Infrared Laser Spectroscopy of Imidazole Complexes in Helium Nanodroplets: Monomer, Dimer, and Binary Water Complexes

Two-Sided Impact of Water on the Relaxation of Inner-Valence Vacancies of Biologically Relevant Molecules

After ionization of an inner-valence electron of molecules, the resulting cation-radicals store substantial internal energy which, if sufficient, can trigger ejection of an additional electron in an Auger decay usually followed by molecule fragmentation. In the environment, intermolecular Coulombic decay (ICD) and electron-transfer mediated decay (ETMD) are also operative, resulting in one or two electrons being ejected from a neighbor, thus preventing the fragmentation of the initially ionized molecule. These relaxation processes are investigated theoretically for prototypical heterocycle-water complexes of imidazole, pyrrole, and pyridine. It is found that the hydrogen-bonding site of the water molecule critically influences the nature and energetics of the electronic states involved, opening or closing certain relaxation processes of the inner-valence ionized system. Our results indicate that the relaxation mechanisms of biologically relevant systems with inner-valence vacancies on their carbon atoms can strongly depend on the presence of the electron-density donating or accepting neighbor, either water or another biomolecule.

Structures of the (Imidazole)nH+ ... Ar (n=1,2,3) complexes determined from IR spectroscopy and quantum chemical calculations

Here, we present new cryogenic infrared spectra of the (Imidazole)$$_{n}\mathrm{H}^{+}$$ n H + (n=1,2,3) ions. The data was obtained using helium tagging infrared predissociation spectroscopy. The new results were compared with the data obtained by Gerardi et al. (Chem. Phys. Lett. 501:172–178, 2011) using the same technique but with argon as a tag. Comparison of the two experiments, assisted by theoretical calculations, allowed us to evaluate the preferable attachment positions of argon to the (Imidazole)$$_{n}\mathrm{H}^{+}$$ n H + frame. Argon attaches to nitrogen-bonded hydrogen in the case of the (Imidazole)H$$^+$$ + ion, while in (Imidazole)$$_{2}\mathrm{H}^{+}$$ 2 H + and (Imidazole)$$_{3}\mathrm{H}^{+}$$ 3 H + the preferred docking sites for the argon are in the center of the complex. This conclusion is supported by analyzing the spectral features attributed to the N–H stretching vibrations. Symmetry adapted perturbation theory (SAPT) analysis of the non-covalent forces between argon and the (Imidazole)$$_{n}\mathrm{H}^{+}$$ n H + (n=1,2,3) frame revealed that this switch of docking preference with increasing complex size is caused by an interplay between induction and dispersion interactions.

How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer

The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.

Setting up the HyDRA blind challenge for the microhydration of organic molecules

The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates...

A New Solid-State Proton Conductor: The Salt Hydrate Based on Imidazolium and 12-Tungstophosphate

We report the structure and charge transport properties of a novel solid-state proton conductor obtained by acid–base chemistry via proton transfer from 12-tungstophosphoric acid to imidazole. The resulting material (henceforth named Imid₃WP) is a solid salt hydrate that, at room temperature, includes four water molecules per structural unit. To our knowledge, this is the first attempt to tune the properties of a heteropolyacid-based solid-state proton conductor by means of a mixture of water and imidazole, interpolating between water-based and ionic liquid-based proton conductors of high thermal and electrochemical stability. The proton conductivity of Imid₃WP·4H₂O measured at truly anhydrous conditions reads 0.8 × 10^–6 S cm^–1 at 322 K, which is higher than the conductivity reported for any other related salt hydrate, despite the lower hydration. In the pseudoanhydrous state, that is, for Imid₃WP·2H₂O, the proton conductivity is still remarkable and, judging from the low activation energy (E_a = 0.26 eV), attributed to structural diffusion of protons. From complementary X-ray diffraction data, vibrational spectroscopy, and solid-state NMR experiments, the local structure of this salt hydrate was resolved, with imidazolium cations preferably orienting flat on the surface of the tungstophosphate anions, thus achieving a densely packed solid material, and water molecules of hydration that establish extremely strong hydrogen bonds. Computational results confirm these structural details and also evidence that the path of lowest energy for the proton transfer involves primarily imidazole and water molecules, while the proximate Keggin anion contributes with reducing the energy barrier for this particular pathway.

