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

Theoretical study on the structures and vibrational spectra of (H2O-Arn)+, n = 1, 2: formation of a hemi-bond of water radical cation

The possible existence of a hemi-bond in the cationic complex of water and Ar has been actively debated in the literature. We simulated vibrational spectra of low-energy conformers of H2O+-Arn (n = 1, 2) in the mid- and near-infrared regions based on ab initio anharmonic algorithms with potential energy at CCSD/aug-cc-pVTZ quality. Decent agreements between experimental data and spectra simulated with four types of normal modes, intermolecular translation, H-O-H bending, and O-H stretching, validate our computational algorithms. By cross-examination of the available experimental data and our simulations, we believe that both the hydrogen-bond and hemi-bond conformers of H2O+-Ar2 should coexist under the experimental conditions. Our simulated spectra of hemi-bond conformers of H2O+-Ar2 further suggest that spectral features in the under-explored part of the near-infrared region may provide additional spectral features to double check the existence of the hemi-bond conformer.

Observation of the hemibond formation in (H2O-Arn)+ radical cation clusters by electronic spectroscopy and ion imaging technique

The hemibond is a non-classical covalent bond formed by the overlap of non-bonding orbitals of a radical (cation) and a closed-shell molecule. For (H2O-Arn)+ radical cation clusters, competition between the hemibonded type and hydrogen-bonded (H-bonded) type isomers has been discussed on the basis of infrared spectroscopy and theoretical computations. It has been commonly recognized that the H-bonded type is predominant, while the coexistence of the hemibonded type remains a topic of debate. Hemibonded species are known to exhibit very strong electronic transitions in the ultraviolet and/or visible (UV-vis) region, which are marker bands for hemibond formation. In this study, we performed electronic spectroscopy and photofragment ion imaging experiments on (H2O-Arn)+ to observe the hemibond formation between H2O+ and Ar. The observed spectra of (H2O-Arn)+ (n = 1-3) exhibit absorption in the UV and visible regions. A comparison with quantum chemical calculations suggests the coexistence of the hemibonded type in (H2O-Arn)+ (n = 1 and 2). In addition, the photofragment ion imaging experiment on (H2O-Ar)+ showed an angular distribution attributed to the absorption of the hemibonded type, providing firm experimental evidence of the coexistence of the hemibonded type.

Infrared Spectroscopy of [H2O-N2O]+-(H2O)n (n = 1 and 2): Microhydration Effects on the Hemibond

The hemibond, a nonclassical covalent bond involving three electrons shared between two centers, has attracted considerable attention due to its significance in radiation chemistry. Water radical cation clusters, [H2O-X]+, exhibit two primary bonding motifs: the hemibond and the hydrogen bond. Although hydrogen bond formation typically dominates, recent studies have identified instances of hemibond formation in some systems involving water molecules. This study focuses on the [H2O-N2O]+ radical cation cluster, a rare system exhibiting hemibond formation. We investigate the stability of this hemibond in [H2O-N2O]+ against microhydration by employing infrared photodissociation spectroscopy and conducting theoretical calculations on [H2O-N2O]+-(H2O)n (n = 1 and 2). By comparing experimental and simulated spectra, we determined the predominant intermolecular bonding motifs in [H2O-N2O]+-(H2O)n (n = 1 and 2). Our analysis revealed that proton-transferred-type isomers are almost exclusively populated for n = 1 and 2, whereas hemibonded-type isomers are energetically unfavorable. These findings indicate that microhydration disrupts the hemibond and shifts the stable structural motifs.

Infrared Spectroscopy of Radical Cation Clusters (NH3)2+ and (NH3)3. J Phys Chem A 2025;129:2472-2481. [PMID: 40009547 DOI: 10.1021/acs.jpca.4c08362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The ionization of protic molecules such as H2O and NH3 in the condensed phase initiates ion-molecule reactions, which remain poorly understood. Studies of the structure and reactivity of small ionic clusters in molecular beams have yielded a wealth of information on protonated clusters. However, unprotonated radical cation clusters have a low concentration in a typical experiment and thus remain challenging. Here we report the infrared spectra of the (NH3)2+ and (NH3)3+ radical cations solvated in helium nanodroplets. Radical cation clusters often have several isomers with different ionic cores, including proton-transferred and hemibonded structures. Infrared spectra of the cations obtained in this work indicate that the formation of the ammonia dimer ((NH3)2+) and trimer ((NH3)3+) cations yields the proton-transferred structures, which correspond to the respective global minima of the calculated structures. Spectral assignments are corroborated by density functional theory calculations. The spectra also indicate that the NH4+ and NH3 moieties within the clusters undergo internal rotation with rotational constants close to those in the gas phase.

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.

