Nucleophilic Aromatic Addition in Ionizing Environments: Observation and Analysis of New C–N Valence Bonds in Complexes between Naphthalene Radical Cation and Pyridine

Formation of complex organics by covalent and non-covalent interactions of the sequential reactions of 1-4 acrylonitrile molecules with the benzonitrile radical cation

Benzonitrile molecules are present in ionizing environments including interstellar clouds and solar nebulae, where their ions can form adducts with neutral molecules such as acrylonitrile leading to the formation of a variety of nitrogen-containing complex organics. Herein, we report on the formation of complex organics by the sequential reactions of 1-4 acrylonitrile (C3NH3) molecules with the benzonitrile radical cation (C7NH5+˙). The results reveal the formation of the covalently bonded N-acrylonitrile-benzonitrile radical cation (C10N2H8+˙) with a rate coefficient of 2.2 (±0.4) × 10-11 cm3 s-1 at 423 K and a calculated collision cross-section of 73.8 Å2 in good agreement with the measured cross-section of 70.7 Å2 of the C10N2H8+˙ adduct. Subsequent reversible association of 1-3 acrylonitrile molecules with the N-acrylonitrile-benzonitrile radical cation (C10N2H8+˙) at lower temperatures (250-200 K) results in the formation of the N-rich clusters (C10N2H8+˙)(C3NH3)1-3 which can be enhanced in the very cold cores of the interstellar medium (ISM) and could offer unique potential candidates for the substantial amount of nitrogen carriers detected in the emission spectra of the ISM. The observed N-acrylonitrile-benzonitrile covalent adduct and its associated acrylonitrile clusters could have significant implications in the formation of different types of complex organics in different regions of outer space. It is anticipated that the current results would have direct implications in the search for nitrogen-containing complex organics in space.

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.

Internal Energy Dependence of the Pyrrole Dimer Cation Structures Formed in a Supersonic Plasma Expansion: Charge-Resonance and Hydrogen-Bonded Isomers

The structures of the pyrrole dimer cation (Py2+) formed in an electron-ionization-driven supersonic plasma expansion of Py seeded in Ar or N2 are probed as a function of its internal energy by infrared photodissociation (IRPD) spectroscopy in a tandem mass spectrometer. The IRPD spectra recorded in the CH and NH stretch ranges are analyzed by dispersion-corrected density functional theory (DFT) calculations at the B3LYP-D3/aug-cc-pVTZ level. The spectra of the cold Ar/N2-tagged Py2+ clusters, Py2+Ln (n = 1-5 for Ar, n = 1 for N2), indicate the exclusive formation of the most stable antiparallel π-stacked Py2+ structure under cold conditions, which is stabilized by charge-resonance interaction. The bare Py2+ dimers produced in the ion source have higher internal energy, and the observation of additional transitions in their IRPD spectra suggests a minor population of less stable hydrogen-bonded isomers composed of heterocyclic Py/Py+ structures formed after intramolecular H atom transfer and ring opening. These intermolecular isomers differ from the chemically bonded structures proposed earlier in the analysis of IRPD spectra of Py2+ generated by VUV ionization of neutral Pyn clusters.

Cu/Biochar Bifunctional Catalytic Removal of COS and H2S:H2O Dissociation and CuO Anchoring Enhanced by Pyridine N

Economic and environmentally friendly strategies are needed to promote the bifunctional catalytic removal of carbonyl sulfide (COS) by hydrolysis and hydrogen sulfide (H2S) by oxidation. N doping is considered to be an effective strategy, but the essential and intrinsic role of N dopants in catalysts is still not well understood. Herein, the conjugation of urea and biochar during Cu/biochar annealing produced pyridine N, which increased the combined COS/H2S capacity of the catalyst from 260.7 to 374.8 mg·g-1 and enhanced the turnover frequency of H2S from 2.50 × 10-4 to 5.35 × 10-4 s-1. The nucleophilic nature of pyridine N enhances the moderate basic sites of the catalyst, enabling the attack of protons and strong H2O dissociation. Moreover, pyridine N also forms cavity sites that anchor CuO, improving Cu dispersion and generating more reactive oxygen species. By providing original insight into the pyridine N-induced bifunctional catalytic removal of COS/H2S in a slightly oxygenated and humid atmosphere, this study offers valuable guidance for further C═S and C-S bond-breaking in the degradation of sulfur-containing pollutants.

The Effect of Cluster Size on the Intra-Cluster Ionic Polymerization Process

Polyaromatic hydrocarbons (PAHs) are widespread in the interstellar medium (ISM). The abundance and relevance of PAHs call for a clear understanding of their formation mechanisms, which, to date, have not been completely deciphered. Of particular interest is the formation of benzene, the basic building block of PAHs. It has been shown that the ionization of neutral clusters can lead to an intra-cluster ionic polymerization process that results in molecular growth. Ab-initio molecular dynamics (AIMD) studies in clusters consisting of 3-6 units of acetylene modeling ionization events under ISM conditions have shown maximum aggregation of three acetylene molecules forming bonded C₆H₆⁺ species; the larger the number of acetylene molecules, the higher the production of C₆H₆⁺. These results lead to the question of whether clusters larger than those studied thus far promote aggregation beyond three acetylene units and whether larger clusters can result in higher C₆H₆⁺ production. In this study, we report results from AIMD simulations modeling the ionization of 10 and 20 acetylene clusters. The simulations show aggregation of up to four acetylene units producing bonded C₈H₈⁺. Interestingly, C₈H₈⁺ bicyclic species were identified, setting a precedent for their astrochemical identification. Comparable reactivity rates were shown with 10 and 20 acetylene clusters.

