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Aug 10, 2016 - M. Jake PushieJulien J. H. CotelesageLinda VogtMonica BarneyIngrid J. PickeringGraham N. George. The Journal of Physical Chemistry A ...
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Insights into the Nature of the Chemical Bonding in Thiophene-2thiol from X‑ray Absorption Spectroscopy Julien J. H. Cotelesage,† M. Jake Pushie,† Linda Vogt,†,¶ Monica Barney,‡ Andrew Nissan,‡ Ingrid J. Pickering,†,¶ and Graham N. George*,†,¶ †

Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada ¶ Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada ‡ Chevron Energy Technology Company, Richmond, California 94802, United States S Supporting Information *

ABSTRACT: Thiophenes are the simplest aromatic sulfur-containing compounds; they are widespread in fossil fuels and a variety of natural products, and they have vital roles in determining characteristic aromas that are important in food chemistry. We used a combination of sulfur K-edge X-ray absorption spectroscopy and density functional theory to investigate the chemical bonding in the novel sulfur-containing heterocycle thiophene-2-thiol. We show that solutions of thiophene-2-thiol contain significant quantities of the thione tautomer, which may be the energetically preferred 5Hthiophene-2-thione or the more accessible 3H-thiophene-2-thione.

1. INTRODUCTION Thiophenes (Figure 1) are the simplest aromatic sulfur compounds. Noted for their stability, thiophenes are wide-

of thiophene-2-thiol, which, combined with density functional theory (DFT), provides insights into the chemical bonding in this novel compound.

2. EXPERIMENTAL SECTION 2.1. Chemicals and Reagents. Thiophene-2-thiol was purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO) at the highest quality available. Caution: Thiophene-2-thiol has a particularly foul stench: the pure compound should be handled in a hood with good ventilation, and any solutions should be enclosed in sealed containers at all times. Samples of 2,2,4,4-tetramethylcyclobutane-1,3-dithione14 were a gift from Prof. Eric Block, Univ. of New York at Albany, and all other compounds and solvents were obtained from Sigma-Aldrich Chemical Co. (St. Louis, MO) and were of the highest quality available. 2.2. X-ray Absorption Spectroscopy. Samples for XAS were prepared in toluene solutions at concentrations of 100 mM or less. Solutions were placed in modified SPEX CertiPrep (Metuchen, NJ) X-cell sample cups with custom-made Teflon inserts to reduce the volume of solution required and employing a 3 μm thick Etnom window (Chemplex Industries, Inc, Palm City, FL) to transmit the fluorescence. XAS spectra were measured at the Stanford Synchrotron Radiation Lightsource (SSRL) on beamline 4−3. In order to minimize atmospheric attenuation of the X-rays the experiment was maintained in an atmosphere of helium gas. A Si(111) double

Figure 1. Schematic structure of the thiophene ring system, showing ring numbering.

spread in natural systems and are found in plants1 (particularly those of the genus Aster), are of interest as potential antiviral drugs,1,2 are important as odorants and flavorants in food science,3 and are widespread in fossil fuels.4 Here we report on a novel thiophene, thiophene-2-thiol, which, despite being among the vilest-smelling of sulfur compounds in a class of compounds that justly have a reputation for unpleasant odors, is, in trace amounts, important in Maillard chemistry and, in particular, in giving roasted meats their characteristic aroma.5 Thiophene-2-thiol is also of interest in the synthesis of possible new polymeric conductors containing polythiophenes.6 Previous work has established that sulfur K-edge X-ray absorption spectroscopy (XAS) can provide a sensitive probe of the sulfur speciation in complex mixtures.7−12 Previously we have explored the sensitivity of sulfur K-edge XAS to a variety of substituents of the thiophene ring system.13 Here we use sulfur K-edge XAS in the direct detection of different tautomers © XXXX American Chemical Society

