Copyright: Copyright ®1997 Hilton Evans


Contents

Copyright Notice

Installing ChemPen

Introduction

2D Drawing Tutorial

3D Basics

3D Drawing Tutorial

Main Menu

Editing

Using the Mouse

Using the Keyboard

Loading / Saving Drawings

Printing

Chemical Properties

Molecular Measurements

Chemical Reactions

Ordering ChemPen3D

Customer Support


Copyright Notice

ChemPen3D
© 1994 -1998 Hilton Evans.
All rights reserved.

Registered or unlocked copies of ChemPen3D are for the use of the original purchaser only.   Registered users of ChemPen3D may install an unlocked copy  of ChemPen3D on more than one computer so long as the it can only be executed on one of the machines at any given time.

Duplicating or copying of registered copies of ChemPen3D for reasons other than back-up is a violation of United States and International  Copyright Laws. The locked , shareware or demo. versions of ChemPen3D may be freely distributed in their original forms with all of their accompanying files but without unlocking codes.


Installing ChemPen3D

Windows 95

1. Make a backup copy of the ChemPen3D Disk

2. Insert the disk into floppy drive A:

3. Double Click the 'My Computer' Icon

4. Double Click the Floppy Disk Icon

5. Double Click Setup.exe

6. Follow the instructions

Windows 3.x

1. Make a backup copy of the ChemPen3D Disk

2. Insert the disk into floppy drive A:

3. Run the File Manager

4. Select File | Run ... and in the text box type A: Install and type Enter

5. Follow the instructions

6. Wait until you are prompted for the Installation Complete Message


Unlocking ChemPen3D

ChemPen3D must be unlocked to save or print  drawings; although you can copy it to the Windows® clipboard.  An Unlock code is supplied when you purchase ChemPen3D. If you have a valid unlock code, enter your first name, last name and unlock code.  All three must be entered to unlock the program. If you have need a code click how to register ChemPen.


Introduction 1
 Introduction

ChemPen3D  combines chemical structure drawing and molecular mechanics in one software application.  ChemPen3D simplifies the illustration of chemistry documentation for chemists, chemistry educators, students and chemical workers. With ChemPen3D you easily create diagrams like the drawing in Figure 1a.

However ChemPen3D is not just a drawing program. ChemPen3D is also a basic molecular mechanics modeling program . ChemPen3D  uses an extended version of the popular  DREIDING molecular mechanics force field to compute molecular geometries. Thus you can create structures such as that in Figure 1b.

By combining the DREIDING force field a partition function ChemPen3D's reaction tool  lets the user build and analyze the energetics of chemical reactions.  With the Measurement Tool bond lengths, bond angles torsion angles and interatomic distances can be displayed.

Next


Introduction cont'd

ChemPen3D is intuitive. Drawings is done with menus and mouse clicks. Special Editors further simplify drawing.  ChemPen3D is chemical aware. That is, the program  tries to keep your structures chemically accurate.

ChemPen3D drawings can be printed or pasted into popular Windows word processors and graphics applications. ChemPen3D uses atom, bond, structure, symbol and label objects to create drawings. Atoms and bonds, the most basic elements, are used to create the other objects. ChemPen3D combines these objects to create a drawing.

Groups, such as t-butyl and CONH2, are collections of atoms and bonds. Rings are a special class of  groups. When groups are created they are added to a group list. This makes selecting them for editing easier. A structure created by cloning an selected group of atoms and bonds is added to the drawing as a new group.

Simple text is added as Labels. A special type of label is the formula text. A formula has the format of a molecular formula but carries no chemical information. Labels are added from the Symbol Palette and edited with the Text Editor

Arrows and arcs are examples of Symbols. Symbols are added from the Symbol Menu. Symbols are edited with a special Symbol Editor. As ChemPen3D is improved, more symbols will be added.

Next


Modified DREIDING Forcefield

The ChemPen3D DREIDING Force Field

The DREIDING(1) force field was developed for calculating the geometries and dynamics of organic, biological and main group inorganic molecules with molecular molecular mechanics(2) methods. Compared with more specialized force fields, DREIDING, sacrifices a little geometrical  accuracy in favor of treating a larger variety of molecules.

The original DREIDING field was parameterized for non metal elements and for Na, Ca, Zn and Fe. The ChemPen3D version of DREIDING is  extended to include the entire Periodic Table. DREIDING uses implicit protons to greatly improve optimization speed .  While  molecules with explicit protons can also be optimized that is not usually necessary.

