Infrared Spectra of Triatomics CH342L: Spectroscopy February 18, 2016

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1 Infrared Spectra of Triatomics CH342L: Spectroscopy February 18, 2016 Infrared (IR) spectroscopy the measurement and analysis of spectral patterns observed as different vibrational modes of molecules absorb IR light is one of several very important ways in which molecular information may be gathered. In this experiment, you ll reach important conclusions about the geometry of four triatomic molecules. This is a puzzle for you to solve based primarily on spectroscopic evidence, your own logic, and rules of rotational and vibrational spectroscopy found in this document. Although we know how to determine the geometries of these small molecules from Lewis structures and VSEPR theory, this exercise will allow you to approach it from the fresh perspective of what you can determine from spectra, which you can then confirm using tools from general chemistry with support from electronic structure modeling. This will introduce you to IR spectroscopy as well as the rudiments of group theory the study of classes of molecular symmetry and manifestations of symmetry in bonding, chemistry, and spectroscopy. Group theory is a powerful mathematical tool used by chemists that you may encounter in inorganic and spectroscopy courses. In two weeks, you ll be analyzing in detail the vibrational spectra of the diatomics HCl, DCl, and Hr. It should be apparent by now that in spectroscopy and quantum mechanics the most progress can be made with simplest molecules. Thus, this exercise on triatomics will be a much more cursory analysis than the exquisite detail you ll encounter in the diatomics lab. Still these experiments serve as an introduction to the quantization of rotational and vibrational motion and how it is observed spectroscopically. Goals To understand the rules of IR spectroscopy in this handout and use them to assign IR spectral peaks supporting your logic and thinking with evidence in the spectra. To conclude the geometry of four gases. All of these are gases at room temperature. With the exception of carbonyl sulfide (which is clearly A C), you ll attempt to determine from spectrographic evidence whether they are linear or bent molecules and whether the atomic arrangement is symmetric ( A ) or asymmetric (A ). To work with Gaussian to gain more experience with electronic structure methods and to use them to interpret or to predict spectra. ackground on vibrational spectroscopy and group theory 1 There are many rules in IR spectroscopy. The most important aspects are organized below in subtopics so you can digest them more easily. How many vibrational modes are possible in a molecule? Molecules rotate and vibrate in distinctly different ways and at different frequencies. However, the total number of different vibrations and rotations is easily determined. A molecule with N atoms has 3N degrees of freedom (independent directions of motion) equivalent to free translational motion of the separated atoms moving in the x, y, and z directions of 3D space. When atoms come together to form

2 Infrared Spectra of Triatomics CH342L: Spectroscopy 2 molecules, the number of degrees of freedom remains the same as for the separate atoms, but these 3N degrees are also distributed among the new internal modes of molecular behavior not available to separated atoms, and 3 degrees of freedom are still needed for the molecule as a whole to move translationally in 3 independent directions. This leaves 3N 3 degrees of freedom for internal motion of the molecule. If the molecule is linear, there are 2 ways it may rotate, both representing identical end-over-end motions. There are 3 possible rotations for nonlinear molecules. All remaining degrees of freedom go to vibrations. So, by way of subtraction, linear molecules have 3N 5 vibrational modes while nonlinear molecules have 3N 6. For triatomics, N = 3, so linear triatomics have 4 vibrational modes and nonlinear triatomics have 3. However, in linear molecules, 2 of the 4 modes both bending motions are identical except for occurring in different perpendicular planes, so they have the same energy (they are degenerate). To conclude, we should expect to see at most 3 different vibrational modes for all possible geometries if all modes are vibrationally active and appear in the IR spectrum. So far, we have no way to distinguish between possible geometries. What are the vibrations? Normal modes The different vibrational modes are called normal modes and are unique to each molecule, although similar types of vibrations occur in characteristic locations in the IR (for example CH stretches). This is the basis of using IR spectroscopy as a diagnostic tool in organic chemistry. In the triatomics, we ll see bending and stretching vibrations. Depending on the geometry or the symmetry the stretches will be called symmetric or antisymmetric stretches for A molecules or A-, -, or -C stretches for A and AC molecules. Ask your lab instructor to demonstrate these motions (classically!) during your lab section. Calculating the actual frequencies of normal modes is possible given a known geometry and access to computational resources. If you can determine the minimum potential energy and the curvature about the minimum, you can diagonalize the Hessian as will be discussed in lecture. This method is called normal mode analysis, and Gaussian will do the math for us. What s group theory? Group theory classifies a molecule according to the types of symmetry operations that leave identical nuclear positions after the operation. These include the identity operation (which does nothing. All molecules possess this symmetry operation), mirror reflection through a plane, inversion through the center of a molecule and two forms of rotation about a molecular axis through some angle. The distinguishing symmetry operations for triatomics are rotations and mirror reflection perpendicular to the plane of the molecule. Each of the four possible molecular geometries will belong to a different symmetry group as a result. Group theory is not the focus of this experiment, but you should be aware that the rules below are derived from it. The name of the symmetry classes given below come from group theory. Which normal modes are IR active? The strongest absorptions encountered in spectroscopy are due to a form of interaction of matter with the electromagnetic field in light through the electric-dipole interaction. As the name implies, the electric part of the light wave (not the magnetic part) couples with a dipole (the separation of negative

