Electronic and vibrational spectroscopy of benzonitrile cation for astrochemical consideration

The electronic and vibrational spectra of benzonitrile cation, C6H5CN+ (BZN+), in the gas phase at low temperatures are reported. Measurements were carried out using a cryogenic ion trapping apparatus. The mid-infrared spectrum shows a strong CN stretch at 2130 ± 1 cm-1 (4.694 ± 0.002 µm). The electronic spectrum is reported in the range 5040-5750 Å. This covers the forbidden B2B2 ← X2B1 and allowed C2B1 ← X2B1 transitions. The spectrum is dominated by a broad absorption feature at wavelengths shorter than 5250 Å, with the strongest absorption located at 5140 Å. Experimental data are complemented with quantum chemical calculations carried out at the density functional theory and extended multi-configurational quasi-degenerate perturbation theory level. The spectroscopic results are discussed in the context of astronomical observations in the infrared and visible.

Noncovalent Interactions Steer the Formation of Polycyclic Aromatic Hydrocarbons

Aromatic molecules play an important role in the chemistry of astronomical environments such as the cold interstellar medium (ISM) and (exo)planetary atmospheres. The observed abundances of (polycyclic) aromatic hydrocarbons such as benzonitrile and cyanonaphthalenes are, however, highly underestimated by astrochemical models. This demonstrates the need for more experimentally verified reaction pathways. The low-temperature ion-molecule reaction of benzonitrile•+ with acetylene is studied here using a multifaceted approach involving kinetics and spectroscopic probing of the reaction products. A fast radiative association reaction via an in situ experimentally observed prereactive complex shows the importance of noncovalent interactions in steering the pathway during cold ion-molecule reactions. Product structures of subsequent reactions are unambiguously identified using infrared action spectroscopy and reveal the formation of nitrogen-containing, linked bicyclic structures such as phenylpyridine•+ and benzo-N-pentalene+ structures. The results, contradicting earlier assumptions on the product structure, demonstrate the importance of spectroscopic probing of reaction products and emphasize the possible formation of linked bicyclic molecules and benzo-N-pentalene+ structures in astronomical environments.

Growth mechanism of aromatic prebiotic molecules: insights from different processes of ion-molecule reactions in benzonitrile-ammonia and benzonitrile-methylamine clusters

Benzonitrile (BN, C6H5CN) has been detected in the cold molecular cloud Taurus molecular cloud-1 (TMC-1) in 2018, which is suggested to be a precursor in the formation of more complex nitrogen-containing aromatic interstellar compounds. In this study, we utilized mass-selected infrared (IR) photodissociation spectroscopy and quantum chemical calculations to investigate the structures and gaseous ion-molecule reactions of benzonitrile-ammonia (BN-NH3) and benzonitrile-methylamine (BN-MA) clusters. The spectral observations indicate that the cyclic hydrogen bonding structure predominates in both neutral clusters. After VUV (118 nm) single-photon ionization, a new C-N covalent bond formed between BN and NH3 in the (BN-NH3)+ cluster. However, proton sharing constitutes the primary structure of the (BN-MA)+ cluster. The two nitrogen-containing interstellar molecules react with BN to yield distinct products due to difference in charge distribution and molecular polarity in the ionized clusters. The reactions of BN with other molecules contribute to our understanding of the growth mechanisms of complex interstellar molecules.

Proton Transfer Processes in 2-Butenenitrile Dimer Cation Studied by Mass-Selective Infrared Spectroscopy

2-Butenenitrile (2-Bu) is a recently discovered crucial interstellar molecule. Herein, an abnormal NH band was observed in the infrared spectrum of the 2-Bu dimer cation, suggestive of a proton transfer reaction within the cluster. Through a comprehensive theoretical analysis of the IR spectrum of (2-Bu)2+, we discovered not only the formation of a new C-N bond through the attachment of one 2-Bu to another but also the occurrence of a proton transfer reaction in the cluster. This proton was identified as originating from the methyl group of the attaching 2-Bu in the cluster based on the analysis of IR spectra of (2-Bu)+ and [2-Bu-acrylonitrile (AN)]+. Furthermore, the detailed reaction process of this ion-molecule reaction is examined with theoretical calculation. This finding contributes significantly to our deeper understanding of ion-molecule reactions in the gas phase and the formation of nitrogen-containing prebiotic molecules in the interstellar medium.

