Lab 6: Determination of Molecular Structure

Lab 6: Determination of Molecular Structure Laboratory Goals In this lab, you will: Determine the infrared spectrum of a polymer sample Learn how to use a Fourier Transform Infrared Spectrometer to obtain information about molecular structure Use GaussView and a molecular model kit to visualize the specific bonds stretching associated with the major peaks for a simple molecule observed Pull a thread of freshly made nylon Introduction In the previous laboratories, you have used spectroscopy to investigate the electronic structure of atoms and to make quantitative determinations of solution concentrations. In this laboratory we return once again to the relationship between spectroscopy and structure, the new feature being that today you will use infrared (IR) radiation light with wavelengths longer than the red portion of the visible spectrum to help you determine molecular structures. Appendix I explains the basics of how an infrared spectrometer works. IR spectroscopy is an extremely powerful tool that is commonly used by chemists. It can be used quantitatively since Beer s law holds for any type of radiation, but its most prevalent use is in the determination of how molecules are put together, so it is usually thought of as a qualitative technique. IR spectroscopy works exactly the same way as visible light absorption spectroscopy in that both involve a transition from a lower energy level to a higher energy level upon the absorption of a photon. The difference lies in which energy levels are involved. In visible absorption spectroscopy, it is excitation of electrons from one orbital to another. Infrared light, being of longer wavelengths and hence smaller energies than red light, does not have the energy to cause this electronic excitation (see Figure 1). 2s 2s 2p ΔE=hc/λ; λ=600nm, ΔE=2.1 ev 2p a) ΔE=hc/λ; λ=5000nm, ΔE=0.25 ev b) Figure 1. The shorter-wavelength photon in a) has enough energy to excite an electron from the 2s orbital to the 2p, whereas the longer-wavelength photon in b) has insufficient energy to cause this excitation. 2s 2s 2p 2p 6-1

So what kind of energy levels can be excited by infrared radiation? As you know, molecules are not stationary, but are dynamic they are constantly moving. This motion really breaks down into three different types (called degrees of freedom): translation, vibration, and rotation, and it is the vibrations that are excited when IR radiation is absorbed. It turns out that, like electronic energy levels, the translational, vibrational, and rotational motions are all quantized as well hence we can talk about vibrational energy levels. Consider what this means for a typical bond, say a C-H bond in methane, CH 4. If we think of the C-H bond as a spring connecting two masses (here the masses are the C and H atoms while the spring represents the bonding electrons; this model is called the harmonic oscillator, which you will see again in physics): Figure 2. Two masses on a spring are a model for a chemical bond. We know that there must be some frequency (ν) of vibration corresponding to the stretching motion of the spring. In classical physics (also called Newtonian physics, in comparison to relativistic or quantum physics) ν can take on any value, and the masses can vibrate as fast or as slow as the energy allows. In quantum physics, ν is quantized which means that only certain frequencies are allowed this directly results from the Planck equation ΔE = hv and the fact that energy levels are quantized. Aside from the existence of vibrational energy levels, bond vibrations are very similar to normal vibrations. Consider the system in Figure 2 again: How would the vibration be affected if the two masses on the spring were very heavy? You would probably expect the vibration to be very slow because of the large mass. The same is true for atoms of greater mass the heavier the atoms, the slower the bond vibration and hence the smaller the vibrational frequency. Now, again thinking of the system in Figure 2, how do you think the vibration would be affected if the spring were very tight? You would now probably expect the vibration to be very fast if you have ever had a Slinky and tried to make it vibrate you know that it doesn t vibrate very fast because it is a very loose spring. The same is true of molecular bonds stronger bonds, like double or triple bonds, vibrate faster than weaker bonds, like single bonds. So the stronger the bond, the faster the vibration and the higher the frequency; the heavier the atoms, the slower the vibration and the smaller the frequency. Mathematically, 2

