Thiols as Hydrogen Bond Acceptors and Donors: Spectroscopy of 2

Subscriber access provided by Karolinska Institutet, University Library

A: Spectroscopy, Molecular Structure, and Quantum Chemistry

Thiols as Hydrogen Bond Acceptors and Donors: Spectroscopy of 2-phenylethanethiol Complexes Isabella Antony Lobo, Patrick A. Robertson, Luigi Villani, David J. D. Wilson, and Evan G. Robertson J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.8b06649 • Publication Date (Web): 16 Aug 2018 Downloaded from http://pubs.acs.org on August 19, 2018

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The Journal of Physical Chemistry

1.

Introduction

Hydrogen bonding is an important subject of study due to its role in solute-solvent interactions and in the biological mechanisms taking place in the living world. Hydrogen bonds stabilize and determine the three-dimensional structure of many macromolecules such as proteins and nucleic acids. The weakness of the hydrogen bond somewhat obfuscates its power to control many of the vital phenomena of nature. It would be surprising not to find hydrogen bonding in a biological structure or function and so Linus Pauling notably observed that “…the significance of the hydrogen bond for physiology is greater than that of any other single structural feature”.1

Our knowledge of hydrogen bonds has evolved through the efforts of countless researchers since its conceptualization more than a century ago.2,3 In simple terms, when a polarized XH bond of the hydrogen-bond donating moiety points towards an electron rich atom Y, an XH…Y hydrogen bond is formed. In his book, The Nature of the Chemical Bond, Pauling concluded that the hydrogen bond has to be electrostatic as it cannot be chemical (covalent).4 On the other hand del Bene and Pople,5 Gilli et al,6 Weinhold and Landis,7 and many others have stressed the importance of the partial covalent nature in the hydrogen bond. Today, hydrogen bonding is viewed as a complex phenomenon that cannot be attributed to a single factor. Concepts like blue shifting8-12 and σ holes13-14 have added significantly to current understanding and recently the IUPAC has proposed a new definition of a hydrogen bond.15

Hydrogen bonds have touched numerous elements, with the most extensively studied being with the electron-rich atoms like O, N and F. Early on it was thought that thiols do not form hydrogen bonds.16-17 In one of the traditional indicators of hydrogen bonding, H2O has a boiling point which is 160 °C high than that of H2S. The difference in the electronegativity of H and S is small (∆~ 0.38 on the Pauling scale) and the intermolecular SH interactions are weaker. Although early infrared (IR) studies provided evidence consistent with SH hydrogen bonds,18-21 the subject has since been paid little attention.

ACS Paragon Plus Environment

2

The Journal of Physical Chemistry 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The need to study hydrogen bonds involving sulfur is clear; sulfur is an essential element in many biomolecules and biochemical processes. Sulfur is a component of the amino acids cysteine and methionine and antioxidant molecules like glutathione and thioredoxin.22 It is present in the vitamins biotin and thiamine,23 and is an important constituent of agrochemicals like the 1,2dithiolanes.24 Disulfide bonds partially govern the tertiary structure of proteins25 and give the mechanical strength to keratin present in hair and skin of animals and in feathers of birds.26

The advent of spectroscopic techniques capable of probing specifically prepared weakly bound complexes together with the availability of sophisticated theoretical methods has led to a greater understanding of intermolecular interactions. There are a number of experimental and theoretical studies on the X-H….S system where the sulfur atom acts as the H acceptor.27-35 In their book, The hydrogen bond, Pimentel and McClellan specifically mentioned the S-H group as a possible H-bond donor with the S-H stretching mode broadening, shifting to lower frequency and becoming much more intense.36 However, few recent studies have been reported for complexes with the sulfur atom playing the role of H-bond donor in S-H…Y type interactions,37-44 with the efforts of Wategaonkar and co-workers a notable exception.

It has been asserted that IR spectroscopy provides the best evidence for H-bonding.15 In the present study, new experimental IR data is obtained from IR-UV ion depletion studies on isolated molecular conformers and complexes of 2-phenylethanethiol (PET), a molecule previously studied using R2PI spectroscopy.29 In that work two conformers were definitively identified and a number of water clusters tentatively assigned on the basis of partially resolved contours of S1 ←S0 band origins and excited state lifetimes. In the present study we confirm that the dominant hydrate cluster of PET has an S…HO linkage, so PET is made to complex with diethylether (DEE) in order to form a thiol donor SH…O complex. The following work explores the role of thiols as both hydrogen bond donors and acceptors.


3

Page 2 of 37

Page 3 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Scheme 1. Carbon atom labelling scheme for PET

2.

Methodology

2.1

Spectroscopy

Electronic spectra were measured using R2PI spectroscopy coupled with a time-of-flight mass spectrometer (TOF-MS). PET was purchased from Acros Organic (98%) and used as received. Liquid PET was introduced into the sample reservoir and heated to 85 °C and the resultant vapor carried by argon gas (1.2 bar) and pulsed into a diffusion-pumped vacuum chamber through a nozzle (General Valve series 9) with an orifice diameter of 0.8 mm. The supersonic jet is skimmed (Beam Dynamics skimmer, 1.5 mm) and the resulting molecular beam is intersected at right angles by a UV laser beam within the ionization region of the Wiley-Maclaren TOF-MS. Tunable UV light of wavelength 260-275 nm and energy of ca. 0.5 mJ per pulse was generated by frequency doubling of the output of a dye laser (Sirah Cobra Stretch with Coumarin 153 dye) pumped by the third harmonic of a Nd:YAG laser (Spectra Physics Quanta Ray GCR-130) operating at 10 Hz. The ions produced by one-colour R2PI are detected by a microchannel plate detector placed at the top end of a 1.1 m long TOF tube. The signal from the detector is averaged by an oscilloscope and uploaded to a personal computer. To help form PET-water and PET-DEE clusters, water and DEE respectively, are introduced into the line of argon supply. Conformer-specific IR spectra of the PET monomer and its clusters were recorded using IR-UV ion depletion spectroscopy. The Sirah dye laser acts as the probe laser with its wavelength fixed to the electronic origin band of the target species, whether the PET monomer or one of its clusters. Tunable, pulsed IR radiation in the required 2500-3800 cm-1 region is generated by a Laser Vision OPO/OPA pumped by the fundamental (1064 nm) of a Nd:YAG laser (Continuum Surelite II-EX) ACS Paragon Plus Environment

4


operating at 10 Hz. The IR radiation from the scanning “burn laser” (ca. 20 mJ per pulse and loosely focused using a CaF2 lens of focal length 1 m) is timed to arrive ca. 400 ns prior to the UV beam, inducing depopulation of the ground vibrational state with consequent depletion of the R2PI ion signal when an IR transition of the selected conformer is excited. IR spectra are calibrated to vacuum wavenumber values by comparison with water absorption line positions from the HITRAN database.45

2

Computational

The Gaussian09 programme suite46 was employed to carry out the ab initio calculations unless specified. Ground state geometries of the PET conformers, PET-water and PET-DEE complexes were optimized using density functional theory (B3LYP with and without the D3 dispersion correction47 and M06-2X), as well as MØller-Plesset second-order perturbation (MP2) theory. Harmonic vibrational frequencies were calculated at the same level of theory to ensure that the optimized structures were true minima on the potential energy surface (PES), as well as to determine vibrational and thermochemical data. Harmonic frequency scaling factors were determined empirically, and are shown in table S1. The 6-311+G(d,p), def2-TZVPP (abbreviated to TZVPP throughout) and aug-cc-pVTZ (abbreviated to AVTZ) basis sets were employed for geometry optimizations and vibrational frequency analysis. Since the MP2 method was quite expensive for the larger PET-DEE cluster, the basis set was limited to TZVPP. The MP2/AVTZ optimized geometries were employed in subsequent single-point energy calculations at higher levels of theory, including CCSD and CCSD(T). Explicit correlation was considered with the CCSD(T)-F1248-49 methods as implemented within Molpro.50 Results and the calculation of vibration scaling factors are provided in the supplementary data table S1. Binding energies of the selected PET clusters were calculated using single point energy calculations at the CCSD(T)-F12b/cc-pVDZ-F12//MP2/AVTZ level.


