Chemistry 130 course documents archive

Frequently asked questions

Contents

Getting started

Where’s the window with all the programs?

In Swain Library, to bring up the CD User window, click on the START button (lower left corner of the screen) and select CD USER. The window with the program icons should now appear.

In Meyer Library’s PC clusters, select the CHEMISTRY APPLICATIONS icon from the desktop. If programs will not launch from that window, then choose the CITRIX icon on the desktop and open programs from the CITRIX window.

I’m getting a “C:\AUTOEXEC.BAT” error when I try to launch any program.

Sounds like you are using a bad link under the START button. Try going through the CD User window instead. (START button > PROGRAMS > START UP > CD USER. Then double click on desired program.) Or, you can just restart the machine; the CD User window will launch automatically at start-up.

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Combined Chemical Dictionary (CCD) on CD-ROM (Version 4:1)

How do I launch the program?

  • Click START (lower left corner of screen) > CD-User
  • Open Citrix
  • Select Combined Chemical Dictionary
  • Click on Compound Search (right side of screen)

or

  • Click START > CD-User
  • Open Chapman_Hall Dicts.
  • Click on Compound Search (right side of screen)

How do I search by physical property?

  • Click cursor into blank window next to the property to search
  • Type in numerical range with blank spaces before and after the hyphen (e.g. “45 - 50”)

or

  • Click on the Browse Index button next to the physical property name > Highlight and select the desired search term(s)
  • Click on Back to Search
  • Click on Search icon (second from left)

How do I select the search term by browsing an index?

Click on the Browse Index button next to the desired physical property (e.g. molecular formula) > Highlight and select the desired search term(s) (e.g. -only-C H N O) so that term(s) appear in bottom window > Click on Back to Search

How do I search for certain numbers of elements? (e.g. 15 Hydrogens)

You can search fragments of chemical formulas. From the Compound Search screen, type “H15” in the molecular formula field. (NOTE: Formula fragments are case sensitive.)

How do I search for certain numbers and types of elements? (e.g. 15 Hydrogens and only specific elements)

Use Boolean operators. Type “H15” AND “-ONLY -C H N O” in the molecular formula field. Or, use the browse index screen to select “H15”, then change the operator via the pull down menu to “AND”, and then select “-only- C H N O”. The complete search term should appear in the box at the bottom of the browse screen. Select “Back to Search” to add your search to the main search menu.

How do I search for a range of element numbers? (e.g. 15–18 Hydrogens)

Type “H15” or “H16” or “H17” or “H18”. To search C1 - C5, type “C” or “C2” or “C3” or “C4” or “C5”. Do not type “C1”. (Remember, molecular formulas and formula fragments are CASE SENSITIVE!) You can also use the browse index screen to select terms, create your search statement, and paste the statement back into the main search screen.

How do I limit my search to organic compounds?

In the main search window, edit the search window to include the option Dictionary Subset. Browse the index to select Organic Compounds and add to your search.

How do I use “NOT” in a text search?

In the lower text search area of the main search window, click on the left column box until it reads “NOT”. (Each click cycles the box through “AND”, “OR”, then “NOT”.) Enter your search term(s). [note: if you are entering a Chemical Name, MF, Type of Compound, or Type of Compound Words, then browse and select your term from the index for proper capitalization and punctuation.] Run your search.

How do I refine a text search with a structure/substructure search using “NOT”?

In the main search window, click on the AND until it becomes NOT. Be sure the arrow between the text and structure search windows is pointing up. If it is pointing down, click on the arrow to change its direction.

How do I draw a ring?

Click on the “Structure Drawing” button to enter the structure drawing window. Click on ring tool (next to pencil tool). Click on desired ring. Click on work surface to paste into structure search window. When finished drawing the structure, click on the green arrow to add the structure to your search query.

How do I draw chains/functional groups?

Click on the “Structure Drawing” button to enter the structure drawing window. Click on pencil tool. From the top menu bar, choose Draw and select Shortcuts (for functional groups) or Atoms. Click on desired elements. Click on to work surface to paste into structure search window. When finished drawing the structure, click on the green arrow to add the structure to your search query.

How do I draw structural fragments not connected to one another?

