Laser-desorbed quinine and quinidine have been studied in the gas phase by combining supersonic expansion with laser spectroscopy, namely, laser-induced fluorescence (LIF), resonance-enhanced multiphoton ionization (REMPI), and IR-UV double resonance experiments. Density funtional theory (DFT) calculations have been done in conjunction with the experimental work. The first electronic transition of quinine and quinidine is of π-π* nature, and the studied molecules weakly fluoresce in the gas phase, in contrast to what was observed in solution (Qin, W. W.; et al. J. Phys. Chem. C2009, 113, 11790). The two pseudo enantiomers quinine and quinidine show limited differences in the gas phase; their main conformation is of open type as it is in solution. However, vibrational circular dichroism (VCD) experiments in solution show that additional conformers exist in condensed phase for quinidine, which are not observed for quinine. This difference in behavior between the two pseudo enantiomers is discussed.

The observation of the light absorption of neutral biomolecules has been made possible by a method implemented for their preparation in the gas phase, in supersonically cooled molecular beams, based upon the work of Focsa et al. [C. Mihesan, M. Ziskind, B. Chazallon, E. Therssen, P. Desgroux, S. Gurlui, and C. Focsa, Appl. Surf. Sci. 253, 1090 (2006)]. The biomolecules diluted in frozen water solutions are entrained in the gas plume of evaporated ice generated by an infrared optical parametric oscillators (OPO) laser tuned close to its maximum of absorption, at ~3 μm. The biomolecules are then picked up in the flux of a supersonic expansion of argon. The method was tested with indole dissolved in water. The excitation spectrum of indole was found cold and large clusters of indole with water were observed up to n = 75. Frozen spinach leaves were examined with the same method to observe the chlorophyll pigments. The Q(y) band of chlorophyll a has been observed in a pump probe experiment. The Q(y) bands of chlorophyll a is centred at 647 nm, shifted by 18 nm from its position in toluene solutions. The ionization threshold could also be determined as 6.1 ± 0.05 eV.

In order to assess the ability of theory to describe properly the dispersive interactions that are ubiquitous in peptide and protein systems, an isolated short peptide chain has been studied using both gas-phase laser spectroscopy and quantum chemistry. The experimentally observed coexistence of an extended form and a folded form in the supersonic expansion was found to result from comparable Gibbs free energies for the two species under the high-temperature conditions (< or = 320 K) resulting from the laser desorption technique used to vaporize the molecules. These data have been compared to results obtained using a series of quantum chemistry methods, including DFT, DFT-D, and post-Hartree-Fock methods, which give rise to a wide range of relative stabilities predicted for these two forms. The experimental observation was best reproduced by an empirically dispersion-corrected functional (B97-D) and a hybrid functional with a significant Hartree-Fock exchange term (M06-2X). In contrast, the popular post-Hartree-Fock method MP2, which is often used for benchmarking these systems, had to be discarded because of a very large basis-set superposition error. The applicability of the atomic counterpoise correction (ACP) is also discussed. This work also introduces the mandatory theoretical examination of experimental abundances. DeltaH(0 K) predictions are clearly not sufficient for discussion of folding, as the conformation inversion temperature is crucial to the conformation determination and requires taking into account thermodynamical corrections (DeltaG) in order to computationally isolate the most stable conformation.

[2]L. Ragona, M. Catalano, L. Zetta, R. Longhi, F. Fogolari, and H. Molinari. Biochemistry[1]Supported in part by NSF (CHE-0615755)

[2]L. Ragona, M. Catalano, L. Zetta, R. Longhi, F. Fogolari, and H. Molinari. Biochemistry[1]Supported in part by NSF (CHE-0615755)

[2]L. Ragona, M. Catalano, L. Zetta, R. Longhi, F. Fogolari, and H. Molinari. Biochemistry[1]Supported in part by NSF (CHE-0615755)

