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.

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.

International audienceThe present IR-UV depletion spectroscopic study extends the recent data of literature by providing evidence for the existence of a fourth form of guanine in the gas phase. The comparison of the UV and IR signatures of the four forms together with those of the 7- and 9-methylated derivatives allows us to build up a new assignment in terms of enol/keto and 7/9NH tautomerisms. From this complete picture, it turns out that the UV spectroscopy of free guanine is mainly controlled by the 7/9NH tautomerism: both 7NH tautomers observed are red-shifted compared to the 9NH ones, with the following origin transition order, from red to blue: 7NH enol (32864 ± 5 cm-1), 7NH keto (+405 cm-1), 9NH keto (+1046 cm-1), and 9NH enol (+1891 cm-1); 7-, 9- or 1-methylations are found to cause only moderate red shifts (less than 400 cm-1). The opposite trend is observed for the IR spectroscopy, which appears to be essentially controlled by the enol/keto tautomerism. This study exemplifies the need for cross-checked experimental approaches, namely the IR/UV depletion spectroscopy or the study of relevant methylated species, to reach a global and consistent assignment, even in rather simple biological systems such as purine bases

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The conformational landscapes of 2-amino-1-phenylethanol and its 1:1 water complexes have been investigated by UV band contour, UV−UV hole-burning, and IR−UV ion dip spectroscopy, coupled with ab initio computation. The two molecular conformers observed are both stabilized by an intramolecular hydrogen bond, located in the folded (gauche) OCCN side chain, which links the proton donor OH group to the terminal amino group and leads to a significant constriction of the side chain. In the dominant 1:1 water complex, the intramolecular hydrogen bond is disrupted by the first water molecule, which inserts between the OH group and the nitrogen atom, to form a cyclic H-bonded structure. The side chain expands significantly in order to accommodate the water molecule within the neighborhood of both the hydroxyl and amino groups.

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 , XxxϭGly, 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 ␥-fold corresponding to the 2 7 ribbon structure. Topologically, this motif is very close to a ␤-strand backbone conformation. The second conformation observed is the ␤-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 ␤-turn structure, even in the absence of a solvent. The ␤-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 ␤-turn population. This suggests that the intrinsic stabilities of the 2 7 ribbon and the ␤-turn are very similar and that weakly polar interactions occurring between side chains can be a decisive factor capable of controlling the secondary structure.

The present study combines both experiment and molecular dynamics simulations in order to document the ionization behavior of the C 6 H 6 -H 2 O and C 6 H 6 -D 2 O complexes close to the ionization threshold, in particular its nonadiabatic character. Using the two-color two-photon resonant ionization laser technique, the ionization thresholds of these species have been measured together with the threshold for dissociative ionization. A binding energy has been deduced for the neutral species: D 0 (C 6 H 6 -H 2 O) ) 106 ( 4 meV and D 0 (C 6 H 6 -D 2 O) ) 116 ( 5 meV, which significantly increases the precision compared to literature. Using a semiempirical potential model, the minimum energy structures of the neutral and ionic species have been determined, and the potential energy surfaces have been analyzed using a two-dimensional approach. As a result, the formation of a stable C 6 H 6 + -H 2 O complex close to the threshold is found to be controlled by a pure quantum effect and is ascribed to the classically forbidden region of the neutral ground state wave function for the intermolecular vibrational motion. Using classical molecular dynamics simulations in order to sample this region, it has been shown that the neutral conformations involved in the production of stable ions at the ionization threshold exhibit a strong geometry change compared to the neutral equilibrium conformation; i.e., the water molecule is strongly shifted off the benzene C 6 axis and is also flipped over backward the benzene ring. The difference in the ionization energy of the C 6 H 6 -H 2 O and C 6 H 6 -D 2 O complexes, which cannot be explained by the difference in the neutral binding energies alone, supports this result.

The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to visualize weak non-covalent interactions from the topological analysis of the electron density and of its reduced gradient, is applied in the present paper to document intra- and inter-molecular interactions in flexible molecules and systems of biological interest in combination with IR spectroscopy. We first describe the conditions of application of the NCI method to the specific case of intramolecular interactions. Then we apply it to a series of stable conformations of isolated molecules as an interpretative technique to decipher the different physical interactions at play in these systems. Examples are chosen among neutral molecular systems exhibiting a large diversity of interactions, for which an extensive spectroscopic characterization under gas-phase isolation conditions has been obtained using state-of-the-art conformer-specific experimental techniques. The interactions presently documented range from weak intra-molecular H-bonds in simple amino-alcohols, to more complex patterns, with interactions of various strengths in model peptides, as well as in chiral bimolecular systems, where invaluable hints for the understanding of chiral recognition are revealed. We also provide a detailed technical appendix, which discusses the choices of cut-offs as well as the applicability of the NCI analysis to specific constrained systems, where local effects require attention. Finally, the NCI technique provides IR spectroscopists with an elegant visualization of the interactions that potentially impact their vibrational probes, namely the OH and NH stretching motions. This contribution illustrates the power and the conditions of use of the NCI technique, with the aim of providing an easy tool for all chemists, experimentalists and theoreticians, for the visualization and characterization of the interactions shaping complex molecular systems.