Infrared spectrum of the 1-cyanoadamantane cation: evidence of hydrogen transfer and cage-opening upon ionization

The radical cations of diamondoids are important intermediates in their functionalization reactions and are also candidates as carriers for astronomical absorption and emission features. Although neutral diamondoids have been studied extensively, information regarding their radical cations is largely lacking, particularly for functionalized diamondoid derivatives. Herein, we characterize the structure of the 1-cyanoadamantane radical cation (C10H15CN+, AdCN+) using infrared photodissociation (IRPD) spectroscopy of mass selected AdCN+N2 clusters in the XH stretch range (2400-3500 cm-1) and dispersion-corrected density functional theory calculations (B3LYP-D3BJ/cc-pVTZ). A group of three distinct CH stretch bands are observed in the 2800-3000 cm-1 range, in addition to a highly redshifted absorption at 2580 cm-1 attributed to the acidic CH proton predicted by calculations. An unexpected broad absorption peaking at 3320 cm-1 is also detected and assigned to an NH stretch mode based on its width and frequency. Calculations indicate that hydrogen atom transfer (HAT) from the adamantyl cage (C10H15, Ady) to the N atom of the CN group yields lower energy structures, with an open-cage isomer exhibiting such hydrogen transfer being the global minimum on the potential energy surface. The energy barriers involved in the formation of this open-cage isomer are also lower than those calculated for generation of the analogous open-cage 1-amantadine cation isomer which has previously been identified by IRPD. The combined consideration of IRPD spectra and calculations indicates a major population of the nascent canonical closed-cage isomer and a smaller population of the global minimum isomer featuring both cage-opening and hydrogen transfer.

A Facile Route for the Formation of Complex Nitrogen-Containing Prebiotic Molecules in the Interstellar Medium

Prebiotic molecules have often been identified in the interstellar medium and meteorite samples. However, we still have only a fragmentary knowledge of the mechanism of the evolutionary process of these prebiotic molecules. With the aid of state-of-the-art vacuum ultraviolet (VUV)-infrared (IR) spectroscopy and ab initio calculations, we reveal a new pathway leading to the formation of the biorelevant molecules carrying amine groups or peptide bonds via the single-photon ionization induced Michael/cyclization reaction of acrylonitrile (AN)-alcohol heterodimer complexes in the gas phase. In the reactions, not only N-H nitrilium cations with H⁺-N≡C-R Lewis structure but also cyclic amine cations with a peptide bond can be formed when the AN reacts with alcohols of increasing molecular size (such as ethanol, propanol, or butanol). This study suggests the possibility of unsaturated nitriles being reduced by ionized alcohols in space, which can further drive sequential Michael addition/cyclization reactions to form more complex biorelevant molecules.

Simulation Investigation of Bulk and Surface Properties of Liquid Benzonitrile: Ring Stacking-Assessment and Deconvolution