5

Page 4 of 37

Page 5 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


A simplified anharmonic model, developed by Sibert and co-workers for use with CH stretch modes,51-53 was used in conjunction with Gaussian 09 results to predict the aliphatic CH stretch region for conformer-specific IR spectra of PET. The Cartesian force constant matrix and dipole derivatives were obtained from vibrational frequency calculations of optimized geometries at the B3LYP-D3/6-311++G(d,p) level. The Cartesian force constant matrix was mass weighed with the mass of atoms involved in aromatic CH stretch doubled to decouple aromatic modes from aliphatic CH modes. The resulting localised modes including aliphatic CH stretches, bend overtones and bend combinations were then used to construct a Hamiltionian matrix with the addition of Fermi resonance and anharmonic coupling terms.51-52 The addition of these terms results in the generation of anharmonic vibrational modes that, with the use of atom displacement in relation to dipole derivatives, produce mode intensities allowing the construction of an anharmonic vibrational spectrum of the aliphatic CH region.

3.

Results and Discussions

3.1

Ab initio calculations – PET and its clusters

In the previous study of Martin et al.,29 five minimum energy conformers of PET were predicted from MP2/6-311+G(d,p) calculations, while experimentally two conformers were found to be present in the free jet using R2PI and UV-UV hole burning. The two observed conformers were assigned and labelled Ggπ and Ag (see Figure 1). The present study investigates these Ggπ and Ag conformers observed previously, with the At monomer included for comparison. Computed conformational structures of PET and related clusters are illustrated in Figure 1 while relative energies are collated in Table 1.


6


Figure 1. Structures and relative energies of PET monomers and their water clusters at the CCSD(T)-F12b/cc-pVDZ-F12//MP2/AVTZ level of theory. The notation follows the labelling used by Martin et al.29 in their earlier study of PET: Gauche and Anti (G/A) represents the arrangement of the side chain with respect to τ2(SCCC) and gauche/trans (g/t) refers to τ3(HSCC). Ggπ represents the conformer that facilitates SH…π interaction. The structure of cluster Ggπ-DEE is included for comparison.


7

Page 6 of 37

Page 7 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Table 1. Ab initio calculated relative energies of PET conformers and water clusters in kJ mol-1.a Ggπ

Ag

At

Ggπw1-r

Agw1-r

Ggπw1-p

B3LYP/6-311+G(d,p)

0.00

-0.88

2.15

0.00

2.25

4.84

B3LYP/AVTZ

0.00

-1.72

0.84

0.00

0.63

6.19

B3LYP-D3/AVTZ

0.00

3.04

5.78

0.00

6.83

3.81

M06-2X/AVTZ

0.00

3.71

6.34

0.00

5.31

1.19

MP2/TZVPP

0.00

4.74

7.37

0.00

7.21

0.47

0.00

5.30

7.82

0.00

8.15

1.14

0.00

0.85

3.44

0.00

3.17

3.39

0.00

2.08

4.90

0.00

4.58

3.05

B3LYP/6-311+G(d,p)

0.00

-0.93

1.98

0.00

0.95

3.89

B3LYP/AVTZ

0.00

-1.84

0.74

0.00

-0.37

5.12

B3LYP-D3/AVTZ

0.00

2.61

5.33

0.00

5.86

3.05

M06-2X/AVTZ

0.00

2.90

6.69

0.00

2.39

-1.61

MP2/TZVPP

0.00

4.23

6.87

0.00

6.15

-0.29

MP2/AVTZ

0.00

4.59

7.07

0.00

7.09

0.04

B3LYP/6-311+G(d,p)

0.00

-1.47

0.94

0.00

-3.82

2.90

B3LYP/AVTZ

0.00

-2.33

-0.09

0.00

-4.64

4.40

B3LYP-D3/AVTZ

0.00

1.48

3.83

0.00

1.60

3.46

M06-2X/AVTZ

0.00

1.15

5.61

0.00

-0.61

-2.30

MP2/TZVPP

0.00

2.59

4.81

0.00

2.93

-0.07

Conformer/ Clusters

Electronic energy, Ee

MP2/AVTZ CCSD-F12b/cc-pVDZ-F12

b

CCSD(T)-F12b/cc-pVDZ-F12 b Zero-point corrected Energy, E0

Gibbs free energy 298K

MP2/AVTZ

0.00

2.77

4.81

0.00

4.56

0.10

b,c

0.00

0.53

2.95

0.00

-0.65

2.70

CCSD(T)-F12b/cc-pVDZ-F12 b,d

0.00

-0.07

2.34

0.00

0.31

2.52

CCSD(T)-F12b/cc-pVDZ-F12 b,e

0.00

-0.45

1.88

0.00

0.99

2.01

CCSD(T)-F12b/cc-pVDZ-F12

a

b c d e

Geometries are calculated at the same level as the reported energies unless noted. Energies are given relative to the conformer Ggπ or water cluster Ggπw1-r. Single point energy at MP2/AVTZ optimized geometries. B3LYP-D3/AVTZ thermal correction MP2/TZVPP thermal correction MP2/AVTZ thermal correction


8


Electronic energies, Ee, were evaluated using the highest level of theory, CCSD(T)-F12b/cc-pVDZF12, providing a benchmark by which to assess the other methods. At this level of theory, the Ggπ conformer (benefitting from a stabilizing SH…π interaction between the side-chain S-H and the π cloud of the aromatic ring) is preferred over Ag by 2.1 kJ mol-1, with At a further 2.8 kJ mol-1 less stable. The preference for Ggπ is broadly consistent with the observed intensity ratios of the origin bands reported by Martin et al.29 and in the R2PI spectra shown in Figure 2. The comparison of preexpansion populations should ideally be made with Gibbs energy rather than Ee, but Gibbs corrections are highly dependent on the lowest frequency modes that are least reliably calculated.

With B3LYP DFT, conformer Ag is calculated to be the most energetically favored conformer rather than the experimentally observed Ggπ. This anomaly can be attributed to the failure of the DFT method to account for the importance of dispersion in the SH….π type interaction. Inclusion of dispersion (B3LYP-D3) restores the expected energetic ordering. Similar issues with B3LYP relative energies have been noted in recent studies of the conformers of alanine and 2-aminophenethylamine (APEA).54,55 Results with the M06-2X functional, which was parameterized including dispersion-dominated systems,56 gives further justification of the importance of dispersion energy, with the relative energies of Ag and Ggπ being in closer agreement with B3LYP-D3, and subsequently the CCSD(T)-F12 results. The MP2 calculations overestimate the energy differences between the conformers (relative to the CCSD(T)-F12 result of 2.1 kJ mol-1), with MP2/TZVPP and MP2/AVTZ calculations predicting the Ggπ conformer to be more stable than the Ag conformer by ~5 kJ mol-1. At the CCSD-F12B/VDZ-F12 level, the energy difference of just 0.9 kJ mol-1 reflects the absence of the small but non-negligible contribution from triple excitations.

