Isomer-Selective Spectroscopy and Dynamics of Phenol-Arn (n ≤ 5) Clusters

Structures and ionization-induced solvation dynamics of phenol-(argon)_n clusters, PhOH-Ar_n (n ≤ 5), were studied by using a variety of isomer-selective photoionization and vibrational spectroscopic techniques. Several higher-energy isomers were found and assigned for the first time by systematically controlling the experimental conditions of the supersonic expansion. This behavior is also confirmed for the PhOH-Kr₂ cluster. Solvation structures are elucidated by evaluating systematic shifts in the S₁ ← S₀ origin and ionization energies obtained by resonance-enhanced photoionization, in addition to the OH stretching frequency obtained by IR photodissociation. Isomer-selective picosecond time-resolved IR spectroscopy for the n = 2 clusters revealed that the dynamics for the ionization-induced intermolecular π → H site-switching reaction strongly depends on the initial isomeric structure. In particular, the reaction time for the (1|1) isomer is 7 ps, while that for (2|0) is <3 ps. This difference shows that the switching time is determined by the distance of the reaction coordinate between the initial π-site and the final OH-site.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

Mode-Selective Laser Control of Palladium Catalyst Decomposition

It is generally assumed that molecules behave ergodically during chemical reactions, that is, reactivities depend only on the total energy content and not on the initial state of the molecule. While there are a few examples of nonergodic behavior in small (usually electronically excited) species, to date there have been no reports of such behavior in larger covalently bound species composed of several tens of atoms. Here, we demonstrate vibrational mode-selective behavior in a series of palladium catalysts. When we excite solvent-tagged gas-phase Pd catalysts with an infrared laser that is tuned to be resonant with specific molecular vibrations, depending on which vibration we excite, we can select different reaction pathways. We also demonstrate that this behavior can be "turned off" via chemical substitution.

Sugar-peptidic bond interactions: spectroscopic characterization of a model system

Sugars are small carbohydrates which play numerous roles in living organisms such as storage of energy or as structural components. Modifications of specific sites within the glycan chain can modulate a carbohydrate's overall biological function as it happens with nucleic acids and proteins. Hence, identifying discrete carbohydrate modifications and understanding their biological effects is essential. A study of such processes requires of a deep knowledge of the interaction mechanism at the molecular level. Here, we use a combination of laser spectroscopy in jets and quantum mechanical calculations to characterize the interaction between phenyl-β-d-glucopyranoside and N-methylacetamide as a model to understand the interaction between a sugar and a peptide bond. The most stable structure of the molecular aggregate shows that the main interaction between the peptide fragment and the sugar proceeds via a C[double bond, length as m-dash]OH-O2 hydrogen bond. A second conformer was also found, in which the peptide establishes a C[double bond, length as m-dash]OH-O6 hydrogen bond with the hydroxymethyl substituent of the sugar unit. All the conformers present an additional interaction point with the aromatic ring. This particular preference of the peptide for the hydroxyl close to the aromatic ring could explain why glycogenin uses tyrosine in order to convert glucose into glycogen by exposing the O4H hydroxyl group for the other glucoses for the polymerization to take place.

Femtosecond charge and molecular dynamics of I-containing organic molecules induced by intense X-ray free-electron laser pulses

