Infrared absorption of methanethiol clusters (CH3SH)n, n = 2–5, recorded with a time-of-flight mass spectrometer using IR depletion and VUV ionization

Radicals in aqueous solution: assessment of density-corrected SCAN functional

We study self-interaction effects in solvated and strongly-correlated cationic molecular clusters, with a focus on the solvated hydroxyl radical. To address the self-interaction issue, we apply the DC-r2SCAN method, with the auxiliary density matrix approach. Validating our method through simulations of bulk liquid water, we demonstrate that DC-r2SCAN maintains the structural accuracy of r2SCAN while effectively addressing spin density localization issues. Extending our analysis to solvated cationic molecular clusters, we find that the hemibonded motif in the [CH3S∴CH3SH]+ cluster is disrupted in the DC-r2SCAN simulation, in contrast to r2SCAN that preserves the (three-electron-two-center)-bonded motif. Similarly, for the [SH∴SH2]+ cluster, r2SCAN restores the hemibonded motif through spin leakage, while DC-r2SCAN predicts a weaker hemibond formation influenced by solvent-solute interactions. Our findings demonstrate the potential of DC-r2SCAN combined with the auxiliary density matrix method to improve electronic structure calculations, providing insights into the properties of solvated cationic molecular clusters. This work contributes to the advancement of self-interaction corrected electronic structure theory and offers a computational framework for modeling condensed phase systems with intricate correlation effects.

Nature and Strength of Sulfur-Centered Hydrogen Bond in Methanethiol Aqueous Solutions

Methanethiol (M) and water (W) clusters like dimers (M₁W₁, M₂, and W₂), trimers (M₁W₂, M₂W₁, M₃, and W₃), and tetramers (M₁W₃, M₂W₂, M₃W₁, M₄, and W₄) were studied to assess the strength of sulfur-centered hydrogen bonding using different levels of theories, viz, HF, MP2, MP3, MP4, B3LYP, B3LYP-D3, CCSD, CCSD(T)-F12, and CCSD(T) along with aug-cc-pVNZ (where N = D, T, and Q) basis sets. Interaction energies were found to be in the range of -3.3 to -5.3 kcal/mol for the dimers, -8.0 to -16.7 kcal/mol for the trimers, and -13.5 to -29.5 kcal/mol for the tetramers at the B3LYP-D3/CBS limit level of theory. Normal modes of vibrations computed at the B3LYP/cc-pVDZ level of theory were seen to be in good agreement with the experimental values. Local energy decomposition calculations using the DLPNO-CCSD(T) level of theory indicated the domination of electrostatic interactions' contribution to the interaction energy in all cluster systems. Furthermore, atoms in molecules and natural bond orbital calculations both carried out at the B3LYP-D3/aug-cc-pVQZ level of theory aided in visualizing the hydrogen bonds besides proving a rationale for the strength of the hydrogen bonds and thereby the stability of these cluster systems.

Microbial functional communities and the antibiotic resistome profile in a high-selenium ecosystem

Enshi City, in the Hubei Province of China, is known as the world capital of selenium with the most abundant selenium resource. An important selenium hyperaccumulator plant, Cardamine violifolia, was found to naturally grow in this high-selenium ecosystem. However, relatively little is known about the impact of the selenium levels on microbial community and functional shifts in C. violifolia rhizosphere. Here, we tested the hypothesis that underground microbial diversity and function vary along a selenium gradient, including antibiotic resistance genes (ARGs). Comprehensive metagenomic analyses, such as taxonomic investigation, functional detection, and ARG annotation, showed that selenium, mercury, cadmium, lead, arsenic, and available phosphorus and potassium were correlated with microbial diversity and function. Thaumarchaeota was exclusively dominant in the highest selenium concentration of mine outcrop, and Rhodanobacter and Nitrospira were predominant in the high-selenium ecosystem. The plant C. violifolia enriched a high concentration of selenium in the rhizosphere compared to those in the bulk soil, and it recruited Variovorax and Polaromonas in its rhizosphere. Microbial abundance showed a trend of increasing first and then decreasing from low to high selenium concentrations. Annotation of ARGs showed that the multidrug resistance genes adeF, mtrA, and poxtA, the aminoglycoside resistance gene rpsL, and the sulfonamide resistant gene sul2 were enriched in the high-selenium system. It was discovered that putative antibiotic resistant bacteria displayed obvious differences in the farmland and the soils with various selenium concentrations, indicating that a high-selenium ecosystem harbors the specific microbes with a higher capacity to enrich or resist selenium, toxic metals, or antibiotics. Taken together, these results reveal the effects of selenium concentration and the selenium hyperaccumulator plant C. violifolia on shaping the microbial functional community and ARGs. Metalloid selenium-inducible antibiotic resistance is worth paying attention to in future.

