Hydration of the pyrimidine radical cation and stepwise solvation of protonated pyrimidine with water, methanol, and acetonitrile

Gas-Phase External Solvation of Protonated Benzonitrile by Eight Methanol Molecules

The gas-phase sequential association of methanol onto protonated benzonitrile (C₆H₅CNH⁺) and the proton-bound dimer (C₆H₅CN)₂H⁺ have been examined experimentally by equilibrium thermochemical measurements and computationally by density functional theory (DFT). The bonding enthalpy (ΔH°) for the association of methanol with protonated benzonitrile (25.2 kcal mol^-1) reflects the strong electrostatic interaction provided by the formation of an ionic hydrogen bond in the C₆H₅CNH⁺OHCH₃ cluster in excellent agreement with a DFT-calculated binding energy of 24.9 kcal mol^-1. The sequential bonding enthalpy within the (C₆H₅CN)H⁺(OHCH₃)_n clusters decreases from 25.2 to 10.6 kcal mol^-1 for the eighth solvation step (n = 8), which remains more than 25% above the enthalpy of vaporization of liquid methanol (8.4 kcal mol^-1). The nonbulk convergence of ΔH°_n-1,n with eight solvent molecules is attributed to the external solvation of a benzonitrile molecule by an extended hydrogen bonding network of protonated methanol clusters H⁺(CH₃OH)_n. In the external solvation of protonated benzonitrile by methanol, the proton resides on the methanol subcluster and the neutral benzonitrile molecule remains outside and bonded to the surface of the protonated methanol cluster. The bonding enthalpy of methanol to the proton-bound benzonitrile dimer (C₆H₅CN)H⁺(NCC₆H₅) is measured to be 18.0 kcal mol^-1, in good agreement with a DFT-calculated value of 17.1 kcal mol^-1, which reflects the association of the proton with the lower proton affinity methanol molecule, thus forming a highly stable structure of protonated methanol terminated by two ionic hydrogen bonds to the two benzonitrile molecules. The external solvation of benzonitrile by methanol ices in space allows benzonitrile to remain on the ice grain surface rather than being isolated inside the ice. This could provide accessibility for reactions with incoming ions and molecules or for photochemical processes by UV irradiation, leading to the formation of complex organics on the surface of ice grains.

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.

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 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.

Ionic Hydrogen and Halogen Bonding in the Gas Phase Association of Acetonitrile and Acetone with Halogenated Benzene Cations

We report on the gas phase association of the small polar and aprotic solvent molecules acetonitrile (CH₃CN) and acetone (CH₃COCH₃) with the halogenated benzene radical cations (C₆H₅X^•+, X = F, Cl, Br, and I) using the mass-selected ion mobility technique and density functional theory calculations. The association energies (-Δ H°) of CH₃CN (CH₃COCH₃) with C₆H₅F^•+ and C₆H₅I^•+ are similar [13.0 (13.3) and 13.2 (14.1) kcal/mol, respectively] but higher than those of CH₃CN (CH₃COCH₃) with C₆H₅Cl^•+ and C₆H₅Br^•+ [10.5 (11.5) and 10.9 (10.6) kcal/mol, respectively]. However, the electrostatic potentials of the lowest energy structures of C₆H₅Br^•+(CH₃CN) and C₆H₅Br^•+(CH₃COCH₃) or C₆H₅I^•+(CH₃CN) and C₆H₅I^•+(CH₃COCH₃) complexes clearly show the formation of the ionic halogen bonds (IXBs) C-Br^δ+- -NCCH₃ and C-Br^δ+- -OC(CH₃)₂ or C-I^δ+- -NCCH₃ and C-I^δ+- -OC(CH₃)₂ driven by positively charged σ-holes on the external sides of the C-Br and C-I bond axes of the bromobenzene and iodobenzene radical cations, respectively. For the C₆H₅F^•+(CH₃CN) complex, the dominant interaction involves a T-shaped structure between the N atom of CH₃CN and the C atom of the C-F bond of C₆H₅F^•+. The structure of the C₆H₅Cl^•+(CH₃CN) complex shows the formation of unconventional ionic hydrogen bonds (uIHBs) between the N atom of CH₃CN and the C-H bonds of the C₆H₅Cl^•+ cation. Similar results are obtained for the association of acetone with the halogenated benzene radical cations. The formation of IXBs of the iodobenzene cation with acetonitrile or acetone involves a significant entropy loss (-Δ S° = 25-27 cal /(mol K)) resulting from the formation of more ordered and highly directional structures between the nitrogen or oxygen lone pair of electrons of acetonitrile or acetone, respectively, and the electropositive region around the iodine atom of the iodobenzene cation. In comparison, for the association of acetonitrile or acetone with the fluorobenzene, chlorobenzene, and bromobenzene cations, -Δ S° = 16-23 cal/(mol K), consistent with the formation of less ordered structures and loose interactions. The lowest energy structures of the C₆H₅Br^•+(CH₃COCH₃)₂ and C₆H₅I^•+(CH₃COCH₃)₂ clusters show a novel combination of ionic halogen bonding and hydrogen bonding where the oxygen atom of one acetone molecule forms the halogen bond while the oxygen atom of the second acetone molecule becomes the hydrogen acceptor from the methyl group of the first acetone molecule.

Fragment and cluster ions from gaseous and condensed pyridine produced under electron impact

The ion-distribution from condensed pyridine due to 2 keV electron impact shows hydrogenated fragments and clusters with m/z ≤ 320 u and shifts towards higher masses compared to the gas-phase fragmentation. The formation of a bond between the pyridine and a carbenium ion is crucial for the stability of the selected cluster ions.