The content and the molecular dynamics (MD) simulation analysis here are inspired by our recent ab initio calculation on benzonitrile (BZN), whereas the present results are to expand and develop macroscopic documentation involving data verification. MD simulations of the bulk liquid BZN in the range of 293-323 K unravel the hydrogen bond (-C≡N···H) formation with strength in the order of ortho-H ≫ meta-H ∼> para-H. The possibility for ortho-Hs to get involved in the formation of two bonds simultaneously confirms each having σ- and π-bonding features. Accordingly, we used vast efforts for structural analysis particularly based on the deconvolution of the corresponding complex correlation functions. Specific angle-dependent correlation functions led to the recognition of the molecular stacking with a strict anti-parallel orientation. The in-plane dimer and trimer also take part in the structural recognition. A singularity, found in the trend of the simulated temperature-dependent viscosity and diffusion coefficient of liquid BZN, is centered at about 313 K and quite fascinatingly emulates the reported experiment viscosity. An interplay between a small change in the trend of density and a large change in the corresponding viscosity is a key factor in supporting the singularity. Deconvolution of the simulation results allows attributing the singularity to structural alteration involving H-bonding of different types and extent. Approaching the range of 308-313 K, an alteration between hydrogen bond formation involving mostly ortho-Hs and mixed ortho-Hs + meta-H is possible and supports the singularity.

Water-Assisted Proton Transfer in the Sequential Hydration of Benzonitrile Radical Cation C6H5CN•+(H2O)n: Transition to Hydrated Distonic Cation •C6H4CNH+(H2O)n with n ≥ 4

The stepwise hydration of the benzonitrile^•+ radical cation with one-seven H₂O molecules was investigated experimentally and computationally with density functional theory in C₆H₅CN^•+(H₂O)_n clusters. The stepwise binding energies (ΔH_n-1,n^°) were determined by equilibrium measurements for C₆H₅CN^•+(H₂O) and for ^•C₆H₄CNH⁺(H₂O)_n with n = 5, 6, and 7 to be 8.8 and 11.3, 11.0, and 10.0 kcal/mol, respectively. The populations of n = 2 and 3 of the C₆H₅CN^•+(H₂O)_n clusters were observed only in trace abundance due to fast depletion processes leading to the formation of the hydrated distonic cations ^•C₆H₄CNH⁺(H₂O)_n with n = 4-7. The observed transition occurs between conventional radical cations hydrated on the ring in C₆H₅CN^•+(H₂O)_n clusters with n = 1-3 and the protonated radical ^•C₆H₄CNH⁺ (distonic ion) formed by a proton transfer to the CN nitrogen and ionic hydrogen bonding to water molecules in ^•C₆H₄CNH⁺(H₂O)_n clusters with n = 4-7. The measured binding energy of the hydrated ion C₆H₅CN^•+(H₂O) (8.8 kcal/mol) is similar to that of the hydrated benzene radical cation (8.5 kcal/mol) that involves a relatively weak CH^δ+···O hydrogen bonding interaction. Also, the measured binding energies of the ^•C₆H₄CNH⁺(H₂O)_n clusters with n = 5-7 are similar to those of the protonated benzonitrile (methanol)_n clusters [C₆H₅CNH⁺(CH₃OH)_n, n = 5-7] that involve CNH⁺···O ionic hydrogen bonds. The proton shift from the para-^•C ring carbon to the nitrogen of the benzonitrile radical cation is endothermic without solvent but thermoneutral for n = 1 and exothermic for n = 2-4 in C₆H₅CN^•+(H₂O)_n clusters to form the distonic ^•C₆H₄CN···H⁺(OH₂)_n clusters. The distonic clusters ^•C₆H₄CN···H⁺(OH₂)_n constitute a new class of structures in radical ion/solvent clusters.