The fluorescence quenching by oxygen of vapors of nine polycyclic aromatic hydrocarbons with strongly different oxidation potentials 0.44 eV < E ox < 1.61 eV (anthracene, 9-methylanthracene, 2-aminoanthracene, 9,10-dibromanthracene, pyrene, chrysene, phenanthrene, fluoranthene, and carbazole) is studied. From the dependences of the fluorescence decay rates and intensities on the oxygen pressure P O2, the quenching rate constants k S O2 for the excited singlet states S 1 and the fraction f S O2 of the S 1 states quenched by oxygen are estimated. At P O2 = 5 Torr, the k S O2 constants vary from 1.2 × 107 to 3.0 × 105 s−1 Torr−1, while the fraction of the quenched excited singlet states changes from 0.1 (fluoranthene) to 0.7 (chrysene) and 0.8 (pyrene). The dependences of k S O2 on the photophysical and electron-donor characteristics of the fluorescing compounds are analyzed. It is shown that, in the gas phase of anthracene and its derivatives, the magnitudes of k S O2 are limited by the rate constants of gas-kinetic collisions k gk and do not depend on the electron-donor characteristics of fluorophores, while the fraction of quenched states f S O2 changes with the oxidation potential. For compounds with k S O2 < k gk, both the rate constants k S O2 and the fraction of quenched states f S O2 depend on the E ox of sensitizers, which demonstrates an important role played by the charge-transfer interactions in quenching of the S 1 states. The dependence of the rate constants k S O2 on the free energy of electron transfer ΔG et is considered.

{W. Chin, M. Mons, J.-P. Dognon, F. Piuzzi, B. Tardivel and I. Dimicoli, \textit{Phys. Chem. Chem. Phys.{W. Chin, J.-P. Dognon, F. Piuzzi, B. Tardivel, I. Dimicoli and M. Mons, \textit{J. Am. Chem. Soc.

gamma-Turn, the shortest secondary structure of peptides, exists as two helical forms gamma(L) and gamma(D) of opposite handedness. The present gas phase study of capped L-Phe-Xxx peptides (Xxx = L-Ala, D-Ala or Aib: aminoisobutyric acid) provides a unique example of intramolecular chiral recognition of the gamma-turn helicity on Ala or Aib by the neighbouring residue Phe within the chain. With the chiral L- or D-Ala residues, the presence of a side-chain operates a discrimination between the two helical forms: one of them is widely favoured over the other (gamma(L) or gamma(D) respectively). This enables us to validate and calibrate the recognition capabilities of the nearby L-Phe residue. The discriminating interactions have been precisely characterized from their spectroscopic UV and IR signatures and identified by comparison with quantum chemistry calculations. Then, in the case of the non-chiral residue Aib, the two helical forms of the gamma-turn, which are simultaneously observed in the jet, have been discriminated and assigned by comparison with the chiral residues. The relative abundances of the diastereomeric forms L-Phe-Aib(gamma(L)) and L-Phe-Aib(gamma(D)) enable us to determine the most efficient recognition configuration.

Combining laser desorption with a supersonic expansion together with the selectivity of IR/UV double resonance spectroscopy makes it possible to isolate and characterise the gas phase of remarkable backbone conformations of short peptide chains mimicking protein segments. A systematic bottom-up approach involving a conformer-specific IR study of peptide sequences of increasing sizes has enabled us to map the spectral signatures of the intramolecular interactions, which shape the peptide backbone, in particular H-bonds. The precise data collected are directly comparable to the most sophisticated quantum chemistry calculations of these species and therefore constitute a stringent test for the theoretical methods used. One-residue chains reveal the local conformational preference of the backbone and its dependence upon the nature of the residue. The investigation of longer chains provides evidence for a competition between simple successions of local conformational preferences along the chain and more folded structures, in which a new H-bonding network, involving distant H-bonding sites along the backbone, takes place. From three residues, the issue of helical folding can also be addressed. The present review of the gas phase literature data emphasizes the observation of remarkable secondary structures of biology, including short segments of beta-strands, gamma- and beta-turns, combinations of turns, including a 3(10) helix. It also provides evidence for the flexibility of the peptide chains, i.e., a critical influence of rather minor interactions (like side-chain/backbone interactions) on the conformational stability. Finally, the paper will discuss future promising directions of the present approach.

Radiationless deactivation pathways of excited gas phase nucleobases were investigated using mass-selected femtosecond resolved pump-probe resonant ionization. By comparison between nucleobases and methylated species, in which tautomerism cannot occur, we can access intrinsic mechanisms at a time resolution never reported so far (80 fs). At this time resolution, and using appropriate substitution, real nuclear motion corresponding to active vibrational modes along deactivation coordinates can actually be probed. We provide evidence for the existence of a two-step decay mechanism, following a 267 nm excitation of the nucleobases. The time resolution achieved together with a careful zero time-delay calibration between lasers allow us to show that the first step does correspond to intrinsic dynamics rather than to a laser cross correlation. For adenine and 9-methyladenine a first decay component of about 100 fs has been measured. This first step is radically increased to 200 fs when the amino group hydrogen atoms of adenine are substituted by methyl groups. Our results could be rationalized according to the effect of the highly localized nature of the excitation combined to the presence of efficient deactivation pathway along both pyrimidine ring and amino group out-of-plane vibrational modes. These nuclear motions play a key role in the vibronic coupling between the initially excited pipi* and the dark npi* states. This seems to be the common mechanism that opens up the earlier phase of the internal conversion pathway which then, in consideration of the rather fast relaxation times observed, would probably proceed via conical intersection between the npi* relay state and high vibrational levels of the ground state.

