## Handbook of Computational Chemistry, Volume 2The role the Handbook of Computational Chemistry is threefold. It is primarily intended to be used as a guide that navigates the user through the plethora of computational methods currently in use; it explains their limitations and advantages; and it provides various examples of their important and varied applications. This reference work is presented in three volumes. Volume I introduces the different methods used in computational chemistry. Basic assumptions common to the majority of computational methods based on molecular, quantum, or statistical mechanics are outlined and special attention is paid to the limits of their applicability. Volume III is devoted to the important class of Biomolecules. Useful models of biological systems considered by computational chemists are provided and RNA, DNA and proteins are discussed in detail. This volume presents examples of calcualtions of their properties and interactions and reveals the role of solvents in biologically important reactions as well as the structure function relationship of various classes of Biomolecules. |

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### Contents

List of Contributors | |

References | |

Footnotes | |

Atoms | |

Molecules | |

References | |

Footnotes | |

References | |

Practical Aspects | |

References | |

Footnotes | |

References | |

Summary | |

Models and Methodology | |

Calculated Geometries and Properties | |

Summary | |

Footnotes | |

The Local Density Approximation | |

The Generalized Gradient Approximation | |

HyperFunctionals | |

Fifth Rung | |

Bond Lengths | |

Bond Angles | |

Vibrational Frequencies | |

Electron Affinities and Ionization Potentials | |

Atomization Energies | |

Heats of Formation | |

Energy Barriers | |

Bond Energies | |

Hydrogen Bonding | |

Weak Interactions | |

Spin States | |

Excited States | |

References | |

References | |

Footnotes | |

Examples | |

Density Functional Theory | |

SymmetryAdapted Perturbation Theory | |

SymmetryAdapted Perturbation Theory Based on DFT | |

DensityFitting | |

HigherOrder Contributions | |

ChargeTransfer | |

Auxiliary Basis Sets | |

WilliamsStoneMisquitta WSM Distribution | |

Analyzing the Models | |

References | |

BornOppenheimer Approximation | |

BornOppenheimer Molecular Dynamics | |

CarParrinello Molecular Dynamics | |

Verlet Algorithm | |

LeapFrog Algorithm | |

Velocity Verlet Algorithm | |

Partitioning Schemes | |

Bonds Across the QMMM Boundary | |

Nonbonded Interactions | |

Bonded Interactions | |

Angle Bending Interactions | |

Torsional Interactions | |

Building a Molecule | |

Gathering Preliminary Information | |

Building the System | |

Steepest Descent | |

Conjugate Gradient Methods | |

Direct Inversion of the Iterative Subspace | |

Rescale Thermostat | |

Berendsen Thermostat | |

NoséHoover Thermostat | |

Berendsen Barostat | |

NoséHoover Barostat | |

BornOppenheimer MD | |

CarParrinello MD | |

Spatial Distribution Functions | |

Time Correlation Functions | |

References | |

References | |

References | |

References | |

Dipole and Quadrupole Moments | |

Natural Electronic Circular Dichroism | |

TwoPhoton Circular Dichroism | |

Shielding Derivatives | |

SpinOrbit Corrections to Nuclear Magnetic Shielding | |

References | |

Footnotes | |

DFTD | |

Range Separated and Dispersion Functionals | |

References | |

Small Basis Set Study | |

Study with Extended PopleType Basis Sets | |

Effect of Geometry | |

Results from CorrelationConsistent Basis sets | |

References | |

Psoralen | |

Practical Aspects | |

Water | |

Practical Aspects | |

pbenzosemiquinone Radical Anion | |

Practical Aspects | |

Thymine | |

Practical Aspects | |

Cytosine Dimer | |

Psoralen +O2 | |

Computational Details | |

Results and Discussion | |

Summary | |

References | |

References | |

Footnotes | |

VDOS Fingerprints of Nanoparticles | |

Photoluminescence Responses of SiC Nanoparticles | |

References | |

References | |

Selected Structural Studies | |

The Si6and Si36Cases | |

General Features | |

Gallium Arsenide Clusters | |

IIVI Semiconductor Clusters | |

General Trends | |

Selected Studies | |

References | |

Electron Correlation and Orbital Basis Set | |

The Basis Set Superposition Error Correction | |

Extrapolation to the Complete Basis Set Limit | |

References | |

Natural Abundance of Fullerenes | |

Fullerene NanoCapsules | |

Isolated Pentagon Rule IPR in Fullerenes | |

Common Defects in Fullerenes | |

Discovery and Classification of CNTs | |

Various Defects in Carbon Nanotubes | |

Hydrogenation of Graphene with and Without Defects | |

Computational Studies of Fullerene Isomers | |

Giant Fullerenes | |

POAV and PyramidalizationAngle | |

StoneWales Defect in C60 | |

Computational Studies on Vacancy Defects in FullereneC60 | |

H and F Atom Chemisorptions | |

Theoretical Studies on Common Defects in SWCNTs | |

StoneWales Defect | |

Topological Ring Defects | |

Single and DiVacancy | |

References | |

References | |

References | |

Evaluation of the TB representation of the SOinteraction | |

References | |

References | |

References | |

The PCM HarteeFock Reference State | |

The CoupledCluster PCM Free Energy Functional | |

The CoupledCluster PTDE Scheme | |

The CoupledCluster PTE Scheme | |

The PCMEOMCC Eigenvalue Equations | |

References | |

References | |

Protein Crystallography | |

Nuclear Magnetic Resonance Spectroscopy | |

Molecular Mechanics | |

Structure Prediction and Homology Modeling | |

References | |

References | |

References | |

References | |

References | |

References | |

Hydrated Alkaline Earth and ZincGroup Metal Cations | |

Complexes of Hydrated Copper Cations with Guanine | |

The Tautomeric Equilibrium of the Metalated Nucleobases | |

Interaction of Nucleobases with HalfSandwich RuII Complexes | |

Metal Cations From Ia Ib IIa and IIb Groups | |

Enhancement of Base Pairing by Pt Complexes | |

References | |

Continuous QSAR Models | |

Target Functions and Validation Criteria for Classification QSAR Models | |

Target Functions and Validation Criteria for Category QSAR Models | |

Applicability Domains | |

Yrandomization | |

External Validation | |

Using Hybrid Descriptors for QSIIR Modeling of Rodent Carcinogenicity | |

Using Hybrid Descriptors for the QSIIR Modeling of Rodent AcuteToxicity | |

Universal Statistical Figures of Merit for All Models | |

Consensus QSAR Models of Aquatic Toxicity comparison BetweenMethods and Models | |

References | |

Generation of Molecular Descriptors from Structure | |

Selection of Relevant Molecular Descriptors | |

Mapping the Descriptors to Activity | |

References | |

References | |