Wutharath Chin

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.

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 models of γ turns: Effect of side-chain/backbone interactions investigated by IR/UV spectroscopy and quantum chemistry

The conformations of laser-desorbed jet-cooled short peptide chains Ac-Phe-Xxx-NH2 (Xxx=Gly, Ala, Val, and Pro) have been investigated by IR/UV double resonance spectroscopy and density-functional-theory (DFT) quantum chemistry calculations. Singly gamma-folded backbone conformations (betaL-gamma) are systematically observed as the most stable conformers, showing that in these two-residue peptide chains, the local conformational preference of each residue is retained (betaL for Phe and gamma turn for Xxx). Besides, beta turns are also spontaneously formed but appear as minor conformers. The theoretical analysis suggests negligible inter-residue interactions of the main conformers, which enables us to consider these species as good models of gamma turns. In the case of valine, two similar types of gamma turns, differing by the strength of their hydrogen bond, have been found both experimentally and theoretically. This observation provides evidence for a strong flexibility of the peptide chain, whose minimum-energy structures are controlled by side-chain/backbone interactions. The qualitative conformational difference between the present species and the reversed sequence Ac-Xxx-Phe-NH2 is also discussed.

Infrared study of glycolaldehyde isolated in parahydrogen matrix

The infrared spectrum of glycolaldehyde sugar model in solid parahydrogen is reported and interpreted in the light of ab initio anharmonic frequency calculations. The advantages of parahydrogen lead to a simplification of its infrared spectroscopy compared to other conventional matrices. Surprisingly, the sugar molecule is found to display an unexpected large bandwidth compared to the smaller organic molecules studied in parahydrogen so far. Among them, only glycolaldehyde possesses an internal hydrogen-bond. Band broadening in glycolaldehyde is interpreted as originating mainly from the presence of the hydrogen-bond and to a lesser extent from clustering with oH(2) impurities.

Secondary structures of Val–Phe and Val–Tyr(Me) peptide chains in the gas phase: effect of the nature of the protecting groups

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: β-strand and β-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 β-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.

Photochemistry of acetylacetone isolated in parahydrogen matrices upon 266 nm irradiation

The photochemistry of the chelated enol form of acetylacetone (AcAc) was investigated by UV excitation of the S(2) state at 266 nm in parahydrogen matrices, complemented by experiments in neon and normal hydrogen matrices. Infrared (IR) spectroscopy, combined with theoretical calculations, was used to identify the photoproducts. Isomerization towards various non-chelated forms (no intramolecular H-bond) of AcAc is the dominant channel whereas fragmentation is very minor. The isomerization kinetics is monitored by IR spectroscopy. Among the seven non-chelated conformers of AcAc, only three are formed in parahydrogen matrices, whereas four are observed in normal hydrogen matrices. This difference suggests that an active tunnelling process between conformers occurs in parahydrogen but is quenched in normal hydrogen where guest-host interactions are stronger. Fragmentation and isomerization of excited AcAc are discussed in the light of these new data. The role of the intermediate triplet state in the S(2)→ S(0) relaxation is confirmed, as the importance of phonons in the condensed phase.

Nuclear Spin Conversion to Probe the Methyl Rotation Effect on Hydrogen‐Bond and Vibrational Dynamics

A noteworthy example of a molecule with coupled large-amplitude motions is provided by acetylacetone (methyl group torsions and intramolecular hydrogen bonds). The molecule was trapped in solid parahydrogen to investigate the complex proton tunneling processes. Nuclear spin conversion in methyl groups is observed and, combined with IR spectra, documents the coupling between high frequency modes and large amplitude motions.

Unveiled optical properties of tetrapyrollic pigments in cryogenic environments

An unexpected phenomenon was revealed in the laser induced fluorescence spectra of free-base (H2Pc) and zinc (ZnPc) phthalocyanines trapped in rare gas and nitrogen matrices under a moderate increase in the laser intensity. In all matrices the intensity of an emission band near 755nm increased drastically when pumping the S1←S0 transition. This observation was assigned to stimulated emission in a four-level scheme involving a vibronic transition from the lowest electronic state to a vibrational level of the ground state. In the present work, we expose new similar results obtained with porphyrin molecules, i.e. tetra-benzoporphin (TBP). With free-base H2TBP, stimulated emission was observed in Ar or N2 matrices, but not in Xe matrices. A possible reason could be a fast inter-system crossing rate due to the heavy atom effect induced by Xe. We also report the observation of persistent burnt spectral holes, although the low efficiency of this process is not competitive with stimulated emission and no decrease...

Photochemistry of glycolaldehyde in cryogenic matrices

The photochemistry of glycolaldehyde (GA) upon irradiation at 266 nm is investigated in argon, nitrogen, neon, and para-hydrogen matrices by IR spectroscopy. Isomerization and fragmentation processes are found to compete. The hydrogen-bonded Cis-Cis form of GA is transformed mainly to the open Trans-Trans conformer and to CO and CH3OH fragments and their mixed complexes. Different photo-induced behaviours appear depending on the matrix. In nitrogen, small amounts of Trans-Gauche and Trans-Trans conformers are detected after deposition and grow together upon irradiation. The Trans-Gauche conformer is characterized for the first time. In para-hydrogen due to a weaker cage effect additional H2CO and HCO fragments are seen. Calculations of the potential energy surfaces of S0, S1, and T1 states--to analyse the torsional deformations which are involved in the isomerization process--and a kinetic analysis are presented to investigate the different relaxation pathways of GA. Fragmentation of GA under UV irradiation through the CO+CH3OH molecular channel is a minor process, as in the gas phase.