ChemPen3D handles the geometry of metal complexes. The ChemPen3D version of DREIDING  tries to predict the  hybridization of  complexed transition metals based on oxidation number, base electronic configuration, and ligand number.

 1) S.L. Mayo, B. D. Olafson, W. A. Goddard III, J. Phys. Chem., 94, 8897(1990)
2a) N. L. Allinger, J. Am. Chem. Soc., 99, 8127(1977)
2b) N.L. Allinger, Molecular Mechanics, Am. Chem. Soc.; Wash. DC, 1982, ACS Mono. 177

Introduction

Energy and Geometry

The DREIDING Force Field

Intermolecular Interactions

Optimizing Geometry

3D Functions

3D Drawing Tips


Figure 1


Introduction 4
 Introduction - cont'd

Editing is done with  menus and  editors.  Editors  activate if their targets are present. The area where the drawing is displayed is referred to as the Drawing. Up, down, left and right movement is done with the arrow, Tab and Page Up and Page Down keys.

To illustrate the drawing process Figure 1 is drawn. In each step the bold colored words state the  result of  each step. The actions to perform each step follow. Menu commands or button commands are  in bold letters.

Undo and Redo restore a drawing to the its state prior to a drawing operation. Each of the editors has an Undo button to undo the last editing operation.

Click Tutorial for to learn how to draw with ChemPen3D


Drawing Step 1
  Creating a 2D Drawing with ChemPen3D  -

Drawing with ChemPen3D is illustrated with the following example tutorial. Most of the drawing is done with menus  and mouse clicks.

Step 1 - Add a cyclohexane ring From the main menu select Ring,  Add,  6  then click near the left side of the Drawing.

Step 2 - Fuse a second cylclohexane to the right side bond of the first. Select Ring | Fuse | 6 and click to the right of the rightmost bond.

Next Step


Drawing Step 3
Drawing - Step 3 - Fuse a  cyclohexane to the upper rightmost bond

Click near the upper rightmost bond.

Drawing - Step 4 - Fuse a cyclopentyl ring to rightmost bond

Select Ring | Fuse | 5 and click the left most bond bond.

Next Step	Previous Step


Step 5 -Branch two methyls and an OH from the previous structure as shown

1. Select branch | CH3 and click near the two top methines
2. Select branch | OH an click near atom  the upper leftmost methylene
3. Click Reset to stop branching.

Drawing Step - Modify the Methyl bonds
1. Hold Shift and click the right mouse button near the right methyl. The Bond Editor activates
2. Click the cross hatch symbol to change  the bond to an in planebond.
3. Right Click near the left methyl bond and change it to an out planebond.

4. Click the OK button.

Next Step	Previous Step


Step 7 - Clone the Group
1. Drag the mouse from above left to below right of the group activating the   Group Editor
2. Click the Clone button item.
3. Right button click near the new molecule to select it.
4. Type right arrow a couple of times to move the new structure right.

Drawing - Step 8

Create a carbonyl and a double bond
1.  With the mouse pointer near the right structure's OH and type 2 carbonyl.
2. Type 2 while pointing near the left most lowest bond.

Next Step	Previous Step


Step 9 - Add and modify an arrow

1. Select Symbol to activate the Symbol Palette

2. Select the single arrow and click between the structures to place it.

3. Click near the head or tail of the arrow. The symbol editor is activated.

4. Click the style button to change to the style below. Click the OK button.

Step 10 - Add a text label

1. Select Symbol from the main menu.

2. Select Text from the symbol palette and click below the arrow.

3. The text editor activates.. In the editor type the word oxidation

4. Hit Enter or the OK button.

The drawing is done!

Previous Step	Table of Contents


3D Structure Basics

Introduction

Energy and Geometry

The DREIDING Force Field

Intermolecular Interactions

Optimizing Geometry

3D Functions

3D Drawing Tutorial

3D Drawing Tips


Introduction to 3D Structures

While chemists draw chemical reactions as two dimensional images, molecules actually occupy three dimensional space. The atoms in a molecule are distributed in space in ways that minimize the energy of the molecule. In general molecules have more than one minimum energy 3D geometry. Examples are the boat/twist and chair structures of cyclohexane shown in the figure.