Vibrational Spectroscopy of Benzonitrile-(Water)1-2 Clusters in Helium Droplets

Polycyclic aromatic hydrocarbons are considered as primary carriers of the unidentified interstellar bands. The recent discovery of the first interstellar aromatic molecule, benzonitrile (C₆H₅CN), suggests a repository of aromatic hydrocarbons in the outer earth environment. Herein, we report an infrared (IR) study of benzonitrile-(D₂O)_n clusters using mass-selective detection in helium nanodroplets. In this work, we use isotopically substituted water, D₂O, instead of H₂O because of our restricted IR frequency range (2565-3100 cm^-1). A comparison of the experimental and predicted spectra computed at the MP2/6-311++G(d,p) level of benzonitrile-(water)_1-2 clusters reveals the formation of a unique local minimum structure, which was not detected in previous gas-phase molecular beam experiments. Here, the solvent water forms a nearly linear hydrogen bond (H-bond) with the nitrile nitrogen of benzonitrile, while the previously reported most stable cyclic H-bonded isomer is not observed. This can be rationalized by the stepwise aggregation process of precooled monomers. The addition of a second water molecule results in the formation of two different isomers. In one of the observed isomers, a H-bonded water chain binds linearly to the nitrile nitrogen similar to the monohydrated benzonitrile-water complex. In the other observed isomer, the water dimer forms a ring-type structure, where a H-bonded water dimer simultaneously interacts with the nitrile nitrogen and the adjacent ortho CH group. Finally, we compare the water-binding motif in the neutral benzonitrile-water complex with the corresponding positively and negatively charged benzonitrile-water monohydrates to comprehend the charge-induced alteration of the solvent binding motif.

Theoretical investigation of protonated thiophene and two of its nitrile substituted derivatives (2-cyanothiophene and 3-cyanothiophene)

Theoretical and experimental spectroscopic data for protonated cyano-thiophenes (R-CNH⁺ with R = C₄H₃S), which are needed for their interstellar search and/or detection, are still lacking in the literature. Considering the high abundance and reactivity of H₃⁺ in the interstellar medium (ISM), a quantum chemical investigation on protonated thiophene and two of its nitrile-substituted derivatives (2-cyanothiophene and 3-cyanothiophene) is undertaken for their characterization. The geometrical structures for the title species are calculated at the M06-2X/6-31G(d,p) level of theory, followed by an empirical correction for systematic errors. At the same level of theory, IR and Raman spectra are explored and the rotational parameters are calculated. The proton affinity (PA) of R-CN and the enthalpy, entropy and Gibbs free energy changes (Δ_rH, Δ_rS and Δ_rG) of the reactions producing R-CNH⁺ are computed at the G2(MP2) and G3B3 levels of theory and at different temperatures. The PA calculations show that the protonation favors the nitrogen atom, while Δ_rH, Δ_rS, and Δ_rG reveal the spontaneous reactions producing R-CNH⁺ and their neutral forms. In addition, quadrupole hyperfine structures are predicted, while the region where the brightest lines fall at different temperatures is discussed. These results are expected to assist astrophysicists and astrochemists in the search for new species in the ISM.

Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine

Pyrimidine (Pym, 1,3-diazine, 1,3-diazabenzene) is an important N-heterocyclic building block of nucleobases. Understanding the structures of its fragment and precursor ions provides insight into its prebiotic and abiotic synthetic route. The long-standing controversial debate about the structures of the primary fragment ions of the Pym+ cation (C4H4N2+, m/z 80) resulting from loss of HCN, C3H3N+ (m/z 53), is closed herein with the aid of a combined approach utilizing infrared photodissociation (IRPD) spectroscopy in the CH and NH stretch ranges (νCH/NH) and density functional theory (DFT) calculations. IRPD spectra of cold Ar/N2-tagged fragment ions reveal that the C3H3N+ population is dominated by cis-/trans-HCCHNCH+ ions (∼90%) along with a minor contribution of the most stable H2CCCNH+ and cis-/trans-HCCHCNH+ isomers (∼10%). We also spectroscopically confirm that the secondary fragment resulting from further loss of HCN, C2H2+ (m/z 26), is the acetylene cation (HCCH+). The spectroscopic characterization of the identified C3H3N+ isomers and their hydrogen-bonded dimers with Ar and N2 provides insight into the acidity of their CH and NH groups. Finally, the vibrational properties of Pym+ in the 3 μm range are probed by IRPD of Pym+-(N2)1-2 clusters, which shows a high π-binding affinity of Pym+ toward a nonpolar hydrophobic ligand. Its νCH spectrum confirms the different acidity of the three nonequivalent CH groups.

