Modulation of the strength of weak S-H⋯O hydrogen-bond: Spectroscopic study of the complexes of 2-flurothiophenol with methanol and ethanol

Spectroscopic exploration of sulfur-centered hydrogen bonding involving a thiol group (S-H) as the hydrogen bond donor is scarce in the literature. Herein, we have investigated 1:1 complexes of 2-fluorothiophenol (2-FTP) with methanol (MeOH) and ethanol (EtOH) in the gas phase to examine the physical characteristics and strength of the S-H⋯O hydrogen bond. Structures, conformations, and the strength of the S-H⋯O interaction are investigated by measuring the electronic and Infrared (IR) spectra of the two complexes employing resonant two-photon ionization, UV-UV hole-burning, and IR-UV double resonance spectroscopic techniques combined with quantum chemical calculations. Three conformers of 2-FTP⋯MeOH and two conformers of 2-FTP⋯EtOH have been detected in the experiment. A comparison of the IR spectra obtained from the experiment with those of the low-energy conformers of 2-FTP⋯MeOH and 2-FTP⋯EtOH predicted from the theory confirms that all the observed conformers of the two complexes are primarily S-H⋯O hydrogen bonded. The IR red-shifts found in the S-H stretching frequencies in 2-FTP⋯MeOH and 2-FTP⋯EtOH concerning that in 2-FTP are ∼76 and ∼88 cm-1, respectively, which are much larger than that was reported earlier in the 2-FTP⋯H2O complex (30 cm-1). The strength and physical nature of different noncovalent interactions, including the S-H⋯O hydrogen bond existing in the complexes, are further analyzed using natural bond orbital analysis, quantum theory of atoms in molecules, and localized molecular orbital-energy decomposition analysis. The current investigation reveals that the S-H⋯O hydrogen bond can be strengthened by judicial choices of the hydrogen bond acceptors of higher proton affinities.

Competition between O-H and S-H Intermolecular Interactions in Conformationally Complex Systems: The 2-Phenylethanethiol and 2-Phenylethanol Dimers

Noncovalent interactions involving sulfur centers play a relevant role in biological and chemical environments. Yet, detailed molecular descriptions are scarce and limited to very simple model systems. Here we explore the formation of the elusive S-H···S hydrogen bond and the competition between S-H···O and O-H···S interactions in pure and mixed dimers of the conformationally flexible molecules 2-phenylethanethiol (PET) and 2-phenylethanol (PEAL), using the isolated and size-controlled environment of a jet expansion. The structure of both PET-PET and PET-PEAL dimers was unraveled through a comprehensive methodology that combined rotationally resolved microwave spectroscopy, mass-resolved isomer-specific infrared laser spectroscopy, and quantum chemical calculations. This synergic experimental-computational approach offered unique insights into the potential energy surface, conformational equilibria, molecular structure, and intermolecular interactions of the dimers. The results show a preferential order for establishing hydrogen bonds following the sequence S-H···S < S-H···O ≲ O-H···S < O-H···O, despite the hydrogen bond only accounting for a fraction of the total interaction energy.

Energetic electron irradiations of amorphous and crystalline sulphur-bearing astrochemical ices

Laboratory experiments have confirmed that the radiolytic decay rate of astrochemical ice analogues is dependent upon the solid phase of the target ice, with some crystalline molecular ices being more radio-resistant than their amorphous counterparts. The degree of radio-resistance exhibited by crystalline ice phases is dependent upon the nature, strength, and extent of the intermolecular interactions that characterise their solid structure. For example, it has been shown that crystalline CH3OH decays at a significantly slower rate when irradiated by 2 keV electrons at 20 K than does the amorphous phase due to the stabilising effect imparted by the presence of an extensive array of strong hydrogen bonds. These results have important consequences for the astrochemistry of interstellar ices and outer Solar System bodies, as they imply that the chemical products arising from the irradiation of amorphous ices (which may include prebiotic molecules relevant to biology) should be more abundant than those arising from similar irradiations of crystalline phases. In this present study, we have extended our work on this subject by performing comparative energetic electron irradiations of the amorphous and crystalline phases of the sulphur-bearing molecules H2S and SO2 at 20 K. We have found evidence for phase-dependent chemistry in both these species, with the radiation-induced exponential decay of amorphous H2S being more rapid than that of the crystalline phase, similar to the effect that has been previously observed for CH3OH. For SO2, two fluence regimes are apparent: a low-fluence regime in which the crystalline ice exhibits a rapid exponential decay while the amorphous ice possibly resists decay, and a high-fluence regime in which both phases undergo slow exponential-like decays. We have discussed our results in the contexts of interstellar and Solar System ice astrochemistry and the formation of sulphur allotropes and residues in these settings.

