Software for Organic Chemistry
This page gives instructions on how to download the software you will need for organic chemistry labs. All of them are either free for everyone to use, or free for students at CU because we have a site license.
VPN
VPN (Virtual Private Network) software allows you to connect to the internet via the campus servers. Many of CU's resources require you to either be on-campus, or use VPN to access them. Instructions for downloading the recommended VPN program (currently Cisco AnyConnect) are given on the OIT website. Make sure that after you install the program, you set it up according to the instructions OIT gives you at the link above! Otherwise it won't work.
ChemDraw and Other Chemical Drawing Programs
ChemDraw is installed on all the computers in the organic chemistry labs and helproom; feel free to use it at any time that the labs are open. ChemDraw is also installed in a large number of computer labs around campus. To find a computer lab that has ChemDraw, you can use the OIT Lab Software Search Page.
CU Boulder has purchased a site license for the current version of ChemDraw, so it is free to all students. To download and install a copy of this program on your own Mac or PC, go to the OIT ChemDraw page. You can download the program for Mac or PC, plus the activation code. There is also an in-depth User Guide available on the OIT page.
There are also several free alternatives to ChemDraw available, such as MarvinSketch and ChemDoodle. These programs are also perfectly acceptable to use for preparing your lab reports, but the organic lab staff might not have much experience using these programs and will not necessarily be able to help you.
Excel and Other Spreadsheet Programs
Excel is part of Microsoft Office Suite, which is available on the computers in the chemistry labs and help room, as well as most of the computers in the computer labs on campus. To find a computer lab that has Excel, you can use the OIT Lab Software Search Page. CU also allows students to download and use Office 365 ProPlus for free. Instructions on how to do so are located on the OIT website.
There are also several free alternatives to Excel available, such as Google Spreadsheets and LibreOffice Calc. These programs are also perfectly acceptable to use for preparing your lab reports, but the organic lab staff might not have much experience using these programs and will not necessarily be able to help you.
MestreNova
MestreNova (or MNova) is installed on all the computers in the organic chemistry labs and helproom; feel free to use it at any time that the labs are open. CU Boulder has purchased a site license for MestreNova, so you may download and install a copy of this program on your own Mac, PC, or Linux machine. Note that you must be able to connect to the campus servers to download the license file, and also to activate it. If you're on-campus, you must connect to the internet via UCB Wireless, not UCB Guest. If you're not on campus, you will need to use VPN as described above. Make sure that you're actually setting up and running VPN according to OIT's instructions! Just downloading the VPN will not do anything.
First, if you have an older version of MestreNova installed, uninstall it.
To download the software, go to the OIT MestreNova page and save the most recent installation package on your computer, along with the license zip file.
Run the MestreNova installer. When you are asked what modules you want to install, uncheck the entire "MestreNova Plugins" list (every plugin should have a red X next to it), but then select "NMR Plugin". This is the only plugin for which we have a license. Your list should look like this:
If you try to install modules for which we don't have a license, you might have to uninstall and then reinstall correctly. Mac Users: You will need to click on "MestReNova" in the top left corner of the screen (near the apple) and then click "Preferences" from the drop-down list. From the "Preferences" pop-up box you can click "Plug-ins" from the icons at the top of the box and "ignore" everything except the "NMR" option.
When you run MestreNova for the first time, you should see the "Registration Wizard". (If you don't, select "Get/Install Licenses..." under the [Help] pulldown.) Click on [Install], and navigate to wherever you saved the license file. Select that license file (if it asks if you want to replace your previous license file, choose "Yes"). You should see a confirmation message indicating that the license file was installed correctly. Click [OK]. After you have installed all licenses, you will need to restart MNova. Look in the bottom right corner of the window (or check the License Manager under [Help]), and you should see a green checkmark:
If you see the green checkmark, MNova should be ready to use. Mac Users: You may have to go through these steps the first time you run the program. If the "Registration Wizard" window pops up again and again each time you restart MestreNova, it's because you selected the wrong modules to install. Uninstall the program and start over.
If the program was unable to contact the license server, there will be a red X in the bottom right corner and you will see a popup about being unable to contact the server. In this case, first make sure you have followed all the instructions above (especially the part about being connected to UCB Wireless, not UCB Guest!) Mac Users: You may need to go through a few extra steps to fix this issue. First, go to the Help menu, open the License manager, and delete all the licenses. Then, reinstall them from the zip file containing all the licenses, not the extracted folder.
Now that your copy of MestreNova is activated, it will run for up to 90 days without needing to communicate with the license server again. Every time you use the software when you are connected to the campus network, it will automatically update your license extending your time for another 90 days. Therefore, you can use the software offline, away from the campus network for up to 90 days. After this time, however, you will either need to connect by VPN again, or bring your computer onto campus.
What If You Don't Get Your Spectra?
There are several reasons why you might not receive your spectra, or might not be able to open them. This troubleshooting guide should help you fix any issues.
- If you haven’t received an email with your spectrum: You might have input your email incorrectly, or the NMR server might have been unable to send emails for a while. Check to see if your spectrum is available by going to the NMR fileserver page and searching the page for your spectrum. Files are sorted alphabetically, and named as "Semester_SectionNumber_Initials_SampleName". So if it's Spring 2022, you're in section 201, your initials are XYZ, and you named your sample "Acetylferrocene", then your folder will be named 2022S_201_XYZ_Acetylferrocene.
- If you haven’t received an email and your folder is not on the server: One of two things are possible.
- It hasn't been run in the NMR yet. Check to see if any of your classmates have spectra available for this lab yet - if most of them are done, it's possible your sample was skipped for some reason. In this case, visit the NMR room at any time that labs are running so you can resubmit it to the queue, or (with your TA's prior permission) use the example spectra from Canvas.
- Your sample was successfully inserted into the NMR magnet, but the spectrum was never collected. Often this is because something is wrong with the sample preparation (label is badly wrapped, too much solid precipitate in tube, solvent too low, or non-deuterated solvent). In this case you will have to visit the NMR room at any time that labs are running so you can fix whatever needs fixing and resubmit it to the queue.
- If you have your folder and there's a FID file inside it, but MestreNova won't open it: First, check the bottom right corner of MestreNova. If there's a red circle, something went wrong with your installation so you'll have to try again. If there's a green circle, your license is set up properly. There are two options for opening spectra: either open the entire zipped folder, or unzip the folder and then open the FID file. To unzip a folder in Windows, right-click and select Extract All.
SciFinder and ACS Literature
SciFinder is the most powerful literature-search tool available for chemists, and will allow you to find any compounds with the same or a similar structure to your compound. Before you can use SciFinder, you will need to request an account. Go to the CU library's website and follow the directions there. Once your account has been created, you can log in by going to SciFinder's home page. You must be on campus or using VPN.
The CU Boulder Libraries have recently made a change to off-campus access for the American Chemical Society (ACS) publications. ACS publications will no longer be accessible using the campus VPN. Instead, users will need to log-in to the Library’s EZProxy. You can also lookup particular journal titles that are available electronically by going to the Libraries homepage and then clicking on the link to E-Journals (underneath that big box that says Find Articles) and search for the journal you need. If you are off-campus you will be asked for your identikey username and password. For more information, including a link to a browser extension that makes it easier for you to access Library resources off-campus, click here.
Avogadro and GAMESS
Avogadro and GAMESS are free software used for computational chemistry. Avogadro is available for Windows, Mac and Linux; it can be downloaded from the Avogadro website. GAMESS can be downloaded from this website (only accessible from on-campus or via VPN). Once you have installed GAMESS, go to the folder where it is installed and open the README file.