1 f ν = 2πc M xm y M x + M where f is called the force constant and essentially accounts for the strength of the bond. M x and M y are the masses of the two bonded atoms. Let s reiterate this relationship with some specific examples. The mass dependence of ν means that an O-H bond will have a higher frequency than either a C=O or a C-O bond because hydrogen is less massive than carbon. We would also expect the C=O bond to absorb IR light at a higher frequency than the C-O bond because double bonds are stronger than single bonds. The experimental values for these bonds are: Bond Stretch O-H 3200 3650 C=O 1700 1850 C-O 1070 1150 y 1 2 Vibrational Frequency, cm -1 You may be wondering about the strange frequency units of cm -1. These are called wavenumbers. A wavenumber, ν, is equal to 1/λ, where λ is the wavelength of excitation. It is related to the frequency in Hertz (1/s) through the speed of light: ν = ν/c Considering units, this definition makes sense because frequency in Hertz has units of 1/s and the speed of light has units of m/s. Dividing frequency by the speed of light then gives units of 1/m. Traditionally, wavenumbers have units of 1/cm, so we need to divide by 100 to get 1/cm. The truly powerful aspect of this is that these frequency values change only slightly for different molecules with the same pair of atoms bonded. For example, consider pentane, C 5 H 12, and butanol (actually 2-butanol since the OH is on the second carbon), C 4 H 10 O: H H H H H H C C C C C H H H H H H Figure 3. Pentane 6-3 Figure 4. 2-Butanol.

Both are quite different molecules, but both show absorptions at a frequency of 3000 cm -1 due to excitation of the C-H bonds (see Figures 5 and 6). Note that in Figure 5 you can also see an absorption at approximately 1500 cm -1 which is due to an excitation of a C-C bond; in Figure 6 there are absorptions at 1000, 1500, 2950, and 3500 cm -1 corresponding to stretches of C-O, C-C, C-H, and O-H bonds. The process of identifying certain bonding groups by their placement in an IR absorption spectrum is called fingerprinting, and is one method of determining molecular structure, particularly certain reactive groups in organic (carboncontaining) molecules which are termed functional groups. Figure 5: Infrared Spectrum of Pentane 3 Figure 6: Infrared Spectrum of 2-butanol 3 4

In this laboratory you will look at a small organic molecule from the list below, as well a polymer: $ acetone, C 3 H 6 O $ acetaldehyde, C 2 H 4 O $ diethyl ether, C 4 H 10 O $ ethanol, C 2 H 6 O $ methanol, CH 4 O Organic compounds such as these are often classified by the functional groups that they contain. A functional group is a certain arrangement of atoms that is frequently seen in organic molecules, provides many of the molecules properties (both physical and chemical) and is often used as a means of classification. A partial list of functional groups is provided toward the end of these instructions. All of these molecules above obviously have an oxygen in their structures, which is what defines the functional group in each case. Acetone is classified as a ketone, acetaldehyde as an aldehyde, diethyl ether (not surprisingly) is an ether, and both ethanol and methanol are alcohols. You should also bring in a sample of some polymer for which you will find the infrared spectrum (and possibly the formula as well.) From the IR spectrum you will identify many of the bond types present in the polymer as well as potential the actual chemical composition. Prelab Exercise Answer the following and be prepared to turn them in: 1) What changes in the molecule does IR spectroscopy allow us to observe? 2) Energetically, how do these changes compare to the excitation states observed previously in the atomic emission/absorption lab? 3) You should also have drawn the structures for the following compounds: acetaldehyde, acetone, diethyl ether, ethanol, methanol, chloroform Experiment Logistics Your LA will arrange your class into five or six groups, assign each group a specific simple molecule that they will investigate on the computer and also build a model. You will also determine the IR spectrum of this compound as well as the IR for each of your polymer samples. After each group is assigned a molecule, one LA will help rotate the groups through the usage of the IR spectrometer. The three portions of the lab are outlined below. Since one of your LAs will be mainly working with the IR, you are expected to handle the computer aspect mostly on your own. 6-5

Procedure Using the IR spectrometer Liquid Samples For the small organic molecules that you are sampling, you will need to prepare the computer to take a scan (click on the scan button, then enter the name of the compound along with any additional compounds.) You will need to put one or two drops on the center of the metal disk and begin the scan. If you have a particularly volatile sample, you may need to add another drop or two as the sample scans. If you get a warning that the bands are too weak, accept it anyway and look for yourself to see if there are obvious peaks. If the peaks are indeed really weak, then you may need to rescan the sample (be sure that the is liquid on the spot in the center of the disc during the scan. Plastic Sample Again, prepare the computer for a scan by clicking on the scan button then entering the pertinent information about your sample. Then click on the monitor button (within the scan setup window). This should take you to a window that shows the Force Gauge. Place your sample on the center of the disc and then move the pin directly over the sample. Tighten the pin down on your sample and increase the pressure until the force gauge reaches about 75. This pressure should be good for most samples. You can then click on the stop button followed by the scan button to begin the scan. Examining the spectrum The most important information that you will get from your spectrum is the location of the peaks. If you click on the Peaks button, this will automatically label your peaks. If you happen to find that a major peak remains unlabeled, then you will need to click on the VCusr button to bring up a cursor. Move the cursor to the desired local and double click on the green cursor line to label a peak. You can then print out a spectrum of your sample. Assigning Absorptions Once you have your IR spectrum you will want to try to identify what types of bonds are present in your compound (based on the peaks.) Use Table 1 as a reference for matching spectral peaks with bond types. Be careful as you may observe many more peaks than you will be able to assign; focus on the most intense peaks, particularly ones above 1500 cm -1. If a specific recycle symbol is present on your plastic, you should determine what material it is (the internet is good for this) as well as the structural formula. If your polymer does not have a recycle symbol on it, then compare your spectrum to other groups and see if you can find someone else who had the same polymer. Computer Calculations and model building The second portion of the lab will be to use the computer to help you visualize exactly how a molecule reacts to the IR light, specifically trying to identify the atomic movement that results from excitation at the different wavelengths of light. In the lab we will be using the 6

