Investigating Hydrogen Bonding in Phenol Using Infrared

Laboratory Experiment pubs.acs.org/jchemeduc

Investigating Hydrogen Bonding in Phenol Using Infrared Spectroscopy and Computational Chemistry Anna M. Fedor* and Megan J. Toda Department of Chemistry and Biochemistry, Misericordia University, Dallas, Pennsylvania 18612, United States S Supporting Information *

ABSTRACT: The hydrogen bonding of phenol can be used as an introductory model for biological systems because of its structural similarities to tyrosine, a para-substituted phenol that is an amino acid essential to the synthesis of proteins. Phenol is able to form hydrogen bonds readily in solution, which makes it a suitable model for biological interactions. This laboratory experiment studies the phenol monomer, dimer, and trimer using geometry optimization and frequency calculations. The results are validated with the infrared spectra collected over the O−H stretching region (3100−3700 cm−1). Solutions of varying concentrations (0.5−2.0 M) are analyzed with the expectation that the contributions from the phenol dimer and trimer will become more significant as the concentration is increased. The observed peaks in the infrared spectrum are assigned as the “free” O−H stretch at 3579 cm−1 and “bound” O−H stretch at 3390 cm−1. As the concentration increases, the bound O−H stretch is enhanced because of a higher population of dimers and trimers that form in solution, whereas the free O−H stretch only slightly increases in intensity. The harmonic oscillator model and the force constant equation are used, and it is revealed that the O−H bond length is inversely proportional to the observed wavenumber (cm−1), which is supported by the bound O−H stretch appearing at a lower frequency in the infrared spectrum. KEYWORDS: Physical Chemistry, Upper-Division Undergraduate, Laboratory Instruction, Hydrogen Bonding, IR Spectroscopy, Phenols, Hands-On Learning/Manipulatives, Computational Chemistry

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biology.3 An understanding of the behavior of hydrogen bonding in alcohol clusters can provide a more accurate description of such things as the behavior of condensed-phase water or hydrogen bonding in biological systems. The selfassociation of phenol, in particular, can be used as an introductory model for more complex biological systems, such as amino acids, because of its structural similarities to tyrosine. Tyrosine can be described as a para-substituted phenol that is an amino acid essential to the synthesis of proteins.4 The computational portion of this experiment involves the calculation of the optimized geometries and vibrational frequencies of the phenol monomer, dimer, and trimer. The optimized geometries are used to measure the predicted bond lengths of the O−H bond that engages in hydrogen bonding. The vibrational frequencies are used to assign the spectral peaks observed in the IR spectrum.

nfrared spectroscopy is a common technique used in laboratory instruction in both introductory and advanced chemistry courses. It is often used as an investigative tool to connect molecular structure to spectral features. This understanding of molecular structure can be enhanced by electronic structure calculations, in particular, geometry optimization and frequency calculations. Laboratory experiments that combine both experimental infrared (IR) spectra and electronic structure calculations have become more popular in the development of undergraduate lab procedures.1,2 Students who are able to combine experimental and computational chemistry can enhance their understanding through molecular visualization software that animates the motions of the molecules under study. The experimental portion of this lab procedure uses IR spectroscopy to analyze the enhanced hydrogen bonding of phenol in solution with concentration. The hydrogen bond is a unique and necessary phenomenon in structural chemistry and © XXXX American Chemical Society and Division of Chemical Education, Inc.

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Figure 1. Optimized structures [DFT/B3LYP/6-31G(d,p)] of the (a) phenol monomer (free O−H group), (b) dimer (linear, with both free and bound O−H groups), (c) and trimer (cyclic, bound O−H groups) using Gaussian 09/Gaussview 5.

2.0 M in 10 mL volumetric flasks. IR spectra were acquired using a PerkinElmer Frontier Fourier transform infrared/farinfrared (FT-IR/FIR) spectrometer with a liquid demountable cell containing NaCl windows. For concentrations to be compared directly, a fixed path length of 0.05 mm was used during the collection of spectra. Spectra were obtained in absorbance mode, which averaged 16 scans, with a resolution of 2.0 cm−1. Samples were allowed to purge for 5 min prior to scanning to ensure water had been removed from the FT-IR, with backgrounds taken every 30 min. Spectra were collected using the PerkinElmer Spectra software package (version 10.4.2) over the range of 400−4000 cm−1.

