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A: Spectroscopy, Molecular Structure, and Quantum Chemistry

Evidence of C-H O Interactions in the Thiophene : Water Complex
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Joshua G. Wasserman, Keshihito J. Murphy, and Josh J. Newby

J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.9b07355 • Publication Date (Web): 06 Nov 2019
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Page 1 of 35 The Journal of Physical Chemistry

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8 Evidence of C−H···O interactions in the
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thiophene : water complex
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15 Joshua G. Wasserman, Keshihito J. Murphy and Josh J. Newby∗
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18 Department of Chemistry, Hobart and William Smith Colleges, Geneva, NY 14456
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21 E-mail: newby@hws.edu
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23 Phone: 315-781-3757
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26 Abstract
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29 An analysis of the 1:1 complex of thiophene and water is presented. In this study,
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31 computation and matrix isolation FTIR were used to determine stable complexes
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of thiophene : water. Computational studies found six, low-energy complexes that
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34 were differentiated by the interaction present. Three complexes were characterized by
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36 C−H···O interactions, one by O−H···S, one by O−H···π, and one with an unusual, dual
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38 interaction of O−H···S and C−H···O. The O−H···π interaction was found to have the
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40 lowest overall energy at multiple levels of theory (B3LYP, B3LYP-GD3BJ, B97-D3,
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42 M05-2X, ωB97X-D, and MP2). Analysis of matrix isolation FTIR spectra indicated
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44 that the primary experimental geometry was a complex where water interacts through
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C−H···O at the α carbon position of the thiophene ring. This experimental result is not
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47 in line to other related complexes (furan : water and thiophene : methanol) where the
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49 complex formed through more standard interactions (eg. O−H···O, O−H···π). These
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51 atypical differences are explored in our findings.
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Introduction
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6 The role of hydrogen bonding in chemistry cannot be understated. These non-covalent inter-
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8 actions can be found in countless contexts and are often an important aspect for determining
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10 chemical behavior. The common description of a hydrogen bond is that of a hydrogen atom
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12 that is connected to an electronegative atom that interacts with another electronegative
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14 atom (X−H···Y, where X and Y are electronegative atoms). This description, however, can
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16 be expanded to include interactions with π systems and atoms that are not generally thought
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18 of as being electronegative (e.g. C or S). While less common, hydrogen bonding involving C
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20 or S with are known to play a significant role in biochemical processes and supramolecular
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22 features. 1–3
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24 The study of simple aromatics with small molecules has been an area of research ripe
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26 for yielding greater understanding of hydrogen bond interactions. Aromatics are a common
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28 target of interest as they often can support competing interaction types. Aromatics of
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30 interest include benzene, 4–6 phenol, 7,8 indole, 9 and furan. 10 These studies generally involve
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32 a small molecule, such as water, that can act as a hydrogen bond donor or acceptor. In
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34 these studies, quantum chemical calculation often found multiple potential geometries for
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36 the complexes that result from the different types of interactions found in the system. For
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38 example, in the furan : water complex, calculations showed possible O−H···O, O−H···π,
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40 and C−H···O, whereas the spectroscopic analysis indicated that the complex was primarily
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42 O−H···O. 10
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44 While seemingly the weaker of these hydrogen bonds, the C−H···O is commonly found
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46 in larger molecular systems where these interactions can be further stabilized by additional
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48 interactions. 1,2 The C−H···O was first proposed in crystallographic studies by Sutor in the
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50 1960s 11,12 and supported by the work of Taylor and Kennard. 13 Despite its familiarity in
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52 larger systems, C−H···O interactions are not well documented in small molecule studies in
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54 which only one or two interactions are observed. A few examples of small molecule C−H···O
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56 interactions include dimethoxyethane dimer, 14 intermolecular interaction of 1-methoxy-2-
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(dimethylamino)ethane, 15 and formaldehyde dimer. 16 Additionally, a competition between
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C−H···O and O−H···π was observed in the C2 H2 : H2 O and C2 H4 : H2 O complexes. 17 In the
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furan : water complex, the oxygen heteroatom is very electronegative, thus it was a strong
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9 director for the final geometry of the complex. This stronger direction is what led to the
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11 O−H···O interaction being favored over the C−H···O. One might therefore expect thiophene
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13 (C4 H4 S) would have less impact on the geometry of the thiophene : H2 O complex as the
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15 sulfur heteroatom is less electronegative than oxygen, thus potentially favoring a C−H···O
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17 interaction.
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19 There are few studies on complex systems involving thiophene presented in the literature.
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21 The microwave spectroscopy and computational communities have observed complexes of
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23 thiophene, mostly with diatomic halides. 18–21 In these studies, the partially positive hydrogen
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25 of the diatomic halide is found to interact with the π cloud of thiophene. Thiophene dimer,
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27 while not experimentally verified, has been studied theoretically, 22 with specific interest
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29 toward π stacking potential. Matrix isolation FTIR spectroscopy has been used to study
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31 thiophene complexing with copper atoms and copper carbonyl 23 and thiophene complexing
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33 with methanol. 24 In these studies, vibrational frequencies of the thiophene ring experience
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35 little perturbation, but the C−H bonds show some slight vibrational shifts. In the case of
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37 thiophene : methanol, competition between bonding motifs (O−H···S and O−H···π) was
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39 observed with some preference for O−H···S interaction. It is interesting that the thiophene
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41 methanol complex has been studied, whereas the seemingly simpler thiophene : H2 O has not
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43 been reported in the literature.
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45 The aim of the current study is to fill in this gap in the literature of complexes of aromatic
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47 heterocycles and water while exploring potential C−H···O interactions. Here, we present an
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49 investigation of the weakly-bound complexes of thiophene with water as interrogated by
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51 matrix isolation FTIR and computational methods. Potential geometries of the 1:1 complex
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53 of thiophene : water (Tp:H2 O) will be presented and evidence will be given to support an
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55 experimental structure for this complex.
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Methods
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7 Spectroscopy
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The matrix isolation system used in this work has been described in detail elsewhere 10 and
