Anouk M. Rijs

Ir spectroscopy of isolated neutral and protonated adenine and 9-methyladenine

IR spectroscopy is employed to study isolated adenine and its derivative 9-methyladenine in both their neutral and protonated forms. The IR spectra of neutral adenine and 9-methyladenine are measured in a molecular beam expansion via IR-UV ion-dip spectroscopy in the 525 to 1750 cm(-1) region. For adenine, UV excitation selects the 9H tautomer to give a conformer-selective IR spectrum. For 9-methyladenine, only one tautomer exists because of the methyl substitution at the N(9) position. The experimental spectra agree closely with spectra computed for these tautomers at the B3LYP/6-311++G(df,pd) level of theory. These spectra complement previous tautomer-specific IR spectra in the hydrogen stretching range. The 9H-adenine spectrum obtained is compared to a previously recorded FTIR spectrum of adenine at 280 °C, which shows close agreement, although the 7H tautomer cannot be excluded from contributing. Protonated adenine and 9-methyladenine are generated by electrospray ionization and studied via IR multiple-photon dissociation (IRMPD) spectroscopy. Comparison of the experimental spectra with computed spectra allows identification of the protonation site, which suggests that the 1-9 tautomer is the dominant contributor to the spectra.

Gas-Phase IR Spectroscopy and Structure of Biological Molecules

IR spectroscopic techniques to study isolated biomolecules.- Cryogenic methods for the spectroscopy of large, biomolecular ions.- Theoretical Methods for vibrational spectroscopy and collision induced dissociation in the gas phase.- Peptide fragmentation products in mass spectrometry probed by infrared spectroscopy.- Spectroscopy of Metal-Ion Complexes with Peptide-Related Ligands.- Isolated neutral peptides.- Gas-phase IR Spectroscopy of Nucleobases.- Carbohydrates.- Microwave spectroscopy of biomolecular building blocks.

Mid-infrared spectroscopy of molecular ions in helium nanodroplets.

High resolution IR spectra of aniline, styrene, and 1,1-diphenylethylene cations embedded in superfluid helium nanodroplets have been recorded in the 300-1700 cm(-1) range using a free-electron laser as radiation source. Comparison of the spectra with available gas phase data reveals that the helium environment induces no significant matrix shift nor leads to an observable line broadening of the resonances. In addition, the IR spectra have provided new and improved vibrational transition frequencies for the cations investigated, as well as for neutral aniline and styrene. Indications have been found that the ions desolvate from the droplets after excitation by a non-evaporative process in which they are ejected from the helium droplets. The kinetic energy of the ejected ions is found to be ion specific and to depend only weakly on the excitation energy.

Gas-Phase Peptide Structures Unraveled by Far-IR Spectroscopy: Combining IR-UV Ion-Dip Experiments with Born–Oppenheimer Molecular Dynamics Simulations†

Vibrational spectroscopy provides an important probe of the three-dimensional structures of peptides. With increasing size, these IR spectra become very complex and to extract structural information, comparison with theoretical spectra is essential. Harmonic DFT calculations have become a common workhorse for predicting vibrational frequencies of small neutral and ionized gaseous peptides. Although the far-IR region (<500 cm(-1)) may contain a wealth of structural information, as recognized in condensed phase studies, DFT often performs poorly in predicting the far-IR spectra of peptides. Here, Born-Oppenheimer molecular dynamics (BOMD) is applied to predict the far-IR signatures of two γ-turn peptides. Combining experiments and simulations, far-IR spectra can provide structural information on gas-phase peptides superior to that extracted from mid-IR and amide A features.

Internal Proton Transfer Leading to Stable Zwitterionic Structures in a Neutral Isolated Peptide

Decades of gas-phase spectroscopy of small biomolecules have enabled some of the intrinsic physical and chemical properties of the building blocks of life to be unraveled. Bridging the gap towards an understanding of the biological function of these biomolecules has become an essential issue. For the processes that take place in the active sites of functional proteins at the molecular level to be understood, two critical aspects must be taken into account: 1) interactions with the biological environment (protons, electrons, metal ions, water molecules) and 2) the specific organization of a few significant amino acid residues nested in the welldefined local environment shaped by the entire protein. In this context, it is important to pursue a bottom-up approach, whereby elements of the environment can be introduced stepby-step in a controlled fashion until the biological function emerges. A crucial discrepancy between the gas-phase structure of isolated amino acids and peptides and their biologically relevant counterparts is the transition from the canonical to the zwitterionic form. Whereas neutral, isolated amino acids and peptides have always been found in their canonical form, studies on ionic complexes have shown that zwitterionic forms may be stabilized by the addition of a proton, an electron, a metal cation, or a metal dication or by microsolvation. In the case of overall-neutral complexes, the canonical-to-zwitterionic transition was observed upon the stepwise addition of solvent molecules. We report herein the first observation of an “autozwitterion” formed by intramolecular proton transfer between nearby residues in a neutral, isolated peptide. We specifically designed the pentapeptide Ac-Glu-Ala-Phe-Ala-Arg-NHMe (EAFAR; Scheme 1) with an appropriate structure for

