This page contains instructions for using FT-IR, FT-NMR and GC-MS instruments. It also contains instructions for making FT-NMR and FT-IR samples.

FT-NMR

Sample Preparation

The Reed College FT-NMR is an extremely sensitive instrument. Therefore, it is important not to put too much compound in your NMR tube.

It is also important to put the right amount of solvent in the NMR tube. Too much solvent will dilute your compound too much and keep the tube from spinning. Too little solvent will force the vortex (created by the tube’s spinning motion) into the sampling zone and ruin your NMR measurements.

To make an NMR sample for a liquid compound:

These instructions can be used with nearly any NMR solvent, but nearly all samples in Chem 201/202 are made using CDCl₃ (deuterochloroform) impregnated with a small amount of (CH₃)₄Si, which is also known as TMS (tetramethylsilane). CDCl₃ is a highly volatile cancer suspect agent; do not remove it from its fume hood. TMS is even more volatile, so please keep the lid on the bottle as much as you possibly can or this expensive reagent will quickly be ruined. [BACK TO TOP]

Printing your FT-NMR spectrum

The basic operations for processing NMR data consist of calibrating the chemical shift scale so that the TMS peak occurs at 0.0 ppm, defining the appearance of the spectrum for printing, and possibly peak picking and/or integrating. Peak picking is used to print the frequency of each peak (in Hz) directly over the peak which makes it easy to calculate coupling constants (J).

Instructions are under construction.

FT-IR

Thunderdome Attenuated Total Reflectance (ATR) sample accessory

The ThermoNicolet IR100 spectrometer is equipped with an ATR sample accessory. The accessory is useful for a teaching lab because it can be used with both liquid and solid samples, and samples can be prepared and removed quickly.

The ATR accessory looks like a small platform with a circular polished germanium crystal at its center. Briefly, you place your sample on top of this crystal. The spectrometer feeds IR radiation into the crystal from below. Some of the radiation is reflected by the sample back into the crystal and is detected by the spectrometer and converted into an IR spectrum.

Warnings. The ATR accessory is expensive and requires tender, loving care to protect the germanium crystal.

Do not touch the crystal with your fingers, pipets, or spatulas, if you can avoid it.

Do not put corrosive compounds on the ATR (mainly strong acids). Do not put certain organic solvents (acetone, other ketones, chlorinated compounds) on the ATR as they will dissolve adhesives used in the ATR.

Do not wipe the ATR with a Kimwipe as this will scratch the crystal.

Keep the Pressure Tower rotated counterclockwise to its maximum elevation, tilted back and locked, when not in use. Never leave the Tower in contact with the crystal for an extended period; this can etch or crack the crystal.

Always move the Tower carefully; never allow the Tower to drop forward - the tip can crack the crystal.

Sample Preparation

Instructions vary depending on the type of sample. Liquid samples make good contact with the germanium crystal and do not require any special treatment. Solid samples, on the other hand, do not make good contact. A Pressure Tower on the ATR accessory is used to squeeze solid samples against the crystal surface.

Check the crystal surface before you apply a sample. If necessary, clean the accessory before applying a sample (see below).

Liquid samples. Apply 1-2 drops of liquid to the center of the germanium crystal with a disposable pipet (avoid contact between the pipet and crystal). Allow the liquid to spread out to make a thin film (it is ok if the liquid spreads across the entire crystal). Leave the Pressure Tower tilted back.

Solid samples. Place solids on the center of the germanium crystal with a microspatula (avoid contact between the spatula and crystal). Carefully bring the Pressure Tower upright by pulling out the silver release knob and tilting the Tower forward (do not let the tip fall on the crystal).

Use your spatula to position your sample underneath the Tower’s pressure tip. Rotate the knob on top of the Tower clockwise so that the pressure tip presses your sample onto the germanium crystal. Stop rotating the knob when you hear a “click”. These “clicks” are created by a slip-clutch safety mechanism that prevents the tip from applying too much pressure to the crystal.

Cleaning the ATR accessory. If your sample is a solid, first retract the Pressure Tower by rotating the knob on top of the Pressure Tower counterclockwise (NO clicks) as far as you can. This raises the pressure tip to its maximum elevation. Next, pull out the silver release knob and move the Pressure Tower back. Finally, release the silver knob to lock the Tower in place.

Next, moisten an undyed, unscented cotton ball (or soft tissue) with ethanol (or water). Gently wipe the pressure tip and crystal to remove your compound from these surfaces. Repeat with this procedure with a new piece of cotton.

Quick Guide to measuring and printing an FT-IR spectrum

Detailed instructions for using the IR100 are kept by the IR100. They can also be downloaded as a PDF file. The following list is only intended as a quick reminder.

Make sure ATR & spectrometer are ready for use

• ATR should be clean
• Pressure Tower should be tilted back
• IR100 display should be empty (the display should contain two regions, one for a spectrum and one for a report, but both regions should be empty)

Apply sample

Collect and print spectrum

• Collect: Sample
• Analyze: Find Peaks...
• File: Print...

Clear sample spectrum and report for next user

• View: Clear Spectrum
• View: Clear Report

Clean ATR accessory

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GC-MS

Sample Preparation

GC-MS is a combined acronym for two experimental techniques: gas-liquid chromatography (GC) and mass spectrometry (MS). These acronyms are also applied to the instruments used for each technique: gas-liquid chromatograph (GC) and mass spectrometer (MS).

GC-MS samples are typically complex mixtures. A mixture is injected into the GC and separated into its components. As each component exits the GC, it enters the MS and is ionized. A single compound can produce ions of many different masses and the full assortment of ions constitutes a compound’s mass spectrum. In favorable cases, the heaviest ion has the same mass as the compound itself, and the compound’s molecular weight can be established. Carey, Chapter 13.22, and Padias p. 98-106 contain more information on mass spectrometry and GC-MS.

Instructions (under construction) are provided here for the Reed College under construction GC-MS. This instrument is extremely sensitive and only small amounts of material should ever be put through this instrument. Samples should be extremely dilute (typically x mg volatile compound dissolved in xx mL solvent), and only a small volume (typically x mL) of sample should ever be injected into the instrument. Non-volatile compounds should never be put in the GC-MS. [BACK TO TOP]

Recording and printing your GC-MS data

Students may only use the GC-MS instrument under the direct supervision of an instructor or lab assistant.

Before students can use the GC-MS, the instructor should see to it that all electronics have been turned on, all systems have been checked and are in operating order, the MS has been tuned to maximum sensitivity and resolution, and an appropriate parameter for data acquisition has been loaded into the computer (Chem 201/202 students uses a file named under construction that contains settings for both the GC and MS.)

Once the instrument has been properly set-up, students may inject samples into the GC and initiate data runs for themselves. They should also workup data, print Total Ion Count (TIC) vs. time data, and print the mass spectrum of each major peak.

To operate the GC-MS and obtain MS data for your compound:

under construction

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