Characterization and Photofragmentation Studies of the Benzimidazole Homodimer: Evidence for Excited-State Charge-Coupled Proton Transfer

The spectroscopic characterization of the benzimidazole (BIM) homodimer was carried out in a molecular beam in the ground state as well as in the cationic state using the R2PI and RIDIR methods. Primarily, interest in the dimer was due to the observation of a proton-transferred BIM fragment at energies well below its thermodynamic threshold (i.e., barely above the ionization energy of the dimer where fragmentation was not expected). The detailed photofragmentation studies of the homodimer combined with spectroscopic observations and quantum chemical computations of the excited states established that the proton transfer from one subunit to the other occurs via conical intersections connecting the locally excited state, the charge-transfer state, and the ground state. In this study, we have also determined the N-H···N hydrogen bond dissociation energy in the ground state and in the cationic state to be 10.36 ± 0.14 and 27.55 ± 0.20 kcal mol^-1, respectively. Incidentally, this happens to be the first such report on the dissociation energy of the N-H···N hydrogen bond.

Bifunctional Hydrogen Bonding of Imidazole with Water Explored by Rotational Spectroscopy and DFT Calculations

Laser vaporization of imidazole in the presence of an argon buffer gas has allowed the generation and isolation of two isomers of an imidazole monohydrate complex, denoted herein as imid···H₂O and H₂O···imid, within a gas sample undergoing supersonic expansion. Imidazole and water are respectively proton-accepting and proton-donating in imid···H₂O, but these roles are reversed in the H₂O···imid complex. Both isomers have been characterized by chirped-pulse Fourier transform microwave spectroscopy between 7.0 and 18.5 GHz. The ground-state rotational spectra of four isotopologues of imid···H₂O and three isotopologues of H₂O···imid have been measured. All spectra have been assigned and fitted to determine rotational (A₀, B₀, C₀), centrifugal distortion (D_J, D_JK), and nuclear quadrupole coupling constants (χ_aa(N1), [χ_bb(N1) - χ_cc(N1)], χ_aa(N3), and [χ_bb(N3) - χ_cc(N3)]). Structural parameters (r₀ and r_s) have been accurately determined from measured rotational constants for each isomer. The imid···H₂O complex contains a nonlinear hydrogen bond (∠(O-H_b···N3) = 172.1(26)° in the experimentally determined, r₀ geometry) between the pyridinic nitrogen of imidazole and a hydrogen atom of H₂O. The DFT calculations find that the H₂O···imid complex also contains a nonlinear hydrogen bond between the oxygen atom of water and the hydrogen attached to the pyrrolic nitrogen of imidazole (∠(O···H1-N1) = 174.7°). Two states observed in the spectrum of H₂O···imid, assigned as 0^- and 0⁺ states, confirm that large amplitude motions occur on the time scale of the molecular rotation. Density functional theory has been performed to characterize these large amplitude motions.

Direct detection of polar structure formation in helium nanodroplets by beam deflection measurements

Long-range intermolecular forces are able to steer polar molecules submerged in superfluid helium nanodroplets into highly polar metastable configurations. We demonstrate that the presence of such special structures can be identified, in a direct and determinative way, by electrostatic deflection of the doped nanodroplet beam. The measurement also establishes the structures' electric dipole moments. In consequence, the introduced approach is complementary to spectroscopic studies of low-temperature molecular assembly reactions. It is enabled by the fact that within the cold superfluid matrix the molecular dipoles become nearly completely oriented by the applied electric field. As a result, the massive (tens of thousands of helium atoms) nanodroplets undergo significant deflections. The method is illustrated here by an application to dimers and trimers of dimethyl sulfoxide (DMSO) molecules. We interpret the experimental results with ab initio theory, mapping the potential energy surface of DMSO complexes and simulating their low temperature aggregation dynamics.

Strained hydrogen bonding in imidazole trimer: a combined infrared, Raman, and theory study

This is not how three imidazole molecules prefer to arrange, as a combined IR, Raman and computational analysis unambiguously shows.

A HElium NanoDroplet Isolation (HENDI) investigation of the weak hydrogen bonding in the propyne dimer (CH3CCH)2

A HElium Nanodroplet Isolation (HENDI) experiment was performed to explore the absorption spectra of the propyne monomer (CH₃CCH), dimer and (CH₃CCH)_≥3 multimers in the vicinity of the CH stretch region ν₁ of the monomer.

