COMPUTATIONAL CHEMISTRY: THEORIES, METHODS AND APPLICATIONS

COMPUTATIONAL CHEMISTRY: THEORIES, METHODS AND APPLICATIONS

Library of Congress Cataloging-in-Publication Data

Contents

Preface

Chapter 1: Protein Kinase-Targeting Drug Discovery and Design: Computational Chemistry As an Indispensable Tool

Abstract

1. Introduction

2. Binding Site Identification

3. Virtual Screening

3.1. Pharmacophore

3.2. Molecular Docking

3.2.1. Search Algorithm

3.2.2. Scoring Functions

4. Molecular Dynamics

5. Examples of Success

Conclusion

References

Chapter 2: Computational Chemistry Investigation of UV Filters

Abstract

1. Introduction

2. Computational Studies on UVF-DP

2.1. Cinnamates

2.2. Camphors

2.3. Benzophenones

2.4. Dibenzoylmethanes

2.5. Benzimidazoles

Conclusion

References

Chapter 3: Using the Network Simulation Method to Study Ionic Transport Processes in Electrochemical Cells

Abstract

1. Introduction

2. Theoretical Description

3. The Network Model

4. Results and Discussion

4.1. Chronoamperometric Response

4.2. Linear Sweep Voltammetry

4.3. Chronopotentiometric Response

4.4. Electrochemical Impedance

Conclusion

Appendix A

References

Chapter 4: Molecular Simulation of Electron Beam Nanofabrication

1Graduate School of Engineering, Osaka Prefecture University, Sakai, Japan

2National Institute of Technology, Toyama, Japan

Abstract

1. Introduction

2. Methodology

3. Simulation Results

3.1. Carbon Nanomaterials

3.1.1. Electron Irradiation Damages

3.1.2. Electron Beam Fabrication

3.1.3. Nanomechanics

3.2. Polymer Materials

3.2.1. Electron Beam Lithography

3.2.2. Pattern Shrinkage in Scanning Electron Microscopy

3.3. Silicon Oxide

Conclusion

Acknowledgment

References

Chapter 5: Interpretation of Chiral Ordering of Hybrid System of Several AZO Dyes and Chiral Schiff Base Co(II) Complex Induced by Circularly Polarized Light

Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku Tokyo, Japan

Abstract

Introduction

Experimental Section

Materials

Preparations of Bis (N-R-2-Phenlypropyl-Salicydenaminato) Cobalt(II) (Co)

Preparations of Hybrid Materials

Physical Measurements

Computational Methods

Results and Discussion

Computational Results

Linearly Polarized UV Light-Induced Molecular Arrangement

Linearly Polarized UV Light-Induced Molecular Arrangement for AZ+Co+PMMA

Circularly Polarized UV Light-Induced Molecular Arrangement

Examination of the Optical Rotation Strength by Coupled Oscillator Model

Conclusion

Acknowledgment

References

Chapter 6: A General Procedure for a Priori Calculation of Thermochemical Properties of Organic Molecules and Free Radicals

Abstract

Introduction

Theoretical Background

First Approximation (RRHO)

Higher Approximation: Hindered Internal Rotation

Occurrence of Multiple Conformations: Entropy of Mixing Correction

Computational Procedure

Calculation of the RRHO Properties

Calculation of the Hindered Rotation Contribution to Properties

Calculation of the Entropy of Mixing Correction

Results and Discussion

Haloalkyl Radicals

Alkyl and Alkyl Peroxy Radicals

Alkanes

C4-C6 Alkyl Radicals

Comparison with the Published Data

HR Calculation Parameters

Conclusion

Acknowledgment

References

Chapter 7: Strategies for Design of New Organic Molecular Rectifiers: Chemical and Molecular-Simulation Perspectives

1Chemistry Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh, Egypt

2Higher Institute of Engineering and Technology, Kafrelsheikh, Egypt

3The SEC Strategic Research Cluster and the Centre for Synthesis and Chemical Biology, School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin, Ireland

4Chemistry Department, Faculty of Science, El-Menoufia University, Shebin El-Kom, Egypt

Abstract

1. Introduction

2. Classification and Mechanism

Classification Based on Molecular Structure

Mechanism of Rectification

3. Experimental Observations for Molecular Rectifying Diodes

4. Theoretical and Simulation Aspects

Classification Based on the Mechanism of Molecular Rectification

Dual-Functional Device Combining Switch and Diode

Effects of Conformation

Anchor-Rectification Relationship

Conclusion

References

Chapter 8: DFT Studies of 8p,6p-Electrocyclizations of Benzooctatetraenes and Benzodecapentaenes

Abstract

1. Introduction - 8,6-Electrocyclizations

2. Consequences of Incorporation of the Octatetraene -System in the Aromatic Ring on the 8,6- Electrocyclizations of [3,4]-Benzo-(E,Z,Z,E)-1,3,5,7-Octatetraenes [42]

3. Influence of Substituents in 2-Position on 8,6- Electrocyclizations of 2-Substituted [3,4]-Benzo-(E,Z,Z,E)-1,3,5,7-Octatetraenes [53]

4. Influence of Aromatic Ring on 8,6- Electrocyclizations of [3,4]-Aryl-(E,Z,Z,E)-1,3,5,7-Octatetraenes [54]

Conclusion

References and Notes

Index