Conformational stability and structural analysis of methanethiol clusters: a revisit

B3LYP/cc-pV(D/T/Q)Z and CCSD/cc-pVDZ levels of theory predict three minima for both dimers and trimers of methanethiol. Predictions at B3LYP/cc-pVDZ corroborates exceedingly well with the earlier reported experimental value but significantly differ from the previous computational predictions. Interaction energy between the molecules decreases with an increase in the size of the basis set for both the dimer and trimer. The dipole moment of methanethiol dimer gets reduced at the B3LYP/cc-pVDZ level of theory relative to all minima configurations, and the same is seen for trimer also. These new predictions are well supported by atoms in molecules (AIM), frontier molecular orbital (FMO), Mulliken charge (MC), and natural bond orbital (NBO) analysis.

B3LYP/cc-pV(D/T/Q)Z and CCSD/cc-pVDZ levels of theory predict three minima for both dimers and trimers of methanethiol.

IR-VUV spectroscopy of pyridine dimers, trimers and pyridine-ammonia complexes in a supersonic jet

The infrared spectra of the C-H stretching vibrations of (pyridine)m, m = 1-3, and the N-H stretching vibrations of (pyridine)m-(NH3)n, m = 1, 2; n = 1-4, complexes were investigated by infrared (IR)-vacuum ultraviolet (VUV) spectroscopy under jet-cooled conditions. The ionization potential (IP0) of the pyridine monomer was determined to be 74 546 cm-1 (9.242 eV), while its complexes showed only smooth curves of the ionization thresholds at ∼9 eV, indicating large structural changes in the ionic form. The pyridine monomer exhibits five main features with several satellite bands in the C-H stretching region at 3000-3200 cm-1. Anharmonic calculations including Fermi-resonance were carried out to analyze the candidates of the overtone and combination bands which can couple to the C-H stretching fundamentals. For (pyridine)2 and (pyridine)3, most C-H bands are blue-shifted by 3-5 cm-1 from those of the monomer. The structures revealed by random searching algorithms with density functional methods indicate that the π-stacked structure is most stable for (pyridine)2, while (pyridine)3 prefers the structures stabilized by dipole-dipole and C-Hπ interactions. For the (pyridine)m-(NH3)n complexes, the mass spectrum exhibited a wide range distribution of the complexes. The observed IR spectra in the N-H stretching vibrations of the complexes showed four main bands in the 3200-3450 cm-1 region. These features are very similar to those of (NH3)n complexes, and the bands are assigned to the anti-symmetric N-H stretching band (ν3), the symmetric N-H stretching (ν1) band, and the first overtone bands of the N-H bending vibrations (2ν4). The anharmonic calculations including the Fermi-resonance between ν1 and 2ν4 well reproduced the observed spectra.

Effects of solvent molecules on hemi-bonded (CH3SH)2+: infrared absorption of [(CH3SH)2-X]+ with X = H2O, (CH3)2CO, or NH3 and (CH3SH)n+ (n = 3-6)

Three-electron two-center (3e-2c) hemi-bonds play important roles in the oxidation and electron transport of proteins and are implicated to be involved in some neurodegenerative diseases. Our previous investigations on infrared (IR) spectra of (CH3SH)2+ using vacuum-ultraviolet photoionization, infrared dissociation, and time-of-flight detection have shown that (CH3SH)2+ is (3e-2c)-bonded. To investigate the influence of the solvent molecules on the (3e-2c)-bonded (CH3SH)2+ in a supersonic jet, we added H2O or (CH3)2CO or NH3 or (CH3SH)n (n = 1-4) to (CH3SH)2+ and investigated their IR action spectra. The (3e-2c)-bonded (CH3SH)2+ ion core was maintained when a molecule of H2O or (CH3)2CO or CH3SH binds, indicating that the ion core is more stable than the hydrogen bond, whereas the (3e-2c)-bond became broken by a NH3 molecule because the proton transfer led to a more stable hydrogen-bonded structure. The spectral features of the SH-stretching modes of (CH3SH)n+ (n = 3-6) indicate that the (3e-2c)-bonded (CH3SH)2+ ion core is maintained and the first two additional CH3SH are H-bonded to the free SH groups of the ion core. For larger clusters with n = 5 and 6, the additional solvent molecules likely bind to the first solvation shell. These results show also that the (3e-2c)-bonded S∴S structure is more stable than the S∴O and S∴N structures in [(CH3SH)2-X]+ with X = H2O or (CH3)2CO or CH3SH or NH3.

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.

Spectral Characterization of Three-Electron Two-Center (3e-2c) Bonds of Gaseous CH3S∴S(H)CH3 and (CH3SH)2+ and Enhancement of the 3e-2c Bond upon Protonation

The three-electron two-center (3e-2c) bond plays an important role in structures and electron communication in biological systems involving cationic sulfur compounds. Although the nature of 3e-2c bonds and their theoretical formalism have attracted great interest, direct spectral identifications of 3e-2c-bound molecules are scarce. We observed the infrared spectra of the weakly 3e-2c-bound CH₃S∴S(H)CH₃ and the strongly 3e-2c-bound (CH₃SH)₂⁺ in a supersonic jet using infrared (IR) dissociation with vacuum-ultraviolet photoionization and time-of-flight detection. Protonation of CH₃S∴S(H)CH₃ to form [CH₃(H)S∴S(H)CH₃]⁺ significantly enhances the 3e-2c bond, characterized by a large red shift of the SH-stretching band with enhanced IR intensity, shortening of the calculated S-S distance from 3.00 to 2.86 Å, and a dissociation energy increased from ∼23 to 162 kJ mol^-1.

