NMR Tube Cleaner

Congratulations to my student, Richard Marszalek, on his recent publication describing the NMR tube cleaner we developed (Landrie, C.L.; Marszalek, R.M. A Durable and Economical NMR Tube Cleaner. J. Chem. Educ. [Online early access]. DOI: 10.1021/ed200104v. Published Online: October 4, 2011.)  This apparatus can be constructed in less than 15 minutes from easily obtainable materials in the lab and at a significantly lower cost than the fragile glass apparatuses sold by commercial vendors.

Accessing UIC E-Journals On and Off Campus

Did you know that the UIC library subscribes to many online versions of academic journals such as Journal of the American Chemical Society, Journal of Organic Chemistry, Organic Letters, Angewandte Chemie International, Journal of Medicinal Chemistry and Journal of Chemical Education, just to name a few? To search for online subscriptions, direct your web browser to the UIC library website; click on the E-Journals tab; then search for the journal title. 

After you've found the publication you're interested in, simply follow the links to the website for the time range of interest. (Note that many online subscriptions are limited to a range of years and there are often different sources for different time ranges.) If you're on campus, you typically will not have to log in with your NetID. You can then bookmark the website for direct access next time. Once you are within the journal's website you can usually search for an article by year, volume, author and keyword. Most subscriptions also allow you to view and download a pdf version of the article.

As a UIC student or faculty member, you can also access online subscriptions from off-campus. The easiest way to do this is to follow the same instructions above. After clicking on the link to the journal from within the UIC library website, you will be asked to enter your UIC NetID and password. This process will connect you to UIC's proxy server so that the journal's website will "see" you as connecting from the UIC campus. Voila! The key here is you must go through the UIC library website each time.  If you do a lot of online research, this becomes tedious. An alternative is to add ".proxy.cc.uic.edu" to the end of any restricted website's URL. For example, the URL for The Journal of Organic Chemistry (JOC) is:


http://pubs.acs.org/journal/joceah


Since I already know that UIC has a subscription to JOC, I just enter the following into my browser's URL bar:


http://pubs.acs.org.proxy.cc.uic.edu/journal/joceah


Notice the ".proxy.cc.uic.edu" is entered right after the domain name (e.g., .org or .com), not at the end of the URL. An advantage of this method is that you can bookmark the proxy URL on your off-campus devices so that you don't have to go through the library website or enter the ".proxy.cc.uic.edu" each time. This method will only work, however, if UIC has a valid subscription for the site you're trying to access. 


Happy researching!

Dropbox as a File Server for CHEM 333, But Better

As a Mac aficionado and app addict, I have a keen sense as to whether a particular piece of software will increase my productivity and entertainment levels or whether it will just decrease my checking account balance. Not that it matters since I usually buy it anyway. What can I say? I'm a scientist.  Most of those "scientific" purchases, however, are disappointing; the software falls short of my expectations and many don't even deliver the utility they promise. When I do encounter a gem, there is usually an "ah, hah!" moment that justifies all the experimentation until that point. Enter Dropbox.


Given Dropbox's current popularity, I'm a little late in finding this one, but ecstatic nonetheless, especially since it's free.  Dropbox is essentially a web-based file hosting service, which provides you with 2 GB of online storage space. In its most modest application, users can upload and download files to their Dropbox folder through the Dropbox website using any web browser; there's no requirement to download any software.  The real power of the service, however, is unleashed when the Dropbox software is downloaded onto each of the user's computers. The software creates a folder called Dropbox on each computer where it is installed. All files placed or saved into that folder are then synchronized across all machines that also have the Dropbox folder installed. That's it! There are no special synchronization steps or instructions to remember.  Just use your Dropbox folder like you would any other and changes are instantaneously (well, almost) synchronized to all Dropbox folders on other machines.  Don't always have access to a computer? No problem; just download the iPhone or iPad app and you've got access to your files anywhere you go.  Dropbox even keeps track of past versions of each file, so that users can revert to older versions if they need.  Worried about losing your files in "the cloud" or when your internet connection is down? No need: All Dropbox files are saved locally on each machine.


As if that weren't enough, you can also share subfolders with other Dropbox members. I am currently using this function in my Advanaced Synthetic Laboratory class (CHEM 333). I set up a shared folder for each of my students where they can save their IR and NMR data files (we have a lot of them!). I can open their files directly from my computer's Dropbox folder, make changes or comments if I want, and then save the file. The changes are immediately available to everyone sharing that folder. You can even set preferences so that you're alerted when a change has been made to a file or folder you're sharing. It's been a great way to keep track of my student's progress in the lab.  It's also a much cheaper (read: free) alternative to setting up a file server, not to mention better.  So far it's worked like a charm and students have been quick to adopt the process.


There are lots of useful applications of Dropbox such as sharing pics with friends, URL links to files, and uploading PDF files to iBooks or PubMed on Tap on your iPad or iPhone.  My favorite so far though is the ability to sync my Bookends reference database and all attached PDFs, which allows me to access and update my reference literature everywhere I go. I just moved the Bookends database and associated Attachments folder to Dropbox and voila. Done!


If I've sold you, then give it a try. Click on the link below and start "Dropboxing" now. If you're on campus and need some assistance or want more information on the applications I mentioned above, send me an email or stop by my office; I'd be happy to help.


Start Dropboxing Now!

Consolidate All Your Webservers with Cyberduck

Disclaimer:  Mac Geeks Only!

