Corey A. Rice

Elementary peptide motifs in the gas phase: FTIR aggregation study of formamide, acetamide, N-methylformamide, and N-methylacetamide.

Cold, isolated peptide model compounds and their aggregates are generated in pulsed supersonic jet expansions and detected by FTIR spectroscopy in the amide-A region, complemented by amide-I spectra. The most stable, symmetric dimer of formamide is unambiguously assigned in the gas phase for the first time, also by comparison to the analogous acetamide dimer. Efficient quenching of a hot-state Fermi resonance by cooling of the dimers is invoked. As the preferred relative orientation of the C=O and N-H groups in N-methylated formamide and acetamide is trans, these compounds show a fundamentally different dimerization pattern. Their most stable dimers, which would be analogous to those of formamide and acetamide, remain undetected as a consequence of kinetic control in the jet. Accurate benchmark quantities for multidimensional vibrational treatments of these peptide models are derived, and the influence of methyl groups on the N-H stretching dynamics is discussed.

Dimerization of Pyrazole in Slit Jet Expansions

Abstract Pyrazole dimer is observed for the first time in a free jet expansion. Its IR-active N–H stretching vibration is shifted by −269 cm−1 relative to the monomer. Along the 600 mm slit jet expansion, the average number density of pyrazole dimers is ∼ 1011 cm−3. Exploratory quantum chemical calculations including electron correlation are in good agreement with the observed frequency shift and confirm reciprocal hydrogen bonding with bent hydrogen bonds in a planar C2h structure, as postulated by W. Hückel 65 years ago in this journal. Nanomatrix isolation spectra can be obtained by using Ar as the carrier gas. The more strongly coupled vibrational dynamics in pyrazole trimer is illustrated.

Infrared spectroscopy of pyrrole-2-carboxaldehyde and its dimer: A planar β-sheet peptide model?

Intermolecular interactions relevant for antiparallel beta-sheet formation between peptide strands are studied by Fourier transform infrared spectroscopy of the low temperature, vacuum-isolated model compound pyrrole-2-carboxaldehyde and its dimer in the N-H and C=O stretching range. Comparison to quantum chemical predictions shows that even for some triple-zeta quality basis sets, hybrid density functionals and Møller-Plesset perturbation calculations fail to provide a consistent and fully satisfactory description of hydrogen bond induced frequency shifts and intensity ratios in the double-harmonic approximation. The latter approach even shows problems in reproducing the planar structure of the dimer and the correct sign of the C=O stretching shift for standard basis sets. The effect of matrix isolation is modeled by condensing layers of Ar atoms on the isolated monomer and dimer. The dimer structure is discussed in the context of the peptide beta-sheet motif.

Electronic spectroscopy of carbon chains and rings of astrophysical interest.

This perspective is concerned with laboratory measurements of the electronic spectra of carbon chains, rings, and their ions, including derivatives terminated by hydrogen and nitrogen atoms. The selected-species have relevance to astronomical observations through diffuse clouds, absorption features known as diffuse interstellar bands (DIBs). Two indications to decide which molecules should be studied are the observations of polar carbon chains in dense clouds by rotational spectroscopy and the knowledge that a certain number of these have electronic transitions in the DIB region. This information has been obtained initially by measurements of the electronic absorptions in 6 K neon matrixes using mass-selection. This was followed by the gas-phase observations using cavity ringdown and resonance enhanced techniques in combination with pulsed-supersonic discharge sources or via laser vaporization. The gas-phase spectra were then compared with DIB data, all with negative results, except for the detection of C3, but leading to upper limits of their column densities <10(12) cm–2. By reference to mm-wave absorption measurements in the diffuse medium, it is shown that, although species such as H2C3 are present there, the product of the expected column densities and oscillator strength of the transitions will lead to only very weak DIBs. The significant conclusion is that carbon chains and their derivatives containing hydrogen or nitrogen comprising up to a dozen atoms cannot be responsible for stronger DIBs. However, chains with an odd-number of carbon atoms, C17, C19, ···, have very intense transitions in the region above 4400 Å and remain attractive candidates. An uncertainty is the excited electronic state lifetime; if this is less than 70 fs, then the resulting absorptions would be too broad to be astronomically relevant. The electronic absorptions of some of the species studied bear a striking resemblance to DIB data. The two peaked rotational contour of the origin band in the electronic transition of dicyanoacetylene cation is superimposable on a DIB absorption when shifted by 1 Å. The band profiles of cyclic C18 at 100 or 20 K are similar to DIBs but differ in wavelength. This suggests that another set of potential candidates are the carbon rings of sizes up to a hundred of atoms, including ions and heavy atoms, with the requirement of a large oscillator strength. Observations on the absorptions of propadienylidene C3H2 and C60+ are discussed.

