ChemOfice is an universal software package frm the CambridgeSoft Corporation. It is one of the most popular computer program in many chemical laboratories around the world. CS Chem3D program is designed for visualization of chemical compounds, computer simulation and calculations. The main elements of the user interface can be divided as follows: Main menu; Main panel; Control panel. In the center of the screen there is a working window, which displays the process of creating and editing three-dimensional models of molecules.

1. ChemBio3D
Ultra Program

2. Outline
1. CS Chem3D program
2. Graphical interface of Chem3D
program
2.1 Main Menu
2.2 Main Panel
3 Visualization of molecular structures
using Chem3D program
4 Summary
5 References
6 Examples

3. ChemOffice Software
3
ChemOfice is an
universal software package
frm the CambridgeSoft
Corporation. It is one of the
most popular computer
program in many chemical
laboratories around the
world.

4. 1 CS Chem3D program
4
CS Chem3D program
is designed for
visualization of chemical
compounds, computer
simulation and
calculations.

5. 2 Graphical interface of Chem3D program
5
The main elements
of the user interface
can be divided as
follows:
• Main menu;
• Main panel;
• Control panel.
In the center of the
screen there is a
working window,
which displays the
process of creating
and editing three-
dimensional models
of molecules.

6. File - contains a standard set of features for opening, saving and printing files.
Edit - also provides the usual set of copy, paste, undo, and select functions.
View - provides a wide range of settings for the appearance of molecules / bonds
/ panels, etc.
Structure - offers tools for customizing the display of various parameters of a
molecule, as well as measuring bond lengths, interatomic distances and
angles.
Calculations - offer methods for calculating the potential energy of molecules
and other characteristics empirically,semiempirical and ab initio quantum
mechanical methods.
Surfaces - offers tools for analyzing molecules and their calculated properties. 6
2.1 Main Menu

7. Menu File
7
New - opens a new user window. C that Chem3D works
in multi-window mode.
Sample Files - prompts you to open a new window with
predefined settings (for example, background color or
how molecules are displayed) or with presets for
molecular models.
Open / Close Window / Save / Save As… - are standard
functions for opening, closing and saving files.
Revert to Saved - removes all changes since the last
save.
Model Settings - uses this model's settings for the new
model.
Print Setup / Print - opens a standard dialog box for
customizing and then printing the file.

8. Menu Edit
Undo / Redo- undoes or, conversely, redoes the
changes of the last action.
Cut - cuts the selected element of the molecule /
text and copies it to the clipboard.
Copy - copies the selected element of the molecule /
text to the clipboard.
Paste- selected element of the molecule / text from
the clipboard.
Clear - deletes the selected item/text.
8
Copy As...- allows you to copy the selection as ChemDraw- structure or raster (bitmap)
Select All - selects all items.
Select Atoms - allows you to select atoms by a certain attribute: Revers (Select unselected,
i.e. invert selection), SelectC (Select all atoms of one element), Select Adjiacent (Select
all atoms adjacent to the given one), Select Fragment (Select all atoms of the given
fragment).

9. Menu View
9
The first section includes three items:
- Main panel, including the display of the main
panel;
- Control Panel - showing the visibility of the
control panel,
- Settings, which displays a dialog box for
setting the appearance of molecules.
The second section combines the points with
which you can visualize the various calculated
characteristics of the molecular model.
In the last section of the menu item viewlinks to
tables with parameters used in calculations are
given.

10. Menu Structure
• Structure - offers tools for customizing the display
of various parameters of a molecule, as well as
measuring bond lengths, interatomic distances and
angles.
• Measurements - contains a pop-up submenu with
items:
10
• Bond Lengths -
determine lengths connections,
• Bond angles -
determine the angles between the bonds,
• Dihedral angles - define dihedral angles,
• Close Contacts – determine the closest connections,

11. 11
A few more commands main menu
Structure / Measurements-bond length measuring instruments
and angles between bonds
Generate All Bond Lengths-measure bond lengths
Generate All Bond Angles-measure the angles between the bonds
Generate All Dihedral Angles-measure dihedral angles
Measurement results
will be displayed
in the windowmeasurement
in fieldActual, where are they
if necessary
can change.
Checking the box
in fielddisplay,
can be displayed
corresponding measurement
directly on the model

