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E-grāmata: Reviews in Computational Chemistry, Volume 32

Edited by (University of Memphis, TN), Edited by (Office of Naval Research, Arlington, VA, USA)
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REVIEWS IN COMPUTATIONAL CHEMISTRY

THE LATEST VOLUME IN THE REVIEWS IN COMPUTATIONAL CHEMISTRY SERIES, THE INVALUABLE REFERENCE TO METHODS AND TECHNIQUES IN COMPUTATIONAL CHEMISTRY

Reviews in Computational Chemistry reference texts assist researchers in selecting and applying new computational chemistry methods to their own research. Bringing together writings from leading experts in various fields of computational chemistry, Volume 32 covers topics including global structure optimization, time-dependent density functional tight binding calculations, non-equilibrium self-assembly, cluster prediction, and molecular simulations of microphase formers and deep eutectic solvents. In keeping with previous books in the series, Volume 32 uses a non-mathematical style and tutorial-based approach that provides students and researchers with easy access to computational methods outside their area of expertise.

The chapters comprising Volume 32 are connected by two themes: methods that can be broadly applied to a variety of systems, and special considerations required when modeling specific system types. Each in-depth chapter contains background and theory, strategies for using the methods correctly, mini-tutorials and best practices, and critical literature reviews highlighting advanced applications. Essential reading for both newcomers and experts in the area of molecular modeling, this state-of-the-art resource:

  • Covers topics such as non-deterministic global optimization (NDGO) approaches and excited-state dynamics calculations
  • Contains a detailed overview of deep eutectic solvents (DESs) and simulation methods
  • Presents methodologies for investigating chemical systems that form microphases with periodic morphologies such as lamellae and cylinders
  • Features step-by-step tutorials on applying techniques to probe and understand the chemical dynamics exhibited in a system
  • Includes detailed subject indices on each volume in the series and up-to-date compendiums of molecular modeling software, services, programs, suppliers, and other useful information

Reviews in Computational Chemistry, Volume 32 is a must-have guide for computational chemists, theoretical chemists, pharmaceutical chemists, biological chemists, chemical engineers, researchers in academia and industry, and graduate students involved in molecular modeling.