Received: June 10, 2016 Revised: August 8, 2016

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The Journal of Physical Chemistry A crystal monochromator was used with harmonic rejection accomplished by setting the energy cutoff of the beamline 4−3 upstream Ni-coated vertically collimating bent flat mirror to approximately 6 keV. Fluorescence self-absorption artifacts in the XAS spectra15,16 were tested for by sequential dilutions, as previously described, and the data presented in this paper are essentially free from self-absorption artifacts. Spectra of solutions were measured by monitoring the total X-ray fluorescence using a Stern−Heald−Lytle detector (the EXAFS Company, Pioche, NV).17 The incident X-ray energy was calibrated with reference to the spectrum of a solid anhydrous sodium thiosulfate (Na2S2O3) standard using the literature value of 2469.2 eV as the energy of the lowest-energy K-edge absorption peak.18 The spectrum of sodium thiosulfate was also used to optimize the energy resolution, by adjusting apertures. All other experimental parameters were as previously described.16 Analysis of XAS data used the EXAFSPAK program suite, with calculation of higher derivatives achieved using the piecewise cubic spline method embedded within EXAFSPAK.19 Data were normalized to the edge jump to give a per-unit-sulfur absorption spectrum, using the spline method, which employs a rigid spline above the absorption edge to estimate the edge jump. 2.3. Density Functional Theory Calculations. DFT geometry optimizations were performed using DMol3 and Biovia Materials Studio Version 201620,21 using the Perdew− Burke−Ernzerhof functional both for the potential during the self-consistent field procedure, and for the energy. Dmol3 double numerical basis sets included polarization functions for all atoms with all-electron core treatments. Solvation effects were modeled using the Conductor-like Screening Model (COSMO)22 in Dmol3 with a dielectric value representing toluene (ε = 2.38). DFT simulations of near-edge spectra were calculated using the StoBe-deMon code23 employing the socalled half-core-hole approximation for the core−hole, incorporating relaxation of selected excited states at the absorption edge, employing the coordinates from Dmol3 geometry optimizations. StoBe-deMon calculations employed the nonlocal exchange function of Perdew and Wang24 and the Perdew correlation functional.25,26 The (6311/311/1) basis set was used for C, and (311/1) was used for H. To localize the core−hole to the S atom of interest (the absorber) employed the IGLO III basis set,27 while an effective core potential combined with the (311/211/1) basis set was employed for the spectator S center. Interpolation of the exchange-correlation potential employed the auxiliary basis sets (5,4;5,4) for S, (5,2;5,2) for C, and (3,1;3,1) for H. A pseudopotential (4:6,4) was applied to the spectator S atom. Convolution with pseudoVoigt line-shape functions was conducted as previously described.28

Figure 2. Experimental sulfur K-edge XAS spectrum of thiophene-2thiol and selected related compounds, the thione species 2,2,4,4tetramethylcyclobutane-1,3-dithione (red), benzenethiol (blue), 2methyl-thiophene (green), and tetrahydrothiophene (yellow). The broken line shows the linear combination fit discussed in the text.

chemical nature of thiophene ring substituents, while the 1s→(S−C)π* was found to change substantially for different thiophenes.13 The transition energies were found to vary approximately linearly with the Yukawa−Tsuno resonance component29 of the well-known Hammett substituent constant σ,30 often called σR, and we commented that the energies of the major transitions could be predicted for a substituent of known σR.13 Applying this approach to thiophene-2-thiol, we observe that the tabulated σR for the −SH group is small and negative with a value of ca. −0.11, close to the value for a methyl group. On the basis of this, we would therefore predict that the spectrum of the thiophenic sulfur of thiophene-2-thiol would resemble that of 2-methyl-thiophene. The total XAS spectrum of thiophene2-thiol will reflect the presence of two types of sulfur and thus is predicted to include an equal contribution from the thiol substituent, characteristic of an aromatic thiol such as benzenethiol (Figure 2). The experimental spectrum of thiophene-2-thiol, however, is very different from this simple prediction, exhibiting instead distinctive contributions at low energy with a peak energy of 2467.46 eV that are characteristic of the presence of a thione (CS) group.31,32 The spectrum of a solution of 2,2,4,4-tetramethylcyclobutane-1,3-dithione is shown in Figure 2 for comparison, which shows a characteristic low-energy peak attributable to 1s→(CS)π* transitions at the same energy as that observed for thiophene-2-thiol. We hypothesized that the low-energy transition observed for thiophene-2-thiol was due to the presence of thione-containing tautomers, as shown in Figure 3. DFT calculations of the three possible tautomers show that the energies of the two postulated thione entities differ by +1.6 (2) and +25.5 (3) kJ/mol relative to the thiophene-2-thiol. The ring structures of both thione tautomers are planar and, with the exception of the proton directly involved in the transition, show only very subtle shifts in atomic positions on transitioning between tautomers, in most cases less than 0.1 Å. The experimental spectrum of thiophene-2-thiol was fitted with a linear combination of standard compound spectra, using the experimental spectra shown in Figure 2 for representative sulfur functional groups,