program GaussView 2.1 to help us visualize the molecular movements. All the students in the group should take turns using the program. Molecule Loading/Building You will need to start GaussView 2.1 if it is not already running on the computer. Upon starting, an error Cannot find wordpad.exe will come up. Hit okay and the program will start. Three windows will appear. You can then either open an existing molecule file or build a molecule from scratch. You should begin by building your assigned molecule. To build a new molecule, use the builder window to select the atom (and geometry) you wish to add and click in the View window to add the atom. Clicking on a hydrogen (white sphere) will add the atom to an existing atom forming a single bond. You can change atom type by clicking on the periodic table button and selecting a new atom type. You can the change the bonding type by clicking on the bonding button (2 below the periodic table.) [Yes, this is more obvious if you actually have the computer running in front of you.] All single bonds are assumed to be connected to hydrogen (so you do not have to specifically add them.) At any time the molecule that you are building (or viewing) can be rotated by left clicking inside the view box and holding the button down while moving the mouse. This will better allow you to view the molecule in 3D. Performing Calculations Once you have built a molecule you will need to use the program to calculate the IR vibrations. First click on the Clean button on the builder and this should pretty up your structure. You can then start the calculation by opening the Calculate menu and selecting Gaussian. This will bring up a new window called Gaussian Calculation Setup. Here we must instruct the program what to calculate. For Job type select Frequency from the button menu and in the box labeled Method, change the button saying Hartee-Fock to MP2. Click on Submit and let the computer begin its calculations. It will ask you if you want to save the file, click on yes and give the computer a name for the molecule. A Gaussian 98 window will appear and it will begin the calculation (this may take some time. The calculation time for this method increases approximately by the square of the number of atoms.) Meanwhile you may wish to look at some of the other pre-calculated molecules. You will only need to calculate your own molecule. Examining Molecules First you will have to open up a molecule file. Open a (molecule name).log file under the File/Open menu. Upon doing this, the selected molecule should appear in a new View window. This molecule can be rotated as before by using the left mouse button and moving the mouse at the same time. To view the vibrational movements, select Vibrations under the Results menu. This will bring up a new window. You can select any of the calculated vibrations in the pull down menu which shows the frequency and the relative intensity. Click the start button to have the computer put the molecule in motion. You can scroll through the different frequencies 6-7

to see the different ways that the molecule can stretch, bend and twist (and yes, molecule are constantly doing all these.) If you decrease the Frames/Cycle (using the slide bar) the movement will appear to go faster or slower. If you click on spectrum it will show you what the predicted spectrum will look like (though it has no width to the peaks.) You should compare this to your obtained spectrum to see how well they compare. You are highly encouraged to look at other molecules to see a range of different atomic motions. You may also calculate other molecules if you wish. See the section below and keep in mind that molecules with fewer atoms calculate much quicker! General Comments about Calculations It is important to recognize the strength and weakness of calculations. First, the calculations that you are doing are being done on a single molecule (there are no intermolecular interactions present here.) Thus the calculation is most like examining a single molecule in the gas phase. The IR that you are taking on the instrument in lab though, is taken of molecules in the liquid state. Secondly, the MP2 calculations that you are doing (and are done for you) are all based originally on experimental data. This data mostly comes from simple molecules and then is extrapolated to whatever molecules you submit. In this case we would expect fairly accurate calculations since we are using simple molecules. Other more complex calculations can rely less on experimental data, but the computational requirement increase at a power of 3, 4 or more based on the number of atoms. Thus the computer in lab would take days, weeks or months to do some only moderately more complicated molecules. Building the model using the kit Each group will be provided with a molecular model kit. These have balls which represent various atoms (eg yellow-h; black-c; red-o etc) and coils which are used for bonds. You are to build a model of your assigned molecule using the appropriate color balls. Notice how each bond can bend and vibrate. Draw a diagram of the molecule showing the 3-Demensional structure. Give the basis shape of all interior atoms and the hybridization of the orbitals on these atoms (pg 417 of text). Indicate the major vibrational frequency of each bond. Making Nylon Nylon, a common polymer, is formed by a condensation reaction but its structure can vary. Analyzing a piece of nylon fiber using an IR can display the bond structures for that particular sample. Nylon is prepared by combining the two monomer units, sebacoyl chloride in hexane and 1,6 hexanediamine in water. Since the hexane and water are immiscible, an interface is created the polymer is formed. 8