3 Infrared Spectra of Triatomics CH342L: Spectroscopy 3 and positive charge) in the molecule. If the electric field can find even a temporary dipole with the appropriate characteristics and the quantum state is populated, a strong transition may result. For IR spectroscopy specifically, the requirement is not that the molecule have a permanent dipole, but rather that the normal mode must have a changing dipole as the molecule vibrates. Modes in molecules with the most symmetry will have the least possibility of having dipoles. So, in general, the most symmetric molecule will have the fewest normal modes that are IR-active. For the four symmetries listed next with their normal modes, decide for yourself which modes should be IR-active by judging whether the dipole changes as the molecule vibrates, even if the molecule lacks a permanent dipole. Note the numbering of the quantum numbers ν 1, ν 2, ν 3 Linear A molecules: This is the most symmetric of the triatomic symmetries. Molecules of this type belong to the symmetry class D h and have no permanent dipoles. It has 4 normal modes, but the bend is doubly degenerate. You could observe at most 3 distinct normal mode frequencies in your spectra: the doubly degenerate bend (ν 2 ) and the symmetric (ν 1 ) and antisymmetric (ν 3 ) stretches. Linear A or AC molecules: Molecules of this type belong to the symmetry class C v and generally possess permanent dipoles. There are 4 normal modes, by 3 distinct frequencies; the doubly degenerate bend (ν 2 ), the (C) stretch and the A stretch (labeled ν 1 and ν 3 for the higher and lower frequency stretches, respectively). ent A molecules: Molecules of this type belong to the symmetry class C 2v and generally possess permanent dipoles. The three normal modes are the bend (ν 2 ), the symmetric stretch (ν 1 ), and the antisymmetric stretch (ν 3 ). ent A molecules: Molecules of this type are the least symmetric of the four possibilities for triatomics and belong to the class C s and generally possess permanent dipoles. The three normal modes are the bend (ν 3 ), the (C) stretch and the A stretch (labeled ν 1 and ν 3 for the higher and lower frequency stretches, respectively). A A A A C A A C What about IR peak shapes? You ll notice in your spectra that different absorption bands have different types of shapes. These will help you make your final peak assignments. This kind of evidence is best used last, after you have considered the rules above. Each IR-active normal mode should exhibit a strong PR or PQR band at what is called the fundamental frequency, at the energy difference between the ground and first excited state of that mode. For linear molecules, the possible band shapes are extremely regular, and there are only two (see table below). The situation gets a little more complicated for nonlinear molecules, and it is difficult to generalize for

