Benjamin Tardivel

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.

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.

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.

Unraveling the Mechanisms of Nonradiative Deactivation in Model Peptides Following Photoexcitation of a Phenylalanine Residue

The mechanisms of nonradiative deactivation of a phenylalanine residue after near-UV photoexcitation have been investigated in an isolated peptide chain model (N-acetylphenylalaninylamide, NAPA) both experimentally and theoretically. Lifetime measurements at the origin of the first ππ* state of jet-cooled NAPA molecules have shown that (i) among the three most stable conformers of the molecule, the folded conformer NAPA B is ∼50-times shorter lived than the extended major conformer NAPA A and (ii) this lifetime is virtually insensitive to deuteration at the NH(2) and NH sites. Concurrent time-dependent density functional theory (TDDFT) based nonadiabatic dynamics simulations in the full dimensionality, carried out for the NAPA B conformer, provided direct insights on novel classes of ultrafast deactivation mechanisms, proceeding through several conical intersections and leading in fine to the ground state. These mechanisms are found to be triggered either (i) by a stretch of the N(Phe)H bond, which leads to an H-transfer to the ring, or (ii) by specific backbone amide distortions. The potential energy surfaces of the NAPA conformers along these critical pathways have been characterized more accurately using the coupled cluster doubles (CC2) method and shown to exhibit barriers that can be overcome with moderate excess energies. These results analyzed in the light of the experimental findings enabled us to assign the short lifetime of NAPA B conformer to a number of easily accessible exit channels from the initial ππ* surface, most importantly the one involving a transfer of electronic excitation to an nπ* surface, induced by distortions of the backbone peptide bond.

Strength of NH···S Hydrogen Bonds in Methionine Residues Revealed by Gas-Phase IR/UV Spectroscopy

Despite of being ubiquitous in proteins, NHbackbone···S hydrogen bonds linking the sulfur atom of methionine or cysteine to backbone NH groups remain poorly documented. Here, we report vibrationally resolved IR NH stretch spectra of two methionine-containing dipeptides (Ac-Phe-Met-NH2 and Ac-Met-Phe-NH2). The conformations observed for both molecules, assigned with the help of DFT-D quantum chemistry, provide spectroscopic evidence for the formation of NHbackbone···S H-bonds, surprisingly strong enough to challenge the classical intrabackbone NH···O═C H-bonds. The methionine side chain is found to fold locally, forming a H-bond with the neighboring amide groups (NH(i) or NH(i+1)). Comparison with protein data bank structural information shows that such a local folding is also common in proteins where it concerns 24% of the methionine residues that have a sulfur atom linked to a backbone NH group. This convergence between the strength of these NH···S H-bonds and protein structural data illustrates their contribution to the stability of protein chains.

Isolated Monohydrates of a Model Peptide Chain: Effect of a First Water Molecule on the Secondary Structure of a Capped Phenylalanine

The formation of monohydrates of capped phenylalanine model peptides, CH(3)-CO-Phe-NH(2) and CH(3)-CO-Phe-NH-CH(3), in a supersonic expansion has been investigated using laser spectroscopy and quantum chemistry methods. Conformational distributions of the monohydrates have been revealed by IR/UV double-resonance spectroscopy and their structures assigned by comparison with DFT-D calculations. A careful analysis of the final hydrate distribution together with a detailed theoretical investigation of the potential energy surface of the monohydrates demonstrates that solvation occurs from the conformational distribution of the isolated peptide monomers. The distribution of the monohydrates appears to be strongly dependent on both the initial monomer conformation (extended or folded backbone) and the solvation site initially occupied by the water molecule. The solvation processes taking place during the cooling can be categorized as follows: (a) solvation without significant structural changes of the peptide, (b) solvation inducing significant distortions of the backbone but retaining the secondary structure, and (c) solvation triggering backbone isomerizations, leading to a modification of the peptide secondary structure. It is observed that solvation by a single water molecule can fold a β-strand into a γ-turn structure (type c) or induce a significant opening of a γ-turn characterized by an elongated C(7) hydrogen bond (type b). These structural changes can be considered as a first step toward the polyproline II condensed-phase structure, illustrating the role played by the very first water molecule in the solvation process.

Experimental and Theoretical Investigation of the Aromatic−Aromatic Interaction in Isolated Capped Dipeptides†

Among the forces responsible for shaping proteins, interactions between side chains of aromatic residues play an important role as they are involved in the secondary and the tertiary structures of proteins contributing to the formation of hydrophobic domains. The purpose of this paper is to document this interaction in two capped dipeptides modeling a segment of a protein chain having two consecutive Phe residues, Ac-Phe-Phe-NH(2) and Ac-Phe-D-Phe-NH(2). These two molecules have been investigated in the gas phase by IR/UV double resonance spectroscopy, and the assignment of the observed conformers has been done by comparison with quantum chemistry calculations. Both peptides are found to adopt a beta-turn type I conformation stabilized by an edge-to-face interaction between the two aromatic rings. Comparison with other dipeptides in the literature demonstrates the impact of this aromatic-aromatic interaction on the shape adopted by the peptide chain, and its role among the other shaping forces (H-bonds, NH-pi interactions) is discussed. As an illustration, the H-bond strength is found to be significantly lower in the beta-turn type I conformer, in which the two rings interact, as compared to the similar conformer where such an interaction does not exist. This structural feature due to the backbone distortion induced by the interaction between the aromatic rings makes this system a good test for evaluating the ability of computational methods to correctly account for the competition between these forces. MP2, SCS-MP2, DFT, and DFT-D methods have been assessed in this respect. Comparison between geometries, energies, and frequency calculations illustrate their respective limitations in describing conformations resulting from a subtle equilibrium between the several interactions at play.

Energetics of a model NH–π interaction: the gas phase benzene–NH3 complex

The dissociation energy of the benzene–ammonia complex formed in a supersonic expansion has been determined (D0=1.84±0.12 kcal mol−1) from the features of its photoionisation curve as obtained by mass-resolved two-color resonant two-photon ionisation. The complex structure, stabilised by a π-type hydrogen bond between the benzene ring and the ammonia molecule located above, has also been obtained by a semi-empirical model. The neutral structure found is in good agreement with experiment and the best ab initio calculations in the literature. The ionic structures calculated enable us to interpret the slowly increasing photoionisation curve as a consequence of a large equilibrium geometry change between neutral and ion. The present study also shows that the benzene–ammonia complex is less bound than its homologue with water by ca. 0.6 kcal mol−1. However, the value found indicates that the NH–π interaction can be taken into account when modelling the structure of biological systems.

Gas phase folding of an (Ala)4 neutral peptide chain: spectroscopic evidence for the formation of a β-hairpin H-bonding pattern

IR and UV laser spectroscopy of an Ala-based 4-residue model peptide recorded under gas phase isolated conditions provides evidence for the intrinsic stability of compact folded structures resembling the extremity of a beta-hairpin, with a C(14) H-bond bridging the two ends of the chain, and enables us to assess the capabilities of new quantum chemistry techniques to account for dispersive interactions in a medium-size molecule.