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More About This Textbook
Overview
THIS VOLUME, LIKE THOSE PRIOR TO IT, FEATURES CHAPTERS BY EXPERTS IN VARIOUS FIELDS OF COMPUTATIONAL CHEMISTRY. TOPICS COVERED IN VOLUME 20 INCLUDE VALENCE THEORY, ITS HISTORY, FUNDAMENTALS, AND APPLICATIONS; MODELING OF SPINFORBIDDEN REACTIONS; CALCULATION OF THE ELECTRONIC SPECTRA OF LARGE MOLECULES; SIMULATING CHEMICAL WAVES AND PATTERNS; FUZZY SOFTCOMPUTING METHODS AND THEIR APPLICATIONS IN CHEMISTRY; AND DEVELOPMENT OF COMPUTATIONAL MODELS FOR ENZYMES, TRANSPORTERS, CHANNELS, AND RECEPTORS RELEVANT TO ADME/TOX.
FROM REVIEWS OF THE SERIES
"Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."
JOURNAL OF MOLECULAR GRAPHICS AND MODELING
"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
Recent advances in ligand design methods, current issues in de novo molecular design, etc.
Editorial Reviews
From the Publisher
“The editors have done an excellent job and the book is a must on every book shelf of computational chemistry literature.” (ChemPhysChem, 2005; Vol. 6; 7)"…this volume continues the traditions and standards of this series as a prime resource for anyone with an interest in theoretical and computational chemistry…a welcome addition to any library collection." (Journal of the American Chemical Society, March 9, 2005)
Scientific Computing World
...certainly a book that should be considered as an essential component for any complete natural science library.SciTech Book News
Describes computational chemistry tools useful for molecular design and other research applications.SciTech Book News
Describes computational chemistry tools useful for molecular design and other research applications.From The Critics
The field of computational chemistry is defined by Lipkowitz and Boyd (chemistry, Indiana U.Purdue U. at Indiana) as those aspects of chemical research that are rendered practical by computers. In a volume dedicated to late colleagues, the editors compile tutorials in the areas of small molecule docking (as both a design and virtual screening tool) and scoring, proteinprotein docking, spinorbit coupling in molecules, and cellular automata models of aqueous solution systems. A compilation of books published on topics in this field is appended, augmented by a table of relevant journals and book series. The index denotes computer programs, databases, and journals. An ancillary website is available. These reviews have been ranked fourth in impact among serials in the field. Annotation c. Book News, Inc., Portland, OR (booknews.com)Booknews
Aimed at both the novice molecular modeler and the expert computational chemist, five chapters discuss how molecular modeling of peptidomimetics plays a key role in drug discovery with examples of successful computeraided drug design; thermodynamic perturbation and thermodynamic integration approaches in molecular dynamic simulations; and molecular modeling of carbohydrates, the best empirical force fields to use in molecular mechanics, and molecular shape as a useful quantitative descriptor. Annotation c. by Book News, Inc., Portland, Or.Booknews
In four lengthy chapters, tutorials and reviews cover how to obtain simple chemical insight and concepts from density functional theory calculations; strategies for modeling photochemical reactions and excited states; how to compute enthalpies of formation of molecules; and the history of the growth of computational chemistry in Canada (earlier volumes in the series provided similar histories for the US, Great Britain, and France). The preface pays tribute to the Quantum Chemistry Program Exchange (QCPE) and briefly discusses information sources for chemists. Annotation c. Book News, Inc., Portland, OR (booknews.com)Product Details
Related Subjects
Meet the Author
Kenny B. Lipkowitz and Raima Larter are Professors of Chemistry at Indiana University  Purdue University at Indianapolis. Tom Cundari is Professor of Chemistry at the University of Memphis.
Read an Excerpt
Reviews in Computational Chemistry, Volume 19
John Wiley & Sons
Copyright © 2003
Kenny B. Lipkowitz, Raima Larter, Thomas R. Cundari
All right reserved.