4 Infrared Spectra of Triatomics CH342L: Spectroscopy 4 all the different bond angles and atomic masses of atoms A, and C. However, for the case of triatomics, you ll see bands that look somewhat reminiscent of the two linear band shapes but which don t have as nice-looking, even profiles as in the linear cases. The presence of a sharp peak in the middle (a Q branch) still indicates vibrational motion away from the major symmetry axis of the nonlinear molecule. P and R branches: Two rounded or jagged peaks centered about a gap in the middle frequency appear, somewhat resembling mirror images. These peaked are the P and R branches, and are the result of rotational changes in the molecule occurring in addition to the vibrational change, the details of which won t concern us in this experiment (but it will soon!!). This type of shape arises when the vibration occurs along the primary symmetry axis of the molecule as in a stretch. Q branch: The same two rounded or jagged peaks (the P and R branches) are joined by a third sharper spike, roughly in the middle. This is the Q branch. The PQR band system is observed for vibrations departing from the primary axis of symmetry of the molecule as in a bend. R P Energy Q R P Energy What about all those other peaks? Combination and difference bands In addition to the strong fundamental features, you may see weaker features called combination bands that correspond to a simultaneous change in two or more normal modes at once. The frequency of the combination is merely the sum of the separate fundamental frequencies. It is entirely possible by symmetry effects that a mode that is not by itself IR-active as a fundamental will be allowed as a part of a combination band. Combination bands may even involve multiple quanta in 1 or more modes. Only odd numbers of quanta of off-axis motion (where the axis is the major symmetry axis of the molecule) will result in the Q branch appearing. So combinations of on-axis vibrations will always give you P and R branches regardless of the number of quanta involved whereas the off-axis motion alternates between PQR and PR bands depending on whether the number of quanta of the off-axis motion is odd or even. In general, the less symmetry the molecule possesses, the more possible combinations will appear, while a linear A molecule may allow very few. Exact prediction of allowed combinations is certainly possible, but would require more group theory than we can get to at this point. In a few cases, you may even see difference bands that appear at the difference in the frequency between 1 or more quanta of the fundamental frequencies. These bands originate when a vibrationally excited molecule de-excites one mode of vibration while simultaneously exciting another mode. ecause of the unlikelihood of vibrationally excited states in most room temperature samples of gases (unless the molecule is composed of heavier atoms), first attempt to assign all your combination bands based on summed frequencies (as above), then try difference bands if there appear to be no other options.

5 Infrared Spectra of Triatomics CH342L: Spectroscopy 5 Other miscellaneous rules Your spectra are limited by the detector to frequencies between 400 and 4000 cm 1. The low frequencies (on the far IR and microwave side) correspond to smaller energies and motions that in general involve heavier atoms or larger portions of the molecule. ends are always the lowest energy mode in a triatomic, and they are usually substantially lower than the other remaining modes, often pushing the low-frequency limit of our instrument (they may even be below 400 cm 1 ). The high frequencies, on the near IR and visible side, correspond to the highest energies and motions that in general involve small regions of the molecule and the lightest atoms and will always be stretches or combinations. Nothing can beat hydrogen atoms for creating high-frequency vibrations. The symmetric and antisymmetric stretches usually occur at relatively high frequencies and, in many cases, are close to each other in value with the antisymmetric stretch being the higher frequency mode. The - and -A and -C stretches encountered in the less symmetric A and AC molecules also occur at higher frequencies than the bend, but usually have a greater frequency difference between them, particularly when the atoms in the -/-A or A-/-C pairs have widely different masses. This greater difference is directly attributable to the mass of the atom being moved in the stretching motion, with the mode involving the heavier atom occurring at the lower frequency. For combination bands, the experimental frequency is usually a bit less that your prediction based on simple summing of observed fundamental frequencies. This is due to the anharmonicity of the vibrations, which leads to smaller vibrational energy spacings as the molecule engages in more quanta of vibrational motion. Use of Gaussian Follow the instructions in the Appendix for basic operation and visualization of Gaussian using WebMO. Experimental You ll take gas-phase spectra of the five triatomics over the mid-ir range cm 1. Think about error and precision When you set up the instrument to collect spectra, recored the frequency resolution. Allow the frequency resolution to determine both the number of significant figures that you report and to be an indicator of the error in your reported values. ecause you cannot determine the true band center with high accuracy, your error will be somewhat more than the instrument can deliver. Use of the gas cell Since gases are so dilute compared to liquids or solids, a much greater path length is required to gain sensitivity. In this case, a 10-cm cell is used. Carefully evaluate the cell before each gas you run to remove potential interfereing peaks. The Kr windows must be protected from any direct contact with liquid water. At the end of the day, the cell must be stored in a desiccator.