Theoretical Aspects of Nonconventional Hydrogen Bonds in the Complexes of Aldehydes and Hydrogen Chalcogenides

Hydrogen bonds (H-bonds) in the complexes between aldehydes and hydrogen chalcogenides, XCHO...nH₂Z with X = H, F, Cl, Br, and CH₃, Z = O, S, Se, and Te, and n = 1,2, were investigated using high-level ab initio calculations. The C_sp2-H...O H-bonds are found to be about twice as strong as the C_sp2-H...S/Se/Te counterparts. Remarkably, the S/Se/Te-H...S/Se/Te H-bonds are 4.5 times as weak as the O-H...O ones. The addition of the second H₂Z molecule into binary systems induces stronger complexes and causes a positive cooperative effect in ternary complexes. The blue shift of C_sp2-H stretching frequency involving the C_sp2-H...Z H-bond sharply increases when replacing one H atom in HCHO by a CH₃ group. In contrast, when one H atom in HCHO is substituted with a halogen, the magnitude of blue-shifting of the C_sp2-H...Z H-bond becomes smaller. The largest blue shift up to 92 cm^-1 of C_sp2-H stretching frequency in C_sp2-H...O H-bond in CH₃CHO...2H₂O has rarely been observed and is much greater than that in the cases of the C_sp2-H...S/Se/Te ones. The C_sp2-H blue shift of C_sp2-H...Z bonds in the halogenated aldehydes is converted into a red shift when H₂O is replaced by a heavier analogue, such as H₂S, H₂Se, or H₂Te. The stability and classification of nonconventional H-bonds including C_sp2-H...Se/Te, Te-H...Te, and Se/Te-H...O have been established for the first time.

Structural Characterization of 6-Thioguanosine and Its Monohydrate in the Gas Phase

Detailed structural analysis of 6-thioguanosine (6TGs) in relation to its tautomerization and sugar conformation is performed in the gas phase using UV and IR spectroscopy combined with ab initio calculations. We have observed a thiol tautomer of 6TGs with its sugar moiety in the syn conformation that is stabilized by a strong intramolecular H-bonding between O5'H of the sugar and N3 atom of the guanine moiety. This observation is consistent with previous results for guanosine (Gs) in which the corresponding enol form is solely detected. We have also identified a monohydrate of 6TGs consisting of a thiol tautomer with the water linking guanine moiety and sugar OH group. It is demonstrated that hydration behavior of 6TGs is significantly different from that of Gs as a result of a weaker H-bonding ability of the thiol group.

A unified cost-effective method for the construction of reliable potential energy surfaces for H2S and H2O clusters

A DFT-based methodology has been used to construct the potential energy surface of H2S clusters up to pentamers. Geometrical parameters and energetics show very good agreement with the existing experimental and high-level theoretical results. Distinct stable conformers of three dimers, six trimers, eleven tetramers and twenty-three pentamers have been identified. Both S-HS H-bond and SS interactions are identified in dimers, trimers and pentamers, while no SS interactions could be found in any of the 11 tetramer conformers. The binding energies of the most stable dimer, trimer, tetramer and pentamer are -1.66, -5.21, -8.57 and -12.54 kcal mol-1, respectively. The PES has been found to be exceedingly flat and the energy gap between the most and the least stable conformers was found to be only 0.09, 2.13, 1.65 and 1.13 kcal mol-1, from the dimer to the pentamer, respectively. The proposed method has also been used for water clusters up to the pentamer. The results obtained were found to agree closely with the existing results. Only one conformer was found for the water dimer, whereas four, five and fifteen conformers were obtained for the trimer, tetramer and pentamer, respectively. Atoms in molecular calculations were found to corroborate with the geometric and energetic results for both clusters.