Click on the “Structure Drawing” button to enter structure search window and draw the unconnected structural fragments. Click on the green arrow to paste the fragments into your search query.

How do I view all structures in results?

Click on the Hit List button (third from left). Click on the Display Report button (fourth from right, looks like a monitor). If the structure is not available in the Report format, then return to the Hit List, click to highlight on the compound of interest, and then click on the Structure Drawing button (to the right of the benzene ring button). NOTE: this view opens a second structure drawing window which may suddenly disappear, return you to the main query window, and paste the viewed structure into the structure drawing query box. Just click on the Hit List button to return to your previous search result.

How do I view the full entry of results and the structure of parent compounds?

From the main query window, click on the Hit List button (third from left). Double click on the compound of interest to open the full entry. If a structure does not appear, then click on the benzene ring button. If a structure still does not appear, then return to the List Hits view and follow the directions in the previous question.

How do I view my results by molecular formula?

You must use the Report format. From the List Hits display, click on the Report Settings button (fifth from the right). If molecular formula is not in the Selected Fields window on the right, then add it. First click on a blank area of the Selected Fields window. Then click on the pulldown menu under the Current Field window on the right and select Molecular Formula. Once Molecular Formula appears in the Selected Fields window, then click to highlight it. Click on the pulldown menu for Sort Key in the Current Field window and choose Primary (Ascend). Finally choose Preview Report from the bottom set of six buttons to view your results sorted by Molecular Formula.

How do I mark entries for printing?

You can only mark entries in the List Hits or Full Entry view. Click on entry to highlight it. Click on red Check (Bookmark/Unmark) button (5th button from left) to mark or unmark entries for printing

How do I combine two structure search results using “NOT”?

Use the Combine Hits option on the main search query page. First, run the searches you wish to NOT. Then go to the top menu bar and click on Search. Select the last option Combine Hits. Click on a numbered search until its number appears in the top search box. Then click on the NOT operator from the bottom left until it appears in the top search box. Then click on the search you wish to NOT out until its number. e.g. 1 NOT 2. Then click Combine in the lower right corner. The screen will automatically return to the main query window. Go back to the Search menu bar, and this time select Show History. Be sure your NOT search is the highlighted search result. Then close the window. Click on List Hits to see the results of your NOT search.

How do I print results?

You can print three views: hit list (name, CAS registry number, molecular formula), full entry, and report (user defined).

  • List of hits: from the List Hits view, click File on the top menu bar and select Print Hit List.
  • Individual full entry: click on File from the menu bar and select Print Records.
  • Report view: click on Report from the menu bar and select Print. NOTE: Do not use the Print button while looking at the report view. This will not print the report view. Instead, it will only print the full entry of one compound.

DOC seems really slow to log on. Is something wrong?

No, nothing is wrong. DOC seems to take longer to log on than POC.

I’m getting a “DDE” error when I try to search. What’s the problem?

Often, this happens when both DOC and POC (Properties of Organic Compounds) are both open. Check the task bar at the bottom of the screen. If POC is launched, then click on it and quit out of the program. Now go back to DOC. The search should work now.

My search is taking a really long time. I think the computer’s frozen.

Check your molecular weight ranges. Searching a range of 5 whole numbers is the recommended maximum. A range of 10 whole numbers can freeze up the CD-ROM.

Is a range of 10 whole numbers too large for a property search?

Depends on the property. For molecular weight, that is too broad. For melting point, the CD-ROM can handle it. MW is pickier because there are so many compounds found within a 10 whole number range.

What does 9CI in the following name mean: 9CI in H-pyron-3-carboxylioc acid, 9CI?

The “9th CI” is the “9th Collective Index,” a cumulative index for Chemical Abstracts. This means that H-pyron-3-carboxylioc acid is a Chemical Abstracts name (as opposed to a name determined using IUPAC naming rules) and that the CAS rules used were from the time period of the 9th Collective Index.

When I run a search, sometimes the color bar doesn’t move. I tried hitting the “abort” button and re-running the search, but the bar still doesn’t indicate that the search is running. What can I do to make the search work?

