Computer Applications In

Chemistry 2nd Lec

BY: Sadia Haq

Introduction
ChemDraw is a drawing
program that allow the users
to sketch skeletal structure of
chemical compounds which
can then be moved into other
programs like MS-word,
PowerPoint etc. It also allows
to draw chemical structures
and reactions as well as
biological objects and
pathways.
 When starting the ChemDraw program, a
new blank document or a previously used
document opens. In addition to the window
on which to draw, a vertical palette of tools
(“Main Toolbar”) on the left, a main menu
bar at the top of the screen and additional
toolbars below it (usually the General
Toolbar and the Style Toolbar) appear. If
toolbars are missing, they can be activated
from the pull-down menu under “View” in
the main menu bar.
Features of chemdraw
Structure making
• You can draw any structure by using main
toolbar options according to your choice.
You can draw rings, Fischer projections,
Newman projections etc.
• If you want the bond angles and lengths to
be fixed, navigate to Object>Fixed
Lengths and Fixed Angles. This ensures
that bond lengths and bond angles are
consistent throughout the structure.
To create bonds:
 Navigate to View>Show
Main Toolbar.
 On the Main toolbar, select
the Solid Bond tool.
 Click in the document
window. A bond appears.
 To add a second bond, click
the right-end of the bond
you just created. You can
create the rings or structures
from main toolbar by using
the same way.
Features of chemdraw
Cleanup Structure:
The structure cleanup command in chemdraw
is used to neaten the appearance of molecules
by regularizing bond lengths and angles. You
can use structure cleanup to redraw structures
that you may have drawn freehand or to
neaten structures that you may have imported
from other application. If you select only a
part of a structure when you choose structure
cleanup, the other atoms and bonds are not be
effected
 Using structure cleanup
 Select the structure or a part of
the structure you want to cleanup
with a selection tool.
 From the structure menu, choose
structure cleanup.
Convert name to structure and
structure to name
You can convert your structures into their
respective names and can get structures of the
compounds or molecules by inserting their
names on ChemDraw professional. You can
also find the structures of the compounds by
their common or trivial names. ChemDraw
provides stereochemically correct structure
and accurate IUPAC name for structures.
 How to convert?
Structure to name
• Draw the structure of compound or molecule
you want to know the name
• Select the drawn structure, click on “structure
“ icon and convert the structure into name.
Name to structure
• Insert the name of compound you want to
convert into structure by using menu bar and
get the structure you want.
Chemical properties and analysis

You can display the chemical formula, exact

mass, molecular weight, m/z, and elemental
analysis for the entire document, a structure, or
a part of a structure using the Analysis window.
Values for selected objects in the document
window are shown. If no structure is selected
in your document, values for the entire
document are shown. You can have this
window open as you draw in the document.
To open the analysis window:
• Select the entire structure, or part of the
structure. If nothing is selected, the analysis
window displays value for the entire structure.
• Navigate to View>Show Analysis Window. The
analysis windows displays values for the parts
of the drawing you select, or the entire drawing
if nothing is selected.
• (Optional) Select Paste to add the analysis
information to your drawing. The information
appears as a caption that you can edit.
Fragmentation analysis
Mass fragmentation mimics the molecular
fragmentation in a mass spectrometer. When you
apply the mass fragmentation tool to a structure,
you cut through the structure, severing its bonds,
and creating fragments from the original
structure. This is not a predictive tool, you must
specify what bonds are to be broken. To
fragment a structure, use the Mass
Fragmentation Tool to drag the cursor across
one or more bonds. When you release the mouse
button, bonds that you cross are broken.
Data base searches
You can use SciFinder as your search engine for
data and can easily access you data by using
ChemDraw. You can copy your data from your
searches and then can paste easily on your
document in ChemDraw. SciFinder is a research
discovery application created by CAS
(Chemical Abstract Services) that provides
integrated access to the world's most
comprehensive and authoritative source of
references, substances, and reactions in
chemistry and related sciences
NMR prediction
Using ChemNMR, you can estimate and display
proton and Carbon-13 chemical shifts for a
selected molecule. As with ChemDraw, you can
also use Chem3D to predict NMR. Chem3D
includes several interfaces to computational
chemistry packages which predict NMR. Some
packages predict IR spectra and other spectra as
well. ChemNMR estimates chemical shifts for
all hydrogen or carbon atoms for which
additivity rules are available. Following a
hierarchical list, it first identifies key
substructures of a molecule. A substructure
provides the base value for the estimated shift.
To view H or C
NMR
information:
• Select a structure.
• Navigate to
Structure>Predict
1H-NMR Shifts or
Predict 13C-NMR
Shifts.
TLC plate image
The TLC (Thin Layer Chromatography)Tool
lets you depict thin layer chromatography plates.
The tool creates a rectangular plate with an
origin line, solvent front, and one or more lanes.
The lanes can be populated with spots of
different Rf, size, shape, or color. You can
modify the plate as ;Change the height or width
of the plate, Move the origin or solvent front,
Change the order of lanes, Move a spot, Delete a
spot, Change the style or color of a spot etc.
To create a TLC plate:
 Select the TLC tool from the
Chromatography toolbar.
 Drag in any direction from the point of
origin. The width of the plate determines the
number of lanes.
Bio art
ChemDraw includes a variety of tools for
drawing metabolic pathways, such as enzymes
and receptors. To display the BioDraw toolbars,
navigate to View>Show BioDraw Toolbar. You
can also include standard shapes, such as,
circles, ellipses, and arrows, using the Drawing
Elements tool palette or the Arrows tool palette.
You can also create custom shapes using the
Curve tool. You can change the color of an
object, change its line and fill properties, and
rotate it.
Other chemical properties
Other chemical properties like molecular charges,
atomic orbitals, free radicals and individual
electrons can also be drawn by using chemdraw.
You draw orbitals so that the node appears first.
Then you can change the background color,
shading, and solid color using the Color menu.
You can move any attached chemical symbol
(other than H-dot and H-dash) any distance from
its related atom. Use the lone pair symbol to
indicate a lone pair of electrons common in
Lewis structures.
To use the lone pair symbol:
• Hold down the mouse button over the
Chemical Symbols tool and drag to select
the lone pair from the palette.
• Click and drag the atom to where you
want the lone pair. The lone pair is offset
from the atom at a fixed position.
 Use the radical symbol to indicate a single
non-bonded electron.
To use the radical symbol:
• Hold down the mouse button over the
Chemical Symbols tool and drag to select
the radical from the palette.
• Click and drag the atom to where you
want the radical symbol.
To draw a charge and associate
it with a structure:
• Hold down the mouse button over the
Chemical Symbols tool and drag to select
the charge symbol from the palette.
• Click and drag the atom to which you
want the charge to correspond.
Assignment