Microhydration of protonated biomolecular building blocks: protonated pyrimidine

Protonation and hydration of biomolecules govern their structure, conformation, and function. Herein, we explore the microhydration structure in mass-selected protonated pyrimidine-water clusters (H⁺Pym-W_n, n = 1-4) by a combination of infrared photodissociation spectroscopy (IRPD) between 2450 and 3900 cm^-1 and density functional theory (DFT) calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level. We further present the IR spectrum of H⁺Pym-N₂ to evaluate the effect of solvent polarity on the intrinsic molecular parameters of H⁺Pym. Our combined spectroscopic and computational approach unequivocally shows that protonation of Pym occurs at one of the two equivalent basic ring N atoms and that the ligands in H⁺Pym-L (L = N₂ or W) preferentially form linear H-bonds to the resulting acidic NH group. Successive addition of water ligands results in the formation of a H-bonded solvent network which increasingly weakens the NH group. Despite substantial activation of the N-H bond upon microhydration, no intracluster proton transfer occurs up to n = 4 because of the balance of relative proton affinities of Pym and W_n and the involved solvation energies. Comparison to neutral Pym-W_n clusters reveals the drastic effects of protonation on microhydration with respect to both structure and interaction strength.

Ionization-Induced π → H Site Switching in Resorcinol-Arn (n = 1 and 2) Clusters Probed by Infrared Spectroscopy

Infrared (IR) spectra of resorcinol (Rs)-Ar_n clusters (n = 1 and 2) have been measured in the neutral and cationic ground states (S₀ and D₀) by IR dip and resonance-enhanced multiphoton ionization (REMPI)-IR spectroscopy. The OH stretching vibrations in S₀ keep their frequency regardless of the number of Ar atoms and the conformation of the OH groups in Rs (rotamers RsI and RsII), demonstrating that the Ar atoms are attached to the aromatic π-ring (π-bound structure) in S₀. In the D₀ state, the IR spectra of Rs⁺-Ar_n reflect the difference in the Rs conformations (RsI⁺ and RsII⁺). For n = 1, the IR spectra of both rotamers are almost the same as those of the corresponding monomer cations, indicating that Ar ligands essentially remain π-bonded after ionization. In contrast, the IR spectra of Rs⁺-Ar₂ show hydrogen-bonded and free OH stretching vibrations, demonstrating that for a significant fraction of the clusters, the Ar atoms migrate from the π-bound site to the OH groups. The ionization-induced π → H migration yields are not unity for both rotamers RsI⁺-Ar₂ and RsII⁺-Ar₂. This result is in sharp contrast to phenol⁺-Ar₂, in which one of the Ar atoms migrates to the OH site with 100% yield. The mechanism leading to the nonunity yield in Rs⁺-Ar₂ is discussed in terms of the number of OH binding sites and Franck-Condon factors. The ionization excess energy dependence of the IR spectra of Rs⁺-Ar₂ and its Rs⁺-Ar fragments is discussed in terms of the Ar binding energies estimated from the photoionization and photodissociation efficiency spectra.

Unraveling the protonation site of oxazole and solvation with hydrophobic ligands by infrared photodissociation spectroscopy

Infrared spectroscopy reveals exclusive N-protonation of the oxazole ring and bifurcated or linear hydrogen bonding with hydrophobic N₂and Ar ligands.

Intracluster proton transfer in protonated benzonitrile–(H2O)n≤6 nanoclusters: hydrated hydronium core for n ≥ 2

Infrared spectroscopy and density functional theory calculations of protonated benzonitrile–(H₂O)_n clusters reveal proton transfer to solvent for n ≥ 2 and the drastic effects of the aromatic dopant molecule on the network of H⁺(H₂O)_n+1.