Conformational structures of jet-cooled acetaminophen-water clusters: a gas phase spectroscopic and computational study

Jet-cooled acetaminophen (AAP)-water clusters, AAP-(H₂O)₁, were investigated by mass-selected resonant two-photon ionization (R2PI), ultraviolet-ultraviolet hole-burning (UV-UV HB), infrared-dip (IR-dip), and infrared-ultraviolet hole-burning (IR-UV HB) spectroscopy. Each syn- and anti-AAP rotamer has three distinctive binding sites (-OH, >CO, and >NH) for a water molecule, thus 6 different AAP-(H₂O)₁ conformers are expected to exist in the molecular beam. The origin bands of the AAP(OH)-(H₂O)₁ and AAP(CO)-(H₂O)₁ conformers (including their syn- and anti-conformers) in the R2PI spectrum are shifted to red and blue compared to those of the AAP monomer, respectively. These frequency shifts upon complexation between a water molecule and a specific binding site of AAP are also predicted by theoretical calculations. The spectral assignments of the origin bands in the R2PI spectra and the IR vibrational bands in the IR-dip spectra of the four lowest-energy conformers of AAP-(H₂O)₁, [syn- and anti-AAP(OH)-(H₂O)₁ and syn- and anti-AAP(CO)-(H₂O)₁], are aided by ab initio and time-dependent density functional theory (TDDFT) calculations. Further investigation of the IR-dip spectra has revealed a hydrogen-bonded NH stretching mode, supporting the presence of the syn-AAP(NH)-(H₂O)₁ conformer. Moreover, by employing IR-UV HB spectroscopy, we have reconfirmed the existence of the syn-AAP(NH)-(H₂O)₁ conformer, which happened to be buried underneath the broad background contributed by the AAP(OH)-(H₂O)₁ conformers. These observations have led us to conclude that all of the possible conformers of AAP-(H₂O)₁ have been found in this study.

Lack of Aggregation of Molecules on Ice Nanoparticles

Multiple molecules adsorbed on the surface of nanosized ice particles can either remain isolated or form aggregates, depending on their mobility. Such (non)aggregation may subsequently drive the outcome of chemical reactions that play an important role in atmospheric chemistry or astrochemistry. We present a molecular beam experiment in which the controlled number of guest molecules is deposited on the water and argon nanoparticles in a pickup chamber and their aggregation is studied mass spectrometrically. The studied molecules (HCl, CH3Cl, CH3CH2CH2Cl, C6H5Cl, CH4, and C6H6) form large aggregates on argon nanoparticles. On the other hand, no aggregation is observed on ice nanoparticles. Molecular simulations confirm the experimental results; they reveal a high degree of aggregation on the argon nanoparticles and show that the molecules remain mostly isolated on the water ice surface. This finding will influence the efficiency of ice grain-mediated synthesis (e.g., in outer space) and is also important for the cluster science community because it shows some limitations of pickup experiments on water clusters.

Effective doping of low energy ions into superfluid helium droplets

We report a facile method of doping cations from an electrospray ionization (ESI) source into superfluid helium droplets. By decelerating and stopping the ion pulse of reserpine and substance P from an ESI source in the path of the droplet beam, about 10(4) ion-doped droplets (one ion per droplet) can be recorded, corresponding to a pickup efficiency of nearly 1 out of 1000 ions. We attribute the success of this simple approach to the long residence time of the cations in the droplet beam. The resulting size of the doped droplets, on the order of 10(5)/droplet, is measured using deflection and retardation methods. Our method does not require an ion trap in the doping region, which significantly simplifies the experimental setup and procedure for future spectroscopic and diffraction studies.

Effect of kinetic energy on the doping efficiency of cesium cations into superfluid helium droplets

We present an experimental investigation of the effect of kinetic energy on the ion doping efficiency of superfluid helium droplets using cesium cations from a thermionic emission source. The kinetic energy of Cs(+) is controlled by the bias voltage of a collection grid collinearly arranged with the droplet beam. Efficient doping from ions with kinetic energies from 20 eV up to 480 V has been observed in different sized helium droplets. The relative ion doping efficiency is determined by both the kinetic energy of the ions and the average size of the droplet beam. At a fixed source temperature, the number of doped droplets increases with increasing grid voltage, while the relative ion doping efficiency decreases. This result implies that not all ions are captured upon encountering with a sufficiently large droplet, a deviation from the near unity doping efficiency for closed shell neutral molecules. We propose that this drop in ion doping efficiency with kinetic energy is related to the limited deceleration rate inside a helium droplet. When the source temperature changes from 14 K to 17 K, the relative ion doping efficiency decreases rapidly, perhaps due to the lack of viable sized droplets. The size distribution of the Cs(+)-doped droplet beam can be measured by deflection and by energy filtering. The observed doped droplet size is about 5 × 10(6) helium atoms when the source temperature is between 14 K and 17 K.