Synthesis and Single-Electron Oxidation of Bulky Bis(m-terphenyl)chalcogenides: The Quest for Kinetically Stabilized Radical Cations

Sterically encumbered bis(m-terphenyl)chalcogenides, (2,6-Mes₂ C₆ H₃ )₂ E (E=S, Se, Te) were obtained by the reaction of the chalcogen tetrafluorides, EF₄ , with three equivalents of m-terphenyl lithium, 2,6-Mes₂ C₆ H₃ Li. The single-electron oxidation of (2,6-Mes₂ C₆ H₃ )₂ Te using XeF₂ /K[B(C₆ F₅ )₄ ] afforded the radical cation [(2,6-Mes₂ C₆ H₃ )₂ Te][B(C₆ F₅ )₄ ] that was isolated and fully characterized. The electrochemical oxidation of the lighter homologs (2,6-Mes₂ C₆ H₃ )₂ E (E=S, Se) was irreversible and impaired by rapid decomposition.

Infrared Spectroscopy of (Benzene-H2S-Xn)+, X = H2O (n = 1 and 2) and CH3OH (n = 1), Radical Cation Clusters: Microsolvation Effects on the S-π Hemibond

An unconventional covalent bond in which three electrons are shared by two centers is called hemibond. Hemibond formation frequently competes with proton transfer (or ionic hydrogen bond formation), but there have been a few experimental reports on such competition. In the present study, we focus on the (benzene-H₂S)⁺ radical cation cluster, which is a model system of the S-π hemibond. The stability of the S-π hemibond to the microsolvation by water and methanol is explored with infrared spectroscopy of (benzene-H₂S-X_n)⁺, X = H₂O (n = 1 and 2) and CH₃OH (n = 1), clusters. We also perform energy-optimization and vibrational simulations of (benzene-H₂S-X_n)⁺. By comparison among the observed and simulated spectra, we determine the intermolecular binding motifs in (benzene-H₂S-X_n)⁺. While the S-π hemibonded isomer is exclusively populated in (benzene-H₂S-H₂O)⁺, both the hemibonded and proton-transferred isomers coexist in [benzene-H₂S-(H₂O)₂]⁺ and (benzene-H₂S-CH₃OH)⁺. Breaking of the S-π hemibond by the microsolvation is observed, and its solvent and cluster size dependence is interpreted by the proton affinity and the coordination property of the solvent moiety.

Spectroscopic evidence of S∴N and S∴O hemibonds in heterodimer cations

Computational and condensed phase experimental evidence for the existence of S∴N and S∴O hemibonded structures has been reported previously, but no gas phase experimental evidence has been reported. To experimentally explore the existence of the S∴N and S∴O hemibonds in the gas phase, we recorded the infrared photodissociation action spectra of four cationic clusters: [CH₃SH-NH₃]⁺, [CH₃SCH₃-NH₃]⁺, [CH₃SCH₃-H₂O]⁺, and [CH₃OCH₃-H₂O]⁺. Combined with the calculation results, it is found that the S∴N hemibonded structure is competitive with the S⋯HN H-bonded structure, though only the latter structure is actually observed in [CH₃SH-NH₃]⁺. The spectral and theoretical results show that hemibonds can form between the second- (oxygen or nitrogen) and the third-period elements (sulfur) in the heterodimer clusters of [CH₃SCH₃-NH₃]⁺ and [CH₃SCH₃-H₂O]⁺. However, the S∴N and S∴O hemibonded structures are found competitive with the C⋯HN and CH⋯O H-bonded structures, respectively, and both the structures coexist. On the other hand, the O∴O hemibonded structure is much less stable than other hydrogen bonded (H-bonded) structures in [CH₃OCH₃-H₂O]⁺, and it shows no clear contribution to the observed spectrum. This study provides direct spectroscopic evidence for the existence of S∴N and S∴O hemibonds in the gas phase and their competition with the H-bonds, which may be also fundamentally important in biological processes.

On the origins of the mechanistic variants in the thermal reactions of Sx+ (x = 1-3) with benzene

The S-π interaction between sulfur atom(s) and aromatic ring prevails in chemical and biochemical processes. The thermal gas-phase reactions of the S_n⁺ (n = 1-3) ions with benzene have been explored by using Quadrupole-Ion Trap (Q-IT) mass spectrometry complemented by quantum chemical calculations. Charge transfer was found to be the only reaction channel for S₂⁺/C₆H₆, while both charge transfer and bond activation are available for the S⁺/C₆H₆ and S₃⁺/C₆H₆ couples. Upon interrogating the associated electronic origins, multiple factors were found to matter for these processes. In contrast to the σ-type two-center three-electron (2c-3e) S-π hemibond as reported previously, unusual S-π hemibonds were addressed for the S_n⁺/C₆H₆ couples, i.e. the 2c-3e π(S061Eπ) and the three-center three-electron (3c-3e) σ(S₂061Eπ) hemibonds. Such S-π interaction was found to be responsible for the charge transfer processes in S⁺/C₆H₆ and S₂⁺/C₆H₆, but uninvolved in any transformation for S₃⁺/C₆H₆.

