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Practical NMR: Collecting and Interpreting Your Own Spectra

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Practical NMR: Collecting and Interpreting Your Own Spectra Experiment 4 Practical NMR: Collecting and Interpreting Your Own Spectra Reading: Handbook for Organic Chemistry Lab, chapters on NMR Spectroscopy (Chapter 18) and Identification of Compounds (Chapter 20). Organic Chemistry, Marc Loudon, 6th ed., pp. 611-653 (13.1-13.7); pp. 662-667 (13.10-13.11). Previously, you learned how to interpret the 1H NMR spectra of pure compounds. In this experiment, you will learn how to collect and analyze your own spectra and deal with all the complications of impure samples. This way, you can use NMR to assess how successful each of your reactions is in future experiments. There is no prelab or quiz for this experiment. You can save some time by installing MestreNova on your computer before the lab. To do this, go to www.orgchemboulder.com/Labs/Software and follow the instructions for acquiring and installing MestreNova. Note that this software needs to contact a license server which can sometimes be unreliable, so make sure you install this software well in advance of when your writeup is due! Inability to contact the server will not be considered a valid excuse for late work. How to Prepare and Submit an NMR Sample As soon as you arrive in your lab today, clean an NMR tube and cap with acetone and allow them to start drying upside-down in a flask. This will mean that your tube is ready to use when you need it for running your own spectrum. If the cap is stuck to the tube, you can soak it off by filling a vial or small beaker with acetone, and placing the end of the tube upside-down in the acetone for a few minutes. The majority of NMR samples are run in solution – a little of the sample is dissolved in a solvent. Since all hydrogen nuclei (protons) are visible in NMR, any protons in the solvent molecules will likely give off a much stronger signal than protons in the sample, since there are so many more molecule of solvent present, and will drown out the peaks from the sample. The best way to avoid this problem is to use a solvent where all of the protons have been replaced with deuterium, called a deuterated solvent. These deuterium atoms will not interfere with the signal from the protons in the sample. (Another reason why deuterated solvents are necessary is that the instrument needs to “lock on” to the separate signal that comes from the deuterium nuclei, to ensure that it is properly tuned.) Some common deuterated solvents include CDCl 3 (deuterated chloroform), D 2O (deuterated water), and CD 3COCD 3 (deuterated acetone or acetone-d6). Of the deuterated solvents, the most commonly used is CDCl 3, since it has fewer deuterium atoms per molecule and is therefore less expensive (although still fairly expensive). Most compounds will dissolve in CDCl 3 readily, but if not, then D 2O or acetone-d6 can be tried instead. You should already have rinsed your NMR tube with acetone by this point, and allowed it to dry for at least an hour. This is a good idea for any experiment that requires an NMR spectrum. If you ever forget to give it time to dry, you can remove most of the acetone by adding a small amount of CDCl 3 to a depth of half an inch in the tube, and tilting the tube back and forth to rinse it. However, due to cost, this solvent is better to save for actual spectra. It is important to avoid having solid particles in your NMR sample. This is because particles distort the magnetic field in the solution around them, causing all of the spectrum’s peaks to appear broad and smeared-out. For this reason, it is best to make up your sample in a separate vial first before transferring it to the tube. If you have very little sample or if your sample is too gummy to transfer to a vial, you can 39 Experiment 4: Practical NMR also just add solvent directly to the flask that contains it. Then, once your sample has dissolved, you can pipet the solution into your tube, while carefully avoiding the transfer of any particles. Once your sample is dissolved in deuterated solvent, you will place it into an NMR tube, a narrow glass tube that can be capped at one end. To keep track of which tube is yours, you will need to wrap a special NMR tube label around it. When your sample is placed in the instrument, it will be spun very rapidly to cancel out any unevenness in the tube walls. For this reason, you should wrap your label tightly, so that it will not make the tube spin off-balance. These labels are self-laminating: the white half with writing on it is wrapped around the tube first, and then the clear half is wrapped around the outside to prevent the writing from being smudged off. You will need to peel old labels off the tube before applying your own. Do not use regular label tape, do not allow any parts of your label to stick out or bulge, and do not apply your label over any labels that are already present. If you do any of these things, your tube may be pulled out of the NMR queue by the lab staff. The teaching labs at CU have a Bruker Avance-III 300 NMR Spectrometer. This instrument uses an autosampler: a rotating rack capable of holding up to sixty samples, which can place a sample into the NMR and remove it afterwards. This is invaluable for processing the large number of NMR samples produced by the organic teaching labs, since samples can be submitted quickly and then allowed to run overnight. Each sample typically takes two to four minutes for acquisition of a 1H NMR spectrum. When submitting samples, you should type in your email address, so that the instrument will email you your spectrum as soon as it is finished. The drawback is that the autosampler crashes easily if the sample is not prepared according to specifications. If the tube is damaged, if the label is placed incorrectly, or if the sample is placed in the wrong spot on the rack, then the autosampler may crash and stop running samples until it is reset. An even more important reason to be careful is to avoid breaking the NMR machine itself. If your NMR tube is dirty and deposits residue inside the machine, or if it breaks inside the NMR, then the instrument will be unusable for all other organic students, potentially for several months. For this reason, FOLLOW THESE INSTRUCTIONS CAREFULLY. Figure 4-1 and Figure 4-2 below will show you how to prepare, label, and submit your NMR sample. Once you have done this, input your sample information into the computer in the NMR room. How to Input Your Sample Information 1. On the computer next to the carousel, enter your sample details into the form. Make sure that your sample position matches the sample position on the form. Use a unique description for each sample you submit – if you use the same sample name twice, your old spectrum will be overwritten. If you had to put your tube in the overflow rack, use the rows towards the bottom of the form labeled “Overflow 1”, “Overflow 2”, etc. 2. Make sure your tube label is legible! If the spreadsheet is lost for any reason, the lab staff may have to re-enter the information based on what they can read from the labels. If your label doesn’t have your initials and section clearly visible, you may never receive your spectrum, or even your tube back. 3. You should be emailed your spectrum the next time the carousel is run, usually within a day or two. If you are waiting for longer than this, you may need to download it from the server yourself, or come in to resubmit your sample. Instructions are posted at www.orgchemboulder.com/Labs/Software, under “What If You Don't Get Your Spectra?”. 4. All the tubes submitted by your section will be set out in the NMR room, so that you can pick up your tube during the following lab and reuse it. Make sure you pick up your own tube from the rack and not someone else’s. Rinse it with acetone and allow it to dry until you need it again. 40 Experiment 4: Practical NMR Figure 4-1: The steps to prepare and label an NMR sample. 41 Experiment 4: Practical NMR 1 Figure 4-2: The steps to submit an NMR sample to the queue. 42 Experiment 4: Practical NMR Working Up Your Spectrum in MestreNova For the following sections, there are example spectra files available on the orgchem website. You can access them directly by going to www.orgchemboulder.com/Labs/Experiments/PracticalNMR.zip. You should download this file, unzip it, and follow along with the steps to work up the spectrum yourself (you will need to turn it in as part of the experiment). If you haven’t already done so, you should also download and install MestreNova, following the directions at www.orgchemboulder.com/Labs/Software. For this first example, we will be using the spectrum named “1 – Ethyl Benzoate”. The structure of this compound is shown below. Figure 4-3: The crude product of this aldol reaction is the first spectrum you will work up. Getting Started Once you’ve installed MestreNova, open it up. MestreNova will give you the option to pick Modern or Classic interface – this tutorial uses Classic, but you can pick either one.
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