international journal of chem-informatics research vol 2 issue 1
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International Journal of
Cheminformatics Research
IJCR
Jan – Jun 2016
Mechanical Engineering
Electronics and Telecommunication Chemical Engineering
Architecture
Office No-4, 1 Floor, CSC, Pocket-E,Mayur Vihar, Phase-2, New Delhi-110091, India
E-mail: info@journalspub.com
¬ International Journal of Thermal Energy andApplications
¬ International Journal of Production Engineering¬ International Journal of Industrial Engineering
and Design¬ International Journal of Manufacturing and
Materials Processing¬ International Journal of Mechanical Handling and
Automation
« International Journal of Radio Frequency Design« International Journal of VLSI Design and Technology« International Journal of Embedded Systems and Emerging
Technologies« International Journal of Digital Electronics« International Journal of Digital Communication and Analog
Signals
« International Journal of Housing and Human SettlementPlanning
« International Journal of Architecture and InfrastructurePlanning
« International Journal of Rural and Regional PlanningDevelopment
« International Journal of Town Planning and Management
Applied Mechanics
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Computer Science and Engineering « International Journal of Wireless Network Security« International Journal of Algorithms Design and Analysis« International Journal of Mobile Computing Devices« International Journal of Software Computing and Testing« International Journal of Data Structures and Algorithms
Nanotechnology« International Journal of Applied Nanotechnology« International Journal of Nanomaterials and Nanostructures« International Journals of Nanobiotechnology
« International Journal of Solid State Materials« International Journal of Optical Sciences
Physics
« International Journal of Renewable Energy and itsCommercialization
« International Journal of Environmental Chemistry« International Journal of Agrochemistry« International Journal of Prevention and Control of Industrial
Pollution
Civil Engineering« International Journal of Water Resources Engineering« International Journal of Concrete Technology« International Journal of Structural Engineering and Analysis« International Journal of Construction Engineering and
Planning
Electrical Engineering« International Journal of Analog Integrated Circuits« International Journal of Automatic Control System« International Journal of Electrical Machines & Drives« International Journal of Electrical Communication
Engineering« International Journal of Integrated Electronics Systems and
Circuits
Material Sciences and Engineering « International Journal of Energetic Materials« International Journal of Bionics and Bio-Materials« International Journal of Ceramics and Ceramic Technology« International Journal of Bio-Materials and Biomedical
Engineering
Chemistry « International Journal of Photochemistry« International Journal of Analytical and Applied Chemistry« International Journal of Green Chemistry« International Journal of Chemical and Molecular
Engineering
« International Journal of Electro Mechanics andMechanical Behaviour
« International Journal of Machine Design andManufacturing
« International Journal of Mechanical Dynamicsand Analysis
« International Journal of Fracture and damageMechanics
« International Journal of Structural Mechanicsand Finite Elements
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Biotechnology « International Journal of Industrial Biotechnology and
Biomaterials« International Journal of Plant Biotechnology« International Journal of Molecular Biotechnology« International Journal of Biochemistry and Biomolecules« International Journal of Animal Biotechnology and
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International Journal of
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Focus and Scope of the Journal! Chemical databases! Drug discovery! Computer-assisted synthesis design! Computer-assisted molecular design! Organizing chemical facts into databases! Molecular modeling! Structure generators! Modeling 3D structures! Database mining! Graph mining! Molecule mining! Sequence mining! Digital libraries
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Commissioning Editors
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EDITORIAL BOARD MEMBERS
Dr. Yogesh Kumar SharmaSwami Shraddhanand College, Department of
Chemistry, University of Delhi, New Delhi, India
Dr. Monika GuptaDepartment of Chemistry,
University of Jammu, Jammu, India
Dr. P. V. SinghDepartment of Chemistry, Institute of
Technology & Management,Uttar Pradesh, India
Dr. Sandeep RaiDepartment of Chemistry/Polymer and Rubber,
Shroff S.R. Rotary Institute of Chemical Technology, Gujarat, India
Dr. Kishore DasariNavin Fluorine International Limited,
India
Dr. Kaman SinghDepartment of Chemistry (DST-FIST-PURSE Sponsored) Centre of Excellence (U.P. Govt., UGC-DRS (I) –SAP Sponsored Department)Faculty of Science, University of Lucknow,
Lucknow, India
Dr. Ajit Manharlal BhavsarDishman Pharmaceuticals and Chemicals
Limited, Ahmedabad, India
Dr. Satyabrata MohapatraEmami Limited, India
Dr. Susarla Venkata Ananta Rama SastryMVGR College of Engineering, Vizianagaram,
Andhra Pradesh, India
From the Editor's Desk
Dear Readers,
We would like to present, with great pleasure, the inaugural volume of a new scholarly
journal, International Journal of Cheminformatics Research. This journal is part of the
Applied Sciences, and is devoted to the scope of present chemical synthesis and chemical
reactions issues, from theoretical aspects to application-dependent studies and the validation of emerging
technologies.
