international journal of chem-informatics research vol 2 issue 1

International Journal of

Cheminformatics Research

IJCR

Jan – Jun 2016

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Engineering

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International Journal of Cheminformatics Research aims to serve as a platform for the propagation of

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mining in the chemical field. Cheminformatics can also be used in chemical and allied industries in several

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editorial team to ensure the publication of only good quality papers.

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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Technology & Management,Uttar Pradesh, India

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Shroff S.R. Rotary Institute of Chemical Technology, Gujarat, India

Dr. Kishore DasariNavin Fluorine International Limited,

India

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Lucknow, India

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Limited, Ahmedabad, India

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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.

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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

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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


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

http://www.mdurohtak.ac.in/

IJCR (2016) 11–12 © JournalsPub 2016. All Rights Reserved


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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.



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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]

http://www.mdurohtak.ac.in/



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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.



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: [email protected]

¬ 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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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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