Previous cluster studies have demonstrated that each monomeric conformer present in the jet expansion will form only one hydrate cluster for a given stoichiometry unless two competing sites have very similar binding energies, as in the case of N-phenylformamide.57 Sulfur is generally a much better hydrogen bond acceptor than donor, so for conformer Ag there is a clear energetic ACS Paragon Plus Environment

9

Page 8 of 37

Page 9 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


preference for water to bind via the OH…S type interaction seen in cluster Agw1-r. The equivalent complex for the Ggπ conformer is Ggπw1-r, which is also predicted to be the most stable at the highest levels of theory. However, the proximity of the aromatic ring allows the water molecule of complex Ggπw1-p to interact via an SH…OH…π interaction (with the thiol behaving as the H-bond donor). The additional OH…π hydrogen bond makes this complex energetically competitive, within a few kJ mol-1.

Calculations on the PET-DEE cluster were guided by experimental evidence supporting assignment to a structure with a Ggπ host conformation and DEE over the aromatic ring. The arrangement shown in Figure 1 benefits from both SH…O and CH…π interactions. The larger size of the system precluded higher-level energetic calculations, but at the MP2/TZVPP level the binding energy of 31.6 kJ mol-1 is substantial, and considerably more than the corresponding value for Ggπw1-r.

3.2

Survey R2PI spectra

A one-color R2PI survey spectra of PET monomer in the region of the S1←S0 electronic origin transitions is shown in Figure 2(a). The peaks labelled A and G are the origin transitions of the anti Ag and gauche Ggπ conformers at 37569 cm-1 and 37582 cm-1, respectively. To study the binding of water to PET, water was introduced along the argon supply. Cluster features were enhanced by probing the expansion at later delay times. Cooling is enhanced as the expansion progresses; monomer features appear in the early period of expansion, followed by the formation of clusters. This method of producing and diagnosing cluster features has been previously used with N˗benzylformamide58 and is particularly helpful when efficient dissociation of parent cluster ions leads to R2PI peaks in the monomer mass channel only. The mass resolved spectrum of PET+ is presented in Figure 3(a), in which the monomer features A and G are evident, while in Figure 3(b) the appearance of water cluster peaks in the monomer mass channel on increasing the time delay by 100 µs is illustrated. The latter spectrum resembles the one from the previous PET study29 where


10


the Gw1 and Xw1/Yw1 were attributed to singly hydrated clusters on the basis of their populations as a function of valve opening delay time.

Figure 2. One-color R2PI spectra of PET. (a) The peaks denoted by * were identified by Martin et al. as vibronic peaks of the gauche Ggπ conformer by probing the origin band G.29 (b) and (c) show R2PI spectra probing the PET+ and PET-DEE+ mass channels, respectively, when diethyl ether (DEE) is supplied along the inlet line. Wavenumbers are for a vacuum.

Figure 3. One-color R2PI spectra probing the mass channels of (a) PET+ and (b) waterPET+ cluster. The additional features Gw1 and Xw1/Yw1 in (b) are attributed to Ggπw1-r and Ggπw1-p/Agw1-r clusters, respectively.29


11

Page 10 of 37

Page 11 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


To study the H-bond donating characteristics of the thiol group, it is advantageous to have a solvent that can only serve as an H-bond acceptor, for which diethyl ether (DEE) was selected. To help form PET-DEE clusters, diethyl ether was introduced into the line of argon supply. Survey spectra recorded in the PET+ and (PET-DEE)+ mass channels are shown in Figure 2 (b) and (c). The predominant new feature is observed at 37379 cm-1 in 2(c), which is red-shifted by 203 cm-1 with respect to the origin transition of the gauche monomer Ggπ. Many clusters are known to produce S1←S0 electronic origin shifts of a few hundred wavenumbers when there is a close interaction with the chromophore.59 This implies that DEE is in close proximity to the aromatic ring and the redshift implies that DEE interacts with PET more strongly in S1 than in S0. It is also notable that excitation of this cluster generates mostly PET-DEE+ parent ions rather than dissociated PET+ daughter ions. In the ionic state of the (PET-DEE)+ cluster, positive charge builds up in the aromatic ring and possibly the thiol of PET; either way a strong attractive force is expected with the electronrich oxygen of DEE. This observation is in contrast to the efficient dissociation of the H-bond donating hydrate clusters observed for PET and for benzene,60 N˗benzylformamide58 and 2phenethylamine61-62 where the clusters are repulsive in the ionic state.

3.3

IR-UV spectroscopy

PET conformers and the CH stretch region The IR-UV ion-depletion spectra of conformers Ag and Ggπ, and clusters Ggπw1-r and PET-DEE (Figure 4) were measured by probing their electronic origins peak in their R2PI spectra. In the aromatic CH stretch region, only the two lowest frequency modes exhibit minor differences between the conformers: they are split by ca. 5-6 cm-1 in conformer Ggπ but not in conformer Ag. This phenomenon is also observed in the ab initio calculations. In conformer Ag, modes rC2H – r C3H – rC6H – rC6H and rC2H – rC3H + rC6H – rC6H (corresponding to modes 7b and 13 in Wilson’s notation63) are separated by less than 1 cm-1 (at MP2/TZVPP level), but in the gauche conformer Ggπ, disruption of symmetry leads to a partial decoupling of the CH oscillators on either side of the ACS Paragon Plus Environment

12


molecule. This produces one mode (rC2H – rC3H, equivalent to 13 + 7b) that is blue-shifted and another mode (rC5H – rC6H, or 13 - 7b) that is red-shifted. The predicted separation of 11 cm-1 overestimates the observed experimental splitting, although similar compositional changes have been observed in the anti and gauche conformers of substituted ethylbenzene derivatives benzenepropanenitrile,64 and haloethylbenzenes.65

Figure 4. IR-UV spectra of PET conformers and the clusters G-DEE and Gw1 with solution phase spectrum (10% in CCl4) from the NIST database.66 Spectra of the thiol stretch region (2500 – 2640 cm-1), obtained separately by averaging a higher number of scans, are shown on the left with their corresponding MP2/TZVPP calculated IR stick spectra. Scaling factors for calculated IR spectra are provided in supplementary data Table S1. The structures to which the conformers/clusters are assigned are shown in brackets, and the scale is vacuum wavenumbers.


13

Page 12 of 37

Page 13 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


The aliphatic CH stretch region is more useful in distinguishing the side-chain conformation, as the composition of the fundamental modes changes with respect to the coupling of the four internal CH stretch coordinates. It is clear from Figure 4 that the IR-UV spectra of Ag and Ggπ conformers exhibit significant variation in the CH stretch region. In particular, the gauche conformer has three distinctly resolved bands at 2909, 2929 and 2944 cm-1, while the anti conformer has a strong band 2934 cm-1 with nearby shoulders at 2927 and 2940 cm-1. This spectral pattern is very similar to that seen in benzenepropanenitrile.64 Stick spectra from harmonic frequency calculations at several different levels of theory are displayed in Figures S1 and S2, but these fail to satisfactorally replicate the experimental band positions for the aliphatic CH stretch region. The discrepancy between experimental and theoretical band positions and intensities has been observed previously for similar molecules.55 Anharmonic effects such as Fermi resonances, overtone or combination CH bending modes perturb band positions and intensities. Conventional anhamonic calculations did not improve agreement, and poor prediction of the positions of the perturbing states can limit the accuracy of these methods.