Formation of unexpected S-S covalent bonds in H2S dimers under confinement

The present work investigates the effect of confinement on the hydrogen bonding interactions in H2S dimers. The interiors of different sized fullerenes (C60, C70, C84, and C120) have been used to model the effect of confinement. It was found that as the degree of confinement increases, the hydrogen bonding between H2S molecules disappears and sulphur-sulphur interactions appear. We obtained clear computational evidence that, inside C60, the H2S dimer is bound by a covalent bond between two sulphur atoms. It was also found that the strength of the S-S bond inside fullerenes is linked to the amount of charge transfer from the H2S dimer to the fullerene.

Observation of an Unusually Large IR Red-Shift in an Unconventional S-H···S Hydrogen-Bond

The S-H···S non-covalent interaction is generally known as an extremely unconventional weak hydrogen-bond in the literature. The present gas-phase spectroscopic investigation shows that the S-H···S hydrogen-bond can be as strong as any conventional hydrogen-bond in terms of the IR red-shift in the stretching frequency of the hydrogen-bond donor group. Herein, the strength of the S-H···S hydrogen-bond has been determined by measuring the red-shift (∼150 cm^-1) of the S-H stretching frequency in a model complex of 2-chlorothiophenol and dimethyl sulfide using isolated gas-phase IR spectroscopy coupled with quantum chemistry calculations. The observation of an unusually large IR red-shift in the S-H···S hydrogen-bond is explained in terms of the presence of a significant amount of charge-transfer interactions in addition to the usual electrostatic interactions. The existence of ∼750 S-H···S interactions between the cysteine and methionine residues in 642 protein structures determined from an extensive Protein Data Bank analysis also indicates that this interaction is important for the structures of proteins.

Participation of S and Se in hydrogen and chalcogen bonds

The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.

Computational analysis of vibrational frequencies and rovibrational spectroscopic constants of hydrogen sulfide dimer using MP2 and CCSD(T)

Previous studies have shown that the weakly bonded H₂S dimer demands high level quantum chemical calculations to reproduce experimental values. We investigated the hydrogen bonding of H₂S dimer using MP2 and CCSD(T) levels of theory in combination with aug-cc-pV(D,T,Q)Z basis sets. More precisely, the binding energies, potential energy curves, rovibrational spectroscopic constants, decomposition lifetime, and normal vibrational frequencies were calculated. In addition, we introduced the local mode analysis of Konkoli-Cremer to quantify the hydrogen bonding in the H₂S dimer as well as providing for the first time the comprehensive decomposition of normal vibrational modes into local modes contributions, and a decomposition lifetime based on rate constant. The local mode force constant of the H₂S dimer hydrogen bond is smaller than that of the water dimer, in accordance with the weaker hydrogen bonding in the H₂S dimer.

C-HS interaction exhibits all the characteristics of conventional hydrogen bonds

This is a tale of a pair of a hydrogen bond donor and acceptor, namely the CH donor and sulphur acceptor, neither of which is a conventional hydrogen bond participant. Sulfur (S), being less electronegative (2.58) compared to its first row analogue oxygen (3.44), has not been considered as a potential HB acceptor for a long time. The C-HY (Y = HB acceptor) interaction has its own history of exhibiting omnidirectional shifts in the CH stretching frequency upon complex formation. Therefore, a systematic investigation of the C-HS interaction was the primary goal of the work presented here. Together with gas-phase vibrational spectroscopy and ab initio quantum chemical calculations, the nature and strength of the C-HS hydrogen bond (HB) have been investigated in the complexes of 1,2,4,5-tetracyanobenzene (TCNB) with various sulfur containing solvents. Despite the unconventional nature of both HB donor and HB acceptor (C-H and S, respectively), it was found that the C-HS hydrogen bond exhibits all the characteristics of the conventional hydrogen bond. The binding strength of the C-HS H-bond in these complexes was found to be comparable to that of the conventional hydrogen bonds. The unusual stabilities of these HBs have been mainly attributed to the attractive dispersion interaction.