6 Infrared Spectra of Triatomics CH342L: Spectroscopy 6 Filling the cell with gases Take infrared spectra of the gases in the following order to minimize contamination: CO 2, N 2 O, COS, and SO 2. Evacuate the cell thoroughly before you fill it with each gas. Your instructor will walk you through the filling procedure. Some of the gases are toxic. If you smell anything or observe any escaping mist, put the cell in the fume hood until the degassing is done. Occasionally, the gases will be too concentrated and yield absorptions that are off scale to the point that the peak shapes cannot be accurately determined (absorbances above 2). To reduce the concentration, reattach the cell to the vacuum pump and take a quick sip on the vacuum by quickly rotating the stopcock by 180 past its open position. Using the FTIR spectrometer Your instructor will walk you through the procedure to blank the instrument and collect your spectra for the first gas. Take notes, as you ll be on your own for the following gases. Labeling all peaks and zooming in Make sure you have the central frequencies for both strong and weak features of all gases clearly labeled. You will need to zoom in on and print weak bands separately (combinations at high frequency can be very weak) to get a good idea of their peak shapes and exact frequencies. Use the top of the Q branch in a PQR system and the midpoint between the P and R branches for the central frequency. Air contamination It is quite common, with leaky gas cells or by blanking with air, that air will show up as a contaminant in your spectra. Devise a method for handing this problem. Which gases would you expect to see in air? Cross-sample contamination Watch out for interference of strong peaks from previous gases in your next spectrum. Make sure you fully evacuate the cell between runs, admit several cycles of room air, then pump out the cell again before filling with your sample gas. It s critical to keep details like this in mind and record the order of gases in your notes. efore leaving lab You should make sure that you have complete information (frequency location as well as band shape) for all strong and weak features for each gas. Analysis strategy Fill in the Triatomics Worksheet on the next page to organize and process some of the most important facts and rules from this handout. The information summarized on the worksheet should be sufficient to assign the features you observe and to reach the primary conclusions regarding the geometry of the five molecules. For each gas, assign the strongest (highest intensity) features first as presumed fundamentals, noting their frequencies. The response of the FTIR s detector is not flat with frequency and strong fundamental bands at high and low frequencies may appear smaller than centrally located peaks. ands in these outlying locations should still be considered as candidates for fundamentals in spite of their relatively small intensities. Always assume that the lowest frequency feature is a

7 Infrared Spectra of Triatomics CH342L: Spectroscopy 7 bend. Search the remaining features for possible combination and difference bands. You should consider it a potential match if the observed frequency falls within 50 cm 1 of the added fundamental frequencies. Remember that the experimental combination frequency will also be a bit lower than the predicted one due to anharmonicity. Feel free to check in with your instructor on your assignments. Using all of the enclosed information, you should be able to make a strong case for the geometry of each triatomic. In particular, you should consider the number of fundamentals that are IR-active, the presence and number of combinations, the frequency location and separation of different modes, and the shapes of the bands. Remember that this is a puzzle you may have to iterate to figure out the final assignments until everything fits and all rules are obeyed. Use mass trends to correlate with frequency trends (locations and relative ordering of bands). Use Lewis structures, VSEPR theory, and Gaussian calculations to confirm your ideas. What to turn in next week All spectra, annotated with all assignments you can make along with frequency locations. Label all assigned bands with their frequencies and involved modes (for example: 2156 cm 1, combination, 1 bend + 2 symmetric stretches, 1ν 2 +2ν 1 ). Use correct quantum number notation from the table on page 3. A table summarizing your Gaussian results for frequencies of normal modes including a column with comparison to experimental values. Summarize all band assignments and modes in table form (see HCN example on the final page of the handout) with one table per molecule. Sketch the normal modes below. In a page or two, summarize the logic you use to assign the geometry to each of the four gases. Use the spectra as primary evidence supported by the logic you ve mastered working through this manual. Explain the step-by-step logic you used to assign the bands and make conclusions about the geometry. Acknowledge any ambiguities or uncertainties. Use your Lewis structures, VSEPR models and Gaussian results to support these conclusions, not as the primary evidence. References 1. Adapted from: Hollingsworth, W.; Ferrett, T. Manual for Advanced Lab I: Spectroscopy; Carleton College: Northfield, MN, 2002; ch 4.