Vacuum Ultraviolet Photoionization Induced Proton Migration and Formation of a New C-N Bond in Pyridine Clusters Revealed by Infrared Spectroscopy and Mass Spectrometry

The structures and reactions of pyridine (Pyd) cluster cations in a supersonic molecular beam generated upon photoionization at 9.2-9.4 eV were investigated by infrared (IR) action spectroscopy. The mass spectrum showed prominent peaks of (Pyd)_m⁺ and H⁺(Pyd)_m, m = 1-5. In the pyridine/pyridine-d₅ mixture, the mass pattern indicated that H⁺ and D⁺ migrated during the formation and dissociation of the cluster cations. The IR photodissociation spectra of both (Pyd)₂⁺ and H⁺(Pyd)₂ revealed a N-H stretching band near 3400 cm^-1, indicating that their structures are 1-(2-pyridyl)pyridin-1-ium and pyridinium-pyridine, respectively. Observation of the former product implies that the reaction proceeds via an α-distonic cation intermediate, while the latter product is formed via proton migration. The IR spectra of (Pyd)_m⁺ and H⁺(Pyd)_m, m ≥ 3, suggested that these clusters consist of a covalently bound (Pyd)₂⁺ or H⁺(Pyd)₂ core, respectively, with additional pyridines attached to them via hydrogen bonds and/or weak dispersive interactions.

Spectroscopic evidence of the C-N covalent bond formed between two interstellar molecules (ISM): acrylonitrile and ammonia

Acrylonitrile (AN) and ammonia (NH3) are two important nitrogen-containing interstellar molecules in outer space, especially on Titan. Herein, we measured infrared (IR) spectra of neutral and cationic AN-NH3 complexes by VUV single-photon ionization combined with time-of-flight mass spectrometry. On combining IR spectra with the theoretical calculations, we found that the molecules prefer to form a single-ring cyclic H-bonded structure in the neutral AN-NH3 and (AN)2-NH3 clusters. However, after ionization of AN-NH3 and (AN)2-NH3 clusters, a new C-N-covalent bond is confirmed to form directly between AN and NH3, without any energy barrier in the cationic complexes. Moreover, in the ionized (AN)2-NH3 cluster, the covalent C-N bond prefers to form between AN and NH3 rather than the two AN groups. These results provide spectroscopic evidence of AN forming a new molecule with NH3, induced by VUV radiation. The formation of the new C-N bond broadens our knowledge on the evolution of the prebiotic nitrogen-containing molecules in space.

From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis

Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N₂, and BF bound to a [Ru(II)(NH₃)₅]^{2 +} moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential.

Probing radical-molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals

Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical-molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical-molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A "polarize-then-depolarize" (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. These radical extensions are incorporated into the "vertical" and "adiabatic" variants of uALMO-EDA for studies of energy changes and property shifts upon complexation. The EDA is validated on two model complexes, H₂O˙F and FH˙OH. It is then applied to several chemically interesting radical-molecule complexes, including the sandwiched and T-shaped benzene dimer radical cation, complexes of pyridine with benzene and naphthalene radical cations, binary and ternary complexes of the hydroxyl radical with water (˙OH(H₂O) and ˙OH(H₂O)₂), and the pre-reactive complexes and transition states in the ˙OH + HCHO and ˙OH + CH₃CHO reactions. These examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical-molecule interactions.

On the Computational Characterization of Charge-Transfer Effects in Noncovalently Bound Molecular Complexes

Charge-transfer (CT) is an important binding force in the formation of intermolecular complexes, and there have been a variety of theoretical models proposed to quantify this effect. These approaches, which typically rely on a definition of a "CT-free" state based on a partition of the system, sometimes yield significantly different results for a given intermolecular complex. Two widely used definitions of the "CT-free" state, the absolutely localized molecular orbitals (ALMO) method (where only on-fragment orbital mixings are permitted) and the constrained density functional theory (CDFT) approach (where fragment electron populations are fixed), are carefully examined in this work. Natural bond orbital (NBO) and the regularized symmetry-adapted perturbation theory (SAPT) are also briefly considered. Results for the ALMO and CDFT definitions of CT are compared on a broad range of model systems, including hydrogen-bonding systems, borane complexes, metal-carbonyl complexes, and complexes formed by water and metal cations. For most of these systems, CDFT yields a much smaller equilibrium CT energy compared to that given by the ALMO-based definition. This is mainly because the CDFT population constraint does not fully inhibit CT, which means that the CDFT "CT-free" state is in fact CT-contaminated. Examples of this contamination include (i) matching forward and backward donation (e.g., formic acid dimer) and (ii) unidirectional CT without changing fragment populations. The magnitude of the latter effect is quantified in systems such as the water dimer by employing a 3-space density constraint in addition to the orbital constraint. Furthermore, by means of the adiabatic EDA, it is shown that several observable effects of CT, such as the "pyramidalization" of the planar BH₃ molecule upon the complexation with Lewis bases, already appear on the "CT-free" CDFT surface. These results reveal the essential distinctions between the ALMO and CDFT definitions of CT and suggest that the former is more consistent with accepted understanding of the role of CT in intermolecular binding.