Introduction

Energy and Geometry

The DREIDING Force Field

Intermolecular Interactions

Optimizing Geometry

3D Functions

3D Drawing Tips


3D Energy and Geometry

The atoms in a molecule assume a 3D geometry that minimizes the molecule's total energy. The internal energy is the net sum of energy released on bond formation plus the strain energy plus the thermal kinetic energy of the atoms. If other molecules are present, the total energy is composed of the internal energy plus the energy due to interacting with neighboring molecules.

Bond lengths, bond angles, torsion angles, dihedral angles and  non bonded interatomic interactions all have minimum energy values. When a molecule is strained its these values differ from their minima.

Strictly speaking , Quantum chemistry is used to calculate molecular energy and geometry. However, even today, Quantum chemistry overwhelms most PCs for all but the smallest molecules.   Over the last 30 years various empirical  method have been developed that do a good job of predicting molecular geometry and energy. One   the DREIDING generic force field  is used herein. DREIDING approximates molecular internal energy with sums of harmonic terms for bond lengths, bond angles, torsion and dihedral angles.

Introduction

Energy and Geometry

The DREIDING Force Field

Intermolecular Interactions

Optimizing Geometry

3D Functions

3D Drawing Tips


Interatomic Forces

The DREIDING  force field includes interatomic energy terms for non bonded atoms that are not in angles torsions or dihedral coordinates. ChemPen3D uses the Lennard Jones potential for uncharged pairs and a simple coulomb potential for charged pairs.

DREIDING also uses a CHARMM like hydrogen bonding potential. Because non-bonded interactions are included the interaction between pairs or  groups of molecules can be investigated.

Introduction

Energy and Geometry

The DREIDING Force Field

Intermolecular Interactions

Optimizing Geometry

3D Functions

3D Drawing Tips


The 3D Functions

From 3D Function Menu you can optimize the molecular geometry change the 3D  display, and perform some simple animation. Click on each section of the menu to display its function.

Introduction

Energy and Geometry

The DREIDING Force Field

Intermolecular Interactions

Optimizing Geometry

3D Functions

3D Drawing Tips


3D Geometry Optimization
Optimizing 3D Geometry

The search for a minimum energy molecular geometry is 3D geometry optimization. In general, a given molecule will have more than one minimum energy geometry. ChemPen3D iteratively moves atoms to lower energy positions until the internal energy of the molecule has been minimized.

Optimizing Group Geometries-A group selected by the group editor can be individually optimized. This feature is used to optimize the geometries of reaction components.  With the group of atoms selected, click on the appropriate 3D optimization function from the 3D Functions menu.

Modifying 3D Geometries-A molecule can be forced into different minimum energy geometries. For example to the cyclohexane boat can be forced into the chair conformation. Use an editor to alter the molecule until it is close to the desired geometry.  Then apply Refine Geometry

Introduction

Energy and Geometry

The DREIDING Force Field

Intermolecular Interactions

Optimizing Geometry

3D Functions

3D Drawing Tips


 3D Drawing Tips

Draw in Normal View... While drawing can be done in any 3D view it's best to use normal. It's easier to target atoms or bonds with a mouse pointer for branching, fusing or joining of groups.

Save Your 2D Drawing First ...If you have a 2D structure you will be converting to 3D save it  first under a different name and/or extension.

Use 3D Draw Mode ...3D Draw mode simplifies some drawing tasks. Rings are automatically puckered, Joined rings rotate to an orientation close to their minimum energy geometry. Drawing with 3D mode turned on can provide a visually satisfactory drawing that need not be  geometry optimized. However, for energy calculations, geometry optimization should be performed.

Build your molecule piecemeal. For large complex molecules it can help to build your molecule piecemeal. For example to build a  substituted cyclohexane, add and optimize the cyclohexane first.  Then branch the groups. ChemPen3D takes advantage of the  3D geometry when adding a branched or fused structure.

Add Protons Last ... usually...The DREIDING  works best with molecules with implicit protons. Hs should usually be added last. The Add Protons menu command portents a molecule, placing the protons at their correct positions in space.

Introduction

Energy and Geometry

The DREIDING Force Field

Intermolecular Interactions

Optimizing Geometry

3D Functions

3D Drawing Tips


Normal View/Stereo Pair

Stereo Pair view displays two views of the same drawing with slightly different parallaxes. With the proper viewer or crossed  eyes you can combine these to give an apparent 3D image.