A simplified anhamonic method developed for the analysis of aliphatic CH stretch modes has been successfully demonstrated with alkylbenzenes51 and haloethylbenzenes;65 molecules that are structurally similar to PET. It was applied here to the two monomers Ag and Ggπ, in addition to the water cluster Ggπw1-r with the results shown in Figure 5. Immediately evident are the bands associated with CH2 bend overtone and combination bands below 2900 cm-1, which are absent in the harmonic calculations. The one with most intensity is the overtone of the CH2 bending mode on the alpha carbon attached to the phenyl ring. The simplified anharmonic model shows improvement in prediction of band intensities and positions relative to the more expensive ab initio method (MP2/TZVPP) in the harmonic approximation.


14


PET clusters Turning to the water clusters, the most prominent band in the electronic spectrum is that labelled Gw1. In the previous study,29 R2PI measurements at ≈0.10 cm-1 resolution showed that this band has a significant central Q-branch. Of the six monohydrate clusters considered in that study, four were predicted by theory to have mostly µb-type character, inconsistent with an observable Q-branch. Only Ggπw1-r (mostly µa-type) and Ggπw1-p (60% µc-type and 38% µa-type) were feasible, with the former preferred. An increased S1 lifetime for Gw1 also supported assignment to either of these two cluster structures - calculations indicated they both had elevated vertical excitation energies for σ*←n(3py) on the sulfur atom, thereby reducing dissociation via the CS or SH bonds.29

The IR-UV ion dip spectrum of Gw1 in Figure 4 (recorded based on the electronic origin of 37569 cm-1) shows two intense OH stretches at 3540 and 3705 cm-1, thus confirming that it must be a water cluster. The 117 cm-1 red-shift in ν1 compared to the water monomer at 3657 cm-1 is not consistent with an OH…π type bond such as that of the water molecule in Ggπw1-p: for example the observed shift in the corresponding 2-phenylethylalcohol cluster (‘hydrate C*’)67 is just 50 cm-1. Thus, Gw1 must therefore have a structure like Ggπw1-r in which a water molecule acts as hydrogen bond donor to the sulfur lone pair. The ν1 band of Gw1 at 3540 cm-1 is not shifted quite as far as in the analogous 2-phenylethylalcohol cluster (‘hydrate F’, 3519 cm-1),67 because the sulfur is a slightly weaker acceptor. The ν3 red-shift is larger than is typically observed in single-donor systems64,65 but is closer to the analogous PEAL cluster (‘hydrate F’, 3721 cm-1),67 where water is receiving two weak H-bonds from neighbouring aliphatic and aromatic CH groups. In PET, these CH…O bonds are shorter by ca. 0.1 Å than in PEAL and therefore stronger due to the more labile geometry afforded by the diffuse sulfur acceptor atom.


15

Page 14 of 37

Page 15 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


The aromatic and aliphatic CH bands closely resemble those of the Ggπ monomer, indicating the conformation of the PET host. Moreover, the ab initio calculations predict that the Ggπw1-r cluster (with water acting as the H-bond donor to the sulfur atom) is energetically lower lying than Ggπw1-p. All these factors point to Gw1 being the Ggπw1-r cluster, consistent with the assignment proposed by Martin et al.29 The anharmonic stick spectrum of Ggπw1-r shown in Figure 5(c) is not quite as convincing as it is for the two monomers Ag and Ggπ in the combination/overtone region, but it does correctly predict the two most conspicuous changes in this part of the spectrum from Ggπ to Ggπw1-r. The second highest alkyl CH stretch fundamental labelled ▲ in Figure 5 undergoes a significant reduction in intensity and a blue shift (calculated at +14 cm-1, observed +11 cm-1). Also, the third highest alkyl CH stretch fundamental labelled ● becomes more prominent in intensity (calculated as 34% in Ggπw1-r compared to 24% in Ggπ).

Unfortunately, the overlap and low signal strengths of the Xw1/Yw1 bands were a hindrance to the recording of their IR-UV spectra. The spectra shown in Figure S3(a) and S3(b) are noisy, and in the CH stretch region they appear to indicate contributions from clusters with both Ggπ and Ag arrangements of the PET host. In the earlier study,29 partially resolved band contours suggested assignment of these features to Ggπw1-p and Agw1-r structures. In the newly recorded spectra, bands in the OH stretch region at ~ 3725 and 3583 cm-1 are consistent with Agw1-r, however there is no evidence of a band at around 3620 cm-1 that would be expected for the π-bonded water OH in Ggπw1˗p.67 There was also no evidence of an H-bonded SH stretch band that would be expected for such a structure. It is therefore concluded that Agw1-r is the most significant contributor to the overlapping Xw1/Yw1 band system, and that if the Ggπw1-p origin is also located there then its population is too low to be readily detected.


16


Figure 5. IR-UV ion dip spectra of conformers a) Ag, b) Ggπ and c) Ggπw1-r in the aliphatic CH stretch region. Accompanying stick spectra are from the simplified anharmonic model at B3LYP-D3/6-311++G(d,p) level, and scaled harmonic frequency calculations at B3LYP-D3/6-311++G(d,p) and MP2/def2-TZVPP levels.


17

Page 16 of 37

Page 17 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


The aliphatic C-H stretch region in the IR spectrum of PET-DEE cluster is complex due to the coupling of the many C-H vibrations. However, comparison with the phenol-DEE cluster spectrum68 allows a number of these bands to be assigned to DEE, in particular the strong band at 2983 cm-1 and those below 2880 cm-1. The four bands that lie in between have positions and intensities consistent with conformer Ggπ rather than Ag, with some broadening due to overlap with some of DEE’s weaker bands. The broad and doublet aromatic CH stretches at 3029 and 3035 cm-1 also very closely resemble those of the Ggπ conformation. The large red shift of the S1←S0 electronic origin suggests DEE’s proximity to the aromatic ring, and the perturbed SH stretch band indicates an SH…O interaction. Taken together, this evidence allows the host conformation of the PET-DEE cluster to be confidently assigned to Ggπ, with DEE located over the aromatic ring. The assignment of PET conformer and cluster bands is summarized in Table 2.

SH stretch bands Experimental IR-UV and MP2/TZVPP calculated stick spectra of the SH stretch bands are presented in Figure 4. Both experiment and calculations indicate very small intensities for the SH stretching vibrations of the monomers (~1.5 km mol-1 according to calculations, see Table 2), so that it was necessary to average hundreds of laser shots to detect the weak monomer peaks. The assignments indicated by arrows in Figure 4 are supported by comparison with the computed spectra (plotted in Figure 4) and with results from other molecules. For example, the SH stretch band of EtSH with gauche CCSH conformation in the gas phase is 2591 cm-1.69 We have recorded the SH stretch at 2583 cm-1 for the Ggπ conformer (and 2590 cm-1 for conformer Ag) in the gas phase. From the NIST database,66 a weak SH stretch at 2574 cm-1 is reported for PET in solution phase (10% in CCl4). The slightly red-shifted SH stretch in solution phase is expected due to the interaction of the thiol with CCl4. There is a small red shift for the observed band of conformer Ggπ compared to the Ag monomer (7 cm-1 from experiment and 10 cm-1 from MP2/TZVPP calculations), which can be attributed to the SH…π bonding seen in the former.


