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

Protonation and hydration of aromatic hydrocarbon molecules and their derivatives play a key role in many biological and chemical processes. The recent detection of benzonitrile (BN, cyanobenzene, C6H5CN) in the interstellar medium suggests the existence of its protonated form (H+BN) in both the gas phase and in or on ice grains. Herein, we analyze the vibrational signatures of size-selected protonated clusters composed of BN and water (W, H2O), H+(BN–Wn=1–6), in the XH stretch range (X = C, N, O) with the aid of dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). The size-dependent frequency shifts provide detailed insight about the site of protonation and the structure of the hydration shell. For n = 1, the proton is attached to the N atom of the CN group in BN, and W acts as a proton acceptor in an NH⋯O ionic hydrogen bond (H-bond) of a H+BN–W type structure with cation–dipole configuration. For n ≥ 2, the proton is transferred to the H-bonded hydration network, consistent with thermochemical arguments arising from both the relative proton affinities of BN and Wn and the solvation energies. In these proton-transferred BN–H+Wn structures, the excess proton is more or less localized at a H3O+ hydronium core solvated by neutral W and BN ligands. At least for the considered cluster size (n ≤ 6), the BN impurity molecule is located in the first solvation shell of the H3O+ ion, consistent with the larger electric dipole moment and proton affinity of BN as compared to W. However, the energy gap between these structures and surface isomers with BN solvated further away from the charge decreases with cluster size, suggesting that BN is located at the surface in large BN–H+Wn clusters. While for smaller clusters (n ≤ 4) the hydration network prefers branched structures at T = 0 K, in larger clusters (n ≥ 5) cyclic configurations with four- or five-membered H+Wn rings are most stable because they feature more H-bonds than the branched structures. Comparison with bare H+Wn clusters reveals the substantial effects of the perturbation by the BN impurity on the structure of the hydration network.TU Berlin, Open-Access-Mittel - 201

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.TU Berlin, Open-Access-Mittel - 202

Microhydration of protonated 5-hydroxyindole revealed by infrared spectroscopy

Controlled microsolvation of protonated aromatic biomolecules with water is fundamental to understand proton transfer reactions in aqueous environments. We measured infrared photodissociation (IRPD) spectra of mass-selected microhydrates of protonated 5-hydroxyindole (5HIH+–Wn, W = H2O, n = 1–3) in the OH and NH stretch ranges (2700–3800 cm−1), which are sensitive to the spectroscopic characteristics of interior solvation, water network formation, and proton transfer to solvent. Analysis of the IRPD spectra by dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ) reveals the coexistence of C3- and C4-protonated carbenium ions, 5HIH+(C3) and 5HIH+(C4), as well as the O-protonated oxonium ion, 5HIH+(O). Monohydrated 5HIH+–W2/3 clusters are formed by hydrogen-bonding (H-bonding) of the first water to the most acidic functional group, namely, the NH group in the case of 5HIH+(C3), the OH group for 5HIH+(C4), and the OH2 group for 5HIH+(O). The latter benefits from its twofold degeneracy and the outstandingly high binding energy of D0 ∼ 100 kJ mol−1. Larger 5HIH+–W2/3 clusters preferably grow (i) by H-bonding of the second water to the remaining vacant functional group and and/or (ii) by formation of W2 water chains at the respective most acidic functional group. Our IRPD spectra of 5HIH+–Wn do not indicate any proton transfer to the solvent up to n = 3, in line with the proton affinities of 5HI and Wn. Comparison of 5HIH+–Wn to neutral 5HI–W and cationic 5HI+–Wn clusters elucidates the impact of different charge states on the topology of the initial solvation shell. Furthermore, to access the influence of the size of the arene ion and a second functional group, we draw a comparison to microhydration of protonated phenol.TU Berlin, Open-Access-Mittel - 201

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

Protonation and solvation of heterocyclic aromatic building blocks control the structure and function of many biological macromolecules. Herein the infrared photodissociation (IRPD) spectra of protonated oxazole (H+Ox) microsolvated by nonpolar and quadrupolar ligands, H+Ox-Ln with L = Ar (n = 1–2) and L = N2 (n = 1–4), are analyzed by density functional theory calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level to determine the preferred protonation and ligand binding sites. Cold H+Ox-Ln clusters are generated in an electron impact cluster ion source. Protonation of Ox occurs exclusively at the N atom of the heterocyclic ring, in agreement with the thermochemical predictions. The analysis of the systematic shifts of the NH stretch frequency in the IRPD spectra of H+Ox-Ln provides a clear picture of the sequential cluster growth and the type and strength of various competing ligand binding motifs. The most stable structures observed for the H+Ox-L dimers (n = 1) exhibit a linear NH⋯L hydrogen bond (H-bond), while π-bonded isomers with L attached to the aromatic ring are local minima on the potential and thus occur at a lower abundance. From the spectra of the H+Ox-L(π) isomers, the free NH frequency of bare H+Ox is extrapolated as νNH = 3444 ± 3 cm−1. The observed H+Ox-L2 clusters with L = N2 feature both bifurcated NH⋯L2 (2H isomer) and linear NH⋯L H-bonding motifs (H/π isomer), while for L = Ar only the linear H-bond is observed. No H+Ox-L2(2π) isomers are detected, confirming that H-bonding to the NH group is more stable than π-bonding to the ring. The most stable H+Ox-(N2)n clusters with n = 3–4 have 2H/(n − 2)π structures, in which the stable 2H core ion is further solvated by (n − 2) π-bonded ligands. Upon N-protonation, the aromatic C–H bonds of the Ox ring get slightly stronger, as revealed by higher CH stretch frequencies and strongly increased IR intensities.TU Berlin, Open-Access-Mittel - 201

