I would like to thank research group members Keith Hollis, Daniell Mattern, Walter Cleland, Takashi Tomioka, and Susan Pedigo for donating some of the chemicals used in these experiments. I would like to thank Dr. Susan Pedigo for the extended loan of a circulating water bath, without which the Raman spectrometer could not collect data. AUSTIN ARCHIE HOWARD: Upgrade of a Raman spectrometer with modern computer control and data acquisition for hydrogen bonding studies in pyrimidine.
The first chapter is a brief description of the history and theory of Raman spectroscopy as well as some details of the instrumentation used in Raman spectroscopy. The second chapter contains technical details on the restoration and upgrade of the high-resolution Raman spectrometer. The location of the ν1 peak in the Raman spectrum corresponding to the pyrimidine ring-breathing state was used as a marker to monitor the degree of hydrogen bonding and species involved.
History, Theory, and Instrumentation
- Light-Matter Interaction
- The Raman Effect
- Instrumentation
- References
According to Equation 2 above, the induced dipole moment in a molecule is equal to the product of the polarizability and the applied electric field. When light is Rayleigh scattered, the molecule is excited to a quasi-excited state and relaxes, producing a photon of the same frequency. Thus, the frequency of the monochromatic excitation radiation can be used to find the vibrational frequencies of the molecule.
Only one component of the polarizability tensor must change during a normal mode for this mode to be Raman active. The number of counts is directly proportional to the intensity of the light hitting the photocathode and is therefore a measure of signal intensity. Each wavelength of light interferes constructively at a certain angle relative to the normal of the grating with all others interfering destructively.
The first grilles were made by machines that made slots in the surface of the grille. The broken off portion of the material is then dissolved, creating grooves in a sinusoidal pattern on the lattice.
Upgrade of a High Resolution Cold War Era Raman Spectrometer
- Ramanor HG2-S Raman Spectrometer
- The Restoration
- The New Experimental Setup
- References
An optical diagram of the instrument reproduced from the original user manual is shown below in Figure 2.1. The cathode of the photomultiplier tube is held at -1500 V by an Ortec high voltage power supply. The spectrometer, with the exception of the slits, is computer controlled through the Spectra Link interface.
By 2007, the spectrometer described above was in storage at the University of Tennessee, along with many of the components from the experimental setup described in Figure 2.4. In addition, the Hammer group was able to obtain copies of the original user manuals for the spectrometer itself to and from Jobin-Yvon's Spectra Link interface. When disassembling the Spectra Link, it turned out that the original modules discussed in the user manual were no longer present.
The controller is connected to the computer via a native RS-232 serial cable, with only three of the nine pins connected. The movei=[number of revolutions] command moves the desired number of revolutions of the engine. The waitdone command tells the controller to wait until the motor has finished spinning before continuing with program execution.
This program allowed the user to control the destination and scan speed and track the position of the wave number. It should be noted that there is no electronic output from the spectrometer itself for the current wavenumber position. This position is stored in a global variable and displayed on the program's user interface screen.
We also received a NIM tray which contains many of the electronic components required to operate the photomultiplier tube. We made our own half-wave plate using a microscope slide and glossy cellophane tape as suggested in an optics textbook.2 The results are Figure 2.10 The effect of a half-wave plate on two. A commercial grade half-wave plate was purchased for use in the final version of the experimental setup.
Raman Spectroscopic Investigations of Intermolecular Interactions Involving
Introduction
Vibrational spectroscopy, such as infrared (IR) and Raman, lends itself to studies of these interactions.5 Changes in a vibrational spectrum allow us to determine exactly which atoms and bonds are being affected in the intermolecular interactions that occur and to what extent. are these interactions occur. Hydrogen bonds have been investigated with Raman spectroscopy as early as the 1950s when Puranik investigated hydrogen bonds between carbonyl donors and acceptors6-8 and found the first evidence in a Raman spectrum for hydrogen bonds with nitrogen.9 Vibrational spectroscopy has also been used to investigate bonds hydrogen in terms of thermodynamic properties including association constants,10 rate constants,11 and enthalpies of formation.12. Pyrimidine, from which the nucleobases known as pyrimidines are derived, is shown in Figure 3.1 along with the pyrimidine nucleobases cytosine, thymine, and uracil.
Also shown in Figure 3.1 are the remaining nucleobases common in nucleic acids, known as the purines. Note that these molecules also contain six-membered .. w in m F h a. ings consist of ucleic acids yrosine, and ninteractions o nteractions o structural and. Pyrim with the first nvestigate sp mode, in wh. ratiello foun igher freque thorough i Figure 3.1. pyrimidine cl nucleic acids pyrimidine. a) b). ing of two n n similar not s.. of pyrimidine occurring in d chemical si. midine and ot Raman specifically specifically describes all binding and that the r ensions with h .. las of s and cytosine uracil d) Guanine . nitrogen atom n-covalent in more, three nine) contained could the.
