Oleg V. Boyarkin

Spectroscopic studies of cold, gas-phase biomolecular ions

While the marriage of mass spectrometry and laser spectroscopy is not new, developments over the last few years in this relationship have opened up new horizons for the spectroscopic study of biological molecules. The combination of electrospray ionisation for producing large biological molecules in the gas phase together with cooled ion traps and multiple-resonance laser schemes are allowing spectroscopic investigation of individual conformations of peptides with more than a dozen amino acids. Highly resolved infrared spectra of single conformations of such species provide important benchmarks for testing the accuracy of theoretical calculations. This review presents a number of techniques employed in our laboratory and in others for measuring the spectroscopy of cold, gas-phase protonated peptides. We show examples that demonstrate the power of these techniques and evaluate their extension to still larger biological molecules.

Interplay of Intra- and Intermolecular H-Bonding in a Progressively Solvated Macrocyclic Peptide

Hydrated in a Hurry Water has a major influence on the conformation of proteins and related biomolecules. However, so many water molecules participate in the hydrogen bonding networks that it can be difficult to pinpoint which specific interactions play the biggest role. Nagornova et al. (p. 320) sought to answer this question for the case of a 10–amino acid ring—the antibiotic compound Gramicidin S—by probing the conformational impact of successive additions of one to 50 water molecules to the naked gas-phase structure. The primary changes in the overall ring geometry came from the addition of just the first two waters. The main conformational changes associated with the hydration of a peptide ring ensue upon the addition of just two water molecules. Studying solvation of a large molecule on an atomic level is challenging because of the transient character and inhomogeneity of hydrogen bonding in liquid water. We studied water clusters of a protonated macrocyclic decapeptide, gramicidin S, which were prepared in the gas phase and then cooled to cryogenic temperatures. The experiment spectroscopically tracked fine structural changes of the clusters upon increasing the number of attached water molecules from 1 to 50 and distinguished vibrational fingerprints of different conformers. The data indicate that only the first two water molecules induce a substantial change of the gramicidin S structure by breaking two intramolecular noncovalent bonds. The peptide structure remains largely intact upon further solvation, reflecting the interplay between the strong intramolecular and weaker intermolecular hydrogen bonds.

Intramolecular energy transfer in highly vibrationally excited methanol. I. Ultrafast dynamics

Vibrational overtone excitation of jet-cooled methanol, in combination with infrared laser assisted photofragment spectroscopy (IRLAPS) detection, reveals OH stretch bands that are significantly simplified with respect to room-temperature spectra. The simplification afforded by jet-cooling permits the observation of spectral splitting on the order of 50 cm(-1) in the region of the 5 nu(1) OH stretch overtone band. Tracking this splitting as a function of OH stretch vibrational level in combination with isotopic substitution studies allows us to identify the perturbing state as the combination level involving four quanta of OH stretch and one quantum of CH asymmetric stretch, 4 nu(1) + nu(2). Careful examination of the spectra reveals that this strong interaction arises from a fourth-order anharmonic term in the Hamiltonian that couples the OH and CH ends of the molecule. These frequency domain results indicate that subsequent to coherent excitation of the 5 nu(1) band, methanol would undergo energy redistribution to the methyl part of the molecule on a time scale of similar to 130 fs. This work also suggests that similar strong resonances may occur more generally in molecules that possess two different high-frequency oscillators in close proximity

Conformation-specific infrared and ultraviolet spectroscopy of tyrosine-based protonated dipeptides

We present the spectroscopy and photofragmentation dynamics of two isomeric protonated dipeptides, H+AlaTyr and H+TyrAla, in a cold ion trap. By a combination of infrared-ultraviolet double resonance experiments and density functional theory calculations, we establish the conformations present at low temperature. Interaction of the charge at the N-terminus with the carbonyl group and the tyrosine pi-cloud seems to be critical in stabilizing the low-energy conformations. H+AlaTyr has the flexibility to allow a stronger interaction between the charge and the aromatic ring than in H+TyrAla, and this interaction may be responsible for many of the differences we observe in the former: a significant redshift in the ultraviolet spectrum, a much larger photofragmentation yield, fewer stable conformations, and the absence of fragmentation in excited electronic states.

Highly resolved spectra of gas-phase gramicidin s: a benchmark for peptide structure calculations.

We have measured a vibrationally resolved UV spectrum of doubly protonated gramicidin S (GS) in the gas phase and, subsequently, a highly resolved, conformer-specific IR spectrum in the 6 mum fingerprint region, using a cold ion trap in combination with table-top lasers. The study has revealed at least three conformational states of GS populated under our experimental conditions, with the major one showing evidence of a symmetric three-dimensional structure similar to that in the condensed phase. The derived qualitative constraints, along with the measured vibrational frequencies, serve as a benchmark for computations of peptide structure.