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–Wn, 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 Wn and the involved solvation energies. Comparison to neutral Pym–Wn clusters reveals the drastic effects of protonation on microhydration with respect to both structure and interaction strength.TU Berlin, Open-Access-Mittel - 202

Vibronic optical spectroscopy of cryogenic flavin ions: the O2+ and N1 tautomers of protonated lumiflavin

Flavins are key compounds in many photochemical and photophysical processes used by nature, because their optical properties strongly depend on the (de-)protonation site and solvation. Herein, we present the vibronic optical spectrum of protonated lumiflavin (H+LF), the parent molecule of the flavin family, obtained by visible photodissociation (VISPD) spectroscopy in a cryogenic ion trap. By comparison to time-dependent density functional theory (TD-DFT) calculations at the PBE0/cc-pVDZ level coupled to multidimensional Franck–Condon simulations, the spectrum recorded in the 420–500 nm range is assigned to vibronic bands of the optically bright S1 ← S0(ππ*) transition of the two most stable H+LF tautomers protonated at the O2+ and N1 position. While the most stable O2+ protomer has been identified previously by infrared spectroscopy, the N1 protomer is identified here for the first time. The S1 band origins of H+LF(O2+) and H+LF(N1) at 23 128 and 23 202 cm−1 are shifted by 1617 and 1691 cm−1 to the blue of that of bare LF measured in He droplets, indicating that the proton affinity of both tautomers is slightly reduced upon S1 excitation. This view is consistent with the molecular orbitals involved in the assigned ππ* transition. The spectrum of both protomers is rich in vibrational structure indicating substantial geometry changes by ππ* excitation. Interestingly, while the O2+ protomer is planar in both electronic states, the N1 protomer is slightly nonplanar giving rise to large vibrational activity of low-frequency out-of-plane modes. Comparison with protonated lumichrome and metalated lumiflavin reveals the impact of functional groups and the type of the attached cation (proton or alkali ion) on the geometric and electronic structure of flavins.TU Berlin, Open-Access-Mittel - 202

Structures and IR/UV spectra of neutral and ionic phenol-Ar-n cluster isomers (n <= 4): competition between hydrogen bonding and stacking

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.The structures, binding energies, and vibrational and electronic spectra of various isomers of neutral and ionic phenol–Arnclusters with n ≤ 4, PhOH(+)–Arn, are characterized by quantum chemical calculations. The properties in the neutral and ionic ground electronic states (S0, D0) are determined at the M06-2X/aug-cc-pVTZ level, whereas the S1 excited state of the neutral species is investigated at the CC2/aug-cc-pVDZ level. The Ar complexation shifts calculated for the S1 origin and the adiabatic ionisation potential, ΔS1 and ΔIP, sensitively depend on the Ar positions and thus the sequence of filling the first Ar solvation shell. The calculated shifts confirm empirical additivity rules for ΔS1 established recently from experimental spectra and enable thus a firm assignment of various S1 origins to their respective isomers. A similar additivity model is newly developed for ΔIP using the M06-2X data. The isomer assignment is further confirmed by Franck–Condon simulations of the intermolecular vibrational structure of the S1 ← S0 transitions. In neutral PhOH–Arn, dispersion dominates the attraction and π-bonding is more stable than H-bonding. The solvation sequence of the most stable isomers is derived as (10), (11), (30), and (31) for n ≤ 4, where (km) denotes isomers with k and m Ar ligands binding above and below the aromatic plane, respectively. The π interaction is somewhat stronger in the S1 state due to enhanced dispersion forces. Similarly, the H-bond strength increases in S1 due to the enhanced acidity of the OH proton. In the PhOH+–Arn cations, H-bonds are significantly stronger than π-bonds due to additional induction forces. Consequently, one favourable solvation sequence is derived as (H00), (H10), (H20), and (H30) for n ≤ 4, where (Hkm) denotes isomers with one H-bound ligand and k and m π-bonded Ar ligands above and below the aromatic plane, respectively. Another low-energy solvation motif for n = 2 is denoted (11)H and involves nonlinear bifurcated H-bonding to both equivalent Ar atoms in a C2v structure in which the OH group points toward the midpoint of an Ar2 dimer in a T-shaped fashion. This dimer core can also be further solvated by π-bonded ligands leading to the solvation sequence (H00), (11)H, (21)H, and (22) for n ≤ 4. The implications of the ionisation-induced π → H switch in the preferred interaction motif on the isomerisation and fragmentation processes of PhOH(+)–Arn are discussed in the light of the new structural and energetic cluster parameters