We studied the electronic and nuclear dynamics of I-containing organic molecules induced by intense hard X-ray pulses at the XFEL facility SACLA in Japan. The interaction with the intense XFEL pulse causes absorption of multiple X-ray photons by the iodine atom, which results in the creation of many electronic vacancies (positive charges) via the sequential electronic relaxation in the iodine, followed by intramolecular charge redistribution. In a previous study we investigated the subsequent fragmentation by Coulomb explosion of the simplest I-substituted hydrocarbon, iodomethane (CH₃I). We carried out three-dimensional momentum correlation measurements of the atomic ions created via Coulomb explosion of the molecule and found that a classical Coulomb explosion model including charge evolution (CCE-CE model), which accounts for the concerted dynamics of nuclear motion and charge creation/charge redistribution, reproduces well the observed momentum correlation maps of fragment ions emitted after XFEL irradiation. Then we extended the study to 5-iodouracil (C₄H₃IN₂O₂, 5-IU), which is a more complex molecule of biological relevance, and confirmed that, in both CH₃I and 5-IU, the charge build-up takes about 10 fs, while the charge is redistributed among atoms within only a few fs. We also adopted a self-consistent charge density-functional based tight-binding (SCC-DFTB) method to treat the fragmentations of highly charged 5-IU ions created by XFEL pulses. Our SCC-DFTB modeling reproduces well the experimental and CCE-CE results. We have also investigated the influence of the nuclear dynamics on the charge redistribution (charge transfer) using nonadiabatic quantum-mechanical molecular dynamics (NAQMD) simulation. The time scale of the charge transfer from the iodine atomic site to the uracil ring induced by nuclear motion turned out to be only ∼5 fs, indicating that, besides the molecular Auger decay in which molecular orbitals delocalized over the iodine site and the uracil ring are involved, the nuclear dynamics also play a role for ultrafast charge redistribution. The present study illustrates that the CCE-CE model as well as the SCC-DFTB method can be used for reconstructing the positions of atoms in motion, in combination with the momentum correlation measurement of the atomic ions created via XFEL-induced Coulomb explosion of molecules.

Structure and hydrogen-bonding ability of estrogens studied in the gas phase

The structures of estrogens (estrone(E1), β-estradiol(E2), and estriol(E3)) and their 1:1 hydrogen-bonded (hydrated) clusters with water formed in supersonic jets have been investigated by various laser spectroscopic methods and quantum chemical calculations. In the S1-S0 electronic spectra, all three species exhibit the band origin in the 35,050-35,200 cm(-1) region. By use of ultraviolet-ultraviolet hole-burning (UV-UV HB) spectroscopy, two conformers, four conformers, and eight conformers, arising from different orientation of OH group(s) in the A-ring and D-ring, are identified for estrone, β-estradiol, and estriol, respectively. The infrared-ultraviolet double-resonance (IR-UV DR) spectra in the OH stretching vibration are observed to discriminate different conformers of the D-ring OH for β-estradiol and estriol, and it is suggested that in estriol only the intramolecular hydrogen bonded conformer exists in the jet. For the 1:1 hydrated cluster of estrogens, the S1-S0 electronic transition energies are quite different depending on whether the water molecule is bound to A-ring OH or D-ring OH. It is found that the water molecule prefers to form an H-bond to the A-ring OH for estrone and β-estradiol due to the higher acidity of phenolic OH than that of the alcoholic OH. On the other hand, in estriol the water molecule prefers to be bound to the D-ring OH due to the formation of a stable ring-structure H-bonding network with two OH groups. Thus, the substitution of one hydroxyl group to the D-ring drastically changes the hydrogen-bonding preference of estrogens.

Mimicking anaesthetic-receptor interaction: a combined spectroscopic and computational study of propofol···phenol

Propofol is a general anaesthetic that exerts its action by interaction with the GABA(A) receptor. Crystallographic studies suggest that there is a direct interaction between propofol and the phenolic residue of a tyrosine in the channel. In this study we create propofol···phenol clusters by their co-expansion in jets. The complex is probed using a set of mass-resolved spectroscopic strategies: 2-color REMPI, UV/UV hole-burning, IR/UV double resonance and the novel technique IR/IR/UV triple resonance. The existence of at least six different isomers in the expansion is demonstrated. All the isomers are stabilized by interactions between their aromatic rings. Additionally, in some conformers the OH moieties form hydrogen bonds in some of the isomers, with propofol and phenol alternating their donor-acceptor roles, while in others the -OH···OH angle points to a dipole-dipole interaction. Interpretation of the data in the light of dispersion-corrected DFT calculations shows that shallow barriers separate all the isomers, both in the ground and excited electronic states. Comparison of the structures of the complex with the X-ray diffraction data is also offered.