A direct measurement of the dissociation energy of water

We have performed a direct measurement of one of the most fundamental thermochemical values: the O-H bond energy in water. Using a triple-resonance laser excitation scheme, we excite the molecule through a series of vibrational overtone transitions to access directly the onset of the dissociative continuum. The dissociation energy obtained from our experiments, 41145.94+/-0.15 cm(-1), is approximately 30 times more accurate than the currently accepted value and has important implications for other thermochemical quantities linked to the bond energy of water.

Intramolecular energy transfer in highly vibrationally excited methanol. II. Multiple time scales of energy redistribution

State-selected spectra of the OH stretch overtones of methanol in the range of upsilon(1) = 3-8 reveal spectral splittings and broadenings that result from vibrational couplings within the molecule. We employ a two-color excitation technique in which an infrared pulse promotes jet-cooled methanol molecules to a single rotational state in upsilon(1) = 1 or 2 and a second visible or near-infrared laser pulse is scanned to record a vibrational overtone spectrum. The final vibrationally excited species are detected by infrared laser assisted photofragment spectroscopy. The implications of the spectra for vibrational dynamics in the time domain can be understood in terms of a hypothetical coherent excitation of relevant portions of the spectrum. The observed splittings and widths correspond to three time scales. The largest splittings imply subpicosecond oscillation of energy between the OH stretch and a combination with the C-H stretch (5 nu(1) double left right arrow 4 nu(1) + nu(2) and 6 nu(1) double left right arrow 5 nu(1) + nu(2)) or a combination with the COH bend (7 nu(1) double left right arrow 6 nu(1) + 2 nu(6)). Secondary time scales correspond to finer splittings and are thought to arise from low-order resonances with other vibrational states. We argue that the nonmonotonic energy dependence of the presence and extent of such secondary structure throughout the recorded spectra reflects the requirement of resonance with important zeroth-order states. The third time scale, represented by the widths of the narrowest features at each overtone level, reflects the onset of vibrational energy randomization. These widths increase exponentially with vibrational energy in the range 2 nu(1) up to 8 nu(1). At the highest energy (25 000 cm(-1)) the three time scales begin to converge, implying an irreversible decay of the OH stretch overtone in 300 fs

UV and IR Spectroscopic Studies of Cold Alkali Metal Ion-Crown Ether Complexes in the Gas Phase

We report UV photodissociation (UVPD) and IR-UV double-resonance spectra of dibenzo-18-crown-6 (DB18C6) complexes with alkali metal ions (Li(+), Na(+), K(+), Rb(+), and Cs(+)) in a cold, 22-pole ion trap. All the complexes show a number of vibronically resolved UV bands in the 36,000-38,000 cm(-1) region. The Li(+) and Na(+) complexes each exhibit two stable conformations in the cold ion trap (as verified by IR-UV double resonance), whereas the K(+), Rb(+), and Cs(+) complexes exist in a single conformation. We analyze the structure of the conformers with the aid of density functional theory (DFT) calculations. In the Li(+) and Na(+) complexes, DB18C6 distorts the ether ring to fit the cavity size to the small diameter of Li(+) and Na(+). In the complexes with K(+), Rb(+), and Cs(+), DB18C6 adopts a boat-type (C(2v)) open conformation. The K(+) ion is captured in the cavity of the open conformer thanks to the optimum matching between the cavity size and the ion diameter. The Rb(+) and Cs(+) ions sit on top of the ether ring because they are too large to enter the cavity of the open conformer. According to time-dependent DFT calculations, complexes that are highly distorted to hold metal ions open the ether ring upon S(1)-S(0) excitation, and this is confirmed by extensive low-frequency progressions in the UVPD spectra.

Cold Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide

Keywords: spectroscopy, peptides, cold ion traps, mass spectrometry Reference EPFL-ARTICLE-164212doi:10.1002/anie.201100702View record in Web of Science Record created on 2011-03-11, modified on 2017-11-27

Structure and Bonding of Isoleptic Coinage Metal (Cu, Ag, Au) Dimethylaminonitrenes in the Gas Phase

Dimethylaminonitrene complexes of IMesM(+) (IMes =1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene; M = Cu, Ag, Au) were prepared in the gas phase and structurally characterized by high-resolution infrared spectroscopy of the cold species, ion-molecule reactions, and DFT computations. We measured the binding energies of the nitrene fragment to the IMesM(+) moiety by energy-resolved collision-induced dissociation experiments in the gas phase, affording a trend in bond strength of M = Cu ≈ Au > Ag. This trend is explained in terms of a detailed metal-nitrogen bonding analysis, from which relativistic effects on the bonding were assessed. Various density functionals were evaluated for reproducing the observed thermochemical data and Truhlars M06 functional was found to give the best agreement.