Microhydration Structures of Protonated Oxazole

The initial microhydration structures of the protonated pharmaceutical building block oxazole (Ox), H+Ox-Wn≤4, are determined by infrared photodissociation (IRPD) spectroscopy combined with quantum chemical dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). Protonation of Ox, achieved by chemical ionization in a H2-containing plasma, occurs at the most basic N atom. The analysis of systematic shifts of the NH and OH stretch vibrations as a function of the cluster size provides a clear picture for the preferred cluster growth in H+Ox-Wn. For n = 1–3, the IRPD spectra are dominated by a single isomer, and microhydration of H+Ox with hydrophilic protic W ligands occurs by attachment of a hydrogen-bonded (H-bonded) Wn solvent cluster to the acidic NH group via an NH···O H-bond. Such H-bonded networks are stabilized by strong cooperativity effects. This is in contrast to previously studied hydrophobic ligands, which prefer interior ion solvation. The strength of the NH···O ionic H-bond increases with the degree of hydration because of the increasing proton affinity (PA) of the Wn cluster. At n = 4, proton-transferred structures of the type Ox-H+Wn become energetically competitive with H+Ox-Wn structures, because differences in solvation energies can compensate for the differences in the PAs, and barrierless proton transfer from H+Ox to the Wn solvent subcluster becomes feasible. Indeed, the IRPD spectrum of the n = 4 cluster is more complex suggesting the presence of more than one isomer, although it lacks unequivocal evidence for the predicted intracluster proton transfer

Effect of alkali ions on optical properties of flavins: vibronic spectra of cryogenic M+lumiflavin complexes (M = Li–Cs)

Flavin compounds are frequently used by nature in photochemical processes because of their unique optical properties which can be strongly modulated by the surrounding environment such as solvation or coordination with metal ions. Herein, we employ vibronic photodissociation spectroscopy of cryogenic M+LF complexes composed of lumiflavin (LF, C13H12N4O2), the parent molecule of the flavin family, and alkali ions (M = Li–Cs) to characterize the strong impact of metalation on the electronic properties of the LF chromophore. With the aid of time-dependent density functional theory calculations (PBE0/cc-pVDZ) coupled to multidimensional Franck–Condon simulations, the visible photodissociation (VISPD) spectra of M+LF ions recorded in the 500–570 nm range are assigned to the S1 ← S0 (ππ*) transitions into the first optically bright S1 state of the lowest-energy M+LF(O4+) isomers. In this O4+ structure, M+ binds in a bent chelate to the lone pairs of both the O4 and the N5 atom of LF. Charge reorganization induced by S1 excitation strongly enhances the interaction between M+ and LF at this binding site, leading to substantial red shifts in the S1 absorption of the order of 10–20% (e.g., from 465 nm in LF to 567 nm in Li+LF). This strong change in M+⋯LF interaction strength in M+LF(O4+) upon ππ* excitation can be rationalized by the orbitals involved in the S1 ← S0 transition and causes strong vibrational activity. In particular, progressions in the intermolecular bending and stretching modes provide an accurate measure of the strength of the M+⋯LF bond. In contrast to the experimentally identified O4+ ions, the predicted S1 origins of other low-energy M+LF isomers, O2+ and O2, are slightly blue-shifted from the S1 of LF, demonstrating that the electronic properties of metalated LF not only drastically change with the size of the metal ion but also with its binding site.TU Berlin, Open-Access-Mittel - 201

Photoionization-induced pi <-> H site switching dynamics in phenol(+)-Rg (Rg = Ar, Kr) dimers probed by picosecond time-resolved infrared spectroscopy

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.The ionization-induced pi H site switching reaction in phenol(+)-Rg (PhOH+-Rg) dimers with Rg = Ar and Kr is traced in real time by picosecond time-resolved infrared (ps-TRIR) spectroscopy. The ps-TRIR spectra show the prompt appearance of the non-vanishing free OH stretching band upon resonant photoionization of the pi-bound neutral clusters, and the delayed appearance of the hydrogen-bonded (H-bonded) OH stretching band. This result directly proves that the Rg ligand switches from the pi-bound site on the aromatic ring to the H-bonded site at the OH group by ionization. The subsequent H pi back reaction converges the dimer to a pi H equilibrium. This result is in sharp contrast to the single-step pi H forward reaction in the PhOH+-Ar-2 trimer with 100% yield. The reaction mechanism and yield strongly depend on intracluster vibrational energy redistribution. A classical rate equation analysis for the time evolutions of the band intensities of the two vibrations results in similar estimates for the time constants of the pi H forward reaction of tau(+) = 122 and 73 ps and the H pi back reaction of tau_ = 155 and 188 ps for PhOH+-Ar and PhOH+-Kr, respectively. The one order of magnitude slower time constant in comparison to the PhOH+-Ar-2 trimer (tau(+) = 7 ps) is attributed to the decrease in density of states due to the absence of the second Ar in the dimer. The similar time constants for both PhOH+-Rg dimers are well rationalized by a classical interpretation based on the comparable potential energy surfaces, reaction pathways, and density of states arising from their similar intermolecular vibrational frequencies