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You can use ChemSketch to draw chemical structures, and to view them as three dimensional (3D) models.

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The approach here is to show by example. I will lead you through one example in some detail, showing how to draw the structure. After that, I will briefly show some other features.

Entered: Fri Oct 22 2010. Operating systems: MS Windows. Distribution: Free. Application fields:.

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No attempt is made here to teach all of ChemSketch. The idea is to guide you to some basics. If you can do the things shown here, you should then be ready to pursue more features of the program on your own -- as you need them.

DRAWING YOUR FIRST MOLECULE

In this section, you will draw a simple organic molecule, to get started with the basic features of ChemSketch. The molecule is propane, CH₃CH₂CH₃.

Open ChemSketch (for example, by clicking on its icon).

Single click anywhere on the main screen. You should see CH₄ appear on the screen.

Position the pointer over that CH₄. You will know when the pointer is properly positioned because a faint box will appear around the C atom (along with its hydrogens). Single click. You should now seeH₃C-CH₃ (which is ethane).

Position the pointer over either C-region of that H₃C-CH₃. You will know when the pointer is properly positioned because a faint box will appear around the C atom you have chosen (along with its hydrogens). Single click. You should now see a 2D structure of propane (Fig 3):

As you draw the propane structure, note the following general points:
To add a Carbon, you click on the place where you want it added. You use the C tool -- the default -- for this.
Each time you add a C, the number of hydrogens shown will adjust appropriately.Try yourself.....it's just easy...

MORE BASIC FEATURE

1. Double bonds (propene)

Propene (propylene; CH₂=CH-CH₃) differs from propane in having a double bond. The drawing strategy is to draw propane, then change one C-C single bond to a double bond.

First, draw propane,

Now, put the pointer on one of the C-Cbonds in the propane structure. You will know when the pointer is properly positioned, because a faint box will appear around the bond. Single click. The bond will change to a double bond, and the CH₃ will change to CH₂. You now have the 2D structure for propene (Fig 5):

Each time you click on a bond, it will increase from single to double to triple bond, or will change from triple back to single. Just click on the bond over and over, and you will toggle among these choices.

2. Heteroatoms (ethanol)

The 'skeleton' of ethanol (ethyl alcohol; CH₃CH₂OH) differs from propane in having an O atom instead of one of the C atoms. That is, ignoring the hydrogens, propane is C-C-C and ethanol is C-C-O. The drawing strategy is to draw propane, then change one carbon atom to an oxygen atom.

A 'heteroatom' is an atom other than C or H. Chemistry drawing programs usually draw C atoms by default, and they usually provide the proper number of hydrogen atoms. It is up to the user to specify atoms other than C or H.

First, draw propane,

Now, click on the O tool (for oxygen), on the toolbar along the left side; the O tool will light up. (The O tool is a little below the C tool, which you have been using so far, by default.) Then, put the pointer on one of the C atoms at either end of the propane structure. You will know when the pointer is properly positioned, because a faint box will appear around the atom (with its hydrogens). Single click. The C will change to an O, and the number of hydrogens will adjust appropriately. That is, the CH₃ will change to OH. You now have the 2D structure for ethanol (Fig 6):

This illustrates the general procedure for changing one atom to another in a ChemSketch structure.

In this case, if you changed the middle C to an O, you would make dimethyl ether, H₃C-O-CH₃.

If the heteroatom you want is not shown at the left, click on the periodic table button at the top of that column of tool buttons (just left of the 'mm'; see Fig 2); it lights up as 'Periodic Table of Elements'. Choose the element you want from the periodic table. (The elements directly available at the left, with their own tool buttons, will vary.)

3. Rings and templates

ChemSketch provides templates of several 'complex' structures, allowing you to add these structures as a unit. We illustrate that here with a ring.

Go to Templates menu, and choose Table of Radicals. (You can also reach this by pressing F6. There is also a tool button for this feature: it is along the right side, just below the ruler and just above tool buttons for some specific ring templates; it lights up as Table of Radicals.)

Find the section of the Table of Radicals called Cycles. Move the pointer to the benzene ring, and click on it. You will now be returned to the main screen. Position the pointer as desired, and single click. The benzene ring will be put on the screen.

The pointer will still carry the benzene ring. To add a second benzene ring to your structure, position the pointer over any specific atom of the first ring, and single click. To fuse two rings, position the pointer over a bond in one ring, and single click.

And the pointer still carries the benzene ring! How do you get it to stop? Click something else. For example, you might click the C tool, at the left, to go back to adding individual carbon atoms. (Or, click on the lasso tool, so the pointer no longer carries anything. You can also right click, but this does not work for other tools, such as the common C tool.)

Notes about drawing this structure:
* You can do the last two steps in either order. That is, you can add ring 2 at a bond, and ring 3 at an atom.
* Regardless of the order, when you do the final step, you can make either 2-phenylnaphthalene (shown) or 1-phenylnaphthalene; this depends on the positioning for the third step.

More sets of templates are available from the Template Window, which is also on the Templates menu. Once you get to the Template Window, some template sets are listed along the left side, but many more are available from the drop down menu at the top (near 'Draw' button). Explore!

4. Stereochemistry: Drawing cis-trans isomers at double bonds

Sometimes you want a particular group to point in a certain direction, and the drawing program may insist it point in another direction. This section presents one simple but versatile little trick to deal with this. The specific example is drawing cis-2-butene. By default, ChemSketch seems to want to draw the trans isomer.

