Frequently Asked Questions

ChemSketch

Q: How do I Insert Markush bonds into ChemSketch diagrams?

A:

  1. Draw the molecule on which you want to add the Markush bond.
  2. Hold SHIFT and select the atoms which are to be included in the Markush bond.
  3. Click the Markush Bond button on the Structure toolbar.

Q: How do I show all the explicit carbons in a structuer?

A:

  1. On the General Toolbar in ChemSketch, choose Structure mode.
  2. From Tool menu, choose Structure Properties. The Properties dialog box appears.
  3. In the Properties dialog box, click the Common tab.
  4. Under Show Carbons, select the All checkbox
  5. On the bottom of the Properties dialog box, click Set Default.

Q: How do I show Newman projections?

A: In ACD/3D Viewer, rotate the molecule so that the viewer is looking down the desired bond. There are also Newman Projection templates in newer versions of ACD/ChemSketch. From the Templates menu, choose Templates Window. In the dialog box that appears, select Newman Projections from the drop-down list.

Q: How do I hide an allyl anion or radical "CH2"?

A:

  1. Select the structure in Structure mode by clicking the Select/Move button.
  2. When the Select/Move button is active, double-click the structure to open the Properties dialog box.
  3. In Properties dialog box, click the Common tab.
  4. Under Show Carbons, clear the All and Terminal checkboxes.
  5. Click the Atom tab.
  6. Ensure that the C atom is selected on the left-hand side. Then clear the Show checkbox.
  7. Click Apply. The CH2 will disappear, leaving the charge or radical in the structure.

Q: How do I change how an atom label is attached to a bond?

A: Atom labels can be connected to the bond with any of its atoms. To be able to adjust the position of the label, it must be entered with the Edit Atom Label tool.

To change the connect, please use the following steps:

  1. Click on the Change Position button in structure toolbar to make it active.
  2. Click on the atom label while holding down the SHIFT key on computer keyboard.
  3. For other atom labels in the structure, click on the atom label repeatedly with Change Position button active while holding down the SHIFT key until the desired connected atom to bond is obtained.

To change how Hydrogens are positioned around an atom, the SHIFT key is not required. Instead, simply click the Change Position button in the Structure toolbar and then click on the atom repeatedly.

Q: How do I view the chair or boat conformations in 3D?

A: The easiest way to do this is to use the stereobonds, clean the structure, and then optimize it. There will be a prompt asking if the stereobonds should be changed to single bonds. Click No.

The ‘up’ stereobonds are the solid wedge and come out of the page. The ‘down’ stereobonds are the dashed wedge that go into the page.

Q: What is the temperature used to predict densities in ChemSketch?

A: A temperature of 20 degrees Celsius is used for density prediction.
ChemSketch uses the following definition to predict density:

Density = Mw/Mv

where Mw is the molecular weight, and My is the predicted molar volume.
All the properties for liqiuds were calculated at 20°C.

Q: How do I insert Greek letters and symbols in ACD/ChemSketch?

A:

  1. In Draw mode, click the Edit Text button.
  2. In the Font list, choose Symbol.

If for some reason teh Symbol font is not listed in the dropdown box, the Greek letters can be ontarined by using the following steps:

  1. From Start/Programs/Accessories/System Tools, select Character Map.
  2. From the Character Map window that appears, select the needed symbol and copy it to clipboard by clicking the corresponding buttons.
  3. Switch to the ACD/ChemSketch window and from the Edit menu, choose Paste.

Q: When attempting to generate SMILES notation for a ring structure with "down stereo bonds" coming off of it, no @ or @@ is placed in the SMILES string. If I draw a structure with "up stereo bonds" first and replace the bonds with "down stereo bonds" then it generates half of the @ or @@ expected. This works fine using just the "up stereo bonds". Why is this?

A: The reason is that ACD/Labs' SMILES procedure (and not only ACD/Labs) takes into account only the sharp ends of stereobonds. It defines what atom is the stereo center. A different drawing of the same structure leads to different SMILES.

  1. If somebody draws 'down wedges' with the narrow end attached to the cyclic atom, the SMILES include all the stereo names.
  2. If the structure is drawn with wide ends of the stereo bond attached to the cyclic atoms, no stereobond is encoded in SMILES.
  3. If the user uses "undirected" stereobonds (for example, dashed lines), the result will be less predictable when SMILES use the mol file for exchange as this format doesn't support "undirected" stereo bonds. In the resulting mol file they will be replaced by wedges with the direction depending on internal atom numbers (the narrow/sharp end attached to the atom with the lower number).

Try using sharp ends attached to the stereo center to improve the treatment of different stereo designations (for SMILES and for mol file encoding).

Q: When opening ACD/ChemSketch or ACD/3D Viewer, an error message "Cannot create User Styles" is received.

