Michel Mons

Excited states dynamics of DNA and RNA bases: Characterization of a stepwise deactivation pathway in the gas phase

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.

Probing the competition between secondary structures and local preferences in gas phase isolated peptide backbones

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.

Resonant two‐photon ionization spectra of the external vibrational modes of the chlorobenzene‐, phenol‐, and toluene‐rare gas (Ne, Ar, Kr, Xe) van der Waals complexes

Using resonant two‐photon ionization and time‐of‐flight mass spectrometry techniques, original spectra of the external vibrational modes of ten van der Waals (vdW) complexes are presented. The complexes are formed in a pulsed supersonic expansion between a rare gas atom (Ne, Ar, Kr, Xe) and a monosubstituted benzene derivative chlorobenzene, phenol, or toluene. For each complex, the red shift of the S1←S0 000 energy due to complexation, and the vdW stretching and bending frequencies are determined. In some cases, the bending mode anharmonicity and Fermi resonances could be analyzed from the extended progressions observed for the bending vibration. The diatomic model is used to estimate the stretching force constant. Intensity, mass, and dissymmetry effects induced by the X substituent on the benzene ring are analyzed. In particular, in these Cs symmetry complexes, every bending A’ level is observed, not just the even bending levels found in C6v or C2v complexes. Finally, some correlations are shown from t...

A simple laser vaporization source for thermally fragile molecules coupled to a supersonic expansion: application to the spectroscopy of tryptophan

Abstract The mass resolved electronic spectrum of cold tryptophan molecules has been obtained using a novel desorption method as a vaporization source coupled with a supersonic expansion. This desorption device is characterized by its simplicity, stability suitable for spectroscopic studies and by a very low yield of fragmentation products. The unique performance of the desorption source is demonstrated by the possibility to measure hole-burning spectra of tryptophan by resonance enhanced two-photon ionization which confirms strongly the presence of only a small number of stable conformers for this species in its ground state.

Gas-Phase Folding of a Two-Residue Model Peptide Chain: On the Importance of an Interplay between Experiment and Theory

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.

Angular correlation between photofragment velocity and angular momentum measured by resonance enhanced multiphoton ionization detection

REMPI detection of photofragments is discussed as a probe technique to measure the angular distribution of the velocity as well as the angular correlation between velocity and angular momentum existing in fragments formed during a polarized photolysis. The symmetry properties of the REMPI probe process induced by polarized light are expressed in terms of sensitivity to the moments of the rotational angular momentum distribution and the angular state of the photofragment is described in the formalism of bipolar moments. Original explicit expressions of the ion velocity profiles are given with probe geometry characteristics as parameters for two kinds of fragment detection (time‐of‐flight mass spectrometry and angular measurements of the ion yield) and the consequences of the v–J correlation on the observed profiles are discussed. Some experimental geometries are proposed in order to either determine the angular correlation or to avoid its effects.

Competition between local conformational preferences and secondary structures in gas-phase model tripeptides as revealed by laser spectroscopy and theoretical chemistry

The gas-phase model tripeptides N-acetyl-Phe-Pro-NH2 and N-acetyl-Pro-Phe-NH2 have been studied experimentally and theoretically in order to investigate the local conformational preferences of the peptide backbone and their competition with secondary structures under solvent-free conditions. The combination of UV and IR spectroscopies shows that, under supersonic beam conditions, only a reduced number of conformations are formed, indicating efficient conformational relaxation processes in these species. IR spectroscopy in the NH stretch spectral range combined with density functional theory calculations proves to be a very efficient tool to assign the structure of these species in terms of intramolecular H-bonding. Classical secondary structures of biology, like repeated γ-turns are observed as major conformations. Only one minor conformation of N-Ac-Phe-Pro-NH2 was assigned to a β-turn structure. According to the nature of the main conformers, the backbone conformational trends on the phenylalanine (Phe) residue is shown to be very dependent upon the neighbouring residues: Phe adopts a β conformation when alone (in N-acetyl-Phe-NH2) or when followed by a proline residue (in N-acetyl-Phe-Pro-NH2) but favours a γL conformation when preceded by proline (in N-acetyl-Pro-Phe-NH2). These subtle preferences, resulting from a competition between weakly polar or dispersive interactions, constitute a very stringent test of the theoretical tools for protein modelling and simulation.

Secondary structures of short peptide chains in the gas phase: double resonance spectroscopy of protected dipeptides

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.

Gas phase hydrogen-bonded complexes of aromatic molecules: Photoionization and energetics

The present review discusses the possibility of measuring the dissociation energy of gas phase complexes from their dissociative photoionization. A compilation of recent results on hydrogen-bonded complexes of aromatic molecules, with a polar solvent molecule (water, alcohol, NH 3, HCl, etc.), playing the role of either proton donor or proton acceptor is presented. We show that laser experiments begin to provide a consistent set of energetic data that can be considered as benchmarks to assess quantum calculations as well as to parametrize the force field models used in biochemistry.

Ab Initio Kinetic Simulation of Gas-Phase Experiments: Tautomerization of Cytosine and Guanine

A novel kinetic approach based on ab initio calculated rate constants has been developed and implemented in the kTSim program. The proposed approach allows prediction of the distribution of reactant and product concentrations over time, based exclusively on computationally obtained rate constants. The newly developed methodology was used to simulate the process of evaporation and tautomerization of guanine and cytosine under thermal (T = 490 K, cytosine; T = 620 K, guanine) and laser (T = 1000 K, 24 ns laser pulse) desorption conditions. Both monomolecular and bimolecular mechanisms of the tautomerization were considered simultaneously. The rates of the reactions were estimated using the values of Gibbs free energies calculated at the MPWB1K/aug-cc-pVDZ level and specified in a kTSim input. We expect that the proposed approach can also be used for accurate kinetic simulation of a wide range of processes.