Sulfur hydrogen bonding and internal dynamics in the monohydrates of thenyl mercaptan and thenyl alcohol

Water forms weak H-bonds with thenyl compounds, simultaneously retaining internal mobility in the dimer.

Cooperative nature of the sulfur centered hydrogen bond: investigation of (H2S)n (n = 2-4) clusters using an affordable yet accurate level of theory

Existing studies have shown that appreciably high level quantum chemical calculations are required to reproduce experimental energetic and geometric features of a H₂S dimer. This condition severely restricts any practical possibility of obtaining reliable results for higher order H₂S clusters. We have shown here that the binding energies calculated at the CCSD(T)/CBS level with counterpoise corrected geometries calculated at the MP2/aug-cc-pV(Q+d)Z level of theory excellently match with the experimental results for the H₂S dimer. Subsequently, the above mentioned levels of theory were used for trimers and tetramers. (H₂S)_n (n = 2-4) clusters were found to show cooperative strengthening of S-HS hydrogen bonds, which is clearly evident from the evolution of binding energies and hydrogen bond lengths, with increasing cluster size. Localized molecular orbital energy decomposition analyses have been carried out to understand how the contributions of various energy components modulate with the size of the clusters and what are their relative contributions towards the overall stabilization of the clusters. Natural bond orbital and atoms in molecules analyses were also carried out in order to look into the evolution of the electronic charge transfer and electron density topology with cluster size.

The S∴π hemibond and its competition with the S∴S hemibond in the simplest model system: infrared spectroscopy of the [benzene-(H2S) n ]+ (n = 1-4) radical cation clusters

The S∴π hemibond (two-center three-electron, 2c-3e, bond) is an attractive interaction between a sulfur atom and π electrons. The S∴π hemibond is of essential importance in understanding chemistry of sulfur radical cations, and its roles in biochemistry have recently attracted much interest. In the present study, we observe the S∴π hemibond in the simplest model system in the gas phase. Infrared spectroscopy is applied to the [benzene-(H2S) n ]+ (n = 1-4) radical cation clusters. In n = 1, the CH stretch and SH stretch bands of the benzene and H2S moieties, respectively, are clearly different from those of the neutral molecules but similar to those of the ionic species. These vibrational features show that the positive charge is delocalized over the cluster due to the S∴π hemibond formation. In n = 2-4, the S∴S hemibond and S-π-S multicenter hemibond (three-center five-electron, 3c-5e, bond) can compete with the S∴π hemibond. The observed vibrational features clearly indicate that the S∴S hemibond formation is superior to the S∴π hemibond and S-π-S multicenter hemibond. Calculations of several dispersion-corrected density functionals are compared with the observations. While all the tested functionals qualitatively catch the feature of the S∴π hemibond, the energy order among the isomers of the different hemibond motifs strongly depends on the functionals. These results demonstrate that the [benzene-(H2S) n ]+ clusters can be a benchmark of density functionals to evaluate the sulfur hemibonds.

Thiols as Hydrogen Bond Acceptors and Donors: Spectroscopy of 2-Phenylethanethiol Complexes

Evidence and understanding of sulfur-centered hydrogen bonding, especially where the donor is a thiol, lags far behind that for conventional OH interactions. To help address this deficiency, conformer specific IR spectra of 2-phenylethanethiol (PET) and associated 1:1 solvent complexes have been measured in SH, OH, and CH stretch regions using resonant-two-photon-ionization (R2PI) and IR-UV ion dip spectroscopic techniques. The aromatic and aliphatic CH stretch regions show signature differences between anti and gauche conformers. Supported by ab initio calculations, a PET-water cluster with an OH···S arrangement and a PET-diethyl ether cluster expressing an SH···O interaction were identified. The SH stretch band of the SH···O complex is red-shifted and undergoes significant intensity enhancement compared to the bare molecule, which is characteristic of hydrogen bonding. These findings offer insight into the nature of the thiol functional group as a potential hydrogen bond donor and acceptor.