18

The Journal of Physical Chemistry 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47

Page 18 of 37

Table 2. Comparison between experimental and calculated wavenumbers values (cm-1) for fundamental SH, CH and OH stretch bands of PET monomers (Ag, Ggπ) and clusters with water (Ggπw1-r) and diethylether (Ggπ-DEE). Assignment SH

Ag

Ggπ a

Expt.

Calc.

2590

2591 (1.1)

b

Calc.

Ggπw1-r a

Expt.

Calc.

2583

2581 (1.5)

Calc.

b

Ggπ-DEE a

Expt.

Calc.

2574

2571 (6.2)

Calc.

b

Expt. c

Calc.a

2559

2527 (114)

CH aliphatic 2850 (0.6) Overtone/ Combination

2864

2872 (6.5)

2886

2895 (1.0)

2844 (1.8) 2852

2855 (9.0)

2848 (5.4) 2859

2863 (1.0)

2875 (0.3)

2894 (6.0)

CH aliphatic

2927

2888 (8.9)

2937 (8.6)

2909

2879 (21)

2916 (17)

2911

2881 (17)

2915 (14)

2912

2874 (85)

CH aliphatic

2934

2905 (17)

2950 (14)

2929

2902 (17)

2945 (18)

2931

2904 (18)

2953 (20)

2930

2898 (19)

CH aliphatic

2940

2939 (2.7)

2957 (7.5)

2944

2940 (6.3)

2959 (13)

2955

2949 (1.7)

2973 (1.6)

2943

2936 (6.9)

CH aliphatic

2963

2964 (7.1)

2990 (11)

2961

2959 (11)

2985 (17)

2966

2963 (6.1)

2992 (10)

2961

2955 (13)

CH aromatic

3029

3045 (6.7)

3028

3043 (5.7)

3028

3041 (6.2)

3029

3038 (4.8)

3029

3046 (4.6)

3033

3054 (1.6)

3033

3055 (2.3)

3035

3050 (0.4)

3064 (3.1)

3059

3063 (5.9)

3062 (1.5)

3059 (3.9)

3069

3072 (17)

3068

3072 (16)

3069

3071 (8.1)

3068

3067 (16)

3089

3084 (11)

3087

3084 (9.6)

3086

3082 (14)

3088

3077 (8.2)

3540 3705

3516 (236) 3715 (115)

OH a

MP2/TZVPP calculated results, with computed IR intensities (km mol-1) given in parentheses. The SH, CH and OH vibrational scaling factors are given in supplementary data Table S1. b Simplified anharmonic results at the B3LYP-D3/6-311++G(d,p) level. Vibrational wavefunctions are somewhat mixed so the largest component is used to assign as fundamental or combination/overtone mode.c The aliphatic CH stretches are assigned to the PET side chain. Other observed bands in this region at 2805, 2815, 2859, 2871 and 2983 cm-1, are assigned to the DEE molecule. 19 ACS Paragon Plus Environment

Page 19 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Studies of hydrogen bonded XH…Y(H) systems usually focus on the more dramatic changes in the donor XH bond, but the acceptor YH can also be affected. The modest red shift of 9 cm-1 measured for the SH stretch band of the Ggπw1-r cluster is consistent with the formation of an OH…S bond. The calculated intensity of the SH stretching vibration increases from 1.5 to 6.2 km mol-1, while the measured intensity increases by a factor of three when monomer Ggπ forms the Ggπw1-r cluster. A similar trend is observed in the equivalent ('hydrate F’) cluster of 2-phenylethanol, with the alcohol OH stretch band red-shifting from 3626 to 3607 cm-1 and increasing in intensity.67 It is also evident from the structures in Figure 6 that the bound water molecule donor has the effect of strengthening the SH…π interaction with the side chain being distorted to accommodate the SH…π interaction.

In the Ggπ-DEE complex, the interaction between the SH proton and the electronegative oxygen atom of DEE can be understood as arising from both dispersion and charge transfer due to electron density transfer from oxygen to the thiol. The increase in electron density in the S-H σ* antibonding orbital causes a weakening of the S-H bond with a resultant red shift, elongation of the S-H bond and higher intensity in the SH stretch band. This is quite evident in the red shift of 24 cm-1 when Ggπ forms the Ggπ-DEE cluster. Furthermore, the measured intensity of the SH stretch band of the Ggπ-DEE cluster increases about 20-fold, while the MP2/TZVPP calculated intensity increases from 1.5 to 114 km mol-1. It is worthwhile to note here that the thiol hydrogen directed towards the aromatic ring in Ggπ, instead tends to point towards the oxygen in the Ggπ-DEE cluster. As illustrated in Figure 6, there are changes in the Ggπ geometry when it forms the complex with DEE, with the SH…π distance increasing markedly and thus the SH…π interaction is weakened in the cluster. In order to obtain a more indicative value of the red shift in the SH band that results from the formation of the OH…S hydrogen bond in this cluster, an alternative comparison would be with the Ag monomer where the latter is devoid of any SH….π interactions, which suggests the SH stretching red shift is 31 cm-1 in Ggπ-DEE.

20 Environment ACS Paragon Plus


Figure 6. Change in geometry in Ggπ on cluster formation (MP2/AVTZ optimized structures). Bond distances are in units of Å.

A recent IR-VUV photoionization study on H-bond donor complexes of H2S found that binding to DEE resulted in an SH band being red shifted by 46 cm-1 with respect to the mean of ν1 and ν3 in the H2S monomer.42 If only ν1 is considered rather than the mean, the shift is 39 cm-1. The VUV photoionization technique employed lacks the preselection of a specific conformer through S1←S0 excitation and hence the resultant IR spectra are broad due to the presence of multiple conformers and possibly even dissociating clusters with more than one solvent molecule. This drawback is quite evident in the SH stretch band where the full width at half maximum (FWHM) is 46 cm-1. Coplanar and perpendicular structures are obtained from the calculations, with MP2/AVTZ predicting the presence of only the latter conformer. Moreover, the calculated shifts at this level were much greater than the observed shifts, by 70 – 105 cm-1. In comparison, the IR spectra recorded by our technique are conformer/cluster specific. As a result, the SH stretch of Ggπ-DEE is narrow (with FWHM < 5cm-1, see Figure 5) and well defined so it may be directly compared with a particular ab initio structure. However, setting aside the considerable inhomogeneous broadening in the H2SDEE spectrum, it appears that the red shift is somewhat greater for an H2S donor than an R-SH donor.

Vibrational spectroscopic data and computed parameters comparing the PET clusters and monomers are summarized in Table 3. The properties of the SH donor Ggπ-DEE complex supports 21 Environment ACS Paragon Plus

Page 20 of 37

Page 21 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


the case that it is H-bonded according to the new IUPAC criteria;70 the SH stretch is red-shifted, much more intense and the computed SH bond distance has increased (by 0.6 pm). The higher binding energy of Ggπ-DEE (32 kJ mol-1) than Ggπw1-r (19 kJ mol-1) can be attributed to additional (DEE)CH…π(PET) interactions that probably account for at least half of the total. It could also be noted that the MP2/TZVPP binding energies are overestimated given that the more accurate CCSD(T)-F12b/cc-pVDZ-F12//MP2/AVTZ U0 value for cluster Ggπw1-r is 13.7 kJ mol-1.