Characterization of Znq+–imidazole (q = 0, 1, 2) organometallic complexes: DFT methods vs. standard and explicitly correlated post-Hartree–Fock methods

Benchmarking DFts for the characterization of the Zn^q+–imidazole (q= 0, 1, 2) complexes.

Conformational preferences of monohydrated clusters of imidazole derivatives revisited

IR-UV double resonance spectroscopy was used to identify the conformers of monohydrated benzimidazole andN-methylbenzimidazole in a supersonic jet. A new OH–N bound conformer relevant to histidine containing proteins was discovered. The long standing differences in the literature about the relative energies and abundance of the monohydrated imidazole derivatives have also been resolved.

NMR studies of active-site properties of human carbonic anhydrase II by using (15) N-labeled 4-methylimidazole as a local probe and histidine hydrogen-bond correlations

By using a combination of liquid and solid-state NMR spectroscopy, (15) N-labeled 4-methylimidazole (4-MI) as a local probe of the environment has been studied: 1) in the polar, wet Freon CDF3 /CDF2 Cl down to 130 K, 2) in water at pH 12, and 3) in solid samples of the mutant H64A of human carbonic anhydrase II (HCA II). In the latter, the active-site His64 residue is replaced by alanine; the catalytic activity is, however, rescued by the presence of 4-MI. For the Freon solution, it is demonstrated that addition of water molecules not only catalyzes proton tautomerism but also lifts its quasidegeneracy. The possible hydrogen-bond clusters formed and the mechanism of the tautomerism are discussed. Information about the imidazole hydrogen-bond geometries is obtained by establishing a correlation between published (1) H and (15) N chemical shifts of the imidazole rings of histidines in proteins. This correlation is useful to distinguish histidines embedded in the interior of proteins and those at the surface, embedded in water. Moreover, evidence is obtained that the hydrogen-bond geometries of His64 in the active site of HCA II and of 4-MI in H64A HCA II are similar. Finally, the degeneracy of the rapid tautomerism of the neutral imidazole ring His64 reported by Shimahara et al. (J. Biol. Chem.- 2007, 282, 9646) can be explained with a wet, polar, nonaqueous active-site conformation in the inward conformation, similar to the properties of 4-MI in the Freon solution. The biological implications for the enzyme mechanism are discussed.

Electron Diffraction of Superfluid Helium Droplets

We present experimental results of electron diffraction of superfluid helium droplets and droplets doped with phthalocyanine gallium chloride and discuss the possibility of performing the same experiment with a laser aligned sample. The diffraction profile of pure droplets demonstrates dependence on the nozzle temperature, that is, on the average size of the droplets. Larger clusters demonstrate faster decay with increasing momentum transfer, whereas smaller clusters converge to isolated gas phase molecules at source temperatures of 18 K and higher. Electron diffraction of doped droplets shows similar modified molecular scattering intensity as that of the corresponding gas phase molecules. On the basis of fittings of the scattering profile, the number of remaining helium atoms of the doped droplets is estimated to be on the order of hundreds. This result offers guidance in assessing the possibility of electron diffraction from laser aligned molecules doped in superfluid helium droplets.

Molecular recognition in glycolaldehyde, the simplest sugar: two isolated hydrogen bonds win over one cooperative pair

Carbohydrates are used in nature as molecular recognition tools. Understanding their conformational behavior upon aggregation helps in rationalizing the way in which cells and bacteria use sugars to communicate. Here, the simplest α-hydroxy carbonyl compound, glycolaldehyde, was used as a model system. It was shown to form compact polar C₂-symmetric dimers with intermolecular O–H⋅⋅⋅O=C bonds, while sacrificing the corresponding intramolecular hydrogen bonds. Supersonic jet infrared (IR) and Raman spectra combined with high-level quantum chemical calculations provide a consistent picture for the preference over more typical hydrogen bond insertion and addition patterns. Experimental evidence for at least one metastable dimer is presented. A rotational spectroscopy investigation of these dimers is encouraged, also in view of astrophysical searches. The binding motif competition of aldehydic sugars might play a role in chirality recognition phenomena of more complex derivatives in the gas phase.