Vibrational autoionization of state-selective jet-cooled methanethiol (CH3SH) investigated with infrared + vacuum-ultraviolet photoionization

Vibrational autoionization of Rydberg states provides key information about nonadiabatic processes above an ionization threshold. We employed time-of-flight mass detection of CH₃SH⁺ to record vibrational-state selective photo-ionization efficiency (PIE) spectra of jet-cooled methanethiol (CH₃SH) on exciting CH₃SH to a specific vibrationally excited state with an infrared (IR) laser, followed by excitation with a tunable laser in the vacuum-ultraviolet (VUV) region for ionization. Autoionizing Rydberg states assigned to the ns, np, nd and nf series are identified. When IR light at 2601 (ν₃, SH stretching mode) and 2948 cm^-1 (ν₂, CH₃ symmetric stretching mode) was employed, the Rydberg series converged to the respective vibrationally excited (ν₃ and ν₂) states of CH₃SH⁺. When IR light at 3014 cm^-1 (overlapped ν₁/ν₉, CH₃ antisymmetric stretching and CH₂ antisymmetric stretching modes) was employed, Rydberg series converging to two vibrationally excited states (ν₁ and ν₉) of CH₃SH⁺ were observed. When IR light at 2867 cm^-1 (2ν₁₀, overtone of CH₃ deformation mode) and 2892 cm^-1 (2ν₄, overtone of CH₂ scissoring mode) was employed, both Δν = -1 and Δν = -2 ionization transitions were observed; there is evidence for direct ionization from the initial state into the CH₃SH⁺ (ν₄⁺ = 1) continuum. In all observed IR-VUV-PIE spectra, the ns and nd series show intensity greater than the other Rydberg series, which is consistent with the fact that the highest-occupied molecular orbital of CH₃SH is a p-like lone pair orbital on the S atom. The quantum yields for autoionization of various vibrational excited states are discussed. Values of ν₁ = 3035, ν₂ = 2884, ν₃ = 2514, and ν₉ = 2936 cm^-1 for CH₃SH⁺ derived from the converged limits agree satisfactorily with values observed for Ar-tagged CH₃SH⁺ at 3026, 2879, 2502, and 2933 cm^-1.

Infrared absorption of methanol-water clusters (CH3OH)n(H2O), n = 1-4, recorded with the VUV-ionization/IR-depletion technique

We recorded infrared (IR) spectra in the CH- and OH-stretching regions of size-selected clusters of methanol (M) with one water molecule (W), represented as M_nW, n = 1-4, in a pulsed supersonic jet using the photoionization/IR-depletion technique. Vacuum ultraviolet emission at 118 nm served as the source of ionization in a time-of-flight mass spectrometer to detect clusters M_nW as protonated forms M_n-1WH⁺. The variations in intensities of M_n-1WH⁺ were monitored as the wavelength of the IR laser light was tuned across the range 2700-3800 cm^-1. IR spectra of size-selected clusters were obtained on processing of the observed action spectra of the related cluster-ions according to a mechanism that takes into account the production and loss of each cluster due to IR photodissociation. Spectra of methanol-water clusters in the OH region show significant variations as the number of methanol molecules increases, whereas those in the CH region are similar for all clusters. Scaled harmonic vibrational wavenumbers and relative IR intensities predicted with the M06-2X/aug-cc-pVTZ method for the methanol-water clusters are consistent with our experimental results. For dimers, absorption bands of a structure WM with H₂O as a hydrogen-bond donor were observed at 3570, 3682, and 3722 cm^-1, whereas weak bands of MW with methanol as a hydrogen-bond donor were observed at 3611 and 3753 cm^-1. For M₂W, the free OH band of H₂O was observed at 3721 cm^-1, whereas a broad feature was deconvoluted to three bands near 3425, 3472, and 3536 cm^-1, corresponding to the three hydrogen-bonded OH-stretching modes in a cyclic structure. For M₃W, the free OH shifted to 3715 cm^-1, and the hydrogen-bonded OH-stretching bands became much broader, with a weak feature near 3179 cm^-1 corresponding to the symmetric OH-stretching mode of a cyclic structure. For M₄W, the observed spectrum agrees unsatisfactorily with predictions for the most stable cyclic structure, indicating significant contributions from branched isomers, which is distinctly different from M₅ of which the cyclic form dominates.

Communication: vacuum ultraviolet photoabsorption of interstellar icy thiols

Following the recent identification of ethanethiol in the interstellar medium (ISM) we have carried out Vacuum UltraViolet (VUV) spectroscopy studies of ethanethiol (CH3CH2SH) from 10 K until sublimation in an ultrahigh vacuum chamber simulating astrochemical conditions. These results are compared with those of methanethiol (CH3SH), the lower order thiol also reported to be present in the ISM. VUV spectra recorded at higher temperature reveal conformational changes in the ice and phase transitions whilst evidence for dimer production is also presented.