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a brief description will be given here. Cryogenic temperatures of the sample are maintained
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using a CTI-Cryogenics, Model 22 Cryodyne (Helix Technology Corp.), backed by a 8200
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series compressor. A window mount is attached to the cold finger and holds a CsI window.
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Temperature of the cold finger was measured with a silicon diode monitored by a temperature
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controller (Lakeside, 335). The sample window and cold finger are contained in a vacuum
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chamber (Janis, CCS-350R). This chamber has four, o-ring sealed optical ports and two o-
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ring sealed sample injection ports on a rotatable shroud. For FTIR spectroscopy experiments,
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two opposing optical ports are fitted with KBr windows. The two injection ports are at 45◦
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angles to the CsI cold window during depositions.
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Thiophene (> 99 %, Sigma Aldrich) was dried over molecular sieves (3 Å) prior to
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introduction to the vacuum system. Water (18 MΩ) was obtained from an in-house purifier.
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Isotopic studies utilized D2 O (99.9 % D, Sigma Aldrich). All samples were degassed using
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standard freeze-pump-thaw cycling before use. Despite these precautions, samples of neat
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thiophene contain small amounts of water. When using D2 O, this small amount of water
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39 also yields HOD in spectra. Mixtures of thiophene, water, and matrix gases (nitrogen or
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41 argon, 99.9999 %, Linde) were prepared using standard manometric techniques. Samples
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43 were deposited in nitrogen at 15 K at a rate of 5 - 10 mm/hr for 4 - 8 hrs. Matrices were
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45 then annealed at 30 K for 15 minutes. Annealing was used to soften the matrix and allow
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47 for diffusion in order to facilitate complexation. Final spectra of the annealed matrix were
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49 recorded at 15 K. Matrices of Ar were deposited at 20 K to reduce the scattering of the
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51 matrix. These samples were annealed at 35 K and final spectra were recorded at 15 K.
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53 Sample spectra were recorded on a nitrogen purged, Nicolet iS50 (ThermoScientific) FTIR
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55 using 128 scans at 0.5 cm−1 resolution in the 4000 - 600 cm−1 region.
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Computational details
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6 Ground state geometries, energies, and harmonic frequencies were calculated using the Gaus-
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8 sian suite of programs. 25,26 Multiple levels of theory, including density functional theory
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10 (DFT) and Møller-Plesset second-order, perturbation theory (MP2) 27 calculations, were
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12 employed . Density fucntional theory calculations employed the B3LYP, 28,29 M05-2X, 30
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14 B97-D3 31,32 and ω-B97XD 33 functionals. As B3LYP does not account for dispersion forces,
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16 empirical corrections were made using GD3BJ. 32 These levels of theory were chosen as they
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18 address varying levels of dispersion interaction, which may be important in molecular com-
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20 plexes. A wide variety of complex geometries were sampled to best ensure that our study
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22 found the lowest energy configurations.
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24 Calculations were performed using the Pople type basis set 34 6-311++G(d,p) and the
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26 Dunning type aug-cc-pVTZ. 35 Tight convergence criteria and an ultra-fine grid were em-
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28 ployed in all density functional calculations. Energies for complexes were corrected for zero
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30 point energy (ZPE), as well as basis set superposition error (BSSE), using the procedure
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32 of Boys and Bernardi. 36 For simplicity, vibrational frequencies presented here are all from
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34 B3LYP/aug-cc-pVTZ calculations and have all been scaled by 0.968 as suggested by CC-
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36 CDBD. 37
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38 Atoms in molecules (AIM) analysis was used to find bond critical points (BCPs), ring
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40 critical points (RCPs), and associated electron density values. This analysis was performed
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42 using AIMAll. 38 Input wave function files were supplied by the output of Gaussian.
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Results and Discussion
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7 Calculation
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Energetics of Tp:H2 O complexes
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12 A major challenge in determining the structure of a weakly-bound complex is that it is often
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14 hard to predict which intermolecular interactions will dominate in the final structure. As
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16 such, it can be unclear which levels of theory and basis sets will most appropriately describe
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18 the complex. To limit bias in our analysis, we chose to calculate structures using multiple
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20 levels of theory and basis sets that have been used to successfully describe other weakly-
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22 bound complexes. 33,39–41 As may be expected, each calculation set (level of theory plus basis
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24 set) will yield slightly different results, but it is believed that a holistic analysis of these
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26 calculations will yield the most probable interpretation for the minimum energy structure.
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28 In essence, the more calculations that predict a preferred interaction, the more likely we are
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30 to know the true structural preference.
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32 Six unique, minimum energy structures were found across all levels of theory when calcu-
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34 lated using the 6-311++G(d,p) and aug-cc-pVTZ basis sets. All minimum energy structures
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36 found were within 10 kJ/mol of the global minimum (Table 1) and had no negative (imag-
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38 inary) frequencies. All energies reported here have been corrected for ZPE and BSSE. The
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40 six structures were neither found equally across every level of theory, nor every basis set,
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42 but are thought to represent the most likely minimum energy structures of Tp:H2 O. The
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44 geometry of these structures are shown in Figure 1. Two structures (V and VI) were found
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46 to be minima in only a few of the calculations,as discussed below, and are not expected to
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48 be the most likely experimental structures.
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50 B3LYP found four stable structures using both 6-311++G(d,p) and aug-cc-pVTZ basis
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52 sets. Both basis sets predict structure III to be the minimum energy structure (ZPE and
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54 BSSE corrected). Structure I is calculated to be 0.04 kJ/mol higher in energy whereas
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56 structures II and IV are 1.29kJ/mol and 0.97 kJ/mol higher in energy, respectively, when
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10 Table 1: Calculated relative energies and interaction energies of Tp:H2 O
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6-311++G(d,p) aug-cc-pVTZ
13 I II III IV Va VI I II III IV V VI
14 B3LYP
15 Rel. E (kJ/mol)b 0.55 2.29 0.00 1.66 - - 0.15 1.45 0.00 1.03 - -
16 BSSE corr. (kJ/mol)c 0.80 2.43 0.00 1.58 0.04 1.29 0.00 0.97
17 Interaction E (kJ/mol)d -6.82 -4.81 -7.74 -5.86 -5.61 -3.93 -6.95 -5.73
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B3LYP-GD3BJ
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21 Rel. E (kJ/mol) 5.36 7.54 0.00 - - - - - 0.00 - - -
22 BSSE corr. (kJ/mol) 4.70 6.85 0.00 0.00
23 Interaction E (kJ/mol) -9.83 -7.32 -15.10 -14.31
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25 B97-D3
26 Rel. E (kJ/mol) - 9.54 0.00 - - - - - 0.00 - - -
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BSSE corr. (kJ/mol) 8.48 0.00 0.00
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Interaction E (kJ/mol) -6.19 -15.82 -14.90
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31 M05-2X
32 Rel. E (kJ/mol) 3.84 8.55 0.00 - - 8.15 4.03 7.44 0.00 - 4.62 7.13
33 BSSE corr. (kJ/mol) 3.10 7.65 0.00 6.94 3.66 6.93 0.00 4.24 6.60
34 Interaction E (kJ/mol) -11.63 -7.32 -15.27 -8.33 -10.25 -6.07 -14.73 -10.54 -6.95