+ + You will be provided with solutions of 0.05 M 1,6 hexanediamine and 0.02 M sebacoyl chloride in hexane. Place 25 ml of the 1,6 hexanediamine in a 100 ml beaker. Place a stirring rod in the center of the beaker and carefully pour 25 ml of the sebacoyl chloride solution down the glass rod taking care not to disrupt the interface. Carefully remove the glass rod and use a forceps to pull a string of the nylon. How long can you make a single strand? To do this, follow the example that will be done by the LA in lab. Rinse the nylon in an ethanol/water bath. Examine the FTIR spectrum of the nylon. After you are done observing and stretching the sample, dispose of the nylon in the solid waste container. Report This report will be written with the other members of your group. Your report will consist of the following: 1. The spectrum of your small organic molecule with labeled peaks (indicating bond type they correspond to) as well as the molecular structure. For one peak you will also need to indicate the molecular motion that gives rise to that peak. 2. The drawing of the 3-Demensional structure of your molecule, showing the angles and shape of all internal atoms and the hybridization of the orbitals. 3. The spectrum of the nylon you made. This should have the type of bond indicated by each peak above 1400 cm -1 labeled. 4. The spectrum of your plastics. This should have on it labeled the type of bond indicated by each peak above 1400 cm -1. Additionally you should include small description of what the plastic was as well as the structural formula (if determined.) Also, answer the following questions: 1. How does the molecular structure of the nylon account for its resistance to tearing? 2. Where does the formation of nylon occur? 3. You know that an interface is formed between the immiscible liquids hexane and water. Why is it necessary that the liquids be immiscible and what would happen if they were miscible? 4. What are the bond types for the nylon? What intermolecular forces are present? 6-9

Lastly, draw out the step by step mechanism to show how two monomers combine to form a dimer of the polymer. Although this lab report will not be due until the following week, you may wish to treat yourself and sit down with your partners and try to finish it before then end of the lab session. Once the LA has helped everyone collect their data and pull the nylon, they will then be available for any questions you might have. Chemicals acetaldehyde, acetone, diethyl ether, ethanol, methanol, chloroform. Chemical Disposal Dispose of chemicals in the appropriate waste container. Equipment 50 ml volumetric for organic solutions, pipets, salt windows, cell holder, o-ring, pens for plotter. References 1. A. Streitwieser, Jr., and C. H. Heathcock, Introduction to Organic Chemistry; Macmillan: New York, 1985. 2. J. E. Swartz and K. Schladetzky, J. Chem. Ed., 73 188 (1996). 3. SDBS Spectral Data Base for Organic Molecules, http://riodb01.ibase.aist.go.jp/sdbs/cgibin/cre_index.cgi?lang=eng accessed on October 21, 2000. 10

Table 1: Some common bond types and IR stretching frequencies C-H C=C C C C=O O-H N-H C-O Bond Type of bond Alkyl (saturated) methyl Alkyl (unsaturated) alkynes aldehydes Specific type of bond benzene/sub. benzene Absorption range and intensity 1380 cm -1 (weak), 1460 cm -1 (strong) and 2900-3000 cm -1 (strong to medium) 3000-3050 cm -1 (weak to medium) 3300 cm -1 (medium) 2720, 2820 cm -1 (medium) acyclic C=C alkenes 1650 cm -1 (medium) aromatic C=C alkyne aldehyde/ketone alcohols primary amines secondary amines saturated aliph./cyclic 6- membered 1450, 1500, 1580, 1600 cm -1 (strong to weak) - always ALL 4! 2050 cm -1 (weak) 1650-1775 cm -1 alcohols primary 1050±10 cm -1 3500-3700 cm -1 (concentrating samples broadens the band and moves it to 3200-3400 cm -1 ) doublet between 3400-3500 cm -1 and 1560-1640 cm -1 (strong) above 3000 cm -1 (medium to weak) secondary around 1100 cm -1 tertiary 1150-1200 cm -1 ethers aliphatic 1120 cm -1 aromatic 1220-1260 cm -1 carboxylic acids 1250-1300 cm -1 esters 1100-1300 cm -1 (two bands - distinction to ketones, which do not posess C-O!) C-N aliphatic amines 1020-1220 cm -1 (often overlapped) C=N 1615-1700 cm -1 6-11