A:The default setting for the “User Styles” may be pointing to a write protected (or deleted) directory. Change the value to a directory where the user has writing privileges (for example c:\temp).

From within ChemSketch, from the Options menu, choose Preferences. Click on the General tab, and under Directories, enter the desired path in the Private box.

Q: How do I draw structures in ACD/ChemSketch in a notation style, like NH2CH2CH2CH2OH (Condensed Formula)?

A:

  1. Double-click on the hidden CH part of the molecule to bring up the Properties window.
  2. Click on the C button at the bottom left of the Properties window. This will display a Show check box.
  3. Select this box and it will display the hidden atoms as CH or CH2.
  4. Repeat this for all atoms to be displayed in the chain.
  5. Next click on the atom and drag the bond so that it is now in line with the other atoms.
  6. Repeat until all are aligned.
  7. Move the H atom so that the chain reads NHCHCH2 rather than NHHCCH2. To do this, enable the Change Position button on the toolbar. Now select the atom you want to change the position of. Keep clicking until the H is oriented the correct way.

Drawing a structure with an end group as (CH3)3C is not possible with the described method. If it is written as (CH3)3C this will not allow you to calculate the PhysChem Properties. At this moment in time, there is no solution for this problem.

Q: Is it possible to read an *.sdf file containing multiple molecules where some of the molecules contain counterions and then generate an *.sdf file where all of the molecules have had counterions removed?

A: Yes, it is possible.
If the *.sdf file was created including the molecules with and without counter ions, use the Remove Spectator Ions goodie.

Click on this button and specify the path and the name of *.sdf file. The new *.sdf file will be in the same folder with the desired result.
If there is no *.sdf file already prepared, follow the steps below:

  1. Draw the structures (with and without counter ions).
    Note: Only put one structure on a page. It is possible to draw up to 100 structures, because the ChemSketch document can have 100 pages maximum.
  2. Click on the Sketch-to-SDF Converter button. Then in the Export to an SDF File window, type in ‘1’ for the whole document.
  3. Click on the Remove Spectator Ions button.
  4. Click on the SDF-to-Sketch Converter button. In the Import SDF Data window, define how many molecules per page you need.

Q: Connecting an R group to a nitrogen atom in a shorthand formula always connects the R group to the first carbon. How can I change that?

A: Atom labels can be connected to the bond with any of its atoms. Please follow the procedures below to change the connected atom to the bond.

  1. Click the Change Position button in structure toolbar to make it active.
  2. Click on any of the atom labels in the formula, while holding down SHIFT. The connection point of R changes to the next atom label, i.e., H.
  3. For other atom labels in the structure, click on the atom label repeatedly with Change Position active while holding down SHIFT until the desired connected atom to -R is obtained.

Q: How do I delete the bond only so the attached groups or atoms stay?

A: Click the Delete button, then navigate to the bond and hold CTRL while clicking the bond.

Q: How do I draw a molecule which is a zigzag but has no terminal group at the end, just an empty bond? This is used for polymer notation.

A: The easiest way to accomplish this is to simply turn off the label display through the Properties dialog box.

With a ChemSketch structure displayed:

  1. Switch to Structure mode.
  2. Click the Select/Move button.
  3. Double-click the CH3 group to be hidden.
  4. Click the Atom tab in the Properties dialog box that appears.
  5. Click on the small C icon (under the box with the CH3 label in it).
  6. Click the Show checkbox twice so that there is no checkmark in the box.
  7. Click Apply, then close the dialog box.

The second method turns off labeling for all termini currently drawn on the structure.

  1. Switch to Structure mode.
  2. Click the Select/Move button.
  3. Select the entire structure.
  4. Move the mouse over the structure until all the squares turn black.
  5. Double-click to open the Properties dialog box.
  6. On the Common tab of the dialog box, click the Terminal checkbox until it is empty.
  7. Click Apply, and close the dialog box.

Finally, the following method will prevent the 'not shown' label from appearing when the mouse is over the terminus:

  1. Click the ABC icon on the left vertical toolbar.
  2. Click the terminus to be altered.
  3. In the Label box, hold ALT and enter the number 255. This will enter a blank space in the box.
  4. Click Save. (This will add this label to the list as an invisible entry after the last visible one. If another label is added, the line will appear as a blank line in the list of user labels.)
  5. Click Insert; the label will be inserted and the dialog box will close.
  6. The label should stay in the label menu; the next time it is needed, click the ABC button, the group to hide, the blank entry from the list, and finally Insert.

Q: How do I calculate internuclear distance in ACD/3D Viewer?

A:

  1. Switch to Balls and Sticks view mode.
  2. From the Tools menu, choose Change Geometric Parameter OR on the top toolbar, click Bond Length.
  3. Click on an atom to select it.
  4. Click on the atom at the other end of the bond. The Internuclear Distance dialog box appears. The distance between the atoms will also appear on the Status bar.
  5. To exit the Internuclear Distance dialog box, click OK.