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ωB97X-D
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Rel. E (kJ/mol) 6.23 8.15 0.00 - - 8.66 5.64 - 0.00 0.27 - -
39 BSSE corr. (kJ/mol) 5.70 7.59 0.00 7.46 5.38 0.00 0.26
40 Interaction E (kJ/mol) -9.33 -6.95 -15.19 -7.28 -8.91 -13.93 -13.89
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42 MP2
43 Rel. E (kJ/mol) 3.71 5.97 0.00 0.54 - 6.50 - - 0.00 - - -
44 BSSE corr. (kJ/mol) 1.43 3.41 0.00 0.34 3.34 0.00
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Interaction E (kJ/mol) -6.99 -4.90 -9.37 -8.83 -5.02 -13.84
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48 Structure V was not found to a minimum when using the 6-311++G(d,p) basis set. b Relative
49 energies corrected for ZPE. c Relative energies corrected for ZPE and BSSE. d Interaction
50 energies are corrected for BSSE according to procedure of Boys and Bernardi. 36
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6 Cα2 Cα1
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9 Cβ2 Cβ1
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11 I III V
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24 II IV VI
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27 Figure 1: Calculated structures of the Tp:H2 O complex. Structures I - IV were optimized
28 using B3LYP/aug-cc-pVTZ. Structures V and VI were optimized at M05-2X/aug-cc-pVTZ as
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they were not found when using B3LYP. All other levels of theory produced geometries very
31 similar to those shown here. For labeling purposes, α carbons indicate the carbons closest to
32 the sulfur atom, whereas β indicates the farther carbons. The 1 and 2 designations indicate
33 if the carbon is on the same side (1) as the complexing water or on the opposing side (2).
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36 using aug-cc-pVTZ. As B3LYP calculation ignore dispersion interactions, B3LYP-GD3BJ
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38 was used to correct for the effect of dispersion that may be present in these structures. These
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40 calculations show a simpler picture with only 3 stable structures at the 6-311++G(d,p) basis
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42 set. This set collapses into one minimum upon optimization with the larger aug-cc-pVTZ
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44 basis set. This minimum energy structure is a π bound OH as seen in structure III (Figure
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46 1). It is not surprising that the dispersion corrected calculation favors structure III as this
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48 structure interacts through the π cloud of thiophene and would seemingly be the strongest
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50 influenced by dispersion forces.
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52 The Cartesian coordinates describing the B3LYP/aug-cc-pVTZ structures can be found
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54 in the Supporting Information.
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56 M05-2X found four minima using the Pople basis set and five using the Dunning. Both
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basis sets found the lowest energy complex to be a π bound OH interaction (like structure
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III), however at this level of theory, both OHs were found to be interacting with the π
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cloud of thiophene in a symmetric fashion. The next lowest energy structure is the C−H···O
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9 interaction (I) and was found to be roughly 4 kJ/mol higher in energy. Structures II and IV
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11 were found to be over 6 kJ/mol higher in energy than the minimum. M05-2X also found a
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13 stable structure unlike all other calculations (structure V). This structure is unusual as it has
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15 no obvious interaction between the two monomer units. This structure only converged to a
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17 minimum using M05-2X with the triple zeta Dunning set. Attempts to find this structure
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19 at all other levels of theory and basis sets were unsuccessful, thus it seems that this minima
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21 is an artifact of this specific level of theory and basis set. M05-2X also found a minimum
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23 (designated VI) where the water monomer was positioned between the two hydrogens at the
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25 Cβ position leading to a C2v symmetry. This structure was found to be a transition state
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27 according to B3LYP, B3LYP-GD3BJ, and B97-D3, and MP2.
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29 Two structures (II and III) were found using B97-D3/6-311++G(d,p), but were found to
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31 collapse to one minimum (structure III) when refined with the aug-cc-pVTZ basis set. Cal-
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33 culations employing ωB97-XD/6-311++G(d,p) found structures I, III, IV, and VI. Structure
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35 VI was found to collapse into structure III when employing the larger aug-cc-pVTZ basis
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37 set. Again, structure III was the lowest energy structure, with structures I and IV being
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39 5.38 and 0.26 kJ/mol higher in energy, respectively.
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41 In MP2 calculations, structure III was again found to be the lowest energy structure
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43 with structure IV 0.34 kJ/mol higher in energy and structures I and II being over 1.43 and
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45 3.41 kJ/mol higher in energy when using 6-311++G(d,p). These structures collapse into
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47 structure III when the aug-cc-pVTZ basis set is applied. MP2 calculations using the Pople
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49 basis set also found structure VI, which was observed to be a transition state at other levels
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51 of theory. This structure showed water acting as a double acceptor from Cβ1 −H and Cβ2 −H.
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53 This structure was found to be 3.34 kJ/mol higher in energy than the MP2 global minimum
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55 (structure III) at 6-311++G(d,p) but optimized to structure III with the aug-cc-pVTZ basis
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set.
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It should be noted that several of the calculations showed a slightly altered version of
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complexes shown in Figure 1. This is not unexpected as each level of theory emphasizes dif-
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9 ferent aspects of the potential energy surface. None of these alterations are significant as they
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11 can still be described with the same interactions. The interaction seen in these structures
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13 were all determined to be the same and therefore we chose to group them accordingly. The
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15 largest deviation was found to be connected to structure III. Here, a double donor structure
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17 with the water monomer bridging across the thiophene ring and interact with both double
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19 bonds was found at multiple levels of theory. This structure was only seen when using the
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21 6-311++G(d,p) basis set and was found to always converge to the asymmetric structure III
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23 when the larger aug-cc-pVTZ basis set was used. For simplicity, a selection of geometric
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25 parameters for the four major complexes calculated at the B3LYP/aug-cc-pVTZ level of
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27 theory can be found in Table 2.
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29 In this dense data set (Table 1), there are few key points to consider. 1.) Complex
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31 III is the lowest energy complex at all levels of theory and basis sets utilized in this work.
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33 2.) Complex I was the next lowest in energy across six of the twelve calculated sets, but
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35 was not a converged minimum in four sets. 3.) In general, the calculated relative energy
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37 correlates with the interaction energy in that low energy complexes have higher (more neg-
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39 ative) interaction energy. There are exceptions to this correlation as observed in B3LYP
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41 and M05-2X calculation with the aug-cc-pVTZ basis set. This oddity was also observed in
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43 the calculated interaction energy for the furan:water complex. 10 The most likely source of
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45 this aberration is the lack of ZPE correction in the interaction energy. For simplicity, future
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47 energetic arguments will use the values from the aug-cc-pVTZ calculations unless otherwise
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49 stated.
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10 Table 2: Selected geometric parameters of Tp:H2 O complexes calculated with B3LYP/aug-
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13 I II III IV