Gas phase hydration of halogenated benzene cations. Is it hydrogen or halogen bonding?

Halogen bonding (XB) non-covalent interactions can be observed in compounds containing chlorine, bromine, or iodine which can form directed close contacts of the type R1-XY-R2, where the halogen X acts as a Lewis acid and Y can be any electron donor moiety including electron lone pairs on hetero atoms such as O and N, or π electrons in olefin double bonds and aromatic conjugated systems. In this work, we present the first evidence for the formation of ionic halogen bonds (IXBs) in the hydration of bromobenzene and iodobenzene radical cations in the gas phase. We present a combined thermochemical investigation using the mass-selected ion mobility (MSIM) technique and density functional theory (DFT) calculations of the stepwise hydration of the fluoro, chloro, bromo, and iodobenzene radical cations. The binding energy associated with the formation of an IXB in the hydration of the iodobenzene cation (11.2 kcal mol^-1) is about 20% higher than the typical unconventional ionic hydrogen bond (IHB) of the CH^δ+OH₂ interaction. The formation of an IXB in the hydration of the iodobenzene cation involves a significant entropy loss (29 cal mol^-1 K^-1) resulting from the formation of a more ordered structure and a highly directional interaction between the oxygen lone pair of electrons of water and the electropositive region around the iodine atom of the iodobenzene cation. In comparison, the hydration of the fluorobenzene and chlorobenzene cations where IHBs are formed, -ΔS° = 18-21 cal mol^-1 K^-1 consistent with the formation of less ordered structures and loose interactions. The electrostatic potentials on the lowest energy structures of the hydrated halogenated benzene radical cations show clearly that the formation of an IXB is driven by a positively charged σ-hole on the external side of the halogen atom X along the C-X bond axis. The size of the σ-hole increases significantly in bromobenzene and iodobenzene radical cations which results in strong interaction potentials with the electron lone pairs of the oxygen atom of the water molecules and thus IXBs provide the most stable hydrated structures of the bromobenzene and iodobenzene radical cations. The results clearly distinguish the hydration behaviors resulting from the ionic hydrogen and halogen bonding interactions of fluorobenzene and iodobenzene cations, respectively, and establish the different bonding and structural features of the two interactions.

Unconventional CH(δ+)···N hydrogen bonding interactions in the stepwise solvation of the naphthalene radical cation by hydrogen cyanide and acetonitrile molecules

Equilibrium thermochemical measurements using the mass-selected ion mobility (MSIM) technique have been utilized to investigate the binding energies and entropy changes of the stepwise association of hydrogen cyanide (HCN) and acetonitrile (CH3CN) molecules with the naphthalene radical cation (C10H8˙(+)) in the gas phase forming the C10H8˙(+)(HCN)n and C10H8˙(+)(CH3CN)n clusters with n = 1-3 and 1-5, respectively. The lowest energy structures of the C10H8˙(+)(HCN)n and C10H8˙(+)(CH3CN)n clusters for n = 1-2 have been calculated using the M062X and ω97XD methods within the 6-311+G** basis set, and for n = 1-6 using the B3LYP method within the 6-311++G** basis set. In both systems, the initial interaction occurs through unconventional CH(δ+)···N ionic hydrogen bonds between the hydrogen atoms of the naphthalene cation and the lone pair of electrons on the N atom of the HCN or the CH3CN molecule. The binding energy of CH3CN to the naphthalene cation (11 kcal mol(-1)) is larger than that of HCN (7 kcal mol(-1)) due to a stronger ion-dipole interaction resulting from the large dipole moment of CH3CN (3.9 D). On the other hand, HCN can form both unconventional hydrogen bonds with the hydrogen atoms of the naphthalene cation (CH(δ+)···NCH), and conventional linear hydrogen bonding chains involving HCN···HCN interactions among the associated HCN molecules. HCN molecules tend to form "externally solvated" structures with the naphthalene cation where the naphthalene ion is hydrogen bonded to the exterior of an HCN···HCN chain. For the C10H8˙(+)(CH3CN)n clusters, "internally solvated" structures are favored where the acetonitrile molecules are directly interacting with the naphthalene cation through CH(δ+)···N unconventional ionic hydrogen bonds. In both the C10H8˙(+)(HCN)n and C10H8˙(+)(CH3CN)n clusters, the sequential binding energy decreases stepwise to about 6-7 kcal mol(-1) by three HCN or CH3CN molecules, approaching the macroscopic enthalpy of vaporization of liquid HCN (6.0 kcal mol(-1)).

Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport

Results from condensed phase ab initio molecular dynamics (AIMD) simulations suggest a proton transfer reaction is facilitated by "presolvation" in which the hydronium is transiently solvated by four water molecules, similar to the typical solvation structure of water, by accepting a weak hydrogen bond from the fourth water molecule. A new version 3.2 multistate empirical valence bond (MS-EVB 3.2) model for the hydrated excess proton incorporating this presolvation behavior is therefore developed. The classical MS-EVB simulations show similar structural properties as those of the previous model but with significantly improved diffusive behavior. The inclusion of nuclear quantum effects in the MS-EVB also provides an even better description of the proton diffusion rate. To quantify the influence of anharmonicity, a second model (aMS-EVB 3.2) is developed using the anharmonic aSPC/Fw water model, which provides similar structural properties but improved spectroscopic responses at high frequencies.