CHEM 333, Spring 2012: Course Info, Manual/Syllabus and To-Do List

Welcome to CHEM 333 

Welcome to CHEM 333, Advanced Synthetic Laboratory.  As we approach the start of the summer 2011 semester, I want to welcome you to the course and also to give you a list of tasks that should be completed in the coming weeks.  Most of these should be completed before the first lab session so that you are adequately prepared and do not fall behind.  I encourage you to read all of the resources here on the course website as well as on Blackboard that are discussed in the to-do list below.  If you have any questions, my door--and e-mail inbox--are already open and waiting to assist you.    

I'm looking forward to sharing my passion for the exciting world of organic chemistry with you.  This semester I aim not only to teach you the chemistry content and laboratory techniques that you require for your academic endeavors, but also to train you in the type of analytical thinking that is required for approaching challenges in the synthesis of organic molecules.  As part of the four projects in this course you will learn how to devise efficient syntheses of organic molecules from simple starting materials; how to search the scientific literature in order to find precedents for your intended synthetic steps; how to implement complex laboratory techniques; how to identify the products of chemical reactions through analytical techniques such as TLC, GC, IR and NMR; how to record and report the results of your experimental work; and finally, how to conduct authentic research to answer relevant questions in organic chemistry.  While you may not aspire to be an organic chemist, I hope that this course will be a rewarding experience nonetheless.  The practical application of technical knowledge in a laboratory setting and the analytical thinking used to approach problems in organic synthesis involves many general skills that  you will undoubtedly employ in your future careers.  

Cheers,  
Dr. Chad Landrie  

To Do List: 

1.  Become acquainted with the resources available on the course website (www.chadlandrie.com).  

2.  Purchase the  required texts and materials   for the course including the textbook, a lab notebook and goggles.  All of these items are available at the UIC bookstore.  You will need your goggles on the first day of lab.  

3.  Carefully read the course syllabus and front material in the lab manual.  The lab manual and syllabus ( 333manual_SP12.pdf) can be downloaded from the  File Sharing page .  

4.  Review the principles of infrared spectroscopy and recrystallization as well as the common functional groups in organic chemistry.  During your first laboratory session, you will participate in an introductory activity in which you will separate a mixture of fluorenone and fluorene by column chromatography. This activity can be found at the end of the laboratory manual.  Through this process you will learn the basics of column chromatography and thin-layer chromatography.  You will also become acquainted with the rotovaps in the laboratory that you will use countless times during the semester to remove volatile solvents.  Following the separation, you will then recrystallize both products and obtain the m.p. and IR spectrum of each.  These tasks--separation by chromatography, purification by recrystallization and analysis by m.p. and IR--will be repeated in almost every synthesis during the semester.  Therefore, it is essential that you use this time to master these techniques now.  Ask lots of questions; don't be afraid to make mistakes; and review the theories of all theses techniques before your first lab session so that you are prepared to participate in an informed manner. 

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!

ACD/Labs NMR Processor & ChemSketch

The academic version of the ACD/Labs NMR Processor is now available for free to students and instructors. It may be downloaded from the ACD/Labs website after creating a user account. This is great news for instructors and students alike. Instead of spending hours acquiring and processing student NMR data, I am now requiring my Advanced Organic Lab students to process their own FIDs. I anticipate that this software will reinforce concepts taught in class as students perform tasks such as Fourier transformation, phasing, peak picking, integration and proton assignment. The download also includes ChemSketch, an industry standard for drawing chemical structures. ChemSketch can be used simultaneously with the NMR Processor to make proton assignments as well as create professional quality spectral reports.


I have posted a short presentation on using the NMR Processor for my CHEM 333 students on the course website's File Sharing page. The instructions within are basic and only scratch the surface of the software's functionalities. What makes it a great application, however, is that you don't need to know much to create a professional looking spectrum in a matter of minutes.  CHEM 333 students should use the ChemSketch template (ACD_333nmrtemplate.sk2) that I've also posted on the File Sharing page when creating their reports. For a sample FID folder to practice with, download the file, ACD_samplefid.fid.zip, on the File Sharing page.


Although ACD/Labs software does not support Mac OS X, I have been using the processor and ChemSketch on my Intel iMac running Windows XP with the Parallels virtualization application. Parallels can be purchased from the UIC Webstore at a reduced price by UIC students and faculty. The only downside to this solution is that I have been unable to cut-and-paste into native OS X Microsoft Office apps like Work and Powerpoint.

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.

Lidocaine NMR Samples

The latest spectra are now posted online.  The lidocaine specs look pretty good!!  The final product, lidocaine bisulfate, is not very soluble in CDCl3, which is why some of you may have observed cloudy NMR sample solutions.  The book uses dimethyl sulfoxide (DMSO) for the NMR sample, which is much more polar and better able to dissolve your final product.  We don't have any DMSO currently, so CDCl3 will have to do; Navid's spectra turned out great in CDCl3 anyway.  Just be aware that the chemical shift values (ppm) for each proton signal will be slightly different than those reported in your textbook since chemical shift is solvent dependent.

Project Two: LFER of Benzanilides

The slides for Friday's (Feb. 15) lecture are now posted. Also, I updated the slides with each student's synthetic target assignments for Project Two. Plan your syntheses so that you will obtain approximately 200 mg of product. Because deciding on a recrystallization solvent system can be time consuming, I will tell you what system works best for the final product: water/ethanol.

NMR spectra online

NMR spectra for CHEM 333 will be acquired by Maria or Brooke each week. These spectra are later processed with iNMR and saved as a pdf file, which will be posted on this website. Each student is responsible for downloading and printing their own spectra each week. If you would like your spectra reprocessed, expanded, etc., send me an email and I'll get right on it. Free versions of iNMR are available (MAC only). If you'd like to upload your own data from the server and process it yourself with iNMR, stop by my office and I'll show you how.

All of your 1H-NMR spectra for benzocaine looked excellent. Great job on your Fischer esterification. We'll discuss the interpretation of 1H-NMR in class on Friday. See you then.