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CH···O 2.412 CH···O 2.504 OH···π 2.805 OH···S 2.686
16 Cα1 −H 1.078 Cα1 −H 1.077 Cα1 −H 1.077 Cα1 −H 1.077
17 Cβ1 −H 1.080 Cβ1 −H 1.080 Cβ1 −H 1.080 Cβ1 −H 1.080
18 Cα2 −H 1.077 Cα2 −H 1.077 Cα2 −H 1.077 Cα2 −H 1.077
19 Cβ2 −H 1.080 Cβ2 −H 1.080 Cβ2 −H 1.080 Cβ2 −H 1.080
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21 Cα −Cβ 1.363 Cα −Cβ 1.364 Cα −Cβ 1.365 Cα −Cβ 1.362
22 6 C-S-C 91.9 6 C-S-C 91.6 6 C-S-C 91.7 6 C-S-C 91.7
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24 O−H1 0.962 O−H1 0.962 O−H1 0.961 O−H1 0.962
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O−H2 0.962 O−H2 0.962 O−H2 0.965 O−H2 0.965
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6 HOH 105.3 6 HOH 105.3 6 HOH 105.1 6 HOH 104.9
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29 6H2 O tilt 161.5 6H2 O tilt 178.7 6κc C···H 92.0 6κS···H 104.3
30 Point Group Cs Point Group Cs Point Group C1 Point Group Cs
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33 thiophene furan H2 O
34 C−S 1.726 C−O 1.362 O−H 0.962
35 C−C 1.363 C−C 1.355 6 HOH 105.1
36 C−C 1.423 C−C 1.432
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Cα −H 1.077 Cα −H 1.075
39 Cβ −H 1.080 Cβ −H 1.076
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41 6 C−C−C 112.7 6 C−C−C 106.2
42 6 C−S−C 91.7 6 C−O−C 106.8
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44 a
45 All bond lengths are in angstroms and all angles are in degrees. b For labeling purposes,
46 α carbons indicate the carbons closest to the sulfur atom, whereas β indicates the farther
47 carbons. The 1 and 2 designations indicate if the carbon is on the same side (1) as the
48 complexing water or on the opposing side (2) as indicated in Figure 1.
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κ - centroid of the thiophene ring.
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Vibrational Structure of Complexes
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6 As only structures I, II, III, and IV were reliably found to be minima, we elect to focus the
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8 vibrational analysis of these structures (Table 3). The calculated, harmonic frequencies of the
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10 four complexes were expected to show diagnostic perturbation when compared to monomers.
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12 Only the B3LYP calculated vibrational frequency shifts of interest to this study are presented
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14 as they have been shown to be useful in previous work. 10 For simplicity, we will refer to the
15
16 vibrational modes of the water monomers using standard Mulliken designations (ν1 is the
17
18 symmetric stretch, ν2 is the bend, and ν3 is the asymmetric stretch). The vibrational modes
19
20 for complexes III and IV will also be described as bound or unbound stretches, with the
21
22 bound stretch being essentially ν1 and the unbound is ν3 .
23
24 As might be expected, the four structures of Tp:H2 O show potentially diagnostic shifts
25
26 of vibrational modes of each monomer. In Table 3, we show those frequencies that could
27
28 potentially be diagnostic. In this table, only vibrations that show significant intensity or shift
29
30 upon complexation are reported. Of particular note are the OH stretches. In complexes I
31
32 and II, subtle red shifts are noted (∆ν < 1.5 cm−1 ), whereas complexes III and IV show
33
34 more substantial shifts (∆ν > 20 cm−1 ). This difference in shift is due to the nature of
35
36 the interaction observed. In complexes I and II, H2 O acts as an H-bond acceptor from the
37
38 weakly polar C-H of thiophene whereas complexes III and IV show water acting as an H-
39
40 bond donor to the π cloud and S atom of thiophene, respectively. The H2 O bending mode
41
42 was also observed to shift in a similar, but less substantial manner for the two types of water
43
44 behavior (donor or acceptor).
45
46 Thiophene has several bands that show potentially diagnostic shifts upon complexation.
47
48 The transitions that show the potential diagnostic shifts are given in Table 3. Vibrational fre-
49
50 quency shifts of the thiophene monomer tend to be much smaller than those observed in the
51
52 water monomer. These shifts were also observed to be less connected to the donor/acceptor
53
54 nature of water. For example, ν13 shows a noticeable blue-shift (∆ν > 10 cm−1 ) in complexes
55
56 I and III, whereas complex II and IV are much less perturbed (∆ν < 5 cm−1 ). Additionally,
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Table 3: Calculated frequenciesa of Tp:H2 O, monomers, and isotpologoues.
8
9
monomer I II III IV
10 mode Freq. (cm−1 ) ∆b ∆ ∆ ∆
11 Thiophene ν13 674.6 10.9 0.2 10.2 4.0
12 ν15 706.1 28.0 9.7 9.2 3.2
13
ν2 811.8 -2.1 -0.4 -0.2 -4.7
14
15 ν14 1240.4 3.3 4.3 0.7 0.1
16 ν5 1394.9 -0.2 0.1 -1.3 2.5
17 CH str. 3094.5 -3.1 -0.7 2.0 1.2
18 CH str. 3107.1 -2.6 -1.9 1.7 1.1
19
CH str. 3141.7 -9.5 -1.7 -0.4 1.5
20
21 CH str. 3144.3 -2.3 -1.8 -0.3 1.4
22
23 H2 O ν2 1575.3 0.6 0.3 5.2 4.6
24 ν1 3675.1 -0.5 -0.4 -39.1 -37.8
25
ν3 3774.5 -1.2 -0.7 -22.6 -23.2
26
27
28 D2 O ν2 1153.2 0.7 0.4 3.0 2.8
29 ν1 2648.6 -0.4 -0.3 -24.9 -24.1
30 ν3 2766.3 -0.7 -0.3 -19.4 -19.8
31
32
33 HODc bend 1381.0 1.0 0.6 -4.7 -3.5
34 OD str. 2705.7 -0.6 -0.4 -46.3 -45.1
35 OH str. 3726.7 -0.9 -0.5 2.8 1.8
36
37
38
DOHd bend 1381.0 1.0 0.6 12.1 11.5
39 OD str. 2705.7 -0.6 -0.4 2.4 1.7
40 OH str. 3726.7 -0.9 -0.5 -64.8 -63.2
41
42 Freq. (cm−1 ) Freq. (cm−1 ) Freq. (cm−1 ) Freq. (cm−1 )
43
44
IM1 e 20.5 18.9 22.0 16.1
45 IM2 27.5 19.4 26.6 20.6
46 IM3 54.1 48.3 59.9 67.7
47 IM4 66.0 57.8 79.9 72.7
48 IM5 71.6 59.8 192.9 162.4
49
50
IM6 128.1 103.8 270.6 286.6
a
51 All frequencies calculated using B3LYP/aug-cc-pVTZ and were scaled by 0.968.
b
52 ∆ = νcomplex − νmonomer . c HOD interacts through H. d DOH interacts through D.
53 e
Intermolecular vibration.
54
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the ν15 show a noticeable blue-shift (∆ν = +28.0 cm−1 ) in complex I, moderate blue-shifts
4
5
in complex II and III (∆ν = +9.7 and +9.2 cm−1 , respectively) and a small blue-shift in
6
7
complex IV (∆ν = +3.2 cm−1 ). Given these calculated shifts, it would seem that experi-
8
9 mentally determined vibrational shifts could be used to determine the overall geometry of
10
11 the complex.
12
13 The ν15 transition is the in-phase, out-of-plane flapping motion of the hydrogen atoms.
14
15 This transition is calculated to be the strongest transition in the infrared spectrum thus
16
17 seeming to be a logical point to start as any complex bands would seemingly be easily
18
19 apparent. This band shows a wide range of blue-shifting (3.2 - 28.0 cm−1 ) between the four
20
21 complexes. The ν13 vibration is of interest as it shows substantial shifts for complexes I
22
23 and III, but nearly negligible shifts for complexes II and IV. This band is also symmetry
24
25 forbidden (A2 symmetry), but can get turned on in the IR if the symmetry is broken. In
26
27 this way, if a band were observed at this location (near 700 cm−1 ) it could only be due to
28
29 complex I as it is the only complex that has significant intensity in this vibration. The C−H
30
31 stretch region was also observed to have potentially diagnostic shifts, but this region is often
32
33 congested and is prone to matrix broadening effects and thus would seem less likely to be
34
35 useful in our spectral analysis.
36
37 The intermolecular vibrational frequencies were observed to be diagnostic of the complex
38
39 geometry (Table 3). The specific pattern of these six vibrational transitions would be useful
40
41 in assigning the complexes, if low frequency measurements could be made. Our experimen-
42
43 tal setup currently only goes down to 600 cm−1 , but these vibrational frequencies could
44
45 potentially be useful in future work and analysis.
46
47
48
49 Isotopic Substitution of H2 O
50
51 As the water monomer was shown to be perturbed upon complexation, isotopic substitution
52
53 effects on vibrational frequencies were also calculated. In addition to the normal isotopomer,
54
55 D2 O and HOD were also calculated. As complexes I and II interact through the O atom,
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the HOD isotopologue is symmetric with respect to HOD rotation. Complexes III and IV,
4
5
however, interact through the H atom, thus yielding two unique structures when the HOD
6
7
monomer interacts through the H or D atom (Figure 2).
8
9 The shifts in frequency are generally reproduced when comparing the isotopologues. For
10
11 example, ν3 of the water monomer was found to redshift by approximately 1 cm−1 across
12
13 the isotopologues (H2 O, HOD, and D2 O) in complex I. The most variation in shift is seen
14
15 in complexes III and IV as the H/D is interacting directly with the thiophene monomer. In
16
17 complex III, the bound stretch will shift by 20 - 70 cm−1 depending on the isotopologue.
18
19 Also of note, the unbound stretch of HOD is found to blue-shift upon complexation. This
20
21 blue-shifting was found to be diagnostic in the furan : water complex and was used to help
22
23 identify the geometry of this complex. 10
24
25
26
27 Electron Topology of the Complexes
28
29 AIM analysis was used to further characterize the observed interactions of Tp:H2 O. Koch and
30
31 Popelier proposed several criteria to validate the hydrogen bonding interactions, including
32
33 the existence of a bond critical point (BCP) between the donor and acceptor atoms with
34
35 electron density (ρ) and the Laplacian of the charge density (∇2 ρ) values at this point being
36
37 within reasonable ranges. 42
38
39
40
Table 4: AIM properties for the B3LYP calculated structures of Tp:H2 O.
41
42
structure I II III IV
43 ρ (a.u.) 0.0090 0.0074 0.0094 0.0100
44 ∇2 ρ (a.u.) 0.0342 0.0278 0.0269 0.0266
45 interaction C−H···O O−H···π O−H···S C−H···S
46
47
48
AIM analysis of the four complexes shows a single bond critical point between the two
49
50
monomers (Figure 3). This would indicate that all four geometries only have a single in-
51
52
teraction between the two monomers. Values of ρ are all small (0.0074 - 0.0100 a.u.) and
53
54
the values of the Laplacian (∇2 ρ ) are small, positive values (0.0266 - 0.0342 a.u.) for the
55
56
complexes indicating a similar degree of interaction in all four geometries (Table 4). It
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4 a.) b.)
I I
5 200 200 200
6
7 II II
8 100 100 100
9
Absorbance