The self-association of phenol was readily studied in the gas phase, in particular the linear dimer and the cyclic trimer.5,6 Phenol engages in strong (∼10 kcal/mol) O−H---O hydrogen bond interactions when forming clusters in solution.7 These interactions work to stabilize certain cluster sizes and geometries, in particular, the phenol trimer.5,6 The optimized structure of the phenol trimer is strong visual for students in understanding how multiple hydrogen bonds can form, a direct example of the hydrogen bond cooperative effect.8 The elongation of the O−H bond during a hydrogen bond is simulated by the harmonic oscillator as a model for vibrations. Atoms vibrate relative to one another with the bond acting as a spring. The larger the force constant (k), the stiffer the spring, which is representative of a shorter bond length.9 The wavenumber (cm−1) is related to the force constant (k), the reduced mass (μ), and the speed of light (c) by the following eq:10

v ̃ (cm−1) =

1 2πc

k μ

Computational Calculations

Geometry optimizations and frequency calculations were performed on the phenol monomer, dimer, and trimer (Figure 1) using Gaussian 09W and viewed in Gaussview 5.11 Other computational programs are readily available to calculate these parameters, which makes this part of the experiment adaptable to the resources available. Density functional theory (DFT) was the level of theory chosen because of its accuracy at predicting IR frequencies12 and the calculation time required. The geometry optimizations generated the lowest energy cluster for each one of the structures calculated and were modeled after the accepted optimization of the phenol dimer and trimer.5,6 The functional and basis set that was used in the this study was B3LYP/6-31G(d,p),13 which is moderately sized. Computational time varies depending on the size of the cluster and can be reduced if the starting structure is closer to the optimized geometry. The data that was compiled from these calculations consists of optimized geometries with structural information including O−H bond lengths of each structure and vibrational frequencies.

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According to the harmonic oscillator model and eq 1, the O−H bond length is shown to be inversely proportional to the observed wavenumber. After spectra of phenol is aquired at varying concentrations, the intensity of the “free” O−H stretch of the monomer and dimer and the “bound” O−H stretch of the dimer and trimer are monitored with increased concentration. The observed peaks in the IR spectrum are then compared to the predicted vibrational frequencies from computational data. Conclusions about the effect of concentration on the population of the monomer, dimer, and trimer in the IR spectrum are then made. This integrated laboratory exercise combines both computational and experimental techniques to quantitatively describe the effects of hydrogen bonding on the force constant of a molecule, and therefore, its vibrational frequencies. Students will also gain insight on the important structures that result, in particular, the phenol trimer, from hydrogen bonding interactions. This approach helps to visually describe the effects of self-association via hydrogen bonding, a common occurrence in biological systems.

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Execution of Experimental and Computational Measurements

This lab was facilitated in two sections of a physical chemistry laboratory over a 2 year period, with sections in the range of 6− 8 students with two students per group. This laboratory is recommended to be completed in a 2 week time period to provide adequate time for calculations and analysis of the IR spectra. Three research computers and two FT-IR spectrometers were available to the students, which made it possible for groups to evenly distribute usage of the equipment. Each group required approximately 45 min to collect all spectra. Calculation time was minimized by providing a handout of optimized structures to be used as the initial guess for the input files in Gaussian 09W. Suggestions for instructors and further details are available in the Supporting Information.

EXPERIMENTAL PROCEDURE

Experimental Measurements

Solutions of phenol (loose crystals, 99+%) were prepared in dichloromethane (CHROMASOLV, for high-performance liquid chromatography (HPLC), >99.8%); both of which were purchased from Sigma-Aldrich and used as received. Solutions were prepared at concentrations of 0.5, 1.0, 1.5, and B