Laser desorption single-conformation UV and IR spectroscopy of the sulfonamide drug sulfanilamide, the sulfanilamide-water complex, and the sulfanilamide dimer

We have studied the conformational preferences of the sulfonamide drug sulfanilamide, its dimer, and its monohydrated complex through laser desorption single-conformation UV and IR spectroscopy in a molecular beam. Based on potential energy curves for the inversion of the anilinic and the sulfonamide NH₂ groups calculated at DFT level, we suggest that the zero-point level wave function of the sulfanilamide monomer is appreciably delocalized over all four conformer wells. The sulfanilamide dimer, and the monohydrated complex each exhibit a single isomer in the molecular beam. The isomeric structures of the sulfanilamide dimer and the monohydrated sulfanilamide complex were assigned based on their conformer-specific IR spectra in the NH and OH stretch region. Quantum Theory of Atoms in Molecules (QTAIM) analysis of the calculated electron density in the water complex suggests that the water molecule is bound side-on in a hydrogen bonding pocket, donating one O-HO[double bond, length as m-dash]S hydrogen bond and accepting two hydrogen bonds, a NHO and a CHO hydrogen bond. QTAIM analysis of the dimer electron density suggests that the C_i symmetry dimer structure exhibits two dominating N-HO[double bond, length as m-dash]S hydrogen bonds, and three weaker types of interactions: two CHO bonds, two CHN bonds, and a chalcogen OO interaction. Most interestingly, the molecular beam dimer structure closely resembles the R dimer unit - the dimer unit with the greatest interaction energy - of the α, γ, and δ crystal polymorphs. Interacting Quantum Atoms analysis provides evidence that the total intermolecular interaction in the dimer is dominated by the short-range exchange-correlation contribution.

Exploring the rare S—H...S hydrogen bond using charge density analysis in isomers of mercaptobenzoic acid

Experimental and theoretical charge density analyses on isomers of mercaptobenzoic acid have been carried out to quantify the hydrogen bonding of the hitherto less explored thiols, to assess the strength of the interactions using the topological features of the electron density. The electron density study offers interesting insights into the nature of the S—H...S interaction. The interaction energy is comparable with that of a weak hydrogen bond. The strength and directionality of the S—H...S hydrogen bond is demonstrated to be mainly due to the conformation locking potential of the intramolecular S...O chalcogen bond in 2-mercaptobenzoic acid and is stronger than in 3-mercaptobenzoic acid, which lacks the intramolecular S...O bond. Thepara-substituted mercaptobenzoic acid depicts a type I S...S interaction.

Spectroscopic Evidences for Strong Hydrogen Bonds with Selenomethionine in Proteins

Careful protein structure analysis unravels many unknown and unappreciated noncovalent interactions that control protein structure; one such unrecognized interaction in protein is selenium centered hydrogen bonds (SeCHBs). We report, for the first time, SeCHBs involving the amide proton and selenium of selenomethionine (Mse), i.e., amide-N-H···Se H-bonds discerned in proteins. Using mass selective and conformer specific high resolution vibrational spectroscopy, gold standard quantum chemical calculations at CCSD(T), and in-depth protein structure analysis, we establish that amide-N-H···Se and amide-N-H···Te H-bonds are as strong as conventional amide-NH···O and amide-NH···O═C H-bonds despite smaller electronegativity of selenium and tellurium than oxygen. It is in fact, electronegativity, atomic charge, and polarizability of the H-bond acceptor atoms are at play in deciding the strength of H-bonds. The amide-N-H···Se and amide-N-H···Te H-bonds presented here are not only new additions to the ever expanding world of noncovalent interactions, but also are of central importance to design new force-fields for better biomolecular structure simulations.

