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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.

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.

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.

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 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:

MestreNove Plugins selected as described above

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:

Successful license installation

If you see the green checkmark, MNova should be ready to use. Mac Users: 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!) If you still can't contact the license server, please email the lab director so the license server can be rebooted. If you get an error message indicating that some features were not activated, it's because you didn't uncheck all the unlicensed modules. You should simply check the two boxes ("I've read the above information", and "Don't show this message again"), and you will not get this error again.

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.

SciFinder

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.

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.