Optimize Geometry

Activates optimization routine. When launched from the main  menu optimizes all atoms. When launched from the group editor  menu optimizes the selected set of atoms.


Scramble and Optimize

Optimizes drawing or structure after displacing atoms by  approximately one C-C bond length in random directions. This  can be useful if you are trying to find other minimum energy  structures.


Anneal Geometry

Annealing is repeated randomization and geometry optimization of a molecule. Annealing is most useful when a molecule is slow converging on an energy minimum.


Refine Geometry

Refine geometry optimizes the drawing or selected structure  after making small random perturbations to each atom. Use refine geometry if you want to nudge a molecule into an alternative geometry. For example a cyclohexane chair can be nudged into a boat if you move the an atom and invoke Refine Geometry.


Animation
Spin, Tumble, Rock, Wag

A dynamic view of a molecule can be had by one of four animation methods. Spin rotates the molecule around the up down(y) axis. Tumble rotates the molecule around its left  right(x) axis. Wag oscillates the molecule around the y axis. Rock oscillates the molecule about the x axis.


3D Views

The right column of the 3D Functions menu selects the various possible the 14 various graphic displays of the structure. The Normal view is the default. When a view is selected it is checked. The various views of glycine appear below in menu order.


Normal and Stereo Pair Views

By default ChemPen3D displays a single structure. Select Stereo pair if you want to display two images that appear 3D when viewed via the 'cross eye' method of view.


Creating a 3D Structure

The techniques for creating a 3D drawing build on those for creating 2D drawings. Thus, you should complete the 2D Drawing Tutorial before doing this tutorial. To illustrate, the following perfluorocyclohexa-1-3-diene tetracarbonyl complex of  cobalt* will be created.

Select 3D Drawing Tutorial to learn how to build a 3D structure.

* R. L. Hunt and G. Wilkinson, Inorg. Chem., 4, 1270(1965),


Overview

Creating a 3D structure starts with the creation of a 2D structure. An additional optimization step converts a structure from 2D to 3D. There are a variety of 3D views that can be accessed via the 3D Functions menu

Step 1

Add a cyclopropane ring by selecting Ring | Add | 4 and  clicking the drawing.

Step 2

Fuse a six membered ring to the upper left bond by selecting Ring | Fuse | 6

Next steps


Steps 3

Change leftmost bond to double by pressing 2 with the mouse pointer over the target bond.

Step 4

Change fusing bond to triple by  typing 3 while the mouse pointer is over that bond.

Next steps


Steps 5

Select the leftmost atom by clicking near it with the right  mouse button. Click CO(cobalt) on the periodic table to change  the atom to cobalt. Repeat the conversion for its lower left neighbor atom.

Step 6

 Branch fluorine atoms from each carbon atom by selecting  branch | F from the main menu then repeatedly clicking near each target atom

Next


Step 7

From each cobalt branch three carbonyls by selecting branch|CO

Step 8

Optimize the three dimensional structure by selecting  File|3D Functions | Optimize Structure. For this structure optimization took about less than a minute on a 75Mhz pentium. Typically, the structure becomes highly distorted during optimization. This is not a problem.

Finally


Final Step

Select File|3D Functions| Color Space Fill  to give...


The Measurement Tool

Four geometric properties, bond length, bond angle, torsion or dihedral angle and interatomic distance are measured with the measurement tool.

To display bond length, bond angle or torsion angle select the appropriate radio button and click near the target internal coordinate. The value is displayed near the target.

To display interatomic distance click near the anchor atom. Click near any other atom  to display the interatomic distance in angstroms. To select another anchor, click near the current anchor to clear it . Then click near the new anchor and repeat the above procedure.


Menu Commands Overview
 Menu Commands

All drawing is done from the Main Menu shown below.

File	Reset
Alkane	Ring
Atoms	Symbol
Branch	Symbol|Text
Benzene	Symbol | Formula
Font	Undo/Redo
Link


Using the Keyboard;
Using the Keyboard

The keyboard can be used to navigate ChemPen3D. The following key commands move the drawing without affecting the scroller.

Arrow keys move the drawing up, down, left and right  by jump units.

Shift | Arrow moves the drawing or selected group by 32 units.

An atom can be  changed to one of several non-metal elements with a single key stroke . Point to the atom and type one of the following:

H-hydrogen, C-carbon,  N-nitrogen, O-oxygen, B-boron, F-fluorine,  X - chlorine,  Y - bromine,  I - iodine ,  Q - silicon,  P - phosphorous,  S - sulfur,  Z- selenium

A bond type can be changed by a single keystroke. Point to a bond and type one of the following keys.