Just don’t abort it. Even though the color bar is not moving across the screen, the search is running. The reason the bar doesn’t always move is the computer’s operating system. DOC is designed to run on Windows 95 so the color bar works when you’re using a Windows 95 machine, like the computers in Meyer. But the color bar does not work on machines running Windows NT, like the machines in Swain Library.

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Properties of Organic Compounds (POC) on CD-ROM

How do I search a substructure?

Sorry. You should be able to, but the substructure section of the program seems to have a few bugs yet. So, don’t do a substructure search in POC. Look at chemical names and molecular formulas after doing a property search to help narrow down results.

How can I print my table of results?

  1. Highlight rows to Copy (50 rows MAX)
    • To highlight a row, click on the box to the left of the row
    • To highlight a block of rows, highlight the first row and then hold the <shift> key down and hightlight the last row desired.
    • To highlight the entire table, click on the top left-hand corner box of the table.
  2. “Edit” Menu > Copy Table
  3. “Start” Button (lower left corner) > Winword
  4. In Word, “Edit” Menu > Paste
    • Special for Excel: POC will not allow pasting directly into Excel
  5. Copy table in Word
    • highlight table
    • “Edit” Menu > Copy
  6. Launch Excel [“Start” Button (lower left) > Excel]
  7. Select a cell
  8. “Edit” Menu > Paste

To Print a Table

From Word:

  1. “File” Menu > Page Setup > Paper Size > Orientation > Select “Landscape”
  2. “File” Menu > Print > OK

From Excel:

  1. Highlight the entire table
  2. “File” Menu > Print > Page Setup > “Page” tab
  3. Under Orientation > Select “Landscape”
    • Under “Scaling” > “Fit to 1 Page”
    • Click “OK”
  4. Under “Print What” > “Selection”
  5. Click “OK”

My search is taking a really long time. I think the computer’s frozen.

Check your molecular weight ranges. Searching a range of 5 whole numbers is the recommended maximum. A range of 10 whole numbers can freeze up the CD-ROM.

Is a range of 10 whole numbers too large for a property search?

Depends on the property. For molecular weight, that is too broad. For melting point, the CD-ROM can handle it. MW is pickier because there are so many compounds found within a 10 whole number range.

DOC has more compounds than POC, but when I ran the exact same searches on both, only one compound overlapped between them.

The total number of compounds in the CD-ROM will not determine which one contains your unknown. It may be listed in both or one of them.

I’m getting a “DDE” error when I try to search. What’s the problem?

Often, this happens when both DOC and POC (Properties of Organic Compounds) are both open. Check the task bar at the bottom of the screen. If POC is launched, then click on it and quit out of the program. Now go back to DOC. The search should work now.

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Beilstein Crossfire

How do I access Beilstein from the dorm?

You can download the client software package to your computer. See Swain Library’s Beilstein and Gmelin Crossfire page.

I ftp’d the Beilstein Crossfire folder onto my Mac but when I try to connect to beilstein.library.wisc.edu it doesn’t work. Here’s the beginning of the script I get on the computer. Can you tell me what’s wrong?

Alx telnet (librover.doit.wisc.edu)
[?7] [?1] (B =[?25h [m (B [H [2J 7 [1;24r 8
-----------------------------------------------------------------
[65DWELCOME TO MADCAT - THE COMPUTER CATALOG OF THE
[45UNIVERSITY OF WISCONSIN-MADISON LIBRARIES
---------------------------CAT6.3-------------------------------------

The computer is going to the wrong telnet port. The way you can tell is that the Macintoshes display all the connection information up front. You are connecting to the library’s catalog instead of Beilstein.

The solution is to copy over the crosslink preferences file from http://minerva.library.wisc.edu/ to your System/Preferences folder. When downloading from the page, the file is actually inside a folder. Copy only the file inside and not the whole folder. You should then be going to the right port.

I’m getting “Slow Response” and “Abort” messages when I try to login to Crossfire. Should I abort and try again or just wait?

Those two messages often appear during login and are mostly due to Internet traffic. Wait for a minute or two before trying again. If you hit “Abort”, then QUIT out of Crossfire and relaunch the program before trying to login again.