This new journal was planned and established to represent the growing needs of Cheminformatics Research
as an emerging and increasingly vital field, now widely recognized as an integral part of scientific and
technical investigations. Its mission is to become a voice of the Cheminformatics Research Science
community, addressing researchers and practitioners in this area.
The core vision of International Journal of Cheminformatics Research in Journals Pub is to propagate novel
awareness and know-how for the profit of mankind ranging from the academic and professional research
societies to industry practitioners in a range of topics in Chem-informatics Research in general. Journals
Pub acts as a pathfinder for the scientific community to published their papers at excellently, well-time &
successfully.
International Journal of Cheminformatics Research focuses on original high-quality research in the realm
of Chemical databases, Drug discovery, Computer-assisted synthesis design, Computer-assisted molecular
design, Structure generators, Modeling 3D structures, Database mining, Digital libraries and many more.
Many scientists and researchers have contributed to the creation and the success of the Cheminformatics
Research community. We are very thankful to everybody within that community who supported the idea of
creating an innovative platform. We are certain that this issue will be followed by many others, reporting
new developments in the field of Cheminformatics Research.
This issue would not have been possible without the great support of the Editorial Board members, and we
would like to express our sincere thanks to all of them. We would also like to express our gratitude to the
editorial staff of JournalsPub, who supported us at every stage of the project.
It is our hope that this fine collection of articles will be a valuable resource for Cheminformatics Research
readers and will stimulate further research into the vibrant area of Cheminformatics Research.
Puneet Mehrotra
Managing Director
1. Calculation of pK Values of Alkanolamines – A DFT-B3LYP Computational Analysisa
V.K. Rajan, K. Muraleedharan 1
2. An Introduction to Homology Modeling Bharat Singh 9
3. Molecular Modeling: An OverviewSona Chahal 11
4. Chemical Database and Its Types: Brief ReviewBharat Singh 13
5. Data Mining and Drug DiscoveryShivani Sharma 15
Contents
IJCR (2016) 1–8 © JournalsPub 2016. All Rights Reserved Page 1
International Journal of Cheminformatics Research
Vol. 2: Issue 1
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Calculation of pKa Values of Alkanolamines – A DFT-B3LYP
Computational Analysis
V.K. Rajan, K. Muraleedharan* Department of Chemistry, University of Calicut, Malappuram, India
Abstract
Greenhouse effect, an important environmental concern today, is particularly due to the
emission of carbon dioxide. Removal of CO2 and its storage called carbon dioxide capture
and storage (CCS) is thus a noble area in research. Many experimental works are done in
this area to screen a suitable solvent for CCS. But the experimental measurements on pKa
values, free energy values, enthalpy values, etc. are very difficult and have less accuracy. The
present work employs a computational analysis to predict the pKa values of alkanolamines, a
suitable candidate for CCS. The poly-functionality makes the alkanolamines as an
industrially important molecule. A DFT-B3LYP level of theory was employed on different
alkanolamines with 6-31+G (d, p) as basis set. Since most of the reactions starts with
protonation or deprotonation reaction, the study of acid dissociation constants, i.e., the pKa
values is very useful. The pKa values of alkanolamines are of importance that they play a
major role in explaining the mechanism of carbon dioxide capture by them. Different
alkanolamine molecules including primary, secondary, and tertiary are studied. The present
method uses the free energy calculation to get the pKa values of alkanolmines. The linear
relationship of the pKa value with the free energy of protonation is verified. Also computed
the gas phase basicity and gas phase proton affinity of different alkanolamines. The structure
of alkanolamin molecule has an effect on their pKa value and this determines the trend in
their pKa values. They have pKa values less than that of corresponding alkylamines. The
hydrogen bonding, sterric effect, etc. have major role in the pKa values of different
alkanolamines. All the values are computed except the Gibb’s free energy (in gas phase and
in solution phase) and the enthalpy values of proton (in gas phase), which is taken from the
literature. The gas phase basicity and gas phase proton affinity are also varied with the
structure of different alkanolamine molecules. The method employed is simple and the results
are in good agreement with the experimental results. The study can further extended to the
temperature dependence of pKa values, as the postcombustion of CCS has temperature
dependence and to screen suitable candidates for carbon dioxide removal.