Table 3. Correlation of MP2/TZVPP calculated zero-point corrected binding energy (BE) with the red shift, intensity and bond length of the SH stretching modes and also with the H-bond angle. Experimental SH stretch data is included for comparison. Assignment

BE / kJ mol

-1

SH stretch

SH stretch

-1

-1

SH intensity Calc / km mol

-1

SH bond length

H-bond

Calc / Å

angle / °

Expt / cm

Calc / cm

Ag

2590

2591

1.1

1.333

Ggπ

2583

2581

1.5

1.335

Ggπw1-r

19.2

2574

2571

6.2

1.336

162

Ggπ-DEE

31.6

2559

2527

114

1.339

167

4. Conclusion The concept of hydrogen bonding is over a century old, yet it remains an active topic of research as ideas continue to evolve. Advances in spectroscopic techniques and theoretical chemistry capabilities have provided new data and analysis that assist in the detailed understanding of Hbonded systems. Hydrogen bonding models are increasingly encompassing non-conventional interactions, although sulfur-centered hydrogen bonding has not received the same intense scrutiny as have other types of interactions. The results for PET-water and PET-DEE clusters presented here add to the relatively sparse treasury of experimental data on sulfur-centered H-bonds, particularly in the case where a thiol is the donor.



As an acceptor, PET was found to be only slightly weaker than its alcohol analogue PEAL,67 as evidenced by the donor HOH band red-shift of 127 cm-1 compared to 149 cm-1. PET also allows for less stringent cluster geometries; the larger, more diffuse electron density of the sulfur atom affords some flexibility in H-bond donor angle of incidence, opening up a greater range of potential secondary interactions to stabilise the cluster. The Ggπw-r cluster in particular, provides a stark example of this directional lability. In this cluster, the H-bond donating water molecule is able to arrange itself closer to the alkyl and aromatic protons, and subsequently receives stronger CH…O type interactions. This is evidenced by the larger red shift in the asymmetric “free OH” stretch (3705 cm-1 vs 3711 cm-1), as compared to the more directionally stringent alcohol analogue.

No definitive spectroscopic evidence was observed for thiols acting as a hydrogen bond donor to water, which may simply speak to the comparative weakness of the group as a donor compared to the strongly donating water. The simplest reason for R-SH acting as a weaker H-bond donor than ROH is that sulfur is less electronegative than oxygen (S 2.58, O 3.44), and so the SH bond is much less polarized and the propensity for charge transfer reduced accordingly. However, provided with a solvent partner devoid of any competitive donor group, the SH functional group will reliably act as a donor to a suitable acceptor atom. The thiol group of the PET-DEE cluster explored in this study is shown to behave analogously to other well-established H-bond donors and in alignment with metrics proposed by the IUPAC to formally define a hydrogen bond.15 We observe and/or predict an elongation of the SH bond upon formation of the H-bond, a 24/31 cm-1 red shift in SH stretch mode which is accompanied by a dramatic increase in intensity. Calculated binding energies of the PET-DEE complex are well within established bounds for a traditional hydrogen bond, and by most measurable metrics it appears that PET is forming an H-bond between the thiol SH group and the oxygen atom of the ether.


Page 22 of 37

Page 23 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Supporting Information. The Supporting Information is available free of charge on the ACS Publications website: Complete Reference Citations, Computed scaling factors for vibrational modes (Table S1), Experimental IRUV and scaled IR stick spectra of conformer Ag (Figure S1) and Ggπ (Figure S2), IR-UV spectra of Xw1 and Yw1 clusters (Figure S3).

Acknowledgements Contributions from the following bodies are gratefully acknowledged: Australia Research Council (ARC) for funding support via project and linkage equipment (DP120100100, LE100100131) grants. La Trobe University for providing postgraduate scholarships for Isabella Lobo, Patrick Robertson and Luigi Villani. Australia’s National Computational Infrastructure National Facility (NCI-NF; grants k02 and ia1), Intersect and La Trobe University for providing facilities with which to perform quantum chemical calculations. The authors also greatly appreciate Dr E. Sibert’s advice and Fortran codes pertaining to the simplified anharmonic model.

5. References 1.

Pauling, L., Nature of Chemical Bond and the structure of Molecules and Crystals. 1939,

265. 2.

Werner, A., Primary and auxillary valencies of ammonium compounds. Liebigs Ann. 1902,

322, 261-296. 3.

Latimer, W. M.; Rodebush, W. H., Polarity and ionization from the standpoint of the Lewis

theory of valence. J. Am. Chem. Soc. 1920, 42, 1419-1433. 4.

Pauling, L., The Nature of the Chemical Bond and the Structure of Molecules and Crystals.

3rd ed.; Cornell University Press: Ithaca, United States, 1960; p 664.



5.

Del Bene, J.; Pople, J. A., Theory of molecular interactions. I. Molecular orbital studies of

water polymers using a minimal Slater-type basis. J. Chem. Phys. 1970, 52 (9), 4858-4866. 6.

Gilli, P.; Bertolasi, V.; Ferretti, V.; Gilli, G., Evidence for resonance-assisted hydrogen

bonding. 4. Covalent nature of the strong homonuclear hydrogen bond. Study of the O-H--O system by crystal structure correlation methods. J. Am. Chem. Soc. 1994, 116 (3), 909-915. 7.

F. Weinfold; C.R. Landis; , Valency and Bonding, Cambridge University Press, Cambridge.

2005. 8.

Hobza, P.; Havlas, Z., Blue-Shifting Hydrogen Bonds. Chem. Rev. 2000, 100 (11), 4253-

4264. 9.

Hermansson, K., Blue-Shifting Hydrogen Bonds. J. Phys. Chem. A 2002, 106 (18), 4695-

4702. 10.

Scheiner, S.; Kar, T., Red- versus Blue-Shifting Hydrogen Bonds: Are There Fundamental

Distinctions? J. Phys. Chem. A 2002, 106 (9), 1784-1789. 11.

Joseph, J.; Jemmis, E. D., Red-, Blue-, or No-Shift in Hydrogen Bonds: A Unified

Explanation. J. Am. Chem. Soc. 2007, 129 (15), 4620-4632. 12.

Karpfen, A.; Kryachko, E. S., Blue-Shifted A-H Stretching Modes and Cooperative

Hydrogen Bonding. 1. Complexes of Substituted Formaldehyde with Cyclic Hydrogen Fluoride and Water Clusters. J. Phys. Chem. A 2007, 111 (33), 8177-8187. 13.

Politzer, P.; Murray, J. S.; Clark, T., Halogen bonding: an electrostatically-driven highly

directional noncovalent interaction. Phys. Chem. Chem. Phys. 2010, 12 (28), 7748-7757. 14.

Politzer, P.; Murray, J. S., Halogen bonding: an interim discussion. ChemPhysChem 2013,

14 (2), 278-294. 15.

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., et al., Defining the hydrogen bond: an account (IUPAC Technical Report). Pure Appl. Chem. 2011, 83 (8), 1619-1636. 25 Environment ACS Paragon Plus

Page 24 of 37

Page 25 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


16.