While you’re waiting, you could also check and make sure that your “Caps Lock” is not on. If it is, release the “Caps Lock”, “Abort” your login attempt, “Quit” Crossfire, and start over. (Login/password are case sensitive and must be in lower case).

How do I find derivative information in Beilstein?

Please refer to Cheatsheet for Finding Derivatives

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ACD/ILab (ACD Interactive Lab)

What does ACD labs have?

For Chem 130/132, ACD Lab’s “Interactive Lab” has 2 types of information that may be of interest to you. For a specific structure, you can look at:

  1. PREDICTED proton NMR (HNMR) spectra, including shift tables
  2. Physical properties such as refractive index and pKa

How do I get to ACD’s Interactive Lab?

Open Netscape > Go to http://www2.acdlabs.com/ilab/ > Click on “Enter as SL User” (left column) > Click on “Enter as SL User” (middle of page)

How do I draw a structure?

To launch the structure drawing applet, click on “Structure” in the top menu frame.

To draw a bond:

Click and hold down the left mouse button on the workplace screen while dragging from one element to another.

To change a bond value (single, double, or triple):

Double click on the bond. The bond value will cycle through from single to double to triple. Stop double clicking when the bond value you want is reached.

To draw a ring:

Click on the “template” button (4th from left, next to the “A-” button) > click on the downward triangle next to “select group” (top left of window) > click on aromatics > wait for the images to load > click on the structure you want > template window will disappear > click on the workplace surface to paste your structure in to the window.

How do I search my structure?

Draw your structure in the structure editor > choose the property of interest (e.g. HNMR Predictor from the top pull down menu) > Enter the appropriate frequency > Click on the “calculate” button.

How do I print search results from ACD Lab predictions (e.g. HNMR spectral diagram)?

Resize and position your spectral diagram to show the data that you want to see. Then, click on the printer icon. Your currently viewed data is turned into an image and pasted on a blank Netscape page. Click on the print button on the browser to print your search results.

How do I make the ILAB windows go away?

The windows won’t collapse unless you exit the ILAB. To exit ILAB, click on the door icon in the top right of the screen.

How do I exit the program?

Click on the door icon in the top right of the screen to exit the program

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Non-database-specific questions

Are all the unknown compounds in POC or DOC?

If you are a 130 student, then the answer is “yes”. If you are a 132 student, then the answer is “no”. However, most of them are. If you suspect that your unknown is not in POC or DOC, then check with the Swain Librarian for more specific search techniques.

Where can I get the IUPAC name?

You can use ACD’s Interactive Web Laboratory Name Program or look at the “AutoNom” name field in Beilstein Crossfire records to get an IUPAC name.

What are “trivial” names?

According to Grant & Hackh’s Chemical Dictionary (5th ed), a “trivial name” is a name that is not systematic and thus devoid of structural significance (p. 604).

Can I identify a compound by odor (e.g. cinnamon)?

Check Aldrich’s Flavors and Fragrances located on Permanent Reserve, under “A” for “Aldrich”. The index of type of smells begins on p. 89.

The chem tutor mentioned a CRC book that might help me. It’s not the index but a thin book. It has just molecular weight and melting point information in there. Do you know what s/he is talking about?

The Chem 130/132 Library resources page lists several resources for identifying parent unknown compounds. The book you are looking for is the CRC Handbook of Organic Compound Identification. It is a single volume and Swain has six copies on reserve. Swain also offers the CRC Handbook online.

Is there a copy of a carboxylic acid book at Swain Library? I asked the person behind the desk and they said there was no such thing, but I can remember you mentioning it at the orientation session.

Students working the reserve desk do not know items on reserve by their contents. What you want is the CRC Handbook of Organic Compound Identification.

The screen shows an overwrite warning: “PKUNZIP: <w18> Warning! Poc5x.mdb already exists. Overwrite <y/n/a/r>?” What should I do?

“POC5restore”, a housekeeping program, was launched, probably accidentally. To close the program, type “n” on the screen for “no” after the “?” prompt.

Are there other sources on the web that I may use to identify my unknown?

There are free physical property databases on the Web. You are not prevented from using them. But please keep in mind that (1) the quality of the data found on the web does vary considerably and (2) your unknown might not be in the web databases that you are searching.

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