Hidden Hemibonding in the Aqueous Hydroxyl Radical

The existence of a two-center, three-electron hemibond in the first solvation shell of ^•OH(aq) has long been a matter of debate. The hemibond manifests in ab initio molecular dynamics simulations as a small-r feature in the oxygen radial distribution function (RDF) for H₂O···^•OH, but that feature disappears when semilocal density functionals are replaced with hybrids, suggesting a self-interaction artifact. Using periodic simulations at the PBE0+D3 level, we demonstrate that the hemibond is actually still present (as evidenced by delocalization of the spin density) but is obscured by the hydrogen-bonded feature in the RDF due to a slight elongation of the hemibond. Computed electronic spectra for ^•OH(aq) are in excellent agreement with experiment and confirm that hemibond-like configurations play an outsized role in the spectroscopy due to an intense charge-transfer transition that is strongly attenuated in hydrogen-bonded configurations. Apparently, 25% exact exchange (as in PBE0) is insufficient to eliminate delocalization of unpaired spins.

Infrared Spectroscopy and Anharmonic Vibrational Analysis of (H2O-Krn)+ (n = 1-3): Hemibond Formation of the Water Radical Cation

The hemibond is a nonclassical covalent bond formed between a radical (cation) and a closed shell molecule. The hemibond formation ability of water has attracted great interest, concerning its role in ionization of water. While many computational studies on the water hemibond have been performed, clear experimental evidence has been hardly reported because the hydrogen bond formation overwhelms the hemibond formation. In the present study, infrared photodissociation spectroscopy is applied to (H₂O-Kr_n)⁺ (n = 1-3) radical cation clusters. The observed spectra of (H₂O-Kr_n)⁺ are well reproduced by the anharmonic vibrational simulations based on the hemibonded isomer structures. The firm evidence of the hemibond formation ability of water is revealed.

An interesting possibility of forming special hole stepping stones with high-stacking aromatic rings in proteins: three-π five-electron and four-π seven-electron resonance bindings

Long-range hole transfer of proteins plays an important role in many biological processes of living organisms. Therefore, it is highly useful to examine the possible hole stepping stones, which can facilitate hole transfer in proteins. However, the structures of stepping stones are diverse because of the complexity of the protein structures. In the present work, we proposed a series of special stepping stones, which are instantaneously formed by three and four packing aromatic side chains of amino acids to capture a hole, corresponding to three-π five-electron (π:π∴π↔π∴π:π) and four-π seven-electron (π:π∴π:π↔π:π:π∴π) resonance bindings with appropriate binding energies. The aromatic amino acids include histidine (His), phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp). The formations of these special stepping stones can effectively reduce the local ionization potential of the high π-stacking region to efficiently capture the migration hole. The quick formations and separations of them promote the efficient hole transfer in proteins. More interestingly, we revealed that a hole cannot delocalize over infinite aromatic rings along the high π-π packing structure at the same time and the micro-surroundings of proteins can modulate the formations of π:π∴π↔π∴π:π and π:π∴π:π↔π:π:π∴π bindings. These results may contribute a new avenue to better understand the potential hole transfer pathway in proteins.

Sulfur-centered hemi-bond radicals as active intermediates in S-DNA phosphorothioate oxidation

Phosphorothioate (PS) modifications naturally appear in bacteria and archaea genome and are widely used as antisense strategy in gene therapy. But the chemical effects of PS introduction as a redox active site into DNA (S-DNA) is still poorly understood. Herein, we perform time-resolved spectroscopy to examine the underlying mechanisms and dynamics of the PS oxidation by potent radicals in free model, in dinucleotide, and in S-oligomer. The crucial sulphur-centered hemi-bonded intermediates -P–S∴S–P- were observed and found to play critical roles leading to the stable adducts of -P–S–S–P-, which are backbone DNA lesion products. Moreover, the oxidation of the PS moiety in dinucleotides d[G_PSG], d[A_PSA], d[G_PSA], d[A_PSG] and in S-oligomers was monitored in real-time, showing that PS oxidation can compete with adenine but not with guanine. Significantly, hole transfer process from A^+• to PS and concomitant -P–S∴S–P- formation was observed, demonstrating the base-to-backbone hole transfer unique to S-DNA, which is different from the normally adopted backbone-to-base hole transfer in native DNA. These findings reveal the distinct backbone lesion pathway brought by the PS modification and also imply an alternative -P–S∴S–P-/-P–S–S–P- pathway accounting for the interesting protective role of PS as an oxidation sacrifice in bacterial genome.

Role of hemibonding in the structure and ultraviolet spectroscopy of the aqueous hydroxyl radical

The presence of a two-center, three-electron hemibond in the solvation structure of the aqueous hydroxl radical has long been debated, as its appearance can be sensitive to self-interaction error in density functional theory.