Plant, D.; Tarbell, D. S.; Whiteman, C., An infrared study of hydrogen bonding involving

the thiol group. J. Am. Chem. Soc. 1955, 77, 1572-1575. 17.

Di Giacomo, A.; Smyth, C. P., Hydrogen bonding and anomalous dielectric dispersion in

long-chain alcohols and mercaptans. J. Am. Chem. Soc. 1956, 78, 2032-2035. 18.

Gordy, W.; Stanford, S. C., Spectroscopic evidence for hydrogen bonds: SH, NH and NH2

compounds. J. Am. Chem. Soc. 1940, 62, 497-505. 19.

Josien, M. L.; Dizabo, P., Formation of molecular complexes with pyrrole, benzenethiol,

phenol, the alcohols, and the monohalogenated alkanes. C. R. Hebd. Seances Acad. Sci. 1956, 243, 44-46. 20.

Wagner, A.; Becher, H. J.; Kottenhahn, K. G., Hydrogen bonds between sulfoxides and

thiophenol or phenol. Chem. Ber. 1956, 89, 1708-1714. 21.

De Deken, R. H.; Broekhuysen, J.; Bechet, J.; Mortier, A., Spectrophotometric study of the

dissociation of the sulfhydryl group and molecular structure of cysteine. Biochim. Biophys. Acta 1956, 19, 45-52. 22.

Lehninger, A. L., Lehninger Principles of Biochemistry. 4th ed.; W. H. Freeman And

Company: New York, 2005. 23.

Begley, T. P.; Xi, J.; Kinsland, C.; Taylor, S.; McLafferty, F., The enzymology of sulfur

activation during thiamin and biotin biosynthesis. Curr. Opin. Chem. Biol. 1999, 3 (5), 623-629. 24.

Lamberth, C., Sulphur chemistry in crop protection. Science (Washington, DC, U. S.) 2004,

25 (1), 39-62. 25.

Sevier, C. S.; Kaiser, C. A., Formation and transfer of disulphide bonds in living cells. Nat.

Rev. Mol. Cell Biol. 2002, 3 (11), 836-847. 26.

Paquin, R.; Colomban, P., Nanomechanics of single keratin fibres: a Raman study of the α-

helix → β-sheet transition and the effect of water. J. Raman Spectrosc. 2007, 38 (5), 504-514.



27.

Wennmohs, F.; Staemmler, V.; Schindler, M., Theoretical investigation of weak hydrogen

bonds to sulfur. J. Chem. Phys. 2003, 119 (6), 3208-3218. 28.

Cocinero, E. J.; Sanchez, R.; Blanco, S.; Lesarri, A.; Lopez, J. C.; Alonso, J. L., Weak

hydrogen bonds C-H···S and C-H···F-C in the thiirane-trifluoromethane dimer. Chem. Phys. Lett. 2005, 402 (1-3), 4-10. 29.

Martin Danielle, E.; Robertson Evan, G.; Thompson Christopher, D.; Morrison Richard, J.

S., Resonant 2-photon ionization study of the conformation and the binding of water molecules to 2-phenylethanethiol (PhCH2CH2SH). The Journal of chemical physics 2008, 128 (16), 164301. 30.

Biswal, H. S.; Chakraborty, S.; Wategaonkar, S., Experimental evidence of O-H-S hydrogen

bonding in supersonic jet. J. Chem. Phys. 2008, 129 (18), 184311/1-184311/7. 31.

Biswal, H. S.; Wategaonkar, S., Nature of the N-H···S Hydrogen Bond. J. Phys. Chem. A

2009, 113 (46), 12763-12773. 32.

Housecroft, E. C.; Constable, C. E., Chemistry: An Introduction to Organic, Inorganic and

Physical Chemistry. 3rd ed.; Pearson Education Ltd: 2006. 33.

Biswal, H. S.; Wategaonkar, S., O-H···O versus O-H···S Hydrogen Bonding. 3. IR-UV

Double Resonance Study of Hydrogen Bonded Complexes of p-Cresol with Diethyl Ether and Its Sulfur Analog. J. Phys. Chem. A 2010, 114 (19), 5947-5957. 34.

Domagala, M.; Grabowski, S. J., Hydrocarbons as proton donors in C-H···N and C-H···S

hydrogen bonds. Chem. Phys. 2010, 367 (1), 1-6. 35.

Biswal, H. S.; Wategaonkar, S., OH···X (X = O, S) hydrogen bonding in tetrahydrofuran

and tetrahydrothiophene. J. Chem. Phys. 2011, 135 (13), 134306/1-134306/10. 36.

Pimental, G. C.; McClellan, A. L., The Hydrogen Bond. W. H. Freeman, San Francisco

1960. 37.

Biswal, H. S.; Wategaonkar, S., Sulfur, Not Too Far Behind O, N, and C: SH···π Hydrogen

Bond. J. Phys. Chem. A 2009, 113 (46), 12774-12782. 27 Environment ACS Paragon Plus

Page 26 of 37

Page 27 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


38.

Bricknell, B. C.; Ford, T. A., An ab initio investigation of some hydrogen-bonded

complexes of methanethiol. J. Mol. Struct. 2010, 976 (1-3), 115-118. 39.

Kieninger, M.; Ventura, O. N., Calculations of the infrared and Raman spectra of simple

thiols and thiol-water complexes. Int. J. Quantum Chem. 2011, 111 (7/8), 1843-1857. 40.

Grzechnik, K.; Rutkowski, K.; Mielke, Z., The S-H···N versus O-H···N hydrogen bonding

in the ammonia complexes with CH3OH and CH3SH. J. Mol. Struct. 2012, 1009, 96-102. 41.

Bhattacherjee, A.; Matsuda, Y.; Fujii, A.; Wategaonkar, S., The Intermolecular S-H···Y

(Y=S,O) Hydrogen Bond in the H2S Dimer and the H2S-MeOH Complex. ChemPhysChem 2013, 14 (5), 905-914. 42.

Bhattacherjee, A.; Matsuda, Y.; Fujii, A.; Wategaonkar, S., Acid-Base Formalism in

Dispersion-Stabilized S-H···Y (Y=O, S) Hydrogen-Bonding Interactions. J. Phys. Chem. A 2015, 119 (7), 1117-1126. 43.

Fu, L.; Han, H.-L.; Lee, Y.-P., Infrared absorption of methanethiol clusters (CH3SH)n, n =

2-5, recorded with a time-of-flight mass spectrometer using IR depletion and VUV ionization. J. Chem. Phys. 2012, 137 (23), 234307/1-234307/11. 44.

Biswal, H. S.; Bhattacharyya, S.; Bhattacherjee, A.; Wategaonkar, S., Nature and strength of

sulfur-centred hydrogen bonds: laser spectroscopic investigations in the gas phase and quantumchemical calculations. Int. Rev. Phys. Chem. 2015, 34 (1), 99-160. 45.

Rothman, L. S.; Gordon, I. E.; Barbe, A.; Benner, D. C.; Bernath, P. F.; Birk, M.; Boudon,

V.; Brown, L. R.; Campargue, A.; Champion, J. P., et al., The HITRAN 2008 molecular spectroscopic database. J. Quant. Spectrosc. Radiat. Transfer 2009, 110 (9-10), 533-572. 46.

