upon Hg(II)-Binding Hg-C Bond Cleavage Catalyzed by the MerB Summary and Conclusions ELUCIDATION OF THE CONFORMATIONAL FREEDOM OF FERROCENE AMINO ACID (BIO)CONJUGATES: A COMPLEMENTARY THEORETICAL AND EXPERIMENTAL APPROACH Introduction Simple Ferrocene Amino Acid (Bio)Conjugates Systems with Amide-Bridged Fca Units Modeling Responses to External Stimuli Conclusions PART IV: Applications in Main Group, Organic, and Organometallic Chemistry THEORETICAL INVESTIGATION OF THE 13C NMR CHEMICAL SHIFT-NCN ANGLE CORRELATION IN N-HETEROCYCLIC CARBENES Introduction Method Validation 13C-NMR Chemical Shift-N-C-N Angle Correlation Within Various Carbene Types N-C-N Angle-Shielding Tensor Correlations: Carbene A Correlation Between N-C-N Angle and HOMO-LUMO Gap DeltaE: Carbene A Correlations in N-Heterocyclic Carbenes STRUCTURES OF AZOLE-CONTAINING MACROCYCLIC PEPTIDES Azoles in Nature and Civilization Azole-Containing Macrocyclic Peptides in Nature: Opening New Boundaries in Science Achiral Applications of Lissoclinum-Related Macrocyclic Peptides Applications of Lissoclinum-Related Macrocyclic Peptides as Chiral Tools MODELING OF COMPLEX POLYKETIDES: STEREOCHEMICAL DETERMINATION BY A COMBINATION OF COMPUTATIONAL AND NMR METHODS Myxobacterial Polyketides Development of Computational and NMR Methods for Stereochemical Determination: Case Studies with the Archazolids Selected Applications of Combined Computational and NMR Methods for Stereochemical Determination Conclusion and Perspectives QUANTIFYING BUILDING PRINCIPLES OF BORANE CLUSTERS Introduction Structural Features and Energy Penalties Macropolyhedral Boranes Conclusions HYDROGENATION AND DEHYDROGENATION OF DINUCLEAR BORON- AND GALLIUM HYDRIDES: QUANTUM CHEMICAL CALCULATIONS AND EXPERIMENTS Dihydrogen Activation with Main-Group Element Compounds Preliminary Quantum Chemical Calculations Experimental Studies in Concert with Quantum Chemical Calculations CAGES AND CLUSTERS OF INDIUM: SPHERICAL AROMATICITY? Introduction Synthesis of Polyhedral Indium Clusters Quantum Chemical Calculations Summary LIPOPHILIC ANIONS