1-single bond,  2-double bond, 3-triple bond, 4-resonance or transition double bond, 5 transition state bond, 6 triple resonance,  A-toggles a bond between aromatic and non aromatic *

K- deletes a bond, L-links the two closest atoms with a new bond

+ , = (plus) increases the charge  of the closest atom by 1,

- (minus) decreases the charge of the closest atom by 1.

Also see: Entering and Editing Text


Editing Overview
Overview of Editing

ChemPen3D editing is done with the editing tools listed below. Each editing tool is activated either by selecting a target atom, bond, group, symbol or label. Selecting the object activates its applicable editor.

Atom Editor

Bond Editor

Group or Ring

Symbol

Text Editor

Also see Introduction


Editing Atoms

Editing atoms is done with the atom editor and the  Atom Editor Menu .To activate the Atom Editor  below right mouse button click near the target atom. Use the Atom Editor's buttons, menus and text editor to change the currently selected atom.

Also see Editing ,Menu Commands


Atom Editor and Atom Editor Menu Commands

Text Window - edit text in the text window.

Menu commands

Text | L/R shifts symbol between left and right.

Text | Reflect reverses order of characters.

Text | Font select to change symbol font

Protons  +H, -H add or an H. +H(+), -H(+) add or subtract a proton.

Charge increase or decrease an atom's charge by one.

X->XH toggle non-metal symbol between  A, AHn and none

Clone generates a clone of the selected atom.

Delete deletes selected atom and deletes any attached bonds.

Undo reverses editing.


Add/Branch Atom

Launches periodic table. From it select an atom to add to the drawing. Click the  spot on the drawing where you want to add or branch the atom.

Also see: Menu Commands


Branch Menu
Branch

Branch a single bond, a hydrogen,  a halogen atom, or one of several common functional groups from an existing atom.


Alkane Menu

Alkanes are added to the  drawing or branched from existing atoms by selecting them from the alkane menu. T-butyl can be added. T-Butyl and i-propyl can also be branched.


Benzene Menu

 Select the appropriate menu item to add  benzene to a drawing, branch benzene from an atom or fuse benzene to a bond.


Ring Menu

 Select the appropriate menu item to add a ring to a drawing, branch a ring from an atom, join a ring to an atom or fuse a ring to a bond.


Entering and Editing Labels
Labels and Formulas

ChemPen3D uses two label types; texts and formulas. Text is entered and edited with the Text Editor below.

To enter text, select label from the Symbol palette and click the spot where you want to add text. To edit and existing click near the label with the right button. Use the same method to create and edit a formula. When the text editor is active a text can be dragged by the mouse.

Also see Editing


Reset

Turns off drawing command repetition. If a drawing command, for example Branch | COOH is invoked, repeated clicking on the drawing will repeat the operation until Reset is pressed. Reset is grayed when inactive. Selection of another menu command replaces the currently active drawing command.


Undo
Undo and Reset

Undo reverses the most recent drawing command.  Undo does not correct the very first drawing action as this can be undone by using File | New. Undo can be undone with the Redo command.


Editing Bonds

The bond editor is used to edit bonds. Click the right mouse button while holding shift and pointing near the target bond to activate the bond editor. Click an area on the image below to learn its function.

Also see Editing , Menu Commands


Bond Editor Data Box

Displays the bond length in angstroms and bond strain energy, as computed by the DREIDING force field in kcal. This only has relevance for 3D structures generated by ChemPen3D.


Bond Type

To change to a  bond type select its image.


Bond Editor Button Functions

Cut deletes bond and updates atoms valences.

<|>toggles multiple bonds between left, right and center.

Line toggles bond thickness between 0,1,2,3.


Bond Editor Slider

The bond editor slider pivots, rotates or zooms the selected bond depending on the setting of the radio buttons. Select Pivot to pivot the bond around one of its atom. Click near the pivot atom to select it.  Rotate rotates bond within the plane and around the bond's center. Zoom increases or decreases the length of the bond around its center.


Editing Groups
Group Editor

Groups are edited with the group editor and its menu. To activate, hold Ctrl and click the right mouse button while pointing near the target group. Alternately drag the mouse from left and above the group to right and below. Click the area on the image at left to learn its function.