Communication: Where does the first water molecule go in imidazole?

Supersonic jet FTIR spectroscopy supplemented by (18)O substitution shows unambiguously that water prefers to act as an O-H···N hydrogen bond donor towards imidazole, instead of acting as a N-H···O acceptor. Previous matrix isolation, helium droplet, and aromatic substitution experiments had remained ambiguous, as are standard quantum chemical calculations. The finding is supported by a study of the analogous methanol complexes and by higher level quantum chemical calculations.

Electronic polarization spectroscopy of metal phthalocyanine chloride compounds in superfluid helium droplets

We report the electronic polarization spectroscopy of two metal phthalocyanine chloride compounds (MPcCl, M=Al,Ga) embedded in superfluid helium droplets and oriented in a dc electric field. For both compounds, the laser induced fluorescence spectra show preference for perpendicular excitation relative to the orientation field. This result indicates that the permanent dipoles of both compounds are predominantly perpendicular to the transition dipole. Since the permanent dipole derives from the metal chloride, while the transition dipole derives from the phthalocyanine chromophore, in the plane of phthalocyanine, this qualitative result is not surprising. However, quantitative modeling reveals that this intuitive model is inadequate and that the transition dipole might have tilted away from the molecular plane of phthalocyanine. The out of plane component of the transition dipole amounts to approximately 10% if the permanent dipole is assumed to be approximately 4 debye. The origin for this tilt is puzzling, and we tentatively attribute it to the transition of nonbonding orbitals, either from the chlorine atom or from the bridge nitrogen atom, to the pi* orbitals of the phthalocyanine chromophore. On the other hand, although unlikely, we cannot completely exclude the possibility that both our high level density functional theory calculation and ab initio results severely deviate from reality. The droplet matrix induces redshifts in the origin of the electronic transition and produces discrete phonon wings. Nevertheless, in dc electric fields, all phonon wings and the zero phonon line demonstrate the same dependence on the polarization direction of the excitation laser. Although electronic excitation does couple to the superfluid helium matrix and the resulting phonon wings add complications to the electronic spectrum, this coupling does not affect the direction of the electronic transition dipole. Electronic polarization spectroscopy in superfluid helium droplets is thus still informative in revealing the permanent dipole and its relation relative to the transition dipole.

Evidence of Rotational Isomerism in 1-Butyl-3-methylimidazolium Halides: A Combined High-Pressure Infrared and Raman Spectroscopic Study

High-pressure methods were applied to investigate the rotational isomerism and the hydrogen-bonding structures of 1-butyl-3-methylimidazolium bromide and 1-butyl-3-methylimidazolium chloride, respectively. Conformation changes of the butyl chain were observed above a pressure of 0.3 GPa. Under ambient pressure, Raman spectra indicate that the more thermodynamically stable butyl structure of the cations is the gauche-anti (GA) and all-anti forms for 1-butyl-3-methylimidazolium bromide and 1-butyl-3-methylimidazolium chloride, respectively. Nevertheless, the high-pressure phases arise from the perturbed GA conformer. The imidazolium C-H bands of 1-butyl-3-methylimidazolium chloride display anomalous nonmonotonic pressure-induced frequency shifts. This discontinuity in the frequency shift is related to the modification of the imidazolium C-H---Cl- contacts upon compression. The alkyl C-H---Cl- interactions are suggested to be a compensatory mechanism to provide additional stability. Density-functional-theory-calculated results also support the high-pressure results that the methyl and butyl C-H groups are suitable proton donor sites for the GA conformer.

Infrared Laser Spectroscopy of Uracil and Thymine in Helium Nanodroplets: Vibrational Transition Moment Angle Study

Vibrational spectra are reported in the N-H stretching region for uracil and thymine monomers in helium nanodroplets. Each monomer shows only a single isomer, the global minimum, in agreement with previous experimental and theoretical studies. The assignment of the infrared vibrational bands in the spectra is aided by the measurement of the corresponding vibrational transition moment angles (VTMAs) and ab initio frequency calculations. The ambiguity in the VTMA assignment of the N3H band for the uracil monomer is explained by the presence of dimer bands, which are overlapped with the monomer band.