Computational Chemistry: Theories, Methods and Applications

217 Pages·2014·5.294 MB·English

by  Daria Bove

CHEMISTRY RESEARCH AND APPLICATIONS

C C
OMPUTATIONAL HEMISTRY

T , M
HEORIES ETHODS
A
AND PPLICATIONS

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C R
HEMISTRY ESEARCH
A
AND PPLICATIONS

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CHEMISTRY RESEARCH AND APPLICATIONS

C C
OMPUTATIONAL HEMISTRY

T , M
HEORIES ETHODS
A
AND PPLICATIONS

DARIA BOVE
EDITOR

New York
Copyright © 2014 by Nova Science Publishers, Inc.

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Library of Congress Cataloging-in-Publication Data

Computational chemistry : theories, methods and applications / [edited by] Daria Bove.
pages cm. -- (Chemistry research and applications)
Includes bibliographical references and index.
ISBN: (cid:28)(cid:26)(cid:27)(cid:16)(cid:20)(cid:16)(cid:25)(cid:22)(cid:22)(cid:21)(cid:20)(cid:16)(cid:22)(cid:25)(cid:28)(cid:16)(cid:21) (eBook)
1. Chemistry--Data processing. 2. Cheminformatics. I. Bove, Daria, editor.
QD39.3.E46C628 2014
541.0285--dc23
2014022559

Published by Nova Science Publishers, Inc. † New York
CONTENTS

Preface vii
Chapter 1 Protein Kinase-Targeting Drug Discovery
and Design: Computational Chemistry
As an Indispensable Tool 1
Pedro M. M. Araújo, Luís Pinto da Silva
and Joaquim C. G. Esteves da Silva
Chapter 2 Computational Chemistry Investigation
of UV Filters 23
Paulo J. O. Ferreira, Luís Pinto da Silva,
Margarida S. Miranda
and Joaquim C.G. Esteves da Silva
Chapter 3 Using the Network Simulation Method to Study
Ionic Transport Processes in Electrochemical Cells 43
A. A. Moya
Chapter 4 Molecular Simulation of Electron
Beam Nanofabrication 63
Masaaki Yasuda and Kazuhiro Tada
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 85
Nobumitsu Sunaga, Shohei Furuya, Maiko Ito,
Chigusa Kominato and Takashiro Akitsu
vi Contents
Chapter 6 A General Procedure for a Priori Calculation
of Thermochemical Properties of Organic
Molecules and Free Radicals 105
Arijit Bhattacharya, Yuvraj Dangat
and Kumar Vanka
Chapter 7 Strategies for Design of New Organic
Molecular Rectifiers: Chemical and
Molecular-Simulation Perspectives 143
Morad M. El-Hendawy, Niall J. English
and Ahmed M. El-Nahas
Chapter 8 DFT Studies of 8,6-Electrocyclizations
of Benzooctatetraenes and Benzodecapentaenes 167
Davor Margetić, Iva Jušinski and Irena Škorić
Index 195
PREFACE

This book begins with a discussion on the protein kinase targeting drug
discovery and design. It continues with topics on computational chemistry
investigation of UV filters; using the network simulation method to study ionic
transport processes in electrochemical cells; molecular simulation of electron
beam nanofabrication; interpreting of chiral ordering of hybrid system of
several AZO dyes; a general procedure for a priori calculation of
thermochemical properties of organic molecules and free radicals; strategies
for design of new organic molecular rectifiers; and DFT studies.
Chapter 1 – The development of new drugs always was time consuming
and costly. With the development in experimental methods was possible to
scan small-compounds libraries in order to find potentially suitable molecules.
Nevertheless, these methods are able to so with a very low rate. Protein
kinases are a class of enzymes involved in the great majority of cellular
process. Due to its presence in many signal pathways, cell cycle and gene
expression control mechanisms, this class is one of the major targets for
pharmaceutical industries today. Aiming the reduction of time and costs in
drug development computational tools started to be used, and commonly
called Computer aided drug design (CADD). These methods can be separated
in two different types of approaches, structure based (SBDD) and ligand based
(LBDD). In order to use structure based methods, information about the 3D
structure of the target is needed, normally obtained through x-ray
crystallography or NMR. Ligand based methods are preferred when this
information is not available. The focus of the present chapter is the structure
based methods used in the computer drug discovery and design process
targeting kinases. Starting with the visual and energetic analysis of the binding
site, it is obtained enough information for the creation of a Pharmacophore
model and the application of Virtual Screening process. The results of the
viii Daria Bove
screening can then be analysed through Molecular Docking process followed
by Molecular Dynamics in order to better simulate the real binding conditions.
The obtained complexes can be analysed using energy calculations, in order to
better understand the binding process. Within the described procedures,
computational tools originate a great amount of useful information since hit
discovery from lead optimization. The data obtained can save time and reduce
costs in the process of drug design and discovery in a large scale.
Chapter 2 – The raising level of awareness regarding the harmful effects
of solar radiation has resulted in an increase in the production and use of
sunscreens. These commercial products contain ultraviolet (UV) filters that
absorb, reflect or scatter UV radiation (290-320 nm for UVB and 320-400 nm
for UVA) therefore preventing sunburn, photo-aging and ultimately skin
diseases such as skin cancer. A high screening efficiency can only be
guaranteed if a UV filter has a high photo-stability. However, UV filters are
known to undergo degradation upon exposure to sunlight and chemical
substances used in water disinfection such as chlorine, leading to the formation
of undesirable byproducts with properties different from the parent
compounds. This chapter presents a comprehensive review on the
computational studies performed so far on the structural, electronic, energetic
and UV absorption properties of some of the most widely used UV-filters and
their degradation products (UVF-DP). Ab initio and density functional theory
(DFT) methods have been used to obtain the molecular structure, energetics
and other molecular properties of UVF-DP. UV-Vis absorption spectra and
excited state properties have been calculated using the time dependent density
functional theory (TD-DFT). The influence of different solvents in these
properties has been studied using solution models. Transformation and
degradation mechanisms have been established with the aid of computational
methods and results indicate that these can be employed to assess the
environmental fate of UV-filters.
Chapter 3 – The network simulation method is used to numerically study
the steady-state, transient and small-signal ac responses of a binary electro-lyte
solution placed between two electrodes. The ionic transport processes in the
solution are described by the Nernst-Planck and Poisson equations, while the
interfacial charge transfer processes are characterized by the Chang-Jaffé
equations. The chronoamperometric, chronopotentiometric, linear sweep
voltammetric, and small-signal ac responses of symmetric cells, the cation
being the only electroactive species at both electrodes, are simulated on the
basis of an only network model. The main advanta-ges of the network
simulation method with respect to other electrochemi-cal numerical methods,