Among many
chemistry softwares, GChem Software
has its own importance. GChem is a part of GNOME ChemistryUtils
and it includes various applications like GChemPaint, GChem3D, GChemCalc,
GSpectrum etc. GChem is a
multi document application and is a bonobo server so that chemistry can be
embedded in other Gnome applications. GChemPaint application is a two dimensional chemical structures editor for
the GNOME2 desktop and allows for two-dimensional structural drawing;
GChem3D application is a three dimensional structure viewer; GChemCalc
application is a simple chemical calculator for molecular formula and for raw
formula calculations; GSpectrum application is a spectrum viewer. GCrystal
helps to edit and display crystalline structures. GChemTable is a chemistry
elements periodic table application. It is free and open online software
distributed under the GNU GPL license and written in C++ but does not use gtkmm. It can be used on Windows OS or LINUX OS. GChem
softwares are very useful for students, teachers, researchers, educators,
computational researchers.
KEYWORDS: GChemPaint;
GChem3D; GChemCalc; GSpectrum; GCrystal; GChemTable.
1. INTRODUCTION:
The Learning Effects of
Computer Simulations in Science Education has become very important for the
past few decades. In recent times, everyone in academics, research and teaching
have been using the World Wide Website evaluation
as an important tool in chemistry. Various transitions and transformations have
been observed nowadays from traditional methods to ICT-enhanced learning
environments in teaching undergraduate chemistry courses. Therefore, the use of
the web has become an essential part in UG teaching, exploring chemistry and resources on the Internet. The
use of visual basic applications
as teaching aids in chemistry are globally observed in industries research and
development wing to academics. With the advent of Computational Chemistry
and Online educational resources, chemistry softwares have become very
important in the lives of students, researchers, educators, tutors
computational chemists, physicist and biologists. The GUI uses multi document
mode and can be used to include some chemistry could be embedded in other GNOME Office applications like AbiWord
(requires version 2.6.0) using the GOffice component API. The Gnome Chemistry
Utils library provides include six chemistry related programs and provides
following widgets:
·
GChemPaint, a 2D chemical formula editor
for drawing the chemical structures.
·
GChemCalc, a chemical calculator (computes
raw formulae, molar weight, mass composition and isotopic pattern).
·
GChem3D, a molecule 3D viewer using OpenGL
to display molecular models.
·
GCrystal, a crystal structure editor and
viewer helps to edit and display crystalline structures.
·
GChemTable, a periodic table available as
a combo box for chemistry element.
·
GSpectrum a spectrum viewer for the
various spectroscopic and other techniques
These programs are based on included C++ libraries
which provide widgets and classes, some related to chemistry and some utility
classes.
1.
GChemPaint:
GChemPaint was developed by
Jean Bréfort in 2001. The GChemPaint application is a simple two dimensional chemical structure editor for Linux Operating
System allows us to draw and display 2D chemical structures. You can use
GChemPaint to create and edit chemistry related files.
It is free and open source software (FOSS) developed in 'C'. It is distributed
under GPL License. It is useful for students, teachers and teacher educators,
researchers.
Features
of GChemPaint:
· GChemPaint allows drawing and displaying
two dimensional chemical structures. Tool box contains various tools to draw
structures, bonds, orbitals and type text.
· It has inbuilt Templates with different
categories of structures to load into GChemPaint Display area.
· It has an inbuilt Modern Periodic Table.
· It supports multiple file formats like
.mol, .pdb, .svg, .pdf etc.
· It has an inbuilt Chemical Calculator to
calculate molecular weight of compounds.
· It helps to convert 2D structures to 3D
structures using GChem3D feature.
· In GChem3D, structures can be viewed in
Ball and sticks, Space filling, Cylinders and Wireframe.
· Periodic table trends and properties can
be shown using the GChemTable feature.
· Different types of charts can be created
and viewed using GChemTable.
Uses
of GChemPaint:
· It views mass spectrum of the molecule
using Chemical calculator.
· Change length, angle and width of the
bonds using Preferences window.
· Structures can be rotated in GChem3D.
· Magnification of structures, automatic
and manual assignment of atoms can be done in the window.
· We can drag and drop Templates and also
create new Templates.
· It allows using various residues and
creating new residues.
· It can group and align different objects
as one single object.
· We can view NIST Web Book page and
PubChem page for a molecule.
·
Images
can be used in print media, journals and publications.
Installation
of GChemPaint:
STEP 1-First
of all install GChemPaint by following the steps given in this sheet. This sheet gives the steps to install GChemPaint software
on Linux and Windows OS. Open the
sheet read the instructions for your OS and installs GChemPaint on your
machine. Cross-verify (as mentioned in the
sheet) to confirm successful installation.
STEP 2- Next the sheet explains how to learn from spoken tutorials.
This sheet also mentions some important information
about the text editors while coding, how to use the command prompt (in Windows
OS), how to use the Code Files, how to do the Assignments, etc. Read this sheet carefully and make a note of all the
information, before you begin.
STEP 3-Follow
the side-by-side learning methodology while learning from spoken tutorials -
watch the video, listen to the instructions, pause the video, try out the
command on your system. You should get the exact same results as shown in the
video. If successful, proceed with the
video. Else, rewind and watch the video again and replicate the commands shown.
