Handbook of Computational Chemistry, Volume 2

Front Cover
Jerzy Leszczynski
Springer Science & Business Media, Jan 13, 2012 - Computers - 1430 pages

The 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 II portrays the applications of computational methods to model systems and discusses in detail molecular structures, the modelling of various properties of molecules and chemical reactions. Both ground and excited states properties are covered in the gas phase as well as in solution. This volume also describes Nanomaterials and covers topics such as clusters, periodic, and nano systems. Special emphasis is placed on the environmental effects of nanostructures.

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.

 

What people are saying - Write a review

We haven't found any reviews in the usual places.

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
Copyright

Other editions - View all

Common terms and phrases

About the author (2012)

Jerzy Leszczynski - Professor of Chemistry and President's Distinguished Fellow at the Jackson State University (JSU) joined the faculty of the JSU Department of Chemistry in 1990. Dr. Leszczynski attended the Technical University of Wroclaw (TUW) in Wroclaw, Poland obtaining his M.S (1972) and Ph.D. (1975) degrees. During the period 1976

-1986 he served as a faculty member at the TUW. In 1986 he moved to USA, initially as a visiting scientist at the University of Florida, Quantum Theory Project (1986-88) and as a research associate at the University of Alabama at Birmingham (1988-1990). During the period 1998 - 2008 Dr. Leszczynski had served as the director for the Computational Center for Molecular Structure and Interactions (NSF-CREST Center). Since October 2008 he directs new Interdisciplinary Nanotoxicity CREST Center at JSU. Dr. Leszczynski is a computational quantum chemist whose vast areas of interest include: nature of chemical bonds, theoretical predictions of molecular potential energy surfaces and vibrational spectra, structures and properties of molecules with heavy elements, properties and structure of DNA fragments, and characteristics of nanomaterials. He also applies computational chemistry methods to environmental problems, surface chemistry and atmospheric chemistry. Two areas of his research contributions are the most noticeable: investigations of DNA fragments and development of novel techniques for investigation of properties and toxicity of nanomaterials.