8 Infrared Spectra of Triatomics CH342L: Spectroscopy 8 Triatomic Worksheet Linear A Linear A ent A ent A Number of vibrational modes Number and names of distinct IR-active frequencies Number and names of IR-inactive modes Predicted band structure of stretches (PQR/PR) and appearance (symmetrical/less symmetrical) Predicted band structure of bends (PQR/PR) and appearance (symmetrical/less symmetrical) Do you expect to see many combination bands? Predicted order of bands if (C) is heavier than A

9 Infrared Spectra of Triatomics CH342L: Spectroscopy 9 IR spectral data from the IR spectrum of HCN (Linear AC) Observed Frequency Observed Intensity Observed and Shape Assignment Calculate Frequency for Comb ands Freq (Obs- Calc) Expected Shape 712 cm 1 Very Strong PQR Fundamental end (ν 2 ) PQR 1412 cm 1 Strong PR 2089 cm 1 Weak PR 2117 cm 1 Medium PQR 2800 cm 1 Strong PQR 3312 cm 1 Strong PR Combination of 2 ends (2ν 2 ) Fundamental HC-N stretch (ν 1 ) Combination of 3 ends (3ν 2 ) Combination of HC-N stretch and a bend (ν 1 + ν 2 ) Fundamental H-CN stretch (ν 3 ) 1424 cm 1 10 cm 1 PR PR 2136 cm 1 19 cm 1 PQR 2801 cm 1 1 cm 1 PQR PR The modes predicted by normal mode analysis performed using Gaussian are: ν 1 H C N CN stretch ν 2 bend H C N ν 3 H C N HC stretch

10 Infrared Spectra of Triatomics CH342L: Spectroscopy 10 Appendix: Running Gaussian on Schupflab This week you ll use Gaussian to a run normal mode analysis on one of 4 assigned gases and visualize the results from yours and your classmates calcluations. Running and Analyzing Vibrational Mode Calculations with Gaussian on Schufplab Set up a folder to run in On a lab machine (or a personal machine with x11 forwarding set up) use terminal to ssh to schupflab with x forwarding. Change directory to the shared course folder Make a folder for your assigned molecule, either,,, or And change directory to it Run GaussView to make an input file In your folder, run GaussView GaussView will open up in an X11 window. Close the pop-up windows, but leave open the purple background window. On the Job Manager page, start a New Job. A viewer window will open. Click on the periodic table tool. Click on the Element Fragment tool ( ) and pick your central atom with the correct geometry in the periodic table that pops up. If VSEPR tells you it s bent, use a bent geometry. Click in the purple window to add the central atom. Pick your other two atoms and add them. If a spurious hydrogen shows up, delete it with the Delete Atom tool ( ). Once you have your triatomic drawn, got to. Calculate. Gaussian Calculation Setup.... Here, you ll set up a calculation that first finds the nuclear coordinates that minimize the electronic energy, then runs a normal mode analysis at the bottom of that basin to estimate the frequencies of the vibrational modes for the molecule. Edit the. Job Type,. Method, and. General tabs to look like

11 Infrared Spectra of Triatomics CH342L: Spectroscopy 11 Explanation: 3LYP is a method to treat the electron exchange term in DFT calculations to approximate solutions to the Schrodinger equation. In part, the energy of the electrons is treated as a function of the density rather than using wavefunctions. Combinations of functions in the asis Set are used to approximate the densities. y setting our basis set to G(2d,p), we include d- and diffuse p-type orbitals on the heavy atoms. This is very overkill for what we re doing, but for a small molecule, we don t have to be cheap. The Multiplicity is Singlet because there is all the electrons are paired. Click. Submit..., save the file as run.com, and submit the job by hitting. OK on the next window. This will take a couple minutes. Analyzing the results When your job is complete you ll be prompted to open a file. Do so with the checkpoint file run.chk. Go to Results. Vibrations...., tick Select Normal Modes set Modes: to 1-4 and Atoms: to 1-3. Hit OK., and another window listing the frequencies (units of cm -1 ) of the calculated normal modes. If you click on a mode, the purple window will move with that vibration allowing you to picture the different modes. You can play with the options in this window to better visualize the modes. Look at the results from your classmates calculations to visualize the modes of all four gases.