3. RESULTS AND DISCUSSION The sulfur K-edge XAS spectrum of a toluene solution of thiophene-2-thiol is shown in Figure 2, compared with several other relevant sulfur compounds. We have previously investigated the sulfur K XAS of a range of different substituted thiophenes.13 The spectra are comprised of two major transitions, which can be assigned as 1s→(S−C)π* and 1s→(S−C)σ* transitions (lower and higher energy peaks, respectively). For the parent compound thiophene, these transitions are close in energy, within 1 eV of each other, at 2471.0 and 2471.7 eV, respectively.13 The energy of the 1s→(S−C)σ* transition was relatively invariant with the B

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Figure 3. Schematic structures of the possible tautomers of thiophene2-thiol (1), 5H-thiophene-2-thione (2), and 3H-thiophene-2-thione (3). DFT-computed equilibrium relative energies and geometries are shown adjacent to the schematic structures.

with the spectrum of tetrahydrothiophene to represent the ring sulfur of tautomers 2 and 3. The components, namely, thiol and thiophene representing 1 and thione and sulfide representing 2 and 3, were independently varied. The resulting linear combination fit is shown in Figure 2 (broken line). Confidence in the validity of the fit was increased by the fact that the resultant fractions of sulfur forms belonging to the different tautomers differed by only 3% (i.e., the fraction of thiol and thiophene were in agreement, as were the fraction for thione and sulfide). This analysis gave an estimate for the proportion of 1 of 68% and for 2 + 3 of 32%. From the ratio of [2 + 3]/[1] = 0.48 we can calculate an approximate ΔG0 value of +0.8 kJ/ mol, which is very close to the computed difference in enthalpy between 1 and 2 of +1.6 kJ/mol, and certainly within the uncertainty of our density functional calculations. Of the two thione tautomers, 2 is energetically preferred over 3. However, the transfer of a proton from the 2-thiol group of 1 to the 3-carbon position to form 3 requires a movement of only ∼3.4 Å, while transfer to the 5-carbon position to form 2 is over a distance of ∼5.1 Å. Preliminary transition-state DFT calculations indicate that interconversion of 1 and 3 proceeds via a relatively simple transition-state in which the proton is bound to C2 in a four-coordinate intermediate, whereas interconversion of 1 and 2 proceeds via two discrete steps with an activation barrier that is 69 kJ/mol higher than that for 1 to 3, in which the translocating proton bridges first between the two sulfurs and then between the ring sulfur and C5. Thus, while the formation of tautomer 2 is energetically favored over 3, the lower activation barrier for 1→3 means that this would be expected to be kinetically favored over 1→2, and 3 may therefore also be present in solution. We note that we neglected the possibility of proton tunneling in these calculations, which, given the low activation energies and the short distances concerned, would also be expected to be an important contributor to the proportions of tautomers in solution. Simulations of the spectra for the two different sulfur atoms in the three tautomers using StoBe-deMon23 are shown in Figure 4, and as expected they predict that the thione sulfur of 2 and 3 will show an isolated peak at low energy, due to a 1s→(CS)π* transition, and that the ring sulfurs of 1, 2, and

Figure 4. Simulated spectra for all of the sulfur atoms in the three tautomers of thiophene-2-thiol, together with the stick spectrum showing the transition energies and intensities computed. Spectra labeled “ext.” are of the external sulfur (ring 2-substituent), while those labeled “ring” are of the sulfur that is an integral part of the ring (at the 1 position). The calculations clearly show the intense 1s→(CS)π* transition and predict that the sulfur K-edge XAS spectra are not expected to be able to distinguish between 2 and 3. A comparison of the sum of the computed spectra of tautomers with the experimental data is shown in Supporting Information.