Adaptive aggregation of peptide model systems.

Jet-cooled infrared spectra of acetylated glycine, alanine, and dialanine esters and their dimers are reported in the amide A and amide I-III regions. They serve as particularly simple peptide aggregation models and are found to prefer a single backbone conformation in the dimer that is different from the most stable monomer backbone conformation. In the case of alanine, evidence for topology-changing chirality discrimination upon dimer formation is found. The jet spectroscopic results are compared to gas phase spectra and quantum chemical calculations. They provide reliable benchmarks for the evaluation of the latter in the field of peptide interactions.

Gas-phase Electronic Spectra of Coronene and Corannulene Cations

Gas-phase electronic spectra of the coronene () and corannulene () cations complexed with helium have been recorded in a quadrupole ion trap at 5 K by photodissociation. The electronic spectrum of with two helium atoms was also measured to estimate the perturbation. This method is sufficient for an astronomical comparison because the shift due to the weakly bound helium is on the order of 0.2 A. has the origin band of the transition at 9438.3 A and that to a much higher state at 4570 A. The corannulene cation is subject to a Jahn–Teller distortion in the electronic ground state, leading to the and transitions with origin band maxima when complexed with helium at 5996.1 and 5882.6 A. These absorptions lie in a region where there is a congestion of diffuse interstellar bands (DIBs). However, the recorded features have no match with astronomical observations, removing coronene and corannulene cations and probably other aromatic hydrocarbons of this size as possible carriers of the DIBs.

ELECTRONIC SPECTRUM OF IN THE GAS PHASE AT 10 K

The analysis of the λ5797.1 diffuse interstellar band (DIB) by Huang & Oka concludes that the carrier is a chain-like molecule with five to seven heavy atoms with a large oscillator strength, f ≈ 1, for the electronic transition. The spectra of carbon chains of this size with transitions in the visible have been obtained in the gas phase, but the f-values are too small. We have now found that certain carbon-chain cations with transitions in the DIB range have large f-values. An example is the origin band at 4387.7 A of the 1 1AA1 electronic transition of the H2C7H+ chain with f ≈ 0.3. This could be measured in the gas phase at 10 K in an ion trap. Astrophysical relevance of such cations is discussed.

Gas-Phase Electronic Transitions of C17H12N+ at 15 K

The electronic spectrum of C17H12N(+), phenanthrene with a side chain, was measured in the gas phase at a vibrational and rotational temperature of ∼15 K in an ion trap using a resonant multiphoton dissociation technique. The C17H12N(+) structure was produced in a chemical ionization source and identified by a comparison with theoretical calculations of stable structures and excitation energies. The (3), (2), (1) (1)A ← X (1)A electronic transitions of this nitrogen-containing aromatic species with 30 atoms have origin band maxima at 23,586 ± 1 cm(-1), 16,120 ± 50 cm(-1), and 14,519 ± 30 cm(-1). Distinct vibrational structure in the (3) (1)A state is observed, and assignments are made. Astronomical aspects are considered.

Electronic absorption spectrum of triacetylene cation for astronomical considerations.

The A(2)Πg ← X(2)Πu electronic transition (4800-6000 Å) of triacetylene cation was measured in an ion trap, where the vibrational and rotational degrees of freedom were equilibrated to 25 K. The rotational profile of the origin band is predicted by a collisional-radiative rate model under conditions expected in diffuse interstellar clouds. Variation in the density of the surrounding gas, rotational temperature, and velocity dispersion are taken into account.

OPTICAL ABSORPTIONS OF OXYGENATED CARBON CHAIN CATIONS IN THE GAS PHASE

The gas-phase electronic spectra of linear OC4O+ and a planar C6H2O+ isomer were obtained at a rotational temperature of ≈10 K. Absorption measurements in a 6 K neon matrix were followed by gas-phase observations in a cryogenic radiofrequency ion trap. The origin bands of the