C N C-X (X=F, Cl, Br, I) nitriles 2210-2260 cm -1 fluoroalkanes ordinary 1000-1100 cm -1 chloroalkanes 540-760 cm -1 (medium to weak) bromoalkanes below 600 cm -1 iodoalkanes below 600 cm -1 Table of some Organic Chemistry Functional Groups (R, R', R" = any organic group; R', R" can be H if attached to N) R H O Alkane Aldehyde -ane R H -al O R Alkene -ene R R' Ketone -one R O Alkyne -yne R OH Carboxylic Acid -ic acid R O Aromatic (Phenyl) R OR' R X Alkyl Halide O (X = F, Cl, Br, I) -halide R NR'R" Ester R R-ate Amide -amide R OH Alcohol -ol R NR'R" Amine -amine R O R' Ether ether R C N Nitrile -nitrile 12

Appendix 1 INFRARED SPECTROSCOPY: Instrumentation An IR spectrometer is similar to the Spec 401s you used last week in that it has a light source, sample holder, and a detector. Like the Spec 401s detector, the IR spectrometer s detector also detects the decrease in light intensity by the presence of an absorbing sample. The only difference between the two detectors is that the IR detector detects light below the visible range. You will note that you do not need to zero the IR spectrometer; this is because the IR spectrometer has its light from the light source split into two beams and one beam passes through the sample (this is I see the Beer s law lab) while the other beam does not (this is I 0 ). The double beam spectrometers typically give more accurate results since the instrument can adjust for zero on the fly. The other major difference between this spectrometer and others is the method by which it scans the IR spectrum. Before the incident light beam is split into two beams, the IR spectrum sends the initial beam into two directions in one direction is simply a mirror which sends the beam back the way it came in, while the other direction has a movable mirror (which also sends the beam back the way it came). The purpose of the movable mirror is to produce interference between the light beam sent to the fixed mirror and the beam sent to the movable mirror, which will produce a (predictable) fluctuation in the power of the radiation ultimately striking the detector. If the movable mirror is translated in either direction by a distance equal to 1/4 of a wavelength, this will change the overall path of this light beam by half a wavelength (remember that the light reflected from the beamsplitter to the movable mirror has to travel this distance twice once to the mirror and once back to the beamsplitter). This results in destructive interference at the detector, and the power of the combined beams will therefore be zero. If the movable mirror is translated a distance of half a wavelength, then the overall path of the light beam is changed by one wavelength. The combined beams will then be back in phase, and the detector will read a maximum value of power due to constructive interference between the two beams. A plot of the detector power versus time (since the movable mirror moves in time) is called an interferogram. The point of all this is that for a polychromatic source, each individual frequency can be considered to have its own sinusoidal oscillation, and the resulting interferogram is the sum of all these oscillations. Thus, when the movable mirror is positioned so that the two paths from the beamsplitter are equal in distance, all the waves are in phase, and constructive interference will produce a maximum at the detector. As the mirror is translated away from this position, the waves damp to an average value. Through the mathematical process known as the Fourier transform, one can obtain the spectrum (a plot of detector power against frequency) from the interferogram. Such an IR spectrometer utilizing a movable mirror and therefore the Fourier transform technique is called a Fourier Transform Infrared Spectrometer or FTIR. For those of you math nerds, this shows that the Fourier Transform is extremely useful here and in other instrumentation. 6-13

Figure 7. Schematic of the Perkin-Elmer 1605 FTIR. References 1. D.A. Skoog, Principles of Instrumental Analysis, Saunders College Publishing, New York: NY, 1985. 2. J.D. Ingle, Jr., and S.R. Crouch, Spectrochemical Analysis, Prentice Hall, Englewood Cliffs: NJ, 1988. 14