Exploring microsolvation of the anesthetic propofol

Propofol (2,6-diisopropylphenol) is a broadly used general anesthetic. By combining spectroscopic techniques such as 1- and 2-color REMPI, UV/UV hole burning, infrared ion-dip spectroscopy (IRIDS) obtained under cooled and isolated conditions with high-level ab initio calculations, detailed information on the molecular structure of propofol and on its interactions with water can be obtained. Four isomers are found for the bare propofol, while only three are detected for the monohydrated species and two for propofol·(H(2)O)(2). The isopropyl groups do not completely block the OH solvation site, but reduce considerably the strength of the hydrogen bonds between propofol and water. Such results may explain the high mobility of propofol in the GABA(A) active site, where it cannot form a strong hydrogen bond with the tyrosine residue.

Encapsulation of Ar(n) complexes by calix[4]arene: endo- vs. exo-complexes

The structure of the calix[4]arene(C4A)-Ar(n) complexes has been investigated by laser induced fluorescence spectroscopy, mass-selected resonant two-color two-photon ionization (2C-R2PI) spectroscopy, fragment detected IR photodissociation (FDIRPD) spectroscopy, and high level first principles electronic structure calculations at the MP2 and CCSD(T) levels of theory. C4A has a very high ability to form van der Waals complexes with rare gas atoms. For the C4A-Ar dimer two isomers are observed. A major species shows a 45 cm(-1) red-shift of its band origin with respect to the monomer, while that of a minor species is 60 cm(-1). The binding energy of the major species is determined to be in the range of 350-2250 cm(-1) from 2C-R2PI spectroscopy and FDIRPD spectroscopy. Two isomers are also identified in the quantum chemical calculations, depending on whether the Ar atom resides inside (endo) or outside (exo) the C4A. We propose a scheme to derive CCSD(T)/Complete Basis Set (CBS) quality binding energies for the C4A-Ar complex based on CCSD(T) calculations with smaller basis sets and the ratio of CCSD(T)/MP2 energies for the smaller model systems benzene-Ar and phenol-Ar, for which the CCSD(T) level of theory converges to the experimentally determined binding energies. Our best computed estimates for the binding energies of the C4A-Ar endo- and endo-complexes at the CCSD(T)/CBS level of theory are 1560 cm(-1) and 510 cm(-1), respectively. For the C4A-Ar(2) trimer the calculations support the existence of two nearly isoenergetic isomers: one is the {2 : 0} endo-complex, in which the Ar(2) dimer is encapsulated inside the C4A cavity, and the other is the {1 : 1} endo-exo-complex, in which one Ar resides inside and the other outside the C4A cavity. However, the experimental evidence strongly suggests that the observed species is the {2 : 0} endo-complex. The endo structural motif is also suggested for the larger C4A-Ar(n) complexes because of the observed systematic red-shifts of the complexes with the number of bound Ar atoms suggesting that the Ar(n) complex is encapsulated inside the C4A cavity. The formation of the endo-complex structures is attributed to the anisotropy of the interaction with C4A during the complex formation in the expansion region.

Structures and encapsulation motifs of functional molecules probed by laser spectroscopic and theoretical methods

We report laser spectroscopic and computational studies of host/guest hydration interactions between functional molecules (hosts) and water (guest) in supersonic jets. The examined hosts include dibenzo-18-crown-6-ether (DB18C6), benzo-18-crown-6-ether (B18C6) and calix[4]arene (C4A). The gaseous complexes between the functional molecular hosts and water are generated under jet-cooled conditions. Various laser spectroscopic methods are applied for these species: the electronic spectra are observed by laser-induced fluorescence (LIF), mass-selected resonance enhanced multiphoton ionization (REMPI) and ultraviolet-ultraviolet hole-burning (UV-UV HB) spectroscopy, whereas the vibrational spectra for each individual species are observed by infrared-ultraviolet double resonance (IR-UV DR) spectroscopy. The obained results are analyzed by first principles electronic structure calculations. We discuss the conformations of the host molecules, the structures of the complexes, and key interactions forming the specific complexes.