ISBN: 0471235857
Chapter One
INTRODUCTION
This chapter is written for the reader who would like to learn how
Monte Carlo methods are used to calculate thermodynamic properties of systems
at the atomic level, or to determine which advanced Monte Carlo methods
might work best in their particular application. There are a number of
excellent books and review articles on Monte Carlo methods, which are generally
focused on condensed phases, biomolecules or electronic structure theory.
The purpose of this chapter is to explain and illustrate some of the
special techniques that we and our colleagues have found to be particularly
well suited for simulations of nanodimensional atomic and molecular clusters.
We want to help scientists and engineers who are doing their first work in this
area to get off on the right foot, and also provide a pedagogical chapter for
those who are doing experimental work. By including examples of simulations
of some simple, yet representative systems, we provide the reader with some
data for direct comparison when writing their own code from scratch.
Although a number of Monte Carlo methods in current use will be
reviewed, this chapter is not meant to be comprehensive in scope.Monte Carlo
is a remarkably flexible class of numerical methods. So many versions of the
basic algorithms have arisen that we believe a comprehensive review would be
of limited pedagogical value. Instead, we intend to provide our readers with
enough information and background to allow them to navigate successfully
through the many different Monte Carlo techniques in the literature. This
should help our readers use existing Monte Carlo codes knowledgably, adapt
existing codes to their own purposes, or even write their own programs. We
also provide a few general recommendations and guidelines for those who are
just getting started with Monte Carlo methods in teaching or in research.
This chapter has been written with the goal of describing methods that
are generally useful. However, many of our discussions focus on applications
to atomic and molecular clusters (nanodimensional aggregates of a finite number
of atoms and/or molecules). We do this for two reasons:
1. A great deal of our own research has focused on such systems,
particularly the phase transitions and other structural transformations induced by
changes in a cluster's temperature and size, keeping an eye on how various
properties approach their bulk limits. The precise determination of thermodynamic
properties (such as the heat capacity) of a cluster type as a function of
temperature and size presents challenges that must be addressed when using
Monte Carlo methods to study virtually any system. For example, analogous
structural transitions can also occur in phenomena as disparate as the denaturation
of proteins. The modeling of these transitions presents similar
computational challenges to those encountered in cluster studies.
2. Although cluster systems can present some unique challenges, their
study is unencumbered by many of the technical issues regarding periodic
boundary conditions that arise when solids, liquids, surface adsorbates, and
solvated biomolecules and polymers are studied. These issues are addressed
well elsewhere, and can be thoroughly appreciated and mastered once
a general background in Monte Carlo methods is obtained from this chapter.
It should be noted that "Monte Carlo" is a term used in many fields of
science, engineering, statistics, and mathematics to mean entirely different
things. The one (and only) thing that all Monte Carlo methods have in common
is that they all use random numbers to help calculate something. What we
mean by "Monte Carlo" in this chapter is the use of randomwalk processes
to draw samples from a desired probability function, thereby allowing one to
calculate integrals of the form [integral] dqf(q) [rho](q). The quantity [rho](q) is a normalized
probability density function that spans the space of a manydimensional
variable q, and f(q) is a function whose average is of thermodynamic importance
and interest. This integral, as well as all other integrals in this chapter,
should be understood to be a definite integral that spans the entire domain of
q. Finally, we note that the inclusion of quantum effects through pathintegral
Monte Carlo methods is not discussed in this chapter. The reader interested in
including quantum effects in Monte Carlo thermodynamic calculations is
referred elsewhere.