Absorbance

Absorbance

Absorbance

Absorbance
10 H 2O D 2O
11 0 0 0
12
13 III III
-100 -100 -100
14
15
16 IV IV
-200 -200 -200
17
18 3800 3750 3700 3650 3600 1600 1580 1560 2800 2800
2750 2750
2700 2700
2650 2650
2600 2600 1160 1140
-1 -1 -1 -1 -1
19 Wavenumbers (cm ) Wavenumbers (cm ) Wavenumbers
Wavenumbers
(cm )(cm ) Wavenumbers (cm )
20
21 c.) I
22
23 II
24
25 HOD
26
Absorbance

Absorbance
Absorbance

27
28 *
29 * *
III
30
31
32 *
33 *
* IV
34
35
3850 3800 2800 2750 1440 1420
36 -1 -1 -1
Wavenumbers (cm ) Wavenumbers (cm ) Wavenumbers (cm )
37
38 Figure 2: Calculated vibrational spectra (B3LYP/aug-cc-pVTZ) of the four Tp:H2 O com-
39
40 plexes. Panel a.) shows the calculated vibrations of Tp:H2 O, panel b.) is Tp:D2 O and panel
41 c.) is Tp:HOD. In Tp:HOD, starred transitions indicate the transition is due to a complex
42 bound through the D atom. In each panel, the top trace (blue) is the predicted vibrations
43 for complex I, the red trace is complex II, the green trace is complex III and the purple trace
44 is complex IV. In all panels, the predicted vibrations of water monomer (H2 O, D2 O, and
45
46 HOD) are included, for reference, as the black trace (middle).
47
48
49 is interesting that complex I shows the largest value of ∇2 ρ, indicating it has the largest
50
51 buildup of electronic charge between the monomers and therefore potentially the strongest
52
53 interaction between monomers.
54
55
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8
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10
11
12 I III
13
14
15
16
17
18
19
20 II IV
21
22 Figure 3: AIM analysis of the B3LYP/aug-cc-pVTZ structures of Tp:H2 O. Bond critical
23
24
points are shown in green and ring critical points are shown in red. The dotted line indicates
25 the electron density path.
26
27
28 FTIR Spectra
29
30 H2 O transitions
31
32
33 The transitions for water monomer (Figure 4 and Table 5) were observed near positions
34
35 previously reported 43 (ν3 3727.4 vs lit. 3726.9, ν1 3634.9 vs lit. 3634.5 , ν2 1597.2 vs
36
37 lit. 1597.6). There are weak indications of water dimer in the H2 O:N2 spectrum and the
38
39 Tp:H2 O:N2 spectrum in the OH stretching region. The strongest (H2 O)2 band is found
40
41 in the water bend region at 1601.1 cm−1 (lit 1601.1 cm−1 ). The water dimer bands were
42
43 found to be weak in all acquired spectra. Transitions assigned to (H2 O)2 and Tp:H2 O were
44
45 found to increase in intensity after annealing. This increase is in agreement with previous
46
47 studies concerning weakly-bound complexes. 10,40 Several stronger bands were observed after
48
49 annealing and could not be attributed to water dimer as the frequencies do not match with
50
51 reported values.
52
53 The strongest of these new transitions are likely due to Tp:H2 O. Three potential complex
54
55 bands of Tp:H2 O can be found near the ν3 of H2 O at -4.7, -23.1, and -30.0 cm−1 with respect
56
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4
5 Table 5: Experimental frequencies and shifts of transitions due to water monomer, Tp:H2 O,
6 Tp:D2 O, and Tp:HOD.
7
8 Tp:H2 O
9 Frequency (cm ) shift (cm−1 )a
−1
assignment
10 3727.4 - ν3 (H2 O)
11
12
3722.7 -4.7 Tp:H2 O
13 3704.3 -23.1 Tp:H2 Ob
14 3697.5 -30.0 Tp:H2 Ob
15 3634.9 - ν1 (H2 O)
16 3632.5 -2.4 Tp:H2 O
17
18
3604.1 -30.7 Tp:H2 Ob
19 1597.2 - ν2 (H2 O)
20 1599.7 2.5 Tp:H2 O
21 1602.6 5.4 Tp:H2 O
22 1607.0 9.8 Tp:H2 O
23
24
25 Tp:D2 O
26 Frequency (cm−1 ) shift (cm−1 ) assignment
27 2765.9 - ν3 (D2 O)
28 2762.7 -3.2 Tp:D2 O
29
30 2759.9 -6.0 Tp:D2 Ob
31 2749.3 -16.6 Tp:D2 Ob
32 2742.6 -23.3 Tp:D2 Ob
33 2655.4 - ν1 (D2 O)
34
2653.8 -1.6 Tp:D2 O
35
36 1178.7 - ν2 (D2 O)
37 1180.6 1.9 Tp:D2 O
38
39 Tp:HOD
40
Frequency (cm ) shift (cm−1 ) assignment
−1
41
42 3681.8 - DO-H str.
43 3679.8 -2.0 Tp:HOD
44 3677.2 -4.6 Tp:HOD
45 2705.7 - HO-D str.
46
2704.5 -1.2 Tp:HOD
47
48 2702.5 -3.2 Tp:HOD
49 1404.6 - HOD bend
50 1406.9 2.3 Tp:HOD
51 1407.7 3.1 Tp:HOD
52 a
Shift is defined as νcomplex − νmonomer .
53 b
54 These transitions are most likely due to higher order multimers of Tp:H2 O, but are at
55 positions that could also be due to minor amounts of complex III.
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0.8
4 i ii
s_0614_05c TP:H2O:N2 1:1:3000
5
s_0614_05c TP:H2O:N2 1:1:3000
s_0614_05c
s_0612_06c TP:H2O:N21:3000
TP:N2 1:1:3000 s_0612_06c TP:N2 1:3000 s_0614_05c TP:H2O:N2 1:1:3000
0.6 s_0615_05c H2O:N2 1:3000