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Here is how you can draw the cis isomer. This is illustrated in Fig 8, below. The three parts of the figure represent three stages in the drawing. To make the figure, I copied each stage into a new position, so you could see each stage. But normally you would just do all the steps sequentially on one drawing.
1. Draw 2-butene, following the usual procedures. This gives you (a) in the figure. The problem is that the right hand methyl group points down, and you want it to point up.
2. Add one more methyl group -- the one that points up. This gives you (b) in the figure.
3. Remove the lower methyl group, the one you do not want. To do this, choose the lasso tool (upper toolbar, near left); using this tool, select the group you want to remove; then remove it with CTRL/X or delete. Now you have (c) in the figure, the desired cis-2-butene.

The procedure described above is useful whenever you want a group to point in a specific direction different from the program default. For example, you may be simply drawing an extended alkyl chain, but want it oriented a certain way.

5. Stereochemistry: Wedge bonds

Wedge bonds allow you to specify that an attached atom is above or below the plane.

Fig 9, below, shows an example. In this example, wedge bonds are used to show a specific stereoisomer at a stereocenter. This was done in three stages. First, I drew an ordinary structure for bromochloroiodomethane (that is, a C with Br, Cl, I, H attached). This is shown at the left. Then, I made two copies of this, on the right. (The copies were for my convenience in making the figure. In normal use, you would just modify the original.) In the top right copy, I changed two of the bonds to up wedges and two to down wedges. In the lower right copy, I did something similar, but switched which bonds are up and which are down.

Procedure for changing an ordinary bond to a wedge bond: To do this, choose a wedge bond tool, and then click on the desired bond. The wedge bond tools are at about 50 on the tool bar just above the ruler; see Fig 2. The solid wedge ('Up Stereo Bonds') is for a bond pointing up, and the dashed wedge ('Down Stereo Bonds') is for a bond pointing down. You can also use the wedge bond tools to draw new bonds.

I have named the structures in Fig 9, using the naming feature of ChemSketch. I showed the names here so you can see that the left hand structure does not get an R/S designation, and the two right hand structures do get R/S designations. Convince yourself that these are correct. The procedure for getting the names is shown below in the section Naming structures.

Caution. ChemSketch will put wedges wherever you tell it to -- even if they are physically unreasonable. For example, you could draw all four bonds around a C with up wedges -- which is not possible. The ChemSketch naming procedure will not put an isomer designation on such an improper structure.

6. Unusual atoms labels (X for halogen, Me, etc)

Sometimes you want to label an 'atom' (a particular position on a structure) with something other than an ordinary element symbol. Examples include: D for deuterium, X for a general halogen, Me for methyl.

The symbols D and T, for the hydrogen isotopes, are available from the regular periodic table (near its lower right). That periodic table was introduced above near the end of the section on Heteroatoms (ethanol).

A more general way to insert an unusual 'symbol' is the feature Edit Atom Label. This tool is on the left tool bar -- but off the screen. So, expand the left tool bar (>> = 'more buttons') and look for the button labeled abc; it will light up as Edit Atom Label. Click on the abc button; the cursor will now have an odd symbol starting with ab attached to it. Click on the atom you want to change (or anywhere on the drawing screen). A new box opens, called Edit Label. You now have two main choices: First, you can type in the label you want, and press insert. Or you can choose an item from the list there, and press insert.

7. Naming structures

To name a structure you have drawn, use the 'Generate name for structure' tool. You can access this from the Tools menu (expand the Generate item), or from the button near the right hand end of the upper toolbar.

If you want to remove a name that ChemSketch has put on the screen... If naming was the most recent action, then using Undo (on the Edit menu) will remove it. More generally, click on the name to select it, then 'delete' it (such as by using CTRL/X).

The 'Name' feature will name geometric isomers of alkenes using the E,Z system.

Example. Draw 2-butene. Name it. ChemSketch seems to draw the E isomer (which is trans), by default, and it properly names it as the E isomer. Now, put a Cl at the 2-position (replacing the H). Replacing an H with a Cl switches the ranking at this position (relative to the methyl group). Name the new compound; it is now, properly, named as Z.

(If you want to learn how you can draw the 'other' isomer, see the section above on Stereochemistry: Drawing cis-trans isomers at double bonds.)

The 'Name' feature will name chiral isomers using the R,S system. This was illustrated in the section Stereochemistry: Wedge bonds.

The naming feature has limitations, such as only naming structures with 50 atoms or fewer. If you try to name a structure beyond its capacity, you will get an appropriate error message.

8. SMILES and InChI

SMILES and InChI are both ways to describe a chemical structure in simple text characters.

SMILES = Simplified Molecular Input Line Entry Specification.
InChI = (IUPAC) International Chemical Identifier.

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This is not the place to try to explain them, but if you want to try them, they are available. Both are available from the Tools menu; expand the Generate item, and you will see SMILES and InChI commands. There are commands for structure-to-code and code-to-structure.

9. Antialiasing

Antialiasing makes lines and edges appear smoother on the screen. Information on how to turn on this feature was introduced in the section Getting and installing ChemSketch; scroll down to Settings, at the end of that section. In version 12, it seems to be on by default.

The smoothing is applied as part of displaying the structure; it is not stored in the file. Thus, one can gain the benefit of antialiasing with pre-existing files, and can turn it on or off as desired.

Since antialiasing is a display feature, not intrinsic to the drawing, it may or may not be included when you copy a structure to another application. A true screen capture will include the smoothing. On the other hand, copying the structure and pasting it into Word or Powerpoint (with Paste Special) does not include the smoothing. (The free program IrfanView contains a good screen capture feature. IrfanView is athttp://www.irfanview.com/.)

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Since antialiasing improves the quality of the screen display, one might just turn it on and leave it on. Exceptions? It is a 'resource hog'; if it slows down your system too much, you can turn it off. If you know of other exceptions, please let me know.

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