M. J. Frisch; G. W. Trucks; H. B. Schlegel; G. E. Scuseria; M. A. Robb; J. R. Cheeseman;

G. Scalmani, V. B.; G. A. Petersson; H. Nakatsuji; X. Li, M. C., et al. Gaussian 09, Revision A.02; Gaussian, Inc.: Wallingford CT, 2009.



47.

Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H., A consistent and accurate ab initio

parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 2010, 132 (15), 154104/1-154104/19. 48.

Adler, T. B.; Knizia, G.; Werner, H.-J., A simple and efficient CCSD(T)-F12

approximation. J. Chem. Phys. 2007, 127 (22), 221106/1-221106/4. 49.

Knizia, G.; Adler, T. B.; Werner, H.-J., Simplified CCSD(T)-F12 methods: Theory and

benchmarks. J. Chem. Phys. 2009, 130 (5), 054104/1-054104/20. 50.

Werner, H.-J.; Knowles, P. J.; Knizia, G.; Manby, F. R.; Schuetz, M., Molpro: a general-

purpose quantum chemistry program package. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012, 2 (2), 242-253. 51.

Tabor, D. P.; Hewett, D. M.; Bocklitz, S.; Korn, J. A.; Tomaine, A. J.; Ghosh, A. K.; Zwier,

T. S.; Sibert III, E. L., Anharmonic modeling of the conformation-specific IR spectra of ethyl, npropyl, and n-butylbenzene. The Journal of chemical physics 2016, 144 (22), 224310. 52.

Buchanan, E. G.; Dean, J. C.; Zwier, T. S.; Sibert III, E. L., Towards a first-principles model

of Fermi resonance in the alkyl CH stretch region: Application to 1, 2-diphenylethane and 2, 2, 2paracyclophane. The Journal of chemical physics 2013, 138 (6), 064308. 53.

Sibert, E. L., Dressed local mode Hamiltonians fo CH stretch vibrations. Mol. Phys. 2013,

111, 2093-2099. 54.

Jaeger, H. M.; Schaefer, H. F., III; Demaison, J.; Csaszar, A. G.; Allen, W. D., Lowest-lying

conformers of alanine: pushing theory to ascertain precise energetics and semiexperimental Re structures. J. Chem. Theory Comput. 2010, 6 (10), 3066-3078. 55.

Lobo, I. A.; Wilson, D. J. D.; Bieske, E.; Robertson, E. G., A sting in the tail of flexible

molecules: spectroscopic and energetic challenges in the case of p-aminophenethylamine. Phys. Chem. Chem. Phys. 2012, 14 (25), 9219-9229.


Page 28 of 37

Page 29 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


56.

Hohenstein, E. G.; Chill, S. T.; Sherrill, C. D., Assessment of the Performance of the M05-

2X and M06-2X Exchange-Correlation Functionals for Noncovalent Interactions in Biomolecules. J. Chem. Theory Comput. 2008, 4 (12), 1996-2000. 57.

Mons, M.; Dimicoli, I.; Tardivel, B.; Piuzzi, F.; Robertson, E. G.; Simons, J. P., Energetics

of the Gas Phase Hydrates of trans-Formanilide: A Microscopic Approach to the Hydration Sites of the Peptide Bond. J. Phys. Chem. A 2001, 105 (6), 969-973. 58.

Robertson, E. G.; Hockridge, M. R.; Jelfs, P. D.; Simons, J. P., IR-UV Ion-Dip

Spectroscopy of N-Benzylformamide Clusters: Stepwise Hydration of a Model Peptide. J. Phys. Chem. A 2000, 104 (50), 11714-11724. 59.

Zwier, T. S., The spectroscopy of solvation in hydrogen-bonded aromatic clusters. Annu.

Rev. Phys. Chem. 1996, 47, 205-241. 60.

Gotch, A. J.; Zwier, T. S., Multiphoton ionization studies of clusters of immiscible liquids. I.

Benzene-(water)n clusters (C6H6-(H2O)n, n = 1, 2). J. Chem. Phys. 1992, 96 (5), 3388-3401. 61.

Dickinson, J. A.; Hockridge, M. R.; Kroemer, R. T.; Robertson, E. G.; Simons, J. P.;

McCombie, J.; Walker, M., Conformational Choice, Hydrogen Bonding, and Rotation of the S1 ← S0 Electronic Transition Moment in 2-Phenylethyl Alcohol, 2-Phenylethylamine, and Their Water Clusters. J. Am. Chem. Soc. 1998, 120 (Copyright (C) 2011 American Chemical Society (ACS). All Rights Reserved.), 2622-2632. 62.

Hockridge, M. R.; Robertson, E. G., Hydrated Clusters of 2-Phenylethyl Alcohol and 2-

Phenylethylamine: Structure, Bonding, and Rotation of the S1 ← S0 Electronic Transition Moment. J. Phys. Chem. A 1999, 103 (19), 3618-3628. 63.

Varsányi, G., Vibrational spectra of benzene derivatives. Elsevier: 2012.

64.

Robertson, P. A.; Lobo, I. A.; Wilson, D. J. D.; Robertson, E. G., Nitriles as directionally

tolerant hydrogen bond acceptors: IR-UV ion depletion spectroscopy of benzenepropanenitrile and its hydrate clusters. Chem. Phys. Lett. 2016, 660, 221-227. 30 Environment ACS Paragon Plus


65.

P. A. Robertson; L. Villani; U. L. M. Dissanayake; L. F. Duncan; D. J. D. Wilson; B. M.

Abbott; E.G. Robertson, Halocarbons as Hydrogen Bond Acceptors: A Spectroscopic Study of Haloethylbenzenes (PhCH2CH2X, X=F, Cl, Br) and their Hydrate Clusters. Phys. Chem. Chem. Phys. 2018, 20, 8218-8227. 66.

NIST Standard Reference Database Number 69.

67.

Mons, M.; Robertson, E. G.; Snoek, L. C.; Simons, J. P., Conformations of 2-phenylethanol

and its singly hydrated complexes: UV-UV and IR-UV ion-dip spectroscopy. Chem. Phys. Lett. 1999, 310 (5,6), 423-432. 68.

R. Kusaka; Y. Inokuchi; T. Haino; Ebata, T., Structures of (3n-Crown-n)−Phenol (n = 4, 5,

6, 8) Host−Guest Complexes: Formation of a Uniquely Stable Complex for n = 6 via Collective Intermolecular Interaction. 2012, 3 (10), 1414-1420. 69.

Miller, B. J.; Howard, D. L.; Lane, J. R.; Kjaergaard, H. G.; Dunn, M. E.; Vaida, V., SH-

Stretching Vibrational Spectra of Ethanethiol and tert-Butylthiol. J. Phys. Chem. A. 2009, 113 (26), 7576-7583. 70.

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., et al., Definition of the hydrogen bond (IUPAC Recommendations 2011). Pure Appl. Chem. 2011, 83 (8), 1637-1641.


Page 30 of 37

Page 31 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Table of Contents Graphic



figure 2 1329x825mm (96 x 96 DPI)


Page 32 of 37

Page 33 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


figure 3 1447x937mm (96 x 96 DPI)



figure 4 1150x696mm (96 x 96 DPI)


Page 34 of 37

Page 35 of 37 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


figure 6 51x31mm (300 x 300 DPI)



Table of contents graphic 172x88mm (300 x 300 DPI)


Page 36 of 37

Thiols as Hydrogen Bond Acceptors and Donors: Spectroscopy of 2

Recommend Documents