6 0.6 s_0612_06c
s_0615_05c TP:N2
H2O:N2
s_0615_05c H2O:N2
1:3000
1:3000
1:3000
0.6 s_0612_06c TP:N2
s_0615_05c H2O:N2
1:3000
1:3000
7 *
* 0.6
8 a.) a.)
* *
9 *
0.4
Absorbance

Absorbance
10 0.4 0.4
Absorbance

Absorbance
n2 (H2O)
11 n3 (H2O) 0.4
12
13
14 0.2 n1 (H2O)
0.2 0.2 0.2 (H2O)2
15 b.) b.)
16
17 c.) c.)
18 0.0 0.0 0.0
0.0
19
20 3740
21 37403720
37203700
37003680
36803660
3660
-1
3640 36403620
36203600
3600 1640 3740 1620
3720 3700 1600
3680 3660
-1
1580
3640 36201560
3600
Wavenumbers (cm ) -1 Wavenumbers (cm ) -1
22 Wavenumbers (cm ) Wavenumbers (cm )
23 Figure 4: Matrix isolation FTIR spectrum of the H2 O i.) stretching and ii) bending regions.
24
25 In both panels, trace a.) is the spectrum of Tp:H2 O:N2 (1:1:3000), trace b.) is H2 O:N2
26 (1:3000), and trace c.) is Tp:N2 (1:3000). Transitions marked with * are signatures of
27 Tp:H2 O complexes. While similar in position, the (H2 O)2 transition in the bend region is
28 distinct from the Tp:H2 O transitions. Spectra are offset for clarity.
29
30
31 to the monomer transition. (An expanded view of this spectral region can be found in
32
33 the Supporting Information.) The later two bands are quite weak, whereas -4.7 is plainly
34
35 observed. Given the low intensity of the weak bands, it is hard to be confident in assigning
36
37 these transitions to Tp:H2 O and as they could also be assigned to trimer or higher order
38
39 complexes. Complex bands shifted from the ν1 of H2 O at can be observed at -2.4 and -
40
41 30.7 cm−1 , with respect to the monomer. Again the slightly shifted band (-2.4 cm−1 ) is
42
43 plainly observed, whereas the the second band is very weak. The slightly red-shifted bands
44
45 are consistent with the calculated shifts for complex I and II, whereas the more significantly
46
47 shifted bands are more consistent with complexes III and IV. As these bands are very weak, it
48
49 would indicate the concentration of this species is likely small compared to the concentration
50
51 of complex I or II. To aid in our assignment, we looked at differing relative concentrations
52
53 of the monomers. By altering one or both concentrations, we would expect to see greater
54
55 modulations of the bands that arise from higher order complexes (more than one water
56
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attached to thiophene) than from transitions due to the 1:1 complex. When less water is
4
5
used in our sample there are no signs of the weak complex bands (ν3 -23.1 and -30.0 cm−1
6
7
and ν1 -30.7 cm−1 ), but the complex transitions at ν3 - 4.7 cm−1 and ν1 - 2.4 cm−1 remain
8
9 quite obvious (spectra found in the Supporting Information). This would seem to imply
10
11 these weak transitions are more likely to be higher order complexes than other geometries of
12
13 the 1:1 complex, however the presence of complexes III and IV cannot be completely ruled
14
15 out.
16
17 In the water bend region, blue-shifted bands are observed at 2.5, 5.4, and 9.8 cm−1 with
18
19 respect to the water bending transition at 1597.2 cm−1 . The band at +2.5 cm−1 is large by
20
21 comparison to the other two bands. As the concentration of water with respect to thiophene
22
23 is lowered, the farther shifted bands appear to decrease in intensity at a faster rate than the
24
25 band at +2.5 cm−1 indicating they are more likely higher order complexes. The +2.5 cm−1
26
27 band would be in reasonable agreement with the predicted shifts for complexes I and II
28
29 (calculated +0.6 and 0.3 cm−1 , respectively) from the unbound position.
30
31
32
33 D2 O and HOD spectra
34
35 The spectra of the HOD and D2 O with Tp were also recorded (Figure 5). HOD was formed
36
37 from small amounts of water in our experimental setup that exchange protons with the D2 O
38
39 sample. In this manner, we record the spectrum of all three isotopologues simultaneously.
40
41 The D2 O monomer transitions were observed at 2765.9, 2655.4, and 1178.7 cm−1 and complex
42
43 transitions were observed at frequencies mirroring those in the normal isotopomer (Table 5).
44
45 For complexes involving HOD, bands are observed at 3679.8 and 3677.2 cm−1 . These bands
46
47 are red-shifted from the OH stretch of HOD by 2.0 and 4.6 cm−1 . In the OD stretch region,
48
49 complex bands are found at 2704.5 and 2702.5 cm−1 . Again, these shifts are only a few
50
51 wavenumbers (< 3.5 cm−1 ) from the HOD monomer frequency and mirror those in the H2 O
52
53 complex.
54
55 Calculations of complexes III and IV showed a blue-shift of the unbound stretch of
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HOD. For example, in complex III, the O−D stretch blue-shifts by 2.8 cm−1 when HOD
4
5
interacts through the H atom, whereas the O−H stretch blue-shifts by 2.4 cm−1 when HOD
6
7
interacts through the D atom. The appearance of these blue-shifted bands was helpful in the
8
9 assignment of furan:H2 O. 10 There was no indication of blue-shifted O−H or O−D stretches
10
11 in our spectra. In furan:H2 O, these bands were very small. If that is also true in this system,
12
13 it is possible that we would not observe the bands if these complexes are in low concentration.
14
15 Interestingly, in OH stretch region of HOD, two peaks are observed after annealing. These
16
17 peaks are red-shifted by 2.0 and 4.6 cm−1 . These two peaks are replicated in the OD stretch
18
19 region at -1.3 and -3.2 cm−1 from the monomer transition. This doubling is not observed
20
21 when Tp:H2 O is formed in Ar matrices. This suggest these transitions most likely arise from
22
23 matrix site splitting.
24
25
26
27 Thiophene transitions
28
29 The most intense transition of thiophene monomer is found near 720 cm−1 . This transition
30
31 is split into multiple components, but the reason for this splitting is not inherently obvious.
32
33 A similar splitting was seen in the ν13 of furan:H2 O. 10 In both complexes, this vibration
34
35 is the out-of-plane hydrogen flapping. As the region is congested, a difference spectrum
36
37 of the region (Tp:H2 O:N2 - Tp:N2 - H2 O:N2 ) is presented (Figure 6). From the difference
38
39 spectrum, clear indications of complex formation are seen at 721.4, 736.3, and 741.2 cm−1 .
40
41 There are other bands in this congested area that could be complex transitions, but the
42
43 identification is challenging due their low intensity and the competing broad background in
44
45 the region these transition are found in. As with the H2 O region, these transitions could
46
47 potentially be connected to signatures of multiple geometries of the Tp:H2 O dimer, or due to
48
49 higher order complexes. The transition at 741.2 cm−1 might be the most useful transition for
50
51 identification. This band is shifted from the clump of transition by at least 17.5 cm−1 which
52
53 is substantially farther than any of the other complex transitions. The largest calculated
54
55 shift, found in complex I, was found to be +28.0 cm−1 . This would seem to point toward
56
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4 0.30
0.6 i ii
5
6 s_0308_05 TP:D2O:N2 1:1:3000
s_0309_05 D2O:N2 1:3000 0.25 s_0308_05 TP:D2O:N2 1:1:3000
s_0309_05 D2O:N2 1:3000