Students from UG, PG
standard and research scholars as well as teachers, educators must be well
aware of the Basic level and Intermediate Level of GChemPaint.
Basic Level of
Knowledge about GChemPaint
Overview of
GChemPaint
Ø It helps in complete installation of
GChemPaint along with utility files and explains about GChemPaint User Manual.
Ø It Views Menubars of GChemPaint appears
on Ubuntu Desktop menubar.
Ø It explains about GChemPaint utility
softwares and what is the relation between GChemPaint and Jmol Application.
Ø It shows various structures that can be
drawn using GChemPaint.
Introduction to
GChemPaint
Ø It
explains about GChemPaint and uses and benefits of GChemPaint Installation
Ø It
explains how to open a new file and a new file from Terminal, about menu bar,
toolbar and status bar, about the display area, Document Properties window and
the use of Tool box items.
Ø It
explains how to Draw structures using "Add a Chain" tool and how to
Save the drawing with .gchempaint extension
Basic Operations
Ø It
explains that how to Open an existing file, addition and editing of text, selection and movement of objects, flipping and rotation of objects,
grouping and alignment of objects
Ø It
explains how to cut, copy and paste operations and Clear Display area
Ø It
explains how to use the Delete key to delete objects, use of "Eraser"
tool, use of Undo operation.
View, Print and
Export structures
Ø It
shows in View options, Zoom factor, How to setup a page and the preview of
structures in different orientations
Ø It
shows how to print the document and how to export the image in SVG and PDF
formats.
Edit Preferences,
Templates and Residues
Ø It
explains how to Edit Preferences, the types of Arrows.
Ø It
explain how to manage Templates, how to Select and use ready Templates and how
to add a New Template
Ø It
explains the Uses of Residues and how to Edit Residues and Add new residues
Formation of
Molecules
Ø It
explains how to change current element using Periodic table combo button and
how to change the current element using Keyboard
Ø It
explains about Alkyl groups, how to use of Add or modify a text tool, the
Demonstration of how to number the chain positions and how to Add and modify
carbon chain from straight chain to branched
Formation of
Bonds:
Ø It
explains how to Add bonds to the existing bond, how to convert saturated
hydrocarbons to unsaturated hydrocarbons
Ø It explains
to Learn about Tetrahedral geometry, how to Orient the bonds, Inverse wedge
hashes, the types of Stereo-chemical bonds and how to Add Stereo-chemical bonds
Editing
Molecules:
Ø It
explain how to Add unbound electrons on an atom and how to Draw Carbonic acid
and Sulphuric acid structures, how to Add and modify a local charge on an atom,
a local charge on a group of atoms
Ø It
explains the use of tools like
“Increment the charge of an atom” and “Decrement the charge of an atom”; how to
Add cyclic molecules and convert monocyclic molecules to bicyclic molecules
Intermediate Level
of Knowledge about GChemPaint:
Aromatic
Molecular structures:
Ø It
explains how to Draw Cyclohexane molecule and how to convert Cyclohexane to
Cyclohexene and how to convert Cyclohexene to Benzene and how to substitute
Hydrogen of Benzene ring with other atoms or with group of atoms
Ø It
explains how to use "Eraser" tool to delete part of the structure
Ø It
explains how to use Add or modify a group of atoms tool to substitute atoms or
how to use tool Merge to merge two molecules
Orbital Overlap
Ø It
explains About Atomic orbital, about different orbital figures, about shapes of
orbitals
Ø It
explains how to use “Add or modify an atomic orbital” tool
Ø It
also explains how to rotate and resize the orbitals, about the positive,
negative and zero overlaps, about the end-on and side-wise overlap.
Analysis of
Compounds:
Ø It
shows Molecular contextual menu, Use templates tool, Open web pages of the
molecule
Ø It
explains how to use Chemical Calculator, Show composition and Isotropic pattern
of the compound
Ø It
explains how to Save the molecule in ".mol" format, how to Open the
molecule in Molecules viewer, how to Add reaction conditions and reagents on
the reaction arrow Convert 2D structures to 3D structures.
Features of
GChem3D
Ø It
explains how to Open a file in GChem3D, where is Menu bar, About VRML document.
Ø It
shows how to Save image in different File types formats or in Model formats,
how to Change Background color.
Features and
Color Schemes
Ø
It
explains About GChemTable and how to open a new GChemTable window.
Ø It explains about Elemental window and how
to use different Color Schemes.
Charts in
GChemTable
Ø It
explains how to make Elemental Charts and how to create Customized Charts
Ø It
explains about “Graph hierarchy” tree, about “Graph preview”and various tabs
and drop downs
Resonance Structure
Ø It
shows electron shift of a pair of electons and show electron shift of an
electron
Ø It
explains how to attach a reaction criteria on the reaction arrow, how to Create
and Destroy a reaction pathway and Mesomeric pathway
Ø It
shows how to draw Resonance structures of Nitromethane and how to create a
Retrosynthetic pathway.
It
shows the images by GChemPaint structure editors, where Figure 1. shows a two
dimensional chemical editor area, Figure 2. shows the two different mesomers of
benzene, Figure 3. shows various tools in a tool box for drawing and editing
the chemical structures, Figure 4. shows the chemical reaction and Figure 5.
shows the retrosynthesis reaction.