Also see Editing ,Menu Commands


Group Editor Buttons

Font - change group font

Clone -duplicate group.

Delete - delete group

Fuse - fuse selected atoms and bonds into new group.

Line - toggle line thickness between 0,1,2,3.

Number numbers atoms in group starting at 1 if the Group radio button is selected or at the highest Drawing number if Drawing is selected..


Group Slider Functions

The function of the slider is determined by the selected radio button.

Fine check box sets the rotation range to ±30° from ±180°. If the Zoom function is selected the zoom range is set to ±10% from ±50%.

Tilt, and Turn rotate the group around vertical or  horizontal axes

Rotate rotates group within drawing plane.

Atom selects pivoting around an atom. Click near the pivot atom to select  it. Pivot the group around the atom by moving the appropriate slider.

Bond selects pivoting around a group. Click the pivot bond to select it. Pivot the group around the bond by moving the Pivot slider.

Zoom continuously enlarges or shrinks the selected group.


Editing Symbols

Use the symbol editing tool to edit symbols such as arrows and arcs. To activate the Symbol Editor click the Right Mouse Button with the cursor near the target symbol. Click each part of the illustration in this figure to learn its function.

Also see Editing


Symbol Editor Menus and Buttons

Rotate	90°,-90°,+45°,-45° rotate some symbols by the angle shown.

Zoom	+50%, -50% zooms the symbol by the amount shown

Reflect and Flip reverse some symbols up/down or left right.

Line 	changes the line thickness

Style	affect depends on the symbol

Clone	creates a duplicate of the selected symbol

Delete	deletes the selected symbol


Symbol Editor Radio Buttons

The radio buttons determine the function of the slider namely Zoom or Rotate The slider rotates or zooms the symbols depending on the setting of the radio buttons.


Managing Files
File Menu

Opening, saving and exchanging ChemPen3D drawings is done, from the File Menu. The relevent parts of the filemenu appear to the left. Click on each menu item to learn its function.

Also see Menu Commands


File New erases the current drawing, if any and starts a new drawing. If there is an unsaved drawing you are prompted to confirm the operation. The new drawing is given the file name untitled.chp.


File Open
File Open executes the file open dialog below. The Preview window lets you see a scaled down view of the selected file. The information button will display any information entered by the creator. Click each part of the figure to learn its function. If you click the OK button the previewed drawing replaces the current drawing on the drawing, if any. If the Drawing contains a drawing you are prompted to erase it and load a file.


File Save
File | Save , File | SaveAs

executes the file save dialog if the name of the file drawing is untitled. Ok saves the drawing to disk. If the filename already exists you are prompted to confirm the saving. File Save is inactive in the demonstration  version of ChemPen3D.


File Information

File Comments ...  executes the Information dialog. Add a title, author and up to 255 characters of notes to your drawing.


File Copy
File | CopyToClipboard

Copy puts a bit map or  metafile image of the drawing on the Clipboard that can be pasted into another application. Metafiles, which often appear on the clipboard as pictures, in general give better quality printed and displayed images than bit maps. Bit maps are included for applications that don't accept Metafiles.


Bit Maps

Bit maps are raster representations of pictures. ChemPen3D copies its drawings to the clipboard in metafile or bit map format. Compared to metafiles, bitmaps draw themselves very fast.  However bitmaps zoom poorly and should not be used where they must be resized.


Metafiles

Metafiles are sets of instructions that represent a drawing. ChemPen3D copies drawings to the clipboard in metafile or bit map format.  Metafiles can be resized continuously but compared to bit maps draw themselves slowly.


File Import
File | Import

File Import opens the file open dialog and lets you load a drawing without erasing the present drawing. The new drawing is inserted to the right of the current drawing.


File Print
File | Print

Opens the print dialog from which you can print your drawing. The printer can also be setup from this dialog assuming you have installed drivers appropriate to your printer. You can also copy and paste a drawing into a graphic word processor, such as Winwrite®  or WordPad ® and printed.


Chemistry Menu

ChemPen3D's chemical property predictions and calculations are accessed from the Chemistry Menu.  Click on each menu item to display its function


File Configure
File Defaults

Use Default Settings to set the default values for line width, jump size, and  bond length. The information is saved in file named chempen3.cfg or chempen3d98.cfg . Chempen3.cfg / chempen3d98.cfg is saved in the Windows directory. The drawing is initialized with the chempen3.cfg / chempen3d98.cfg data. If chempen3.cfg / chempen3d98.cfg  does not exist it is created upon starting ChemPen. with a set of default values.