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Laboratory Experiment

cm−1; the peak was at a higher wavenumber in Figure 2. This applied scaling factor was 0.9365 and is typical for the O−H stretching region when the DFT is used as a computational method.15 The dimer contains both a free and bound O−H stretch and contributes to both peaks observed in the spectrum. It can be concluded from observations made in Figure 2 that there is a greater enhancement of absorption for the bound O− H stretch due to a larger population of dimers and trimers existing at a higher concentration. IR intensities predicted by Gaussian 09W validate this conclusion but are not required in the laboratory protocol. As an example of this, the predicted intensity of the free O−H stretch of the monomer was predicted to be 41.0 km/mol, whereas that of the bound O−H stretch of the trimer was predicted to be 1034.7 km/mol. The predicted O−H bound and free O−H stretches of all of the phenol clusters can be found in Table 1. Students are instructed to animate the vibrational frequencies in Gaussview 5 to locate the relevant O−H stretches of interest. As the size of the cluster is increased from monomer to trimer, the bound O−H stretch shifts to a lower wavenumber because of the elongation of the O−H bond length. The predicted bond lengths in the optimized structures are shown to increase in Table 1. The phenol monomer has a bond length of 0.96622 Å as compared to an average bond length of 0.98034 Å for the phenol trimer. This confirms that the increase in bond length results in a decrease in the vibrational frequency of the O−H stretch. Students can make assignments to the IR spectra similar to what is represented in Figure 3. Once the frequencies have

HAZARDS All chemicals were purchased from Sigma-Aldrich and used as received. Phenol is toxic if swallowed, in contact with skin, or inhaled and can cause skin or eye damage. Dichloromethane can cause skin or eye irritation and should be used with proper ventilation. To ensure safety, solutions can be prepared in the hood, and the sample can be added to the IR demountable liquid cell, capped, and transferred to the FT-IR. Waste should be disposed of properly.

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RESULTS AND DISCUSSION The IR spectra of the 0.5, 1.0, 1.5, and 2.0 M solutions of phenol in dichloromethane were collected from 3100−3700 cm−1 as shown in Figure 2. It should be noted that there are

Figure 2. IR spectra of 2.0, 1.5, 1.0, and 0.5 M solutions of phenol in dichloromethane in the O−H stretching region (3100−3700 cm−1) displayed two observed peaks.

other plausible hydrogen bonds that are observed in the IR region due to the interactions of phenol with dichloromethane and the self-association of dichloromethane.14 However, these absorptions are outside of the experimental range of this study; therefore, the two peaks of varying intensity and shape observed in the IR spectrum are a direct result of the selfassociation of phenol. As the concentration of phenol is increased, there is a subsequent increase in the absorbance of both peaks. It is clear that the increase in concentration has a larger effect on the intensity of the peak observed at the lower wavenumber. To quantify this increase was not an objective of this lab. To understand the observed changes in the absorbance with increased concentration and to identify the peaks, the computational results were combined with the IR spectra and interpreted. Frequency scaling factors were applied to both data sets, which involved scaling the monomer wavenumber to the free O−H stretch, which was found experimentally to be at 3579

Figure 3. Spectral assignments made to the 2.0 M spectrum of phenol using the scaled frequencies in Table 1 (red, monomer; blue, dimer; green, trimer).

been scaled, it becomes evident that the monomer peak (3570.09 cm−1) and the dimer free O−H stretch (3587.55 cm−1) contribute to the higher wavenumber peak in the IR

Table 1. Computational Data of Phenol O−H Stretching Vibrations (Monomer, Dimer, and Trimer) cluster

scaled wavenumber (cm−1)

motion of moleculea

O−H bond length (Å)

monomer dimer

3579.08 3587.55 3453.84 3354.31, 3354.66

free O−H stretch free O−H stretch bound O−H stretch bound O−H stretch

0.96622 0.96581 0.97340 0.98037, 0.98028, 0.98038

trimer a

The motion of molecules can be animated using Gaussview 5 and is described either as free or bound stretching of the phenol clusters. C