Controlled Hydrogen-Bond Breaking in a Rotaxane by Discrete Solvation

Controlling a molecular brake: Binding interactions between the thread and the macrocycle of a [2]rotaxane can be tuned in a quasi-continuous manner by adding hydrogen-bond-forming solvent molecules one at a time to an isolated [2]rotaxane molecule. Conformational changes that detach the thread from the macrocycle can be induced controllably, and the system resembles a molecular version of applying and releasing a brake.

IR Spectroscopy on Jet-Cooled Isolated Two-Station Rotaxanes

High-resolution IR spectroscopy has been employed to study isolated, switchable [2]rotaxanes. IR absorption spectra of two-station rotaxanes, their separate thread, and macrocycle components, as well as those of the individual stations incorporated into the thread, have been measured in the 1800-1000 cm(-1) region. These spectra have been fully analyzed, aided by quantum chemical predictions of the IR spectra. From these analyses, a comprehensive picture emerges of the conformational structure and binding interactions between the mechanically interlocked components of the rotaxane.

Isolated Gramicidin Peptides Probed by IR Spectroscopy

We report double-resonant IR/UV ion-dip spectroscopy of neutral gramicidin peptides in the gas phase. The IR spectra of gramicidin A and C, recorded in both the 1000 cm(-1) to 1800 cm(-1) and the 2700 to 3750 cm(-1) region, allow structural analysis. By studying this broad IR range, various local intramolecular interactions are probed, and complementary IR modes can be accessed. Ab initio quantum chemical calculations are used to support the interpretation of the experimental IR spectra. The comparison of the calculated frequencies with the experimental IR spectrum probed via the strong infrared absorptions of all the amide groups (NH stretch, C=O stretch and NH bend), shows evidence for a helical structure in the gas phase, which is similar to that in the condensed phase. Additionally, we show that to improve the spectral resolution when studying large neutral molecular structures of the size of gramicidin, the use of heavier carrier gas could be advantageous.

Conformational Study of Z-Glu-OH and Z-Arg-OH: Dispersion Interactions versus Conventional Hydrogen Bonding

The gas-phase conformational preferences of the model dipeptides Z-Glu-OH and Z-Arg-OH have been studied in the low-temperature environment of a supersonic jet. IR-UV ion-dip spectra obtained using the free electron laser FELIX provide conformation-specific IR spectra, which in combination with density functional theory (DFT) allow us to determine the conformational structures of the peptides. Molecular dynamics modeling using simulated annealing generates a variety of low-energy structures, for which geometry optimization and frequency calculations are then performed using the B3LYP functional with the 6-311+G(d,p) basis set. By comparing experimental and theoretical IR spectra, three conformations for Z-Glu-OH and two for Z-Arg-OH have been identified. For three of the five structures, the dispersion interaction provides an important contribution to the stabilization, emphasizing the importance of these forces in small peptides. Therefore, dispersion-corrected DFT functionals (M05-2X and B97D) have also been employed in our theoretical analysis. Second-order Møller-Plesset perturbation theory (MP2) has been used as benchmark for the relative energies of the different conformational structures. Finally, we address the ongoing debate on the gas-phase structure of arginine by elucidating whether isolated arginine is canonical, tautomeric, or zwitterionic.

The 'magnetic bottle' spectrometer as a versatile tool for laser photoelectron spectroscopy.

Abstract This paper discusses the use of ‘magnetic bottle’ spectrometers in laser photoelectron spectroscopy. For electron detection both normal time-of-flight methods as well as zero-kinetic energy electron detection with almost laser-limited resolution can be employed. Photofragmentation processes can be monitored via time-of-flight ion detection. A ‘magnetic bottle’ spectrometer can be successfully combined with a molecular beam. To illustrate some of the features, results for the photodissociation of OCS are presented. Highly rotationally excited CO molecules, and S atoms in their excited 1 D 2 state are produced. Rotationally resolved photoelectron spectroscopy of CO is the key to a better understanding of the dynamics of the photoionisation process.