METROPOLIS MONTE CARLO
Monte Carlo simulations are widely used in the fields of chemistry, biology,
physics, and engineering in order to determine the structural and thermodynamic
properties of complex systems at the atomic level. Thermodynamic
averages of molecular properties can be determined from Monte Carlo methods,
as can minimumenergy structures. Let (f) represent the average value
of some coordinatedependent property f(x), with x representing the 3N
Cartesian coordinates needed to locate all of the N atoms. In the canonical
ensemble (fixed N, V and T, with V the volume and T the absolute temperature),
averages of molecular properties are given by an average of f(x) over the
Boltzmann distribution
(f) = [integral] dxf(x)exp[[beta]U(x)]/[integral]dx exp[[beta]U(x)] [1]
where U(x) is the potential energy of the system, [beta] = 1/[k.sub.B]T, and [k.sub.B] is the
Boltzmann constant. If one can compute the thermodynamic average of
f(x) it is then possible to calculate various thermodynamic properties. In
the canonical ensemble it is most common to calculate E, the internal energy,
and [C.sub.v] , the constantvolume heat capacity (although other properties can be
calculated as well). For example, if we average U(x) over all possible configurations
according to Eq. [1], then E and [C.sub.v] are given by
E = 3N[k.sub.B]T/2 + (U) [2]
[C.sub.v] = 3N[k.sub.B]/2 + ([U.sup.2])  [(U).sup.2]/([k.sub.B][T.sup.2]) [3]
The first term in each equation represents the contribution of kinetic energy,
which is analytically integrable. In the harmonic (lowtemperature) limit, E
given by Eq. [2] will be a linear function of temperature and [C.sub.v] from Eq. [3]
will be constant, in accordance with the Equipartition Theorem. For a small
cluster of, say, 6 atoms, the integrals implicit in the calculation of Eqs. [1]
and [2] are already of such high dimension that they cannot be effectively computed
using Simpson's rule or other basic quadrature methods. For
larger clusters, liquids, polymers or biological molecules the dimensionality
is obviously much higher, and one typically resorts to either Monte Carlo,
molecular dynamics, or other related algorithms.
To calculate the desired thermodynamic averages, it is necessary to have
some method available for computation of the potential energy, either explicitly
(in the form of a function representing the interaction potential as in
molecular mechanics) or implicitly (in the form of direct quantummechanical
calculations). Throughout this chapter we shall assume that U is known or can
be computed as needed, although this computation is typically the most computationally
expensive part of the procedure (because U may need to be computed
many, many times). For this reason, all possible measures should be
taken to assure the maximum efficiency of the method used in the computation
of U.
Also, it should be noted that constraining potentials (which keep the
cluster components from straying too far from a cluster's center of mass)
are sometimes used. At finite temperature, clusters have finite vapor pressures,
and particular cluster sizes are typically unstable to evaporation. Introducing
a constraining potential enables one to define clusters of desired sizes.
Because the constraining potential is artificial, the dependence of calculated
thermodynamic properties on the form and the radius of the constraining
potential must be investigated on a casebycase basis. Rather than diverting
the discussion from our main focus (Monte Carlo methods), we refer the
interested reader elsewhere for more details and references on the use of constraining
potentials.
RandomNumber Generation: A Few Notes
Because generalized Metropolis Monte Carlo methods are based on
"random" sampling from probability distribution functions, it is necessary
to use a highquality randomnumber generator algorithm to obtain reliable
results. A review of such methods is beyond the scope of this chapter,
but a few general considerations merit discussion.
Randomnumber generators do not actually produce random numbers.
Rather, they use an integer "seed" to initialize a particular "pseudorandom"
sequence of real numbers that, taken as a group, have properties that leave
them nearly indistinguishable from truly random numbers. These are conventionally
floatingpoint numbers, distributed uniformly on the interval (0,1). If
there is a correlation between seeds, a correlation may be introduced between
the pseudorandom numbers produced by a particular generator. Thus, the
generator should ideally be initialized only once (at the beginning of the random
walk), and not reinitialized during the course of the walk. The seed
should be supplied either by the user or generated arbitrarily by the program
4 Strategies for Monte Carlo Thermodynamic Calculations
using, say, the number of seconds since midnight (or some other arcane formula).
One should be cautious about using the "builtin" randomnumber
generator functions that come with a compiler for Monte Carlo integration
work because some of them are known to be of very poor quality. The
reader should always be sure to consult the appropriate literature and obtain
(and test) a highquality randomnumber generator before attempting to write
and debug a Monte Carlo program.
