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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.

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 CambridgeSoft store. Create an account (you can opt out of email communications), then log in and select the "Site Subscription Program" tab near the top of the page. Then scroll down to CU-Boulder and hit "Click here to download using your CU-Boulder email address." Once you get to this page you should be able to put in your email address. (Alternatively you can log into the site first, and then use this direct link to go to the download page.) Once you input your email address, you will be emailed a serial code for ChemDraw, and you will be sent to a page where you can download the software.

If you already have ChemDraw installed on your computer but the serial code has expired, you will have to go through the above steps to be emailed a new code (you don't have to download the program again, though). Once you have the code, open up ChemDraw on your computer. If you're using the PC version you can go to the "Help" menu in ChemDraw and select "Activate ChemDraw," but if you're using the Mac version you have to go to the "ChemDraw" menu in ChemDraw and select "Activate ChemDraw." Then input the new serial number you were emailed and hit "Activate Over Internet."

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.

To download the software, go to the MestreLabs website and save the installation package on your computer. You will also have to download the license file from the OrgChem virtual server. Save this license file to a convenient location on your computer, and remember the location. Mac Users: Your computer may attempt to save this file with a name that ends in ".lic.html". If this happens, right-click the file and select "Get Info". In the part of the window that says "Name & extension", manually change the file name to delete the ".html" part, so that the file just ends with ".lic".

Run the MestreNova installer. Note that there are modules in this installation for which we do NOT have a license. Specifically, these are the "NMR Predictor Plugin," "Mass Plugin," "DB Plugin," and "Verify Plugin" modules (in other words, everything but the "NMR Plugin"). In this new version, you can uncheck these modules, and only the NMR Processing part will be loaded. When you try to uncheck the Mass module, you might see several popups asking to connect to other network resources; simply select "NO" for these, and you will ultimately be able to uncheck the Mass module. Unchecking the Mass and DB modules makes activating easier, and you will not be asked for additional licenses later. Mac Users: You will need to click [Customize] to uncheck all modules except the "NMR Plugin".

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 green checkmarks. 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, 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.

Downloading your NMR Spectra

If you input your email address when submitting your sample, you should automatically be emailed your spectra. However, if you do not receive it, you can download it from the NMR server instead. To access the server, you must either be on-campus, or using VPN as described above.

The server is located here. Your browser might complain about the website's security certificate, but you should be able to select "Continue to website" or something similar. Depending on your browser, this may be listed under advanced options. Sign in using the username "student" and the password "$NMR300". Double-click the File Station folder. Once it opens, go to OChem_Lab → nmr. Select your folder but don't open it. (Folders are named as "Semester_SectionNumber_Initials_SampleName". So if it's Spring 2016, you're in section 201, your initials are JMR, and you named your sample "Acetylferrocene", then your folder will be named 2016S_201_JMR_Acetylferrocene). Go to Action → Download. The folder should download as a zip file. You can now work up the spectrum in MestreNova.

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.