7 0.5 s_0327_06c TP:N2 1:3000

s_0327_06c TP:N2 1:3000

*
8
0.20
9 0.4
* *
Absorbance

Absorbance
10
11 a.) 0.15 * *a.)
0.3
12
13 DO-H HO-D
0.2 0.10
14 ν3 (D2O)
15
0.1 0.05
16 b.) ν1 (D2O) b.)
17 c.)
0.0 c.)
18 0.00
19
3700 3690 3680 3670 3660 2760 2720 2680 2640
20 -1
Wavenumbers (cm ) -1
21 Wavenumbers (cm )
22
23
24 0.7 0.30
iii iv
25 s_0308_05 TP:D2O:N2 1:1:3000

26 0.6 s_0309_05 D2O:N2 1:3000

s_0327_06c TP:N2 1:3000 0.25 s_0308_05 TP:D2O:N2 1:1:3000

27
s_0309_05 D2O:N2 1:3000

* s_0327_06c TP:N2 1:3000

28 0.5
a.) 0.20
29 *
Absorbance

30 0.4
Absorbance

H-O-D
31 0.15 *
a.)
32 0.3 b.)
33 0.10 ν2 (D2O)
34 0.2 ν6 (Tp)
35 0.05 b.)
36 0.1
37 c.) c.)
38 0.0 0.00
39
40 1440 1430 1420 1410 1400 1390 1380 1200 1190 1180 1170 1160 1150
-1 -1
41 Wavenumbers (cm ) Wavenumbers (cm )
42
43 Figure 5: Matrix isolation FTIR spectra of isotopologues of Tp:H2 O. Panel i shows the OH
44 stretch region of HOD, panel ii is the OD stretch region showing HOD and D2 O, panel iii
45 shows the HOD bend region and panel iv is the D2 O bend region. In all panels, trace a.) is
46
47 the spectrum of Tp:D2 O:N2 (1:1:3000), trace b.) is D2 O:N2 (1:3000), and trace c.) is Tp:N2
48 (1:3000). Transitions marked with * are signatures of Tp complexes with D2 O or HOD.
49 Spectra are offset for clarity.
50
51
52 complex I being in the matrix.
53
54 Additionally, a small transition is found to grow in at 700.5 cm−1 , which is substantially
55
56 red-shifted from the remainder of the cluster of transitions. As there are no predicted red-
57
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shifted bands for ν15 , the most likely assignment of this transition corresponding to ν13 , which
4
5
was previously noted to be symmetry forbidden with significant intensity only showing from
6
7
complex I. Thus, this transition would seem to provide definitive evidence for the existence
8
9 of complex I in the matrix.
10
11
12
13
14
15 1.0
16 *
17
Absorbance

18
19 0.5
20
21
22 * a.)
*
23 0.0
24
25 b.)

26
27
28 740 730 720 710 700 690
-1
29 Wavenumbers (cm )
30
31 Figure 6: Matrix isolation FTIR spectrum of the ν15 region of Tp:H2 O:N2 . Trace a.) is the
32 standard spectrum and trace b.) is the difference spectrum (Tp:H2 O:N2 - Tp:N2 - H2 O:N2 ).
33 Positive going transition indicate growth of complexes whereas the negative going peaks
34 indicate loss of monomer as complexes form. Spectra are offset for clarity.
35
36
37
38 There were other observed transitions of thiophene that showed shifts upon complexation.
39
40 The most apparent shifts were observed with transitions at 837 and 1256 cm−1 , however they
41
42 are less simple to interpret (spectra found in the Supporting Information). In these areas,
43
44 the thiophene transitions show small shifts or are a cluster of multiple, unresolved transi-
45
46 tions, thus making unambiguous assignment challenging. As these bands do not yield clear
47
48 evidence for a complex assignment, they will not be used in our analysis. Additionally, the
49
50 C−H stretch region of thiophene showed potentially diagnostic behavior. Unfortunately, the
51
52 annealed spectra show complex behavior and only minor perturbations in this region, again,
53
54 making unambiguous assignments challenging (the spectrum can be seen in the Supporting
55
56 Information). This region is further complicated as the H atoms of thiophene interact with
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the local matrix, leading to additional splittings and broadening. Due to these difficulties,
4
5
arguments based on C−H stretches will not be presented.
6
7
8
9 Complexes in Ar matrix
10
11
When the spectrum of Tp:H2 O is recorded in an argon matrix, several peaks are seen to grow
12
13
in upon annealing (Figure 7). The most noticeable band was seen at 3731.5 cm−1 , with minor
14
15
bands appearing at 3640.2 and 3610.4 cm−1 . The band at 3731.5 cm−1 is slightly shifted
16
17
from the reported position of the non-rotating (band center) ν3 of water (3733 cm−1 ). 44
18
19
This transition is generally very weak when observed at the temperatures used in our matrix
20
21 experiments as water is known to rotate in an argon matrix. This rotational freedom gives
22
23 rise to rovibrational structure in this region. The Tp: H2 O complex transition is quite
24
25 intense and there are not obvious bands that would mirror the rovibrational structure of the
26
27 water monomer. This would indicate there is no longer any rovibrational structure upon
28
29 complexation. From this, it seems likely the water monomer loses rotational freedom in
30
31 the matrix upon complexation. This would also seem plausible for the transition at 3640.2
32
33 cm−1 as this transition grows substantially in intensity and is near the non-rotating (band
34
35 center) ν1 of water (3638 cm−1 ). 44 These two bands would seem to indicate there is little
36
37 perturbation to the water monomer’s vibrational structure upon complexation as would be
38
39 consistent with structures I and II. The transition at 3610.4 cm−1 is shifted from the non-
40
41 rotating ν1 by 30 cm−1 , indicating a more substantial change in structure. There is a weak
42
43 band 3689.9 cm−1 that could be the analogous band for the non-rotating ν3 as it is red-
44
45 shifted by 40 cm−1 . The intensity of these bands was observed to change in a mostly linear
46
47 fashion with respect to concentration, thus it seems unlikely that they arise from multimers.
48
49 Assuming this is the case, there would seem to be evidence of two complex geometries of
50
51 Tp:H2 O in Ar with one being dominant.
52
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4 * s_0611_06c TP
i
0.35 ii
5 s_0612_06c TP:H2O
s_0611_06c TP
0.40 s_0612_06c TP:H2O
6 s_0613_13 H2O s_0613_13 H2O