The Generalized Metropolis Monte Carlo Algorithm
The Metropolis Monte Carlo (MMC) algorithm is the single most widely
used method for computing thermodynamic averages. It was originally developed
by Metropolis et al. and used by them to simulate the freezing transition
for a twodimensional hardsphere fluid. However, Monte Carlo methods can
be used to estimate the values of multidimensional integrals in whatever context
they may arise. Although Metropolis et al. did not present their algorithm
as a generalutility method for numerical integration, it soon became
apparent that it could be generalized and applied to a variety of situations.
The core of the MMC algorithm is the way in which it draws samples from
a desired probability distribution function. The basic strategies used in
MMC can be generalized so as to apply to many kinds of probability functions
and in combination with many kinds of sampling strategies. Some authors
refer to the generalized MMC algorithm simply as "Metropolis sampling,"
while others have referred to it as the M(RT) method in honor of the five
authors of the original paper (Metropolis, the Rosenbluths, and the Tellers).
We choose to call this the generalized Metropolis Monte Carlo (gMMC) method,
and we will always use the term MMC to refer strictly to the combination
of methods originally presented by Metropolis et al.
In the literature of numerical analysis, gMMC is classified as an importance
sampling technique. Importance sampling methods generate configurations
that are distributed according to a desired probability function rather
than simply picking them at random from a uniform distribution. The probability
function is chosen so as to obtain improved convergence of the properties
of interest. gMMC is a special type of importance sampling method which
asymptotically (i.e., in the limit that the number of configurations becomes
large) generates states of a system according to the desired probability distribution.
This probability function is usually (but not always) the actual
probability distribution function for the physical system of interest. Nearly
all statisticalmechanical applications of Monte Carlo techniques require the
use of importance sampling, whether gMMC or another method is used (alternatively,
"stratified sampling" is sometimes an effective approach).
gMMC is certainly the most widely used importance sampling method.
In the gMMC algorithm successive configurations of the system are
generated to build up a special kind of random walk called a Markov
chain. The random walk visits successive configurations, where each
configuration's location depends on the configuration immediately preceding
it in the chain. The gMMC algorithm establishes how this can be done so as
to asymptotically generate a distribution of configurations corresponding to
the probability density function of interest, which we denote as [rho](q).
We define K([q.sub.j] > [q.sub.j) to be the conditional probability that a
configuration at [q.sub.i] will be brought to [q.sub.j] in the next step of the random walk. This conditional
probability is sometimes called the "transition rate." The probability
of moving from q to [q'] (where q and [q'] are arbitrarily chosen configurations
somewhere in the available domain) is therefore given by P(q > [q'):
P(q > [q') = K(q > [q')[rho](q) [4]
For the system to evolve toward a unique limiting distribution, we must place
a constraint on P(q > [q']). The gMMC algorithm achieves the desired limiting
behavior by requiring that, on the average, a point is just as likely to move
from q to [q'] as it is to move in the reverse direction, namely, that
P(q > [q') = P([q'] > q). This likelihood can be achieved only if the walk is
ergodic (an ergodic walk eventually visits all configurations when started
from any given configuration) and if it is aperiodic (a situation in which no
single number of steps will generate a return to the initial configuration).
This latter requirement is known as the "detailed balance" or the "microscopic
reversibility" condition:
K(q > [q'])[rho](q) = K([q'] > q)[rho]([q']) [5]
Satisfying the detailed balance condition ensures that the configurations
generated by the gMMC algorithm will asymptotically be distributed according
to [rho](q).
The transition rate may be written as a product of a trial probability
and an acceptance probability A
K([q.sub.i] > [q.sub.j]) = [PI]([q.sub.i] > [q.sub.j])A([q.sub.i] > [q.sub.j]) [6]
where [PI] can be taken to be any normalized distribution that asymptotically
spans the space of all possible configurations, and A is constructed so that
Eq. [5] is satisfied for a particular choice of [PI].