Keywords: alkanolamines, density functional theory, gas phase basicity, pKa values, proton
affinity
INTRODUCTION
A large amount of anthropogenic
greenhouse gases are being emitted to the
atmosphere at an increased rate. This
results in an increased atmospheric
temperature and become a great threat to
both human beings and the environment.
Carbon dioxide (CO2), a major greenhouse
gas, partakes about 60% of global
warming. This makes the removal of CO2
from gas streams and thereby reducing the
atmospheric CO2 concentration, an
IJCR (2016) 9–10 © JournalsPub 2016. All Rights Reserved Page 9
International Journal of Cheminformatics Research Vol. 2: Issue 1
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An Introduction to Homology Modeling
Bharat Singh Maharshi Dayanand University, Rohtak, Uttar Pradesh, India
‘Homology modeling’, also known as
comparative modeling or template-based
modeling (TBM) refers to modeling a
protein three-dimensional structure using a
known experimentally determined
structure of a homologous protein as a
template. Identifying the protein structure
has been the ultimate goal in protein
modeling studies. Knowing the protein
structure assists in the study of protein
function and dynamics, generating in silico
protein models, structure-based drug
design, interaction with other ligands,
antigenic behavior and rational designing.
Homology modeling gives the researchers
and scientists the structural information of
proteins in situations when experimental
techniques fail. Many proteins are simply
too large for NMR analysis and cannot be
crystallized for X-ray diffraction. Also, it
provides the molecular biologists and
biochemists with ‘low-resolution’
structures, containing information about
the spatial arrangement of important
residues in the protein macromolecules.
Such information helps in designing of
new set of experiments. As an example,
the design of site-directed mutagenesis
experiments can be significantly
improvised using low-resolution model
structures.
The method of homology modeling is
based on two basic observations:
1. The structure of any protein molecule
is uniquely determined by its amino
acid sequence. So, once the sequence
is known, it would be easier to obtain
the protein structure.
2. Protein structures are believed to be
conserved in nature. During evolution,
the structures are considered more
stable and changes at a much slower
rate than the associated sequences.
This implies that similar sequences
adapt identical structures while
distantly related sequences fold into
similar structures.
Steps involved in homology modeling
include:
1. Identification of the template.
2. Amino acid sequence alignment.
3. Alignment correction.
4. Generation of backbone.
5. Loop generation.
6. Generation and optimization of side
chains.
7. ab initio loop building.
8. Overall model optimization.
9. Final verification of model, quality
criteria and model quality.
Once the template is selected, next step is
to make a multiple sequence alignment
which includes the desired sequence,
sequence of the template and few other
protein sequences belonging to the same
family of proteins. This gives an overview
of the general characteristics of that
protein family including the degree of
conservation, consensus sequence motifs,
secondary structure prediction, etc.
After the sequence analysis is done, and
the alignment is corrected, the next step is
modeling the protein structure. Modeling
softwares are available that will thread the
desired sequence on the template structure
and creates a preliminary model (the
backbone) of the protein in question. Some
of the servers for modeling are: Swiss
IJCR (2016) 11–12 © JournalsPub 2016. All Rights Reserved Page 11
International Journal of Cheminformatics Research Vol. 2: Issue 1
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Molecular Modeling: An Overview
Sona Chahal Department of Electrical and Electronics, Lord Krishna College of Engineering, Ghaziabad, Uttar Pradesh, India
Molecular modeling has now become
today’s one of the hottest themes for drug
discovery and design tools. It has become
an integral part of determining, explaining,
and predicting the properties of small
organic compounds for potential drug
candidates. It has become a valuable and
essential tool to medicinal chemists for the
drug designing process. Molecular
modeling involves a range of
computerized techniques based on
theoretical chemistry methods and
experimental data to predict and determine
the molecular and biological properties.
Molecular Modeling Tools
The tools for molecular modeling have
evolved considerably from physical
models and calculators to computers as
visualization aids, computers running
commercially written analysis packages
and most recently integration using
internet based tools and work benches
based on HTML, Java Script, etc.
Now-a-days, the tools used for drug
modeling using computers include:
hardware and software components.
Modeling Strategies
Two most commonly used modeling
strategies include: direct drug design and
indirect drug design.