*jump size is the distance a drawing or selected group is moved when an arrow key is pressed.


File Exit

Shuts down the application. If a drawing exists you are prompted to save it.


Symbol Palette

Symbols such as, [image], are added to a drawing using the symbol menu. Examples of symbols are arcs, arrows  and the triangle. Symbols can be edited with the Symbol Editor.  As ChemPen3D is developed other symbols will be added.


Atom Menu
Atom

From the Atom Menu you add atoms, link(form single bonds) atoms, add protons to or remove protons from a molecule or add on of several small common molecules. Click on the menu below to learn its function.


Add Hs/Remove Hs

Use Add Hs 2D if you want  protonate a 2D drawing. You can  also protonate a group or individual atom by selecting it. Use  Add Hs 3D to protonate a drawing distributed in 3D. To remove protons select Remove Hs. Molecules with and without explicit protons appear below.


Add Molecule

Add one of several common small 3D molecules from this menu.


Link Atoms

Connects two atoms with a single bond. Select this menu item then click near each atom to be bonded. An error occurs if you click near the same atom twice.


Ring

Adds, branches, links or fuses a ring to an existing structure. If Add is chosen a ring is drawn centered at the point on the drawing where the mouse is clicked. If  Branch is selected, clicking near an atom branches from that atom. Branching  occurs if the valence of the target atom is not exceeded. If Fuse is selected,  clicking near a bond fuses the ring to that bond. The ring will not be fused if  the valence of the atoms will be exceeded. If Join is selected, clicking near an atom joins an apex of the selected ring to the target atom.


Font

Launches the font dialog allowing the user to change the drawing's  font.


Font Dialog


Link

Found under the Atoms menu, Link is used to  form a new bond between two existing atoms select link then click near each of the two atoms. Use RESET to stop linking. You can also link to close neighbor atoms by typing L with the mouse pointer between them.


Using the Mouse

ChemPen3D makes extensive use of the mouse in drawing and editing. Additional functions are provided by  combining the left and right mouse buttons with the shift and control keys.

Clicking the right mouse button - selects the nearest atom or symbol and activates the Atom Editor or the Symbol Editor

The  Shift|right mouse button - selects the nearest bond and activates the  bond editor

The Ctrl |right mouse button - selects the nearest  group and activates the Group Editor.

Dragging the mouse from above and  left of any group of atoms to below and right of the atoms and combines them into a group activating the Group Editor. The selected group is highlighted.

Also see Editing


Molecular Properties

Molecular properties are displayed  in the Molecular Properties Dialog. A molecule should be geometry optimized before its properties are diaplayed.

{moledat3.shg}


Moments of Inertia

ChemPen3D can report the principal moments of inertia, in amu x Å, for a 3D optimized molecule. To display the principal moments of inertia select File | Chemistry | Moments of Inertia


 Strain Energy

Strain energy results when internal coordinates deviate from their minimum energy values. The Bond Editor displays the strain energy of an individual bond.


 Internal Energy

The internal energy of a 3D geometry optimized molecule can be estimated. The internal energy is the sum of the bond energies plus the net steric strain energy plus the kinetic energy of the molecule.


Dipole Moment

Given an optimized 3D structure, ChemPen3D can estimate the dipole moment of a molecule. Select File | Chemistry | Dipole Moment and an estimate of the dipole moment is displayed in a dialog box.


Molecular Data

ChemPen3D calculates a molecules formula weight, chemical formula and  percent chemical composition. To display a molecule's data select File | Chemistry | Molecular Data


Working With Chemical Reactions
Chemical Reactions

Introduction

Building a Reaction

The Reaction Tool

Balancing a Reaction

Reaction Energetics

Protons in Reactions

Reaction Reports

Things to Remember!


Introduction to Chemical Reactions

With ChemPen3D you can analyze reaction energetics. A byproduct of 3D geometry optimization is the internal energy. Herein the internal energy is the  energy released on bond formation + total strain energy + thermal kinetic energy. Strain energy results when bond lengths or angles and torsion or dihedral angles deviate from their minimum energy values.

ChemPen3D does all reaction calculations assuming gas phase. Gibbs free energy, enthalpy, entropy and the equilibrium constant are calculated and displayed by  the reaction tool.  The reaction tool is also used to balance the reaction and adjust temperature and pressure.