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Experimental and Theoretical Infrared and UV-Visible Spectroscopy. J. Chem. Educ. 2014, 91, 883−888. (3) Desiraju, G.; Steiner, T. The Weak Hydrogen Bond in Structural Chemistry and Biology; Oxford Science Publications: Oxford, UK, 1999. (4) Purushotham, U.; Sastry, G. N. Exploration of Conformations and Quantum Chemical Investigation of L-Tyrosine Dimers, Anions, Cations, and Zwitterions: A DFT Study. Theor. Chem. Acc. 2012, 131, 1−14. (5) Ebata, T.; Watanabe, T.; Mikami, N. Evidence for the Cyclic Form of Phenol Trimer: Vibrational Spectroscopy of the OH Stretching Vibrations of Jet-Cooled Phenol Dimer and Trimer. J. Phys. Chem. 1995, 99, 5761−5764. (6) Fuke, K.; Kaya, K. Electronic Absorption Spectra of Phenol(H2O)n and (Phenol)n As Studied by the MS MPI Method. Chem. Phys. Lett. 1983, 94, 97−101. (7) Pimentel, G. C.; McClellan, A. L. The Hydrogen Bond; W.H. Freeman and Co.: New York, 1960. (8) Arunan, E.; Desiraju, G. R.; Klein, R. A.; Sadlej, J.; Scheiner, S.; Alkorta, I.; Clary, D. C.; Crabtree, R. H.; Dannenberg, J. J.; Hobza, P.; Kjaergaard, H. G.; Legon, A. C.; Mennucci, B.; Nesbitt, D. J. Defining the Hydrogen Bond: An Account (IUPAC Technical Report). Pure Appl. Chem. 2011, 83, 1619−1636. (9) Atkins, P. W.; De Paula, J. Physical Chemistry, 9th ed.; W.H. Freeman: Gordonsville, VA, 2009; pp 300−301. (10) Garland, C. W.; Nibler, J. W.; Shoemaker, D. P. Experiments in Physical Chemistry, 7th ed.; McGraw−Hill: New York, 2003; p 406. (11) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, revision D.01; Gaussian, Inc.: Wallingford, CT, 2009. (12) Wong, M. W. Vibrational Frequency Prediction Using Density Functional Theory. Chem. Phys. Lett. 1996, 256, 391−399. (13) Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648−52. (14) Smith, A. L. The Coblentz Society Desk Book of Infrared Spectra, 2nd ed.; The Coblentz Society: Kirkwood, MO, 1982; 1−24. (15) Laury, M. L.; Carlson, M. J.; Wilson, A. K. Vibrational Frequency Scale Factors for Density Functional Theory and the Polarization Consistent Basis Sets. J. Comput. Chem. 2012, 33, 2380− 2387.

spectrum. It was observed that this higher wavenumber peak shifts slightly to a lower wavenumber as the concentration is increased as shown in Figure 2. This shift is the result of the approximate decreased population of free O−H stretches of the dimer as the concentration is increased. There is also a shift that occurs for the same reason at the lower wavenumber peak. The bound dimer peak (3453.84 cm−1) and the bound trimer peaks (3354.31 cm−1 and 3354.66 cm−1) make up the lower wavenumber peak. This peak broadens and shifts to a lower wavenumber because of the fact that both the dimer and trimer contribute to the overall absorbance and occur at different frequencies. The enhanced absorption of the bound O−H stretch is a direct result of a higher population of dimers and trimers present at higher concentrations as compared to lower concentrations.

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SUMMARY Phenol is an inexpensive reagent that can form hydrogen bonds readily in solution. In this laboratory, the phenol monomer, dimer, and trimer were used as simple models of biological interactions. For the experimental measurements, IR spectroscopy was used to observe the effects of hydrogen bonding on the O−H stretching vibration. For the computational measurements, the vibrational frequency calculations and geometry optimizations were used to assign the peaks observed in the IR spectrum. The harmonic oscillator model and the force constant equation were used to show the relationship of the O−H bond length with the wavenumber. It was observed that students were more engaged in this laboratory as compared to other traditional physical chemistry lab protocols because of the added computational component. In particular, biochemistry majors indicated that this laboratory enhanced their understandings of the applications of physical chemistry in biological systems. This demonstrates the advantage of incorporating experimental and computational lab protocols together in upper-level chemistry courses.

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ASSOCIATED CONTENT

* Supporting Information S

Background information, instructions, data forms, and notes for instructors. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Author

* E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS The authors would like to thank Misericordia University for the financial support through the Faculty Summer Research Grants Program and Misericordia University Summer Research Fellowship Program for this project.

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REFERENCES

(1) Conklin, A.; Goldcamp, M. J.; Barrett, J. Determination of Ethanol in Gasoline by FT-IR Spectroscopy. J. Chem. Educ. 2014, 91, 889−891. (2) Costello, K.; Doan, K. T.; Organtini, K. L.; Wilson, J.; Boyer, M.; Gibbs, G.; Tribe, L. Exploration of Thermochromic Materials Using D

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