List of Contributors
ix
Preface xi
Contributors to Previous Volumes xv
1 Non-Deterministic Global Structure Optimization: An Introductory Tutorial
1(44)
Bernd Hartke
List of abbreviations
1(1)
Introduction
2(1)
The Need for Structural Optimization
2(1)
Search Space is Vast
3(2)
Deterministic vs Non-Deterministic Search
5(3)
Fundamental Take-Home Lessons
8(1)
A Closer Look at Some NDGO Background Details
8(1)
Too Inspired by Nature
8(3)
No Free Lunch
11(3)
NDGO Algorithm Comparisons
14(1)
Barrier Crossing
15(4)
Old vs New Machine Learning
19(1)
Take-Home Lessons for NDGO Background Details
20(1)
General Guidelines for NDGO Applications
21(1)
Brief Summary of Some Fundamental NDGO Algorithm Ideas
21(1)
NDGO Method Design Choices
22(6)
NDGO Tips for Absolute Beginners
28(3)
Things to Do, and Pitfalls to Avoid
31(1)
Recent Highlights
32(2)
References
34(11)
2 Density Functional Tight Binding Calculations for Probing Electronic-Excited States of Large Systems
45(36)
Sharma S.R.K.C. Yamijala
Ma. Belen Oviedo
Bryan M. Wong
Introduction
45(1)
Real-Time Time-Dependent DFTB (RT-TDDFTB)
46(1)
Theory and Methodology
46(3)
Tutorial on RT-TDDFTB Electron Dynamics for a Naphthalene Molecule
49(1)
Absorption Spectrum for Naphthalene
49(2)
Electron Dynamics of Naphthalene with a Laser-Type Perturbation
51(1)
RT-TDDFTB Electron Dynamics of a Realistic Large Systems
51(8)
DFTB-Based Nonadiabatic Electron Dynamics
59(1)
Adiabatic vs Nonadiabatic Dynamics
59(2)
Equations Governing Nonadiabatic Electron Dynamics
61(1)
The Classical Path Approximation
62(1)
Surface Hopping and Fewest Switches Criterion
63(2)
Implementation Details of CPA-FSSH-DFTB
65(2)
Post-processing Tools
67(1)
Computational Details
67(1)
An Example on Charge Transfer Dynamics in Organic Photovoltaics
68(4)
Conclusion and Outlook
72(1)
Acknowledgments
72(1)
References
73(8)
3 Advances in the Molecular Simulation of Microphase Formers
81(54)
Patrick Charbonneau
Kai Zhang
Introduction
81(2)
Block Copolymers
83(1)
Surfactants and Microemulsions
84(3)
Lattice Spin Systems
87(1)
Colloidal Suspensions
87(3)
Other Examples
90(1)
Field Theory of Microphase Formation
90(1)
Molecular Simulations and Challenges
91(2)
Simulating Periodic Microphases
93(1)
Expanded Thermodynamics
94(1)
Thermodynamic Integration for Microphases
95(5)
Ghost Particle/Cluster Switching Method
100(3)
Cluster Volume Moves
103(2)
Determining Phase Transitions
105(1)
Simulations of Disordered Microphases
106(1)
Wolff-Like Cluster Algorithms
106(1)
Virtual Cluster Moves
107(2)
Aggregation Volume Biased (AVB) Moves
109(1)
Morphological Crossovers in the Disordered Regime
110(2)
Microphase Formers Solved by Molecular Simulations
112(1)
One-Dimensional Models
112(1)
Lattice Spin Models
113(4)
Colloidal Models
117(1)
Conclusion
118(1)
Free Energy of an Ideal Gas in a Field
119(1)
Constant pressure Simulations of Particles in A Field
120(1)
Virial Coefficients of Particles in a Field
120(2)
Acknowledgments
122(1)
References
122(13)
4 Molecular Simulations of Deep Eutectic Solvents: A Perspective on Structure, Dynamics, and Physical Properties
135(66)
Shalini J. Rukmani
Brian W. Doherty
Orlando Acevedo
Coray M. Colina
Introduction
135(2)
Deep Eutectic Solvents
137(1)
Definition of Deep Eutectic Solvents
137(1)
DES as Ionic Liquid Analogues
137(3)
Molecular Structure of DESs and Type of Interactions
140(2)
Types of DES
142(1)
Molecular Simulation Methods
143(2)
An Overview of Ab Initio Methods
145(4)
Classical Molecular Dynamics at the Atomic Level
149(4)
Nonpolarizable Force Fields used for DES Simulations
153(6)
Physical Properties
159(1)
Liquid Density
159(3)
Volume Expansivity
162(1)
Surface Tension
162(2)
Thermodynamic Properties
164(1)
Heat Capacity
164(4)
Heats of Vaporization
168(1)
Isothermal Compressibility
169(1)
Transport Properties
170(1)
Viscosity
170(8)
Diffusion Coefficients
178(5)
Deep Eutectic Solvent Structure
183(1)
Radial Distribution Functions
183(6)
Hydrogen Bond Analysis
189(7)
Spatial Distribution Functions
196(1)
Application of DES Through Simulation
196(1)
Gas Sorption Studies on DES
196(2)
DES Interactions at Metal Surfaces
198(1)
Proteins in DES
199(1)
Summary
200(1)
Acknowledgments 201(1)
References 201(16)
Index 217
ABBY L. PARRILL, PhD, is Professor of Chemistry in the Department of Chemistry and Dean of the College of Arts and Sciences at the University of Memphis. Her research interests are in bioorganic chemistry, protein modeling, NMR Spectroscopy, and rational ligand design and synthesis. She has given more than 100 presentations and authored numerous papers and books.

KENNY B. LIPKOWITZ, PhD, was one of the founding co-editors of Reviews in Computational Chemistry. He spent 28 years as an academician and then moved to the Office of Naval Research, where he is currently a Program Manager in Computer-Aided Materials Design.