Beginning                   Building A Reaction


Building a Reaction

Building a reaction is simple. Products and reactants are placed to the left and right of an arrow. Arc arrows should not be used. Other symbols, formulas and labels,  are ignored. Only the first arrow added to the drawing is recognized.

Fuse each reactant!
Each reactant or product must be individually 3D geometry optimized and fused. It's a good idea to select and fuse each reactant or product after building a reaction.  The reaction for the combustion of methane is shown below.

Beginning               Balancing Reactions


Balancing Reactions

A reaction is balanced with the Reaction Tool With a reaction built and groups optimized, select File | Chemistry | Reaction Tool to launch the reaction tool.

Adjust the moles of each substance using the scrollers in the Substance Info. box until the  Mass Balance message box reads BALANCED. Balance is also when the elemental molar balances in the lower window all vanish. Balancing takes account of the implicit protonsin certain non metal atoms.

Beginning                   Analyzing Reaction Energetics


Analyzing Reaction Energetics

The energetics of a reaction can be analyzed using the Reaction Tool   ChemPen3D uses its modified DREIDING force field to predict a molecule's heat of formation.  ChemPen3D treats a molecule as forming from individual atoms; each with a zero reference energy. Select the Report button to copy a summary of the reaction's energetics to the clipboard.

Beginning                   Protons in Reactions


Protons In Reactions

Protons can be implicit [image] or explicit [image]. For reaction energy calculations ChemPen3D only takes account of the bond energies of explicit X-H bonds.

1. If proton bonds are broken in a reaction, explicit protons  should be used.

2. You don't necessarily have to protonate every atom when protons are used.
     You need only protonate the atoms that are actually involved in X-H bond
     breakage.

Beginning                   Things to Remember


Things to Remember

1. The reaction tool only works with one reaction per drawing.

2. A  reaction is a set  of  molecules left  and right of an arrow.

3. Only the first arrow is recognized by a reaction.

4. Arc arrows are not recognized

5. Each molecule must be individually 3D optimized, and  fused.

6. In ChemPen3D reactions are treated as gas phase*.

7. Add explicit protons only when needed.

*PChemPen3D, a more sophisticated version of ChemPen3D will lets you treat reactions in solution.

Chemical Reactions


ChemPen3D Reaction Tool

 Once a reaction is built its energetics can be analyzed using the Reaction Tool. To activate the reaction dialog, select File | Chemistry | Reaction Tool. Click on the graphic below to determine each reaction tool function.

Note: The reaction tool switches the drawing to normal view


A Balanced Reaction

The balanced combustion reaction of methane is shown. The coefficient of each reactant or product appears below the reaction.


Substance Information

The Reactant button tabs between reactants. The selected reactant is highlighted in red.

The number of moles of the selected substance is adjusted by the scrollers in this box. Moles can be adjusted to 0.1 mole.

The state  buttons  inactive in ChemPen3D are a feature of the more advanced  PChemPen3D due the second quarter of 1998.


Reaction Summary

An image of the reaction and a summary of its thermodynamic quantities is copied to the clipboard by the Report button. The report can be pasted into a word processor. A copy of the report simultaneously appears on the screen. An example appears below.


Pressure and Temperature

The Pressure and Temperature are set, respectively using the P(atm) and T(K) scrollers.


Reactant Button

The reactant button tabs between reactants and products.

Upon selection the compound is highlighted.


Mass Balance

The mass balance message box aids you in balancing your reaction. The UNBALANCED message changes to BALANCED when the reaction is balanced.The second lower box shows the difference in moles between reactant and product atom counts. The mole difference for each element reads 0.0 when that element is balance. The coefficient of each compound appears below the compound.  A balanced reaction appears below. The reaction tool is not shown.


Thermodynamic Functions

The enthalpy, free energy, entropy and logK  appear in the left column of the Thermochemical Data box. In ChemPen3D all calculations are done in the gas phase. In the more advanced PChemPen3D (available Q2 1998) estimations can be made on reactions in solution


About PChemPen3D

Available the Second Quarter of 1998, PChemPen3D is Physical ChemPen3D. PChemPen3D extends the functionality of ChemPen3D. PChemPen3D adds solution property prediction, reactions in solution and reaction rate constant prediction. News about ChemPen3D and PChemPen3D.

http://home.ici.net/~hfevans/chempen3.htm


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