Direct Drug Design
In this direct approach, the 3-D features of
the known receptor site are determined
from X-ray crystallography and a lead
molecule is designed. In direct design
method, the receptor site geometry is
already known, and the problem is to find
a molecule that fulfills some geometric
constraints and is also a good chemical
match. After finding ideal candidates
according to these criteria, a docking step
with energy minimization can be used to
predict binding strength.
Indirect Drug Design
The indirect drug design approach
involves comparative analysis of structural
features of the already known active and
inactive molecules that are complementary
with a hypothetical receptor site. If the site
geometry is not known, as is often the
case, the designer must base the design on
other ligand molecules that bind well to
the site.
Applications of Molecular Modeling
The starting point for many computer
assisted molecular modeling studies is
generally a two-dimensional drawing of a
required molecule. Then the two-
dimensional structures are transformed
into three-dimensional representations to
study chemical properties. Various
applications of computer assisted
molecular modeling techniques are
reviewed here.
Generation of Chemical Structures
The 3D structures of molecules can be
created by several common building
functions including create-bond, break-
bond, fuserings, delete-atom, add-atom-
hydrogens, invest chiral center, etc.
Computer modeling allows chemists to
build dynamic models of molecules or
compounds which in turn allow them to
visualize molecular geometry and
demonstrate chemical principles.
IJCR (2016) 13–14 © JournalsPub 2016. All Rights Reserved Page 13
International Journal of Cheminformatics Research Vol. 2: Issue 1
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Chemical Database and Its Types: Brief Review
Bharat Singh*
Maharshi Dayanand University, Rohtak, Haryana, India
Abstract
Chemical database is a powerful branch of cheminformatics research and development, the
chief function of which is storing, indexing and searching of information related to chemical
compounds and reaction synthesis using computer science and information technology.
Computer-based representation of chemicals makes it possible to organize data in chemical
databases-collections of chemical structures and associated properties. The typical kinds of
information found in a chemical database are considered-identification, structural, and
associated data. Here, in this brief review, an outline of the objective of chemical databases
and their types is described.
INTRODUCTION
Chemical databases are an important tool
in the field of cheminformatics research
and development. Cheminformatics is that
discipline of science that uses the
techniques of computer science and
informational skills to address a range of
problems in the field of chemistry.[1,2]
The
aim of cheminformatics is to develop
novel techniques foe collection and
manipulation of chemical information as
well as to develop algorithms for
discoveries and predictions from chemical
databases.
A chemical database is a database that is
especially designed to store chemical
information. The chemical information
collected and stored in chemical databases
can be in the form of a structure, spectra,
chemical process or reaction, chemical
synthesis, information on data analysis
from analytical chemistry to make
predictions on the quality, physical,
chemical or biological properties of
compounds, thermodynamical process,
thermophysical, etc.[2-4]
The use of such
information technology has become an
important part of cheminformatics
research.
Types of Chemical Database
Several types of chemical databases are
available depending upon the particular
type of chemical data stored in them.
These include:
Chemical structure database: This
type of chemical databases store
chemical structures and constitutes
molecular geometry, electronic
structure and crystal structure of
molecules. Such databases are capable
to handle the storage and searching of
information on millions of molecules.
ChemSpider is an example of such
type of database.
Literature database: A literature
database stores the chemical data in
context to structures and other
chemical information in relation to
relevant references such as those in
academic papers or patents. Examples
are the STN (Scientific and technical
information network), Reaxys and
Scifinder databases.[4,5]
IJCR (2016) 15–16 © JournalsPub 2016. All Rights Reserved Page 15
International Journal of Cheminformatics Research Vol. 2: Issue 1
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Data Mining and Drug Discovery
Shivani Sharma* Department of Bio Pharma Sciences, C.G.C Gharuan, Mohali, Punjab, India
Abstract
Today, drug discovery makes use of cheminformatics research to overcome the drawbacks
and shortcomings of traditional drug discovery procedure. Cheminformatics utilizes
computer information technology to solve and answer the wide range of queries and
problems in the field of chemistry. With the aid of data mining, data is collected relating
chemical structures to each other. This has proven beneficial in the area of drug discovery
and designing. Here, in this short communication, the use of data mining in context to drug
discovery and its step-by-step procedure is briefed.
INTRODUCTION
Designing new drugs for targeting specific
diseases requires extensive research and
analysis of several bioactive molecules or
chemical compounds that can be used as
ideal candidates as drugs. One approach
towards achieving this objective is to
analyze a database of known and tested
molecules in order to find structural
properties that determine whether the
molecule will be active or inactive, so that
future chemical tests can be focused on the
most promising candidates.[1]
Data mining
generates large numbers of related
chemical compounds that can be used for
drug designing.