3 and the thiol group of 1 should have spectral features shifted to relatively higher energies, as discussed above. The ring sulfurs of 2 and 3 are predicted to show thiophene-like spectra, with a splitting that is due to a lowering of the energy of the 1s→(C−S)π* transition as a result of involvement of the thione group in the π* orbital. While the thione tautomers lack an aromatic ring, so that a comparison with substituted thiophenes is not strictly valid, this is a somewhat similar situation to that observed with 2-substituted thiophenes with substituents having large σR values.13 The spectra of 2 and 3 are therefore predicted to be very similar, and one conclusion from our simulations is that, as expected, these tautomers cannot be distinguished from sulfur K-edge XAS alone. The importance of thiophenes was mentioned in the introductory matter, and thione compounds have a wellestablished important chemistry in their own right.33 In related C

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Purification, Structural Elucidation, and Evaluation of Bioactivities. Phytochem. Rev. 2016, 15, 197−220. (2) Lepri, S.; Nannetti, G.; Muratore, G.; Cruciani, G.; Ruzziconi, R.; Mercorelli, B.; Palù, G.; Loregian, A.; Goracci, L. Optimization of Small-Molecule Inhibitors of Influenza Virus Polymerase: from Thiophene-3-carboxamide to Polyamido Scaffolds. J. Med. Chem. 2014, 57, 4337−4350. (3) Mottram, D. S. Flavour Formation in Meat and Meat Products: A Review. Food Chem. 1998, 62, 415−424. (4) Kropp, K. G.; Fedorak, P. M. A Review of the Occurrence, Toxicity, and Biodegradation of Condensed Thiophenes found in Petroleum. Can. J. Microbiol. 1998, 44, 605−622. (5) Chen, Y.; Xing, J.; Chin, C.-K.; Ho, C.-T. Effect of Urea on Volatile Generation from Maillard Reaction of Cysteine and Ribose. J. Agric. Food Chem. 2000, 48, 3512−3516. (6) Street, G. B.; Clarke, T. C. Conducting Polymers: A Review of Recent Work. IBM J. Res. Dev. 1981, 25, 51−57. (7) George, G. N.; Gorbaty, M. L.; Kelemen, S. R.; Sansone, M. Direct Determination and Quantification of Sulfur Forms in Coals from the Argonne Premium Sample Program. Energy Fuels 1991, 5, 93−97. (8) Pickering, I. J.; Prince, R. C.; Divers, T. C.; George, G. N. Sulfur K-edge X-ray absorption Spectroscopy for Determining the Chemical Speciation of Sulfur in Biological Systems. FEBS Lett. 1998, 441, 11− 14. (9) Gnida, M.; Yu Sneeden, E.; Whitin, J. C.; Prince, R. C.; Pickering, I. J.; Korbas, M.; George, G. N. Sulfur X-ray Absorption Spectroscopy of Living Mammalian Cells: An Enabling Tool for Sulfur Metabolomics - In situ Observation of Taurine Uptake into MDCK Cells. Biochemistry 2007, 46, 14735−14741. (10) Hackett, M. J.; Smith, S. E.; Paterson, P. G.; Nichol, H.; Pickering, I. J.; George, G. N. X-ray Absorption Spectroscopy at the Sulfur K-edge: A New Tool to Investigate the Biochemical Mechanisms of Neurodegeneration. ACS Chem. Neurosci. 2012, 3, 178−185. (11) Gambardella, A. A.; Schmidt Patterson, C. M.; Webb, S. M.; Walton, M. S. Sulfur K-edge XANES of Lazurite: Toward Determining the Provenance of Lapis Lazuli. Microchem. J. 2016, 125, 299−307. (12) Greenfield, M. L.; Byrne, M.; Mitra-Kirtley, S.; Kercher, E. M.; Bolin, T. B.; Wu, T.; Craddock, P. R.; Bake, K. D.; Pomerantz, A. E. XANES Measurements of Sulfur Chemistry during Asphalt Oxidation. Fuel 2015, 162, 179−185. (13) George, G. N.; Hackett, M. J.; Sansone, M.; Gorbaty, M. L.; Kelemen, S. R.; Prince, R. C.; Harris, H. H.; Pickering, I. J. Long-range Chemical Sensitivity in the Sulfur K-edge X-ray Absorption Spectra of Substituted Thiophenes. J. Phys. Chem. A 2014, 118, 7796−7802. (14) Shirrell, C. D.; Williams, D. E. The Crystal Structure of 2,2,4,4Tetramethyl-1,3-Cyclobutanedithione. Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. 1973, 29, 1648−1653. (15) Pickering, I. J.; George, G. N.; Yu, E. Y.; Brune, D. C.; Tuschak, C.; Overmann, J.; Beatty, J. T.; Prince, R. C. Analysis of Sulfur Biochemistry of Sulfur Bacteria Using X-ray Absorption Spectroscopy. Biochemistry 2001, 40, 8138−8145. (16) George, G. N.; Gnida, M.; Bazylinski, D. A.; Prince, R. C.; Pickering, I. J. X-ray Absorption Spectroscopy as a Probe of Microbial sulfur Biochemistry: The Nature of Bacterial Sulfur Globules Revisited. J. Bacteriol. 2008, 190, 6376−6383. (17) Lytle, F. W.; Greegor, R. B.; Sandstrom, D. R.; Marques, E. C.; Wong, J.; Spiro, C. L.; Huffman, G. P.; Huggins, F. E. Measurement of Soft X-ray Absorption Spectra with a Fluorescent Ion Chamber Detector. Nucl. Instrum. Methods Phys. Res., Sect. A 1984, 226, 542− 548. (18) Sekiyama, H.; Kosugi, N.; Kuroda, H.; Ohta, T. Sulfur K-edge Absorption Spectra of Na2SO4, Na2SO3, Na2S2O3, and Na2S2Ox (x = 5−8). Bull. Chem. Soc. Jpn. 1986, 59, 575−579. (19) George, G. N. 2001, http://ssrl.slac.stanford.edu/exafspak.html. (20) Delley, B. An All-Electron Numerical Method for Solving the Local Density Functional for Polyatomic Molecules. J. Chem. Phys. 1990, 92, 508−517.