7 0.30
8 0.35 * *
a.)
9 a.)
0.25
Absorbance

Absorbance
10 0.30
11
12 0.25 b.) 0.20
b.)
13
14 0.20 0.15
15
16
0.15 c.) 0.10
17 c.)
18
19
3800 3750 3700 3650 3600 1640 1630 1620 1610 1600 1590 1580
20 -1 -1
Wavenumbers (cm ) Wavenumbers (cm )
21
22
23
Figure 7: Matrix isolation FTIR spectra of Tp:H2 O in Ar. Panel i shows the OH stretch
24 region and panel ii shows the bend region of H2 O. In both panels, trace a.) is the spectrum
25 of Tp:H2 O:Ar (1:1:3000), trace b.) is H2 O:Ar (1:3000), and trace c.) is Tp:Ar (1:3000).
26 Transitions marked with * are signatures of Tp complexes with H2 O. Spectra are offset for
27 clarity.
28
29
30 Assigning a Structure to Thiophene : Water
31
32
33 The geometry optimizations consistently found structure III to be the global minimum across
34
35 all levels of theory and basis sets used in this work. At the B3LYP and M05-2x levels of
36
37 theory the next lowest energy is complex I, whereas complex IV is the second lowest at the
38
39 ωB97X-D and MP2 levels of theory. However, neither complex (I or IV) is identified as a
40
41 minima when using B3LYP-GD3BJ nor B97-D3 with the aug-cc-pVTZ basis set. Further
42
43 than this, there seems to be little in the way of discernible patterns in the energetics of the
44
45 complexes across different levels of theory. This would seem to indicate that complex III is
46
47 the most likely structure to be observed experimentally.
48
49 In contrast, the largest observed O−H/D transitions show small red-shifts that are more
50
51 similar to the shifts expected for complex I and II than III and IV. By comparison, any
52
53 transition in line with the shift for complex III or IV had low intensity. The significant
54
55 blue-shifted peak in the thiophene C−H symmetric flap region was observed to match best
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with complex I, but evidence for complexes II and III could potentially be seen in bands
4
5
that are only slightly blue-shifted. Also observed in this region was a small band that was
6
7
red-shifted from the C−H flap. As no complexes were calculated to red-shift, the only
8
9 possible assignment for this band is the asymmetric C−H flap of thiophene in complex I.
10
11 This was the only complex to show appreciable intensity in this transition as it is dipole
12
13 forbidden in the monomer. Finally, there were no indication of blue-shifted unbound HOD
14
15 stretches. This observation was was critical in furan : H2 O 10 as it gave definitive proof of
16
17 the complex geometry. As these bands are not observed in Tp:H2 O, it would give evidence
18
19 against complexes III and IV being the most prevalent.
20
21 Our energetic calculations would seem to imply that complex III is the most likely ob-
22
23 served in our experiments. However, this seems to be contrary to comparison of the exper-
24
25 imental and calculated vibrational frequencies. Our spectroscopic studies show conclusive
26
27 evidence for complex I being formed commonly and complex III being a minor, yet detectable
28
29 secondary structure. In our analysis, there is insufficient evidence to confirm complexes II
30
31 or IV exist in the matrix, however it is certainly possible both are obscured within the
32
33 transitions of complexes I and III.
34
35
36
37 Comparison to other related complexes
38
39
40 There are substantial difference between the Fu:H2 O and Tp:H2 O systems, both in com-
41
42 putation and in spectral characteristics. In the above analysis, the geometry of Tp:H2 O
43
44 was characterized as C−H···O with water acting as a hydrogen bond acceptor, whereas the
45
46 Fu:H2 O system was found to be O−H···O with water acting as a hydrogen bond donor. This
47
48 can likely be explained, primarily by the electronegativity differences in O and S. In context
49
50 of the heterocycle, furan has a significant dipole moment whereas thiophene has a smaller
51
52 dipole moment (furan - 0.7460 D, thiophene - 0.5165 D). While this difference may not seem
53
54 like a lot, the impact of the overall electron density around the heterocycle is substantial. As
55
56 can be seen in Figure 8 the bulk of the electron density of furan is found around the oxygen
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atom, whereas the density shifts into the π cloud in thiophene. As the electron density moves
4
5
into the ring of thiophene, it is also more spread out, leading to less concentrated areas of
6
7
negative charge. The hydrogen atoms do not show a significant change in charge between
8
9 furan and thiophene. As such, we see that the relative charge density of the hydrogens in
10
11 thiophene is higher than that of furan. Thus the hydrogens of thiophene are more likely to
12
13 interact with the water monomer than the hydrogens of furan. This shift of relative electron
14
15 density would be a plausible explanation for the large change in behavior between Fu:H2 O
16
17 and Tp:H2 O.
18
19
20 Furan Thiophene
21 C 4H 4O C 4H 4S
22
23
24
25
26
27
28
29
30
31
32
33 Figure 8: Calculated electron densities (B3LYP/aug-cc-pVTZ) of furan and thiophene. The
34 surfaces are presented with the same isovalues for comparison.
35
36
37
The differences observed between thiophene : H2 O and thiophene : methanol 24 (Tp:MeOH)
38
39
are less easy to rationalize. The study of Jiang and coworkers show two geometries in the ma-
40
41
trix with both showing the methanol OH acting as a hydrogen bond donor. In one geometry
42
43
the donation was to the S atom of thiophene, whereas the second complex was interacting
44
45
through the π cloud of thiophene. The AIM calculations presented in this work 24 did not
46
47
indicate any interaction of the methyl group of methanol with thiophene. Steric effects of the
48
49
methyl group or cage effects of the matrix would be plausible explanation for the methanol
50
51
complex adopting a different geometry in the matrix as compared to the water complex.
52
53
Cage effects seem less likely as Tp:H2 O was found to have the same geometry regardless of
54
55
the matrix (N2 vs. Ar). A microwave study of Tp:H2 O and Tp:MeOH could be useful in
56
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elucidating this geometric issue as it would be a matrix free measurement that could directly
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probe the structure of each complex.
6
7
8
9
10 Conclusions
11
12
13 The FTIR spectrum of the thiophene : water complex was recorded in cryogenic matrices at
14
15 15 K. Computational analysis found four low-energy geometries that each showed diagnostic
16
17 vibrational features. The lowest energy complex was found to be a π hydrogen bond where
18
19 water acted as a hydrogen bond donor. The spectroscopic evidence showed some evidence
20
21 for this geometry, but the most prevalent geometry seen in matrices was determined to
22
23 be a C−H···O interaction where water is acting as an acceptor. This is most interesting
24
25 as C−H···O interactions tend to be weak and therefore not routinely observed to be the
26
27 sole interaction in a van der Waals complexes. This complex geometry is also substantially
28
29 different from the related complexes of furan : water and thiophene : methanol. It is also
30
31 unusual that the lowest energy structure (complex III) is not the most prevalent species
32
33 in the matrix. These differences can, however, be rationalized using arguments concerning
34
35 electrostatics and matrix effects.
36
37
38
39 Acknowledgement
40
41
42 The authors gratefully acknowledge support of Hobart and William Smith Colleges for labo-
43
44 ratory funding. Computational resources of the Extreme Science and Engineering Discovery
45
46 Environment (XSEDE), a program supported by National Science Foundation grant number
47
48 OCI-1053575, were used in this work.
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Supporting Information Available
5
6 Supporting information available. This includes the full citation for references 25 and 26,
7
8 Cartesian coordinates for the B3LYP/aug-cc-pVTZ structures, matrix isolation FTIR spec-
9
10 tra of thiophene transition regions of the Tp:H2 O:N2 spectrum.
11
12 This material is available free of charge via the Internet at http://pubs.acs.org/.
13
14
15
16
17 References
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19
20 (1) Derewenda, Z. S.; Lee, L.; Derewenda, U. The Occurence of C... O Hydrogen Bonds in
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Graphical TOC Entry
5
6
7 0.6
s_0614_05c TP:H2O:N2
s_0612_06c TP:N2
1:1:3000
1:3000

8 0.5
* Tp:H2O s_0615_05c H2O:N2 1:3000 Tp:H2O
*

Absorbance
9 0.4
10 0.3
n3 (H2O)
11 0.2 n1 (H2O)
12 0.1
13 3740 3720 3700 3680 3660 3640 3620
14 Wavenumbers (cm )
-1

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