Continues...
Table of Contents
1. Valence Bond Theory, Its History, Fundamentals, and Applications: A Primer (Sason Shaik and Philippe C. Hiberty).
Introduction.
A Story of Valence Bond Theory, Its Rivalry with Molecular Orbital Theory, Its Demise, and Eventual Resurgence.
Roots of VB Theory.
Origins of MO Theory and the Roots of VB–MO Rivalry.
The ‘‘Dance’’ of Two Theories: One Is Up, the Other Is Down.
Are the Failures of VB Theory Real Ones?
Modern VB Theory: VB Theory Is Coming of Age.
Basic VB Theory.
Writing and Representing VB Wave Functions.
The Relationship between MO and VB Wave Functions.
Formalism Using the Exact Hamiltonian.
Qualitative VB Theory.
Some Simple Formulas for Elementary Interactions.
Insights of Qualitative VB Theory.
Are the ‘‘Failures’’ of VB Theory Real?
Can VB Theory Bring New Insight into Chemical Bonding?
VB Diagrams for Chemical Reactivity.
VBSCD: A General Model for Electronic Delocalization and Its Comparison with the PseudoJahn–Teller Model.
What Is the Driving Force, s or p, Responsible for the D6h Geometry of Benzene?
VBSCD: The TwinState Concept and Its Link to Photochemical Reactivity.
The Spin Hamiltonian VB Theory.
Theory.
Applications.
Ab Initio VB Methods.
OrbitalOptimized SingleConfiguration Methods.
OrbitalOptimized Multiconfiguration VB Methods.
Prospective.
Appendix.
A.1 Expansion of MO Determinants in Terms of AO Determinants.
A.2 Guidelines for VB Mixing.
A.3 Computing MonoDeterminantal VB Wave Functions with Standard Ab Initio Programs.
Acknowledgments.
References.
2. Modeling of SpinForbidden Reactions (Nikita Matsunaga and Shiro Koseki).
Overview of Reactions Requiring Two States.
SpinForbidden Reaction, Intersystem Crossing.
Spin–Orbit Coupling as a Mechanism for SpinForbidden Reaction.
General Considerations.
Atomic Spin–Orbit Coupling.
Molecular Spin–Orbit Coupling.
Crossing Probability.
Fermi Golden Rule.
Landau–Zener Semiclassical Approximation.
Methodologies for Obtaining Spin–Orbit Matrix Elements.
Electron Spin in Nonrelativistic Quantum Mechanics.
Klein–Gordon Equation.
Dirac Equation.
Foldy–Wouthuysen Transformation.
Breit–Pauli Hamiltonian.
Z^{eff} Method.
Effective Core PotentialBased Method.
Model Core PotentialBased Method.
Douglas–Kroll Transformation.
Potential Energy Surfaces.
Minimum Energy CrossingPoint Location.
Available Programs for Modeling SpinForbidden Reactions.
Applications to SpinForbidden Reactions.
Diatomic Molecules.
Polyatomic Molecules.
Phenyl Cation.
Norborene.
Conjugated Polymers.
CH(^{2}II) + N2 — HCN + N(^{4}S).
Molecular Properties.
Dynamical Aspects.
Other Reactions.
Biological Chemistry.
Concluding Remarks.
Acknowledgments.
References.
3. Calculation of the Electronic Spectra of Large Molecules (Stefan Grimme).
Introduction.
Types of Electronic Spectra.
Types of Excited States.
Theory.
Excitation Energies.
Transition Moments.
Vibrational Structure.
Quantum Chemical Methods.
Case Studies.
Vertical Absorption Spectra.
Circular Dichroism.
Vibrational Structure.
Summary and Outlook.
Acknowledgments.
References.
4. Simulating Chemical Waves and Patterns (Raymond Kapral).
Introduction.
Reaction–Diffusion Systems.