chemistry to that reported here, thiol−thione tautomers have been previously studied for 1,2,4-triazole-3-thiol species,34 and a thione intermediate has been postulated for the reactions leading to generation of the pungent allylisothiocyanate in both horseradish (Armoracia lpthifolia) and wasabi (Wasabia japonica),35 which has been directly observed by using sulfur K-edge XAS.36

4. CONCLUSION Sulfur K-edge XAS has been used to investigate the novel sulfur-containing heterocyclic compound, thiophene-2-thiol. The spectra directly show the presence of significant quantities of thione-containing tautomers, illustrating the power of the XAS method for probing sulfur chemical forms. The thione spectra are characterized by a low-energy 1s→(CS)π* transition that falls below the majority of spectroscopic absorption. DFT was used to understand the spectra of the tautomers, and the estimated energetic differences indicate that in addition to thiophene-2-thiol, the 5H-thiophene-2-thione tautomer may be the primary tautomer present in toluene solution.



ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpca.6b05874. Comparison of sum of StoBe-DeMon DFT simulated spectra. (PDF)



AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Phone: +1 306 966 5722. Notes

The authors declare no competing financial interest.



ACKNOWLEDGMENTS We thank Prof. L. G. M. Pettersson (University of Stockholm) for helpful advice in operating the StoBe-deMon software. Research at the Univ. of Saskatchewan is supported by a grant from the Chevron Energy Technology Company, the Natural Sciences and Engineering Research Council (G.N.G, I.J.P), the Canadian Institutes of Health Research (CIHR) (G.N.G, I.J.P), the Saskatchewan Health Research Foundation (GNG, IJP), the University of Saskatchewan and by Canada Research Chairs (G.N.G, I.J.P). J.J.H.C. and M.J.P. are Training in Health Research using Synchrotron Techniques (CIHR-THRUST) Associates. Use of the Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-76SF00515, respectively. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (including P41GM103393). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH.



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