Structures of protonated hydrogen sulfide clusters, H+(H2S)n, highlighting the nature of sulfur-centered intermolecular interactions

Though H₂S has the same hydrogen bond coordination property as H₂O, intermolecular structures of H⁺(H₂S)_n are very different from those of H⁺(H₂O)_n, indicating the competition among hydrogen bond and other intermolecular interactions.

Molecular and dissociative adsorption of water and hydrogen sulfide at perfect and defective Cu(110) surfaces

The adsorption of H₂O and H₂S onto Cu(110) surfaces lead to considerably different geometries and surface reconstruction and relaxation mechanisms.

Acid-Base Formalism Extended to Excited State for O-H···S Hydrogen Bonding Interaction

Hydrogen bond can be regarded as an interaction between a base and a proton covalently bound to another base. In this context the strength of hydrogen bond scales with the proton affinity of the acceptor base and the pKa of the donor, i.e., it follows the acid-base formalism. This has been amply demonstrated in conventional hydrogen bonds. Is this also true for the unconventional hydrogen bonds involving lesser electronegative elements such as sulfur atom? In our previous work, we had established that the strength of O-H···S hydrogen bonding (HB) interaction scales with the proton affinity (PA) of the acceptor. In this work, we have investigated the other counterpart, i.e., the H-bonding interaction between the photoacids with different pKa values with a common base such as the H2O and H2S. The 1:1 complexes of five para substituted phenols p-aminophenol, p-cresol, p-fluorophenol, p-chlorophenol, and p-cyanophenol with H2O and H2S were investigated experimentally and computationally. The investigations were also extended to the excited states. The experimental observations of the spectral shifts in the O-H stretching frequency and the S1-S0 band origins were correlated with the pKa of the donors. Ab initio calculations at the MP2 and various dispersion corrected density functional levels of theory were performed to compute the dissociation energy (D0) of the complexes. The quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) method, natural bonding orbital (NBO) analysis, and natural decomposition analysis (NEDA) were carried out for further characterization of HB interaction. The O-H stretching frequency red shifts and the dissociation energies were found to be lower for the O-H···S hydrogen bonded systems compared to those for the O-H···O H-bound systems. Despite being dominated by the dispersion interaction the O-H···S interaction in the H2S complexes also conformed to the acid-base formalism, i.e., the D0 and the O-H red shift scaled with the pKa of the donor, similar to that observed in the O-H···O interaction. However, the two classes of H-bonds follow different correlations. In addition we also discuss the nuances associated with the similarity and differences in the hydrogen bonding properties of the two classes in the ground electronic state as well as in the excited state.

Critical Assessment of the Strength of Hydrogen Bonds between the Sulfur Atom of Methionine/Cysteine and Backbone Amides in Proteins

Gas-phase vibrational spectroscopy, coupled cluster (CCSD(T)), and dispersion corrected density functional (B97-D3) methods are employed to characterize surprisingly strong sulfur center H-bonded (SCHB) complexes between cis and trans amide NH and S atom of methionine and cysteine side chain. The amide N-H···S H-bonds are compared with the representative classical σ- and π-type H-bonded complexes such as N-H···O, N-H···O═C and N-H···π H-bonds. With the spectroscopic, theoretical, and structural evidence, amide N-H···S H-bonds are found to be as strong as the classical σ-type H-bonds, despite the smaller electronegativity of sulfur in comparison to oxygen. The strength of backbone-amide N-H···S H-bonds in cysteine and methionine containing peptides and proteins are also investigated and found to be of similar magnitudes as those observed in the intermolecular model complexes studied in this work. All such SCHBs also confirm that the electronegativities of the acceptors are not the sole criteria to predict the H-bond strength.

Spectroscopic and ab initio investigation of 2,6-difluorophenylacetylene–amine complexes: coexistence of C–H⋯N and lone-pair⋯π complexes and intermolecular coulombic decay

Hydrogen bond and lone-pair⋯π interactions can coexist.