I work with several remote servers during the semester.  These include tigger and iccarus accounts (UIC) that host my websites, a Blackboard webdisk, two servers for NMR data at UIC, my MobileMe iDisk and even a server for my copier scans in the Chemistry Department.  Managing each separately is an annoying and time consuming task.  Not only do I have to remember the addresses and login information for each, but until today I used different access methods (e.g., Fetch, MacFusion and the Mac Finder).  Enter Cyberduck.  With this open source freeware app, I have been able to consolidate all of my server connections in one place.  It's main advantage over Fetch (a common FTP client) is that it supports all of the protocols I require, including: FTP, SFTP, WebDav and MobileMe.  If you work with several servers utilizing more than one file transfer protocol, I highly recommend this app.  It's intuitive, has a clean GI and works as advertised.  If you're looking for an app that will allow you to mount those servers as disk images on your desktop, checkout MacFusion which is built on Google's MacFUSE code.  This app, however, does not currently support OS 10.6 (Leopard).

ATR Arrives in FTIR Lab

Long before I began teaching the undergrad orgo labs full-time, I was a TA for this course when I was a chemistry graduate student at UIC. At the time, there were few analytical techniques available for the characterization of organic molecules: no melting point apparatuses, no IR, no TLC and a sporadically functional GC with an unbearably slow analog plotter. A typical synthesis lab was often concluded by the students proudly shoving a yellow powder at me exclaiming, “See, I did it.” Sadly, I would acknowledge their accomplishment with a solemn nod, after which they would chuck their powder into the waste container with a strange jubilation. What was the point, I wondered. That yellow powder could have been anything. After about three years as a teaching assistant for this course, I was shocked one day when I found an infrared spectrometer in what is now the instrument room. I couldn’t believe we weren’t using this equipment in our labs. When I was hired as the full-time instructor, I made utilizing the IR my first priority.  Of course, I quickly realized why this technique had been left by the wayside for such a large class: time. Time training TA’s and students, time creating instructional handouts, and time maintaining the spectrometer were all factors, but the time that it took students to acquire a decent spectrum was the most formidable challenge of all—primarily because of the difficulty students had with sample preparation. For liquid samples, students sandwiched a thin film between two NaCl plates. After the tenth plate was ruined by accidentally washing with and thereby dissolving in water, we switched to disposable PTFE cards. These worked well enough, but it was difficult to get spectra of volatile samples.

Solid samples had to be ground with anhydrous KBr and pressed with a die into a transparent disc. While seemingly straightforward, a number of conditions had to be met precisely right in order to obtain a disc of sufficient transparency and with a high enough sample concentration to acquire a spectrum in less than 5 minutes. The tension was palpable during these labs, especially when time was running short and the line for the IR wound outside the instrument room like a snake threatening to choke the sanity out of student and TA alike.

I’m happy to say, those days are over. The attenuated total reflectance (ATR) accessory, which I have fought to acquire since I began teaching this course, has arrived thanks to the differential tuition money that was made available to the Chemistry Department this year. After several tedious hours of tuning, aligning and swearing, the Pike Technologies GLADiATR was successfully installed. Then came the time of reckoning. After acquiring 64 background scans, I nervously applied a small amount of solid acetanilide to the 2 mm2 diamond crystal, lowered the pressure clamp and then turned the clamp dial clockwise until the pressure tip had pressed the solid into the diamond at 40 pounds of force. I clicked the scan icon on the screen and one minute later I was looking at my first successful ATR spectrum. The results were amazing. The total acquisition time from start to print was 3 minutes—a far cry from the 20 minute average for the KBr technique. Could it really be this easy? After twenty or so spectra later, the answer was a resounding yes. I was ecstatic. It’s a great feeling to know that this technology will radically change how IR is approached in CHEM 233 and I am anxiously awaiting to see how it will be received by the CHEM 233 students this semester.

Please click here for a full-color version of the instructions for using the GLADiATR accessory.

To iClick or not to iClick

A couple years ago I sat in on a lecture at UIC where the instructor was using technology that allowed her to poll her students during class.  She would ask a multiple-choice question, which was duplicated on the overhead projector, and then her students would punch in A, B, C, D or E on their hand held clickers before the timer expired. Within seconds, the results of the poll flashed on the screen—eerily reminiscent of a Who Wants to be a Millionaire lifeline. I was hooked instantly. Not only do I love gadgets, Millionaire and statistics of every kind, but it also seemed like an ideal method for communicating with students in large lectures. Any teacher worth their salt continually asks themselves, “are they getting it?” Some are even brave enough to ask out loud even though they know the question will likely be regarded as rhetorical and disappear into the echoes of the lecture hall. What better way to find out then a reliable polling system such as iClicker?
You are wondering, of course, how this topic is relevant to the laboratory courses blog. In truth, it isn’t; however, next Spring I will be teaching one lecture of CHEM 232 (Organic I) and I am considering using this system. I’ve considered many of the advantages and disadvantages from my perspective. What I don’t know, however, is what students at UIC think are the primary strengths and weaknesses of this system. I would welcome any comments you have. Some key questions that must be considered are:

• What are good and bad polling questions?
• Should the system be mandatory?
• Should the questions be worth points? If yes, what percentage of the course?
• How many questions are too many in one lecture, one semester?
• Is the technology reliable? Is record keeping feasible?
• Will students remember to bring their clickers?
• How much do the clickers cost? Is this a financial burden?