Takahashi briefly mentions the possibility that the blue shift must be due to a significant shift in electron density, citing a comparison of his spectra with the vibrational spectrum of the pyridinium cation published by Cook.16 Recently, hydrogen bonding in pyridine mixtures has been revealed. investigated by monitoring the shift of the ν1 peak in mixtures of ethanol17 and water18,19 and according to the shift of the water peaks in the vibrational spectrum.20 Pyrimidine was last investigated in 2007, when Schlucker and colleagues theoretically and experimentally investigated the shift of the ν1 peak of the Raman spectrum in mixtures of different amounts of water .5 Their calculations showed that the wavenumber shift, which should be an indicator of the degree of hydrogen bonding, showed a "perfect negative correlation" with the nitrogen-hydrogen bond distance on the water molecules and the position of the wavenumber ν1. The "water concentration" in their calculations was increased by adding more water molecules at pyrimidine hydrogen bond positions or with water molecules already present. The subgroups in which the negative correlation applies are those in which water molecules are added that hydrogen bond to other water molecules rather than to the pyrimidine.
Their conclusions seem to indicate the major role played by a hydrogen-bonded network relative to single hydrogen bonds to the pyrimidine in the wavenumber position of the pyrimidine ring-breathing state. We monitored the position of ν1 in the Raman spectrum of pyrimidine in mixtures of pyrimidine and different concentrations of water, methanol, benzyl alcohol, 1-hexanol, acetic acid, hexylamine (CH3(CH2)5NH2), acetonitrile (CH3CN), ethylene glycol (HOCH2CH2OH ) and 2-mercaptoethanol (HOCH2CH2SH). In addition, we monitored the position of other vibrational modes, and we acquired Raman spectra of pyrimidine under high pressure to investigate the weak hydrogen bonding in pure pyrimidine when the liquid crystallizes.
We also explain below some discrepancies that exist in the literature regarding the symmetry of some normal modes.
Experimental
The piston and the cell were filled with ethanol, and the bottle was placed in the correct position inside the cell. We sealed the entire system, and we used a press to change the height of the piston and thus the pressure in the system.
Results and Discussion…
Figure 3.3 shows the Raman spectra of pyrimidine at pressures of 10,000 psi, 20,000 psi, and 30,000 psi, in addition to the spectrum at atmospheric pressure (14.7 psi), all of which were obtained in the high-pressure cell filled with ethanol. This means that in the crystal structure of pyrimidine a fraction of the pyrimidine molecules must occur in an environment where the vibration shown in Figure 3.5b cannot occur as is the case elsewhere in the crystal. The location of these interactions clearly shows how the modes depicted in Figure 3.5 are disrupted as pressure increases.
Here, we see similar changes occurring, but in the CH stretching region of the spectrum. We prepared mixtures of pyrimidines with different mole fractions of water and collected the Raman spectra of each. Shown in Figure 3.9 are four other regions of the spectrum where similar, though smaller, blue shifts of the pyrimidine peaks occur as more water is added.
There has been some discrepancy in the past literature regarding the correct assignment and symmetry of the peaks shown in the bottom two spectra of Figure 3.9 (e.g. refs and 22). Interestingly, Figure 3.10 indicates that peaks corresponding to ν8b and ν15 shift noticeably, while the adjacent peaks shift very little or not at all. Optimized structures for different configurations of hydrogen hydrogen bonding with pyrimidine are shown in Figure 3.11.
Frequency calculations were performed on both pyrimidine and methanol hydrogen-bonded species and the pyrimidine monomer. This calculated frequency exactly matches the shifted peak seen in the 50% mole fraction spectrum. The spectra of mixtures of pyrimidine and alcohols show similar behavior to the spectra of methanol above.
In Figure 3.17a, the blue-shifted peak can be found between the ν1 ring breathing peak of pyrimidine at 990 cm-1 and the ring breathing peak of benzyl alcohol at 1000 cm-1. The spectra of mixtures of ethylene glycol and pyrimidine shown in Figure 3.15b also contain some interesting features. It would therefore not be expected to cause the shift attributed to hydrogen bonding in the above cases.
Conclusion
These results indicate that the shifts are due to hydrogen bonding rather than the effect of solvent polarity. Our calculations showed that this is due to the formation of hydrogen bonds between the pyrimidine molecules with an average of between one and two methanol molecules. This shift difference may also be due to the inability of methanol to hydrogen bond with itself and with pyrimidine.
Hexylamine was found to cause no change in the pyrimidine peak, presumably because the exposed hydrogen bonds are weaker.