The conformational structure of short peptide chains in the gas phase is studied by laser spectroscopy of a series of protected dipeptides, Ac-Xxx-Phe-NH(2), Xxx=Gly, Ala, and Val. The combination of laser desorption with supersonic expansion enables us to vaporize the peptide molecules and cool them internally; IR/UV double resonance spectroscopy in comparison to density functional theory calculations on Ac-Gly-Phe-NH(2) permits us to identify and characterize the conformers populated in the supersonic expansion. Two main conformations, corresponding to secondary structures of proteins, are found to compete in the present experiments. One is composed of a doubly gamma-fold corresponding to the 2(7) ribbon structure. Topologically, this motif is very close to a beta-strand backbone conformation. The second conformation observed is the beta-turn, responsible for the chain reversal in proteins. It is characterized by a relatively weak hydrogen bond linking remote NH and CO groups of the molecule and leading to a ten-membered ring. The present gas phase experiment illustrates the intrinsic folding properties of the peptide chain and the robustness of the beta-turn structure, even in the absence of a solvent. The beta-turn population is found to vary significantly with the residues within the sequence; the Ac-Val-Phe-NH(2) peptide, with its two bulky side chains, exhibits the largest beta-turn population. This suggests that the intrinsic stabilities of the 2(7) ribbon and the beta-turn are very similar and that weakly polar interactions occurring between side chains can be a decisive factor capable of controlling the secondary structure.

We report the first gas-phase spectroscopic study of a three-residue model of a peptide chain, Ac-Phe-Gly-Gly-NH2 (Ac = acetyl), using the IR/UV double resonance technique. The existence of at least five different conformers under supersonic expansion conditions is established, most of them exhibiting rather strong intramolecular H-bonds. One of the most populated conformers, however, exhibits a different H-bonding network characterized by two weak H-bonds. Comparison of the amide A and I/II experimental data with density functional theory calculations carried out on a series of selected conformations enables us to assign this conformer to two successive beta-turns along the peptide chain, the two H-bonds being of C10 type, i.e., each of them closing a 10-atom ring in the molecule. The corresponding form is found to be more stable than the 310 helix secondary structure (not observed), presumably because of specific effects due to the glycine residues.

Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.

Recent experimental gas-phase studies of very similar peptide chain models (Ac-Val-Tyr( Me)-NHMe and Ac-Val-Phe-NH2) have led to different assignments for the secondary structures adopted: beta-strand and beta-turn, respectively. We present a discussion of the possible causes for such different behaviour in the light of quantum chemistry calculations. The consistent set of data presently obtained ( relative energies and IR calculated spectra) leads us to propose the same structural assignment for the experimentally observed Val-Tyr( Me) and Val-Phe peptide chains, i.e. a beta-turn conformation. In addition, calculations also suggest that the nature of the chemical protection on the C-terminal (-NHMe vs. -NH2) of the chain model does not affect its conformational preference, nor its structure or its energetics, which suggests the less simple, but more informative, -NH2-protected models for the determination of the intrinsic structural properties of a peptide chain.

The issue of the influence of the side chain/backbone interaction on the local conformational preferences of a phenylalanine residue in a peptide chain is addressed. A synergetic approach is used, which combines gas-phase UV spectroscopy as well as gas-phase IR/UV double-resonance experiments with DFT and post Hartree-Fock calculations. N-Acetyl-Phe-amide was chosen as a model system for which three different conformers were observed. The most stable conformer has been identified as an extended beta(L) conformation of the peptide backbone. It is stabilized by a weak but significant NH-pi interaction bridging the aromatic ring on the residue (i) with the NH group on residue (i+1), with the aromatic side chain being in an anti conformation. This stable conformation corresponds to the common NH(i+1)-aromatic(i) interaction encountered in proteins for the three aromatic residues (phenylalanine, tyrosine, and tryptophan), which illustrates the relevance of gas-phase investigations to structural biology issues. The two other less abundant conformers have been assigned to two gamma-folded backbone conformations that differ by the orientation of the side chain. In all cases, the IR data provided spectroscopic fingerprints of these interactions. Finally, the strong conformational dependence of the fluorescence yield found for N-acetyl-Phe-amide illustrates the role of the environment on the excited-state dynamics of these species, which is often exploited by biochemists to monitor protein structural changes from tryptophan lifetime measurements.