12. 12
Standard
Model display
Demo
Building
2.2 Main Panel

13. 13
Building Panel
The tools in this panel allow you to create and edit
3D models of molecular structures
Highlight
Move All
Turn
Scale
Move object
Add
bond
Create a
text
"Eraser"

14. 14
Model Display Panel
Serves to adjust the parameters of the image of a three-dimensional model
Atom
numbers
Atom
symbols
3D Model
Representation
Options
Background
color,
background
color effects
Note. All these features and more are available
in the main menu(paragraph View /Model Display)

15. 15
Demo Panel
Serves for setting demonstration options 3D model
Rotation Axis
selection
Speed
Amplitude
Stop
Note. The same commands can be called from the main menu
(View /Demo)

16. 3 Visualization of molecular structures
using Chem3D program
16
Chem3D Toolbar offers a set of
simple tools for creating and adjusting
simulated structures in the workspace.
The Chem3D allows full 3D modeling
and visualization of chemical
compounds.
Working window of Chem3D program
ToolbarChem3D

17. Visualization of the spatial structure of molecules
17
Sulfuric acid H2SO4 model
Ethylene (C2H4) molecule
sticks balls and cylinders spherical

18. Editing and analysis of the geometry of
3D molecular models
There are several ways to create a three-dimensional
molecule of a chemical compound.
A two-dimensional model in the form of a structural
formula of the corresponding chemical compound can be
created in the application ChemDraw or in any other
"chemical editor", and then copied through the clipboard
Windows using the copy and paste operations.
When inserted into the Chem3D window, the
structural formula is automatically converted into a
three-dimensional model, while the corresponding
lengths of valence bonds and angles between atoms are
assigned standard values ​​for these elements. 18

19. 19
How to create a 3D model
1st way -directly in the working window with
Toolbar building
2nd way-according to the gross formula of the compound
 Click the button on the panelbuilding
 Click in the working window
 In the text field that appears, write the gross formula
corresponding connection
 After pressingEntera 3D model will be created
3rd way-based on a two-dimensional model created inChemDraw
 Select and copy the 2D model fromChemDraw
 Paste into working windowChem3D
 The model is automatically converted to 3D
How to copy3D-model out the window ChemDraw?
Menu Edit/Copy As/ChemDraw structure

20. 20
How to edit a 3D model
 Click the button on the panel building
 Click on the atom to be replaced
 In the text field that appears, enter the symbol of the new atom
 After pressing the key Enter there will be changes

21. 4 Summary
Chem3D is a program for creating and viewing three-dimensional
chemical structures, has a built-inplugin ChemDraw, which
allows you to build a three-dimensional chemical structure using
the structural formula written on the screen. In addition, the
program calculates the physical properties of chemical structures
using various quantum chemical methods (MM3, MOPAC, the
Hückel method, etc.)
21

22. 5 References
1. ChemBioOffice 2014 version 14.0. CambridgeSoft Corporation. 2014.
https://perkinelmerinformatics.com/products/research/chemdraw
2. Архитектура химических соединений и молекулярный дизайн:
методические указания к практическим занятиям обучения [Электронный
ресурс] для обучающихся направления подготовки 18.04.01 Химическая
технология, профиля Технология продуктов основного органического и
нефтехимического синтеза, всех форм обучения / сост. Т. С.
Котельникова КузГТУ. – Электрон. дан. – Кемерово, 2019.
3. Авдеева Л.В., Сидоров В.В. Методические указания по изучению
программного комплекса ChemOffice. – 2012.
4. Моделирование структуры химических соединений с помощью пакетов
программ ACD/Chemsketch, Chemoffice, Hyperchem. Манаенков О.В.,
Косивцов Ю.Ю., Сульман Э.М. Учебное пособие. — Тверь: ТвГТУ, 2013.
— 84 с.
5. Соловьев, М. Е. Компьютерная химия / М. Е. Соловьев, М. М.
Соловьев. – Москва : СОЛОН-Пресс, 2005. – 536 с.
5. Компьютерная химия: основы теории и работа с программами Gaussian
и GaussView [Текст] / Е. В. Бутырская. - Москва : Солон-Пресс, 2011. - 218 с. :

23. 6 Examples

24. Examples

25. 6 Examples
crystal NaCl and dynamycin
Model of the butane molecule (a) and the surface accessible to
the solvent with a resolution of 40 (b)

26. Thank for your attention!