Please note that the distance calculated is center to center of the atoms.

Q: How do I draw an arrow for a null reaction in ChemSketch?

A: After drawing the reaction arrow:

  1. On the general toolbar of ChemSketch, switch to Draw mode.
  2. On the Drawing toolbar located on the left of the screen, click the Line button.
  3. Draw lines or a cross on the reaction arrow in the style required.
  4. With the Select/Move/Resize button active, select the arrow with two lines or a cross.
  5. On the Editing toolbar, click the Group button. The arrow and the two cross lines will become one object.

OR

  1. On the general toolbar of ChemSketch, switch to Draw mode.
  2. On the Drawing toolbar located on the left of the screen, click the Text button.
  3. Click anywhere in the working space of ChemSketch to get the text box.
  4. Type "X" in the text box.
  5. With the Select/Move/Resize button active, select the text box by clicking "X”.
  6. From the Tools menu, choose Font Panel. The Font dialog box appears.
  7. From the size drop-down list, choose the appropriate font size.
  8. Click Apply. The letter"X" will be resized.
  9. With the Select/Move/Resize button active, click on the letter "X" to select it and then move it over the reaction arrow.
  10. Select the arrow with a cross.
  11. On the Editing toolbar, click the Group button. The arrow and the “X” will become one object. (Note: the selection box must be bigger than the text box in order to Group).

Q: How do I switch a polypeptide chain with right-handed alpha helices to left-handed alpha helices?

A: The Flip (on Bond, Top to Bottom, and Left to Right) buttons are located on the Structure toolbar. Please experiment with the different types of flips that can be preformed to achieve the desired result.

Q: How do I draw H-bonds?

A:

  1. In Structure mode draw the molecules that are going to be H-bonded.
  2. In Draw mode, draw a straight line.
  3. Select the line, click the Tools/Pen Style panel. To open this panel press CTRL + SHIFT + P.
  4. In the Pen dialog box, select the dashed line style.
  5. Click Apply.

Q: How do I add deuterium to a molecule instead of hydrogen?

A: his can be done quickly with the atom labels

  1. On the Atoms toolbar, click the Edit Atom Label button.
  2. On the workspace, click the group you want to change, for example CH3.
  3. In the Edit Label dialog box, type 'CD3' in the top box with C and D capitalized.
  4. Click Insert.

This label can be used to represent fully deuteriated methyl groups. Please note that the CD3 label will stay defined, so that the next time it is needed, select it from the list rather than typing it.

Q: How do I link OLE objects between ChemDraw and ACD/ChemSketch?

A: To link OLE objects between ChemDraw and ACD/ChemSketch, use the following steps:

  1. Draw a structure or any other object in ChemDraw.
  2. Select the object and copy it (from the Edit menu, choose Copy).
  3. Go to ACD/ChemSketch window and from the Edit menu, choose Paste/Special.
  4. In the Paste Special dialog box, click Paste, highlight the CS ChemDraw Drawing line, and click OK.
  5. Double-clicking on the pasted object in ACD/ChemSketch will open ChemDraw with the same drawing.

Q: Is there a way to change the size of structures or reactions in ChemSketch without converting to a picture file?

A: To resize structures:

  1. First, draw your structures or reactions in Structure mode.
  2. Press the spacebar to switch to Draw mode, and lasso all the images to be resized.
  3. Point the mouse toward a corner spot until it changes to a diagonal double-sided arrow.
  4. Drag the corner toward the center of the image to reduce its size. Note the percentage reduction should be plainly visible.
  5. Press the spacebar to return to the Structure mode. All the images are back to structures.

As long as a structure is not grouped into a single image with another, that individual structure will inter-convert between structure and image according to the current mode. The only time that the file will fail to transform back to a structure form is if several distinct structures are grouped together into a single master image.

Q: How do I save 3D images from ACD/3D Viewer in GIF format?

I was pleased to read that ChemSketch 5.0 saves structures in GIF format, but I wish that your 3D viewer program, ACD/3D Viewer 5.0, would also save in GIF format. The 3D images are so nice that I would like to put them on my web site!

A:

  1. Start up the ACD/3D Viewer and click on the ChemSketch button at the bottom.
  2. Draw or read in your molecule in ChemSketch, and click on the 3D Optimization button.
  3. Click on Copy to 3D at the bottom of the window.
  4. In the 3D Viewer window, select the display option(s) desired.
  5. From the Edit menu, choose Copy. This will place the 3D image into the Windows Clipboard so that it can be pasted into many things such as MS Word or Paint programs.
  6. Click on the ChemSketch button at the bottom.
  7. Select Draw mode (top left-hand corner).
  8. From the Edit menu, choose Paste. This will place the 3D image into the ChemSketch Window.
  9. From the File menu, choose Export and save the file in GIF format.