Also, if the biological effects of different
molecules are known one can combine
them to make chemicals with desired
biological outcomes.
The data mining technique, also called as
‘Clustering Process’, divides the databases
of unknown drugs in clusters based on
their similarity.[1,2]
The clusters of
unknown but similar drugs are assessed
and compared with the clusters of some
particular such as HIV drugs to discover
from unknown drugs those drugs that are
similar in properties with the already
known and available drugs.
For better understanding, let us first try to
know the steps involved in drug discovery
process.
Data Pre-processing: This defines the
initial pre-processing steps of the data.
Data Selection: In this step, the data to be
used is selected based on its previously
known information and potential to yield
desired product. The selected data sources
are referred as data marts which are then
used in discovery process. Results are
highly dependent on the target dataset;
therefore care should be taken in selecting
the data.[2,3]
Data Integration: At this stage, the entire
multiple data sources are combined in a
common source called the data warehouse.
The data warehouse is the place where all
the data is centralized. The data stored in
the data warehouse possess certain
characteristics viz. they should be time-
dependent, non-volatile, subject orientated
and integrated.
International Journal of
Cheminformatics Research
IJCR
Jan – Jun 2016
Mechanical Engineering
Electronics and Telecommunication Chemical Engineering
Architecture
Office No-4, 1 Floor, CSC, Pocket-E,Mayur Vihar, Phase-2, New Delhi-110091, India
E-mail: info@journalspub.com
¬ International Journal of Thermal Energy andApplications
¬ International Journal of Production Engineering¬ International Journal of Industrial Engineering
and Design¬ International Journal of Manufacturing and
Materials Processing¬ International Journal of Mechanical Handling and
Automation
« International Journal of Radio Frequency Design« International Journal of VLSI Design and Technology« International Journal of Embedded Systems and Emerging
Technologies« International Journal of Digital Electronics« International Journal of Digital Communication and Analog
Signals
« International Journal of Housing and Human SettlementPlanning
« International Journal of Architecture and InfrastructurePlanning
« International Journal of Rural and Regional PlanningDevelopment
« International Journal of Town Planning and Management
Applied Mechanics
5 more...
1 more...
2 more...2 more...
5 more...
Computer Science and Engineering « International Journal of Wireless Network Security« International Journal of Algorithms Design and Analysis« International Journal of Mobile Computing Devices« International Journal of Software Computing and Testing« International Journal of Data Structures and Algorithms
Nanotechnology« International Journal of Applied Nanotechnology« International Journal of Nanomaterials and Nanostructures« International Journals of Nanobiotechnology
« International Journal of Solid State Materials« International Journal of Optical Sciences
Physics
« International Journal of Renewable Energy and itsCommercialization
« International Journal of Environmental Chemistry« International Journal of Agrochemistry« International Journal of Prevention and Control of Industrial
Pollution
Civil Engineering« International Journal of Water Resources Engineering« International Journal of Concrete Technology« International Journal of Structural Engineering and Analysis« International Journal of Construction Engineering and
Planning
Electrical Engineering« International Journal of Analog Integrated Circuits« International Journal of Automatic Control System« International Journal of Electrical Machines & Drives« International Journal of Electrical Communication
Engineering« International Journal of Integrated Electronics Systems and
Circuits
Material Sciences and Engineering « International Journal of Energetic Materials« International Journal of Bionics and Bio-Materials« International Journal of Ceramics and Ceramic Technology« International Journal of Bio-Materials and Biomedical
Engineering
Chemistry « International Journal of Photochemistry« International Journal of Analytical and Applied Chemistry« International Journal of Green Chemistry« International Journal of Chemical and Molecular
Engineering
« International Journal of Electro Mechanics andMechanical Behaviour
« International Journal of Machine Design andManufacturing
« International Journal of Mechanical Dynamicsand Analysis
« International Journal of Fracture and damageMechanics
« International Journal of Structural Mechanicsand Finite Elements
5 more...4 more...
3 more...
Biotechnology « International Journal of Industrial Biotechnology and
Biomaterials« International Journal of Plant Biotechnology« International Journal of Molecular Biotechnology« International Journal of Biochemistry and Biomolecules« International Journal of Animal Biotechnology and
Applications3 more...
Nursing « International Journal of Immunological Nursing« International Journal of Cardiovascular Nursing« International Journal of Neurological Nursing« International Journal of Orthopedic Nursing« International Journal of Oncological Nursing
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