Practical aspects of computational chemistry V / Jerzy Leszczynski, Manoj K. Shukla, editors.

Format:

Book

Contributor:

Leszczynski, Jerzy, 1949- editor.

Shukla, Manoj, editor.

Language:

English

Subjects (All):

Chemistry, Physical and theoretical--Data processing.

Chemistry, Physical and theoretical.

Physical Description:

1 online resource (292 pages)

Other Title:

Practical aspects of computational chemistry 5

Practical aspects of computational chemistry five

Place of Publication:

Cham, Switzerland : Springer, [2022]

Summary:

This book presents contributions on a wide range of computational research applied to fields ranging from molecular systems to bulk structures. This volume highlights current trends in modern computational chemistry and discusses the development of theoretical methodologies, state-of-the-art computational algorithms and their practical applications. This volume is part of a continuous effort by the editors to document recent advances by prominent researchers in the area of computational chemistry. Most of the chapters are contributed by invited speakers and participants to International annual conference "Current Trends in Computational Chemistry", organized by Jerzy Leszczynski, one of the editors of the current volume. This conference series has become an exciting platform for eminent theoretical and computational chemists to discuss their recent findings and is regularly honored by the presence of Nobel laureates. Topics covered in the book include reactive force-field methodologies, coarse-grained modeling, DNA damage radiosensitizers, modeling and simulation of surfaces and interfaces, non-covalent interactions, and many others. The book is intended for theoretical and computational chemists, physical chemists, material scientists and those who are eager to apply computational chemistry methods to problems of chemical and physical importance. It is a valuable resource for undergraduate, graduate and PhD students as well as for established researchers.

Contents:

Intro

Preface

Contents

1 Introductory Roadmap to Current Reactive Force-Field Methodologies

1.1 Introduction

1.2 Bond Order Methodologies

1.3 Valence Bond Models

1.4 Parameterization

1.5 Other Reactive Methods

1.6 Conclusion

References

2 Physics-Based Coarse-Grained Modeling in Bio-and Nanochemistry

2.1 Introduction

2.2 Designing Coarse-Grained Models and Force Fields

2.2.1 Potential of Mean Force as the Origin of CG Force Fields

2.2.2 Derivation of CG Force Fields from PMF Surfaces

2.2.3 Solvent Treatment in CG Force Fields

2.2.4 Force-Field Parameterization

2.2.4.1 Direct Computation of PMF Surfaces

2.2.4.2 Force Matching

2.2.4.3 Iterative Boltzmann Inversion and Inverse Monte Carlo Iteration

2.2.4.4 Fitting Force-Field Parameters to Reproduce the Experimental Data

2.2.4.5 Calibration with Experimental Structures

2.3 Methods of Conformational Search

2.3.1 Canonical Monte Carlo

2.3.2 Molecular Dynamics

2.3.3 Extensions of MC and MD

2.3.4 Global Energy Minimization

2.3.5 Use of Geometrical Restraints in CG Simulations

2.3.5.1 Chemical Cross-Link Mass-Spectroscopy and Fluorescence Energy Transfer

2.3.5.2 Small Angle X-ray/Neutron Scattering

2.3.5.3 Mutagenesis and Hydrogen-Deuterium Exchange (HDX)

2.3.5.4 Nuclear Magnetic Resonance

2.3.6 Contact-Distance and Template-Based Restraints

2.4 Examples of Physics-Based CG Force Fields and Their Applications

2.4.1 AWSEM

2.4.2 MARTINI

2.4.3 OPEP and HiRe-RNA

2.4.4 oxDNA and oxRNA

2.4.5 SIRAH

2.4.6 UNICORN

2.4.7 Structure-Based and Elastic-Network Potentials

2.5 Conclusions and Outlook

3 First-Principles Modeling of Non-covalent Interactions in Molecular Systems and Extended Materials

3.1 Introduction

3.2 Theoretical Models of Non-covalent Interactions.

3.2.1 Modeling van der Waals Interactions

3.2.2 Quantum Chemical Approaches for Non-covalent Interactions

3.2.3 Dispersion Computations in DFT

3.2.4 Dispersion Computation Through MP2 and Higher Correlation Methods

3.3 Non-covalent Interactions in Hydrogen-Bonded (HB) Systems

3.3.1 Hydrogen Bonding and Related Properties of Small Water Clusters

3.3.2 Nature of O-H Stretching Modes

3.3.3 Effect of Halide Ion Interactions with Small Water Clusters

3.3.4 CTTS Properties of Halide-Water Clusters

3.3.5 Effect of Low-Frequency Vibrations of HBs in Fatty Acid Dimers and Their Amides

3.3.6 Empirical Additive Relations of ΔEB for Fatty Acid and Amide Dimers

3.4 Molecular Modeling of Strong and Weak Cation-π Interactions

3.5 Molecular Modeling of π-π Interactions

3.6 Modeling Non-covalent Interactions in Bio-inspired Supramolecular Systems

3.7 Conclusions

4 DNA Damage Radiosensitizers Geared Towards HydratedElectrons

4.1 Introduction

4.2 Nucleoside Derivatives: A Trojan Horse Approach to Radiotherapy

4.2.1 Modified Nucleosides as Radiosensitizers

4.2.2 Nucleoside Derivatives as Trojan Horses

4.2.3 Electron-Induced Degradation of Modified Nucleosides: Experimental Studies

4.3 Computational Studies on Nucleoside Radiosensitizers

4.3.1 5-Bromo-2-Deoxyuridine

4.3.2 Crucial Characteristic of Electron Attachment Process

4.3.3 Bromonucleobases

4.3.4 5-Substituted Uracils as Potential Radiosensitizers

4.3.5 A Need to Expand the Computational Model for Difficult Derivatives

4.4 Oxygen Mimetics

4.5 Metallic Nanoparticles and Metal Complexes

4.5.1 Possible Mechanisms of Radiosensitization

4.5.2 On the Role of Low Energy Electrons in the Radiosensitization of DNA by Metallic Nanoparticles and Complexes

4.5.3 Not only Gold Nanoparticles and Cisplatin

4.6 Summary.

References

5 Application of Computational Chemistry for Contaminant Adsorption on the Components of Soil Surfaces

5.1 Introduction

5.2 Density Functional Theory (DFT)

5.2.1 Preliminaries

5.2.2 Bloch Function

5.2.2.1 Bypassing Periodicity: Cluster Models

5.2.3 K-point Sampling

5.2.4 Density of States (DOS) and Analysis of Orbitals

5.2.5 Self-Interaction Errors

5.2.6 The Problem of Electron Correlation

5.2.7 Forces, Hellmann-Feynman Theorem, and Geometry Optimization

5.3 Case Study: Adsorption of Munitions in Soils

5.3.1 Binding Energies

5.3.2 Cluster Models and Electrochemical Properties

5.3.3 Comparison of Cluster and Periodic Surface Models

5.3.4 Lewis Acidity and Environmental Fate

5.3.5 Environmental Transport

5.4 Looking to the Future

5.4.1 Breathing New Life into an Old Method: Density Functional Tight Binding

5.4.2 Artificial Intelligence and Machine Learning (AI/ML)

5.4.2.1 Machine Learning and Energetics

5.4.2.2 AI/ML and DFT

5.5 Conclusions

6 Application of Computational Approaches to Analysis of Multistep Chemical Reactions of Energetic Materials: Hydrolysis of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine (RDX) and Octahydro-1,3,5,7-Tetranitro-1,3,5,7-Tetrazocine (HMX)

6.1 Introduction

6.1.1 Short Survey of Experimental Data on RDX Hydrolysis

6.1.2 Short Survey of Experimental Data of HMX Hydrolysis

6.2 Computational Modeling of Hydrolysis of RDX

6.2.1 Conformational Analysis of RDX Structure

6.2.2 Mechanism of RDX Alkaline Hydrolysis

6.2.3 Kinetics of RDX Alkaline Hydrolysis

6.2.4 Hydrolysis of HMX

6.2.4.1 Conformational Analysis of HMX Structure

6.2.4.2 Mechanism of HMX Alkaline Hydrolysis

6.2.4.3 Kinetics of HMX Alkaline Hydrolysis

6.2.5 Mechanism of 4-NDAB Decomposition Under Alkaline Conditions

6.3 Conclusion.

7 Dataset Modelability by QSAR: Continuous Response Variable

Abbreviations

7.1 Introduction

7.2 Methods

7.2.1 Datasets

7.2.1.1 Training Set Data

7.2.1.2 Test Set Data (14 Datasets)

7.2.2 Modelability Criteria

7.3 Results and Discussion

7.4 Conclusions

8 A Cluster Model for Interpretation of Surface-Enhanced Raman Scattering of Organic Compounds Interacting with Silver Nanoparticles

8.1 Introduction

8.2 Surface-Enhanced Raman Scattering (SERS) Experiment

8.2.1 General Aspects

8.2.2 Electromagnetic Mechanism of SERS (EM)

8.2.3 Chemical Enhancement Mechanism (CE)

8.2.4 Use of Silver Nanoparticles in SERS Applications

8.3 Geometrical and Electronic Structures of Silver Clusters

8.4 Detection of Single Molecules Using SERS Technique

8.5 Concluding Remarks

Index.

Notes:

Includes bibliographical references and index.

Description based on print version record.

ISBN:

3-030-83244-9

OCLC:

1283860008