Cellular Automata.
Coupled Map Lattices.
Mesoscopic Models.
Summary.
References.
5. Fuzzy SoftComputing Methods and Their Applicationsin Chemistry (Costel Saˆrbu and Horia F. Pop).
Introduction.
Methods for Exploratory Data Analysis.
Visualization of HighDimensional Data.
Clustering Methods.
Projection Methods.
Linear Projection Methods.
Nonlinear Projection Methods.
Artificial Neural Networks.
Perceptron.
Multilayer Nets: Backpropagation.
Associative Memories: Hopfield Net.
SelfOrganizing Map.
Properties.
Mathematical Characterization.
Relation between SOM and MDS.
Multiple Views of the SOM.
Other Architectures.
Evolutionary Algorithms.
Genetic Algorithms.
Canonical GA.
Evolution Strategies.
Evolutionary Programming.
Fuzzy Sets and Fuzzy Logic.
Fuzzy Sets.
Fuzzy Logic.
Fuzzy Clustering.
Fuzzy Regression.
Fuzzy Principal Component Analysis (FPCA).
Fuzzy PCA (Optimizing the First Component).
Fuzzy PCA (Nonorthogonal Procedure).
Fuzzy PCA (Orthogonal).
Fuzzy Expert Systems (Fuzzy Controllers).
Hybrid Systems.
Combinations of Fuzzy Systems and Neutral Networks.
Fuzzy Genetic Algorithms.
NeuroGenetic Systems.
Fuzzy Characterization and Classification of the Chemical Elements and Their Properties.
Hierarchical Fuzzy Classification of Chemical Elements Based on Ten Physical Properties.
Hierarchical Fuzzy Classification of Chemical Elements Based on Ten Physical, Chemical, and Structural Properties.
Fuzzy Hierarchical CrossClassification of Chemical Elements Based on Ten Physical Properties.
Fuzzy Hierarchical Characteristics Clustering.
Fuzzy Horizontal Characteristics Clustering.
Characterization and Classification of Lanthanides and Their Properties by PCA and FPCA.
Properties of Lanthanides Considered in This Study.
Classical PCA.
Fuzzy PCA.
Miscellaneous Applications of FPCA.
Fuzzy Modeling of Environmental, SAR and QSAR Data.
Spectral Library Search and Spectra Interpretation.
Fuzzy Calibration of Analytical Methods and Fuzzy Robust Estimation of Location and Spread.
Application of Fuzzy Neural Networks Systems in Chemistry.
Applications of Fuzzy Sets Theory and Fuzzy Logic in Theoretical Chemistry.
Conclusions and Remarks.
References.
6. Development of Computational Models for Enzymes, Transporters, Channels, and Receptors Relevant to ADME/Tox (Sean Ekins and Peter W. Swaan).
Introduction.
ADME/Tox Modeling: An Expansive Vision.
The Concerted Actions of Transport and Metabolism.
Metabolism.
Transporters.
Approaches to Modeling Enzymes, Transporters, Channels, and Receptors.
Classical QSAR.
Pharmacophore Models.
Homology Modeling.
Transporter Modeling.
Applications of Transporters.
The Human Small Peptide Transporter, hPEPT1.
The Apical SodiumDependent Bile Acid Transporter.
PGlycoprotein.
Vitamin Transporters.
Organic Cation Transporter.
Organic AnionTransporters.
Nucleoside Transporter.
Breast Cancer Resistance Protein.
Sodium Taurocholate Transporting Polypeptide.
Enzymes.
Cytochrome P450.
Epoxide Hydrolase.
Monoamine Oxidase.
FlavinContaining Monooxygenase.
Sulfotransferases.
Glucuronosyltransferases.
Glutathione Stransferases.
Channels.
Human Etheragogo Related Gene.
Receptors.
Pregnane XReceptor.
Constitutive Androstane Receptor.
Future Developments.
Acknowledgments.
Abbreviations.
References.
Author Index.
Subject Index.