Unraveling the internal dynamics of the benzene dimer: a combined theoretical and microwave spectroscopy study.

We report a combined theoretical and microwave spectroscopy study of the internal dynamics of the benzene dimer, a benchmark system for dispersion forces. Although the extensive ab initio calculations and experimental work on the equilibrium geometry of this dimer have converged to a tilted T-shaped structure, the rich internal dynamics due to low barriers for internal rotation have remained largely unexplored. We present new microwave spectroscopy data for both the normal (C6H6)2 and partially deuterated (C6D6)(C6H6) dimers. The splitting patterns obtained for both species are unraveled and understood using a reduced-dimensionality theoretical approach. The hindered sixfold rotation of the stem can explain the observed characteristic 1 : 2 : 1 tunneling splitting pattern, but only the concerted stem rotation and tilt tunneling motion, accompanied by overall rotation of the dimer, yield the correct magnitude of the splittings and their strong dependence on the dimer angular momentum J that is essential to explain the experimental data. Also the surprising observation that the splittings are reduced by 30% for the mixed (C6D6)(C)(C6H6)(S) dimer in which only the cap (C) in the T-shaped structure is deuterated, while the rotating stem (S) monomer is the same as in the homodimer, is understood using this approach. Stark shift measurements allowed us to determine the dipole moment of the benzene dimer, µ = 0.58 ± 0.051 D. The assumption that this dipole moment is the vector sum of the dipole moments induced in the monomers by the electric field of the quadrupole on the other monomer yields a calculated value of µ = 0.63 D. Furthermore, the observed Stark behavior is typical for a symmetric top, another confirmation of our analysis.

Diagnosing the protonation site of b2 peptide fragment ions using IRMPD in the X-H (X = O, N, and C) stretching region.

Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here we report on the characterization of the protonation site of oxazolone b(2) ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier work, here we provide complementary IR spectra in the 2800-3800 cm(-1) range acquired on a table-top laser system. Combining this tunable laser with a high power CO(2) laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it is shown that a band at 3445 cm(-1), corresponding to the asymmetric N-H stretch of the (nonprotonated) N-terminal NH(2) group, is a distinct vibrational signature of the ring-protonated oxazolone structure.

Infrared spectroscopy of fragments of protonated peptides: direct evidence for macrocyclic structures of b5 ions.

b ions are of fundamental importance in peptide sequencing using tandem mass spectrometry. These ions have generally been assumed to exist as protonated oxazolone derivatives. Recent work indicates that medium-sized b ions can rearrange by head-to-tail cyclization of the oxazolone structures generating macrocyclic protonated peptides as intermediates. Here, we show using infrared spectroscopy and density functional theory calculations that the b(5) ion of protonated G(5)R exists in the mass spectrometer as an amide oxygen protonated cyclic peptide rather than fleetingly as a transient intermediate. This assignment is supported by our DFT calculations which show this macrocyclic isomer to be energetically preferred over the open oxazolone form despite the entropic constraints the cyclic form introduces.

Infrared spectroscopy of fragments from doubly protonated tryptic peptides.

Most proteins in proteomics are identified from tandem mass spectra of doubly protonated tryptic peptides. Statistical studies indicate that these spectra fall into two distinct classes. IR spectroscopy experiments and DFT calculations performed on model b(2) ions show that peptides producing Class I spectra form protonated oxazolone ions (see figure) and not protonated diketopiperazines as proposed elsewhere.

IRMPD spectroscopy of a protonated, phosphorylated dipeptide.

The protonated, phosphorylated dipeptide [GpY+H](+) is characterized by mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and quantum-chemical calculations. The ions are generated in an external electrospray source and analyzed in a Fourier transform ion cyclotron resonance mass spectrometer, and their fragmentation is induced by resonant absorption of multiple photons emitted by a tunable free-electron laser. The IRMPD spectra are recorded in the 900-1730 cm(-1) range and compared to the absorption spectra computed for the lowest energy structures. A detailed calibration of computational levels, including B3LYP-D and coupled cluster, is carried out to obtain reliable relative energies of the low-energy conformers. It turns out that a single structure can be invoked to assign the IRMPD spectrum. Protonation at the N terminus leads to the formation of a strong ionic hydrogen bond with the phosphate P=O group in all low-energy structures. This leads to a P=O stretching frequency for [GpY+H](+) that is closer to that of [pS+H](+) than to that of [pY+H](+) and thus demonstrates the sensitivity of this mode to the phosphate environment. The COP phosphate ester stretching mode is confirmed to be an intrinsic diagnostic for identification of which type of amino acid is phosphorylated.

Selector for structural isomers of neutral molecules.

We have selected and spatially separated the two conformers of 3-aminophenol (C(6)H(7)NO) present in a molecular beam. Analogous to the separation of ions based on their mass-to-charge ratios in a quadrupole mass filter, the neutral conformers are separated based on their different mass-to-dipole-moment ratios in an ac electric quadrupole selector. For a given ac frequency, the individual conformers experience different focusing forces, resulting in different transmissions through the selector. These experiments demonstrate that conformer-selected samples of large molecules can be prepared, offering new possibilities for the study of gas-phase biomolecules.

Cold collisions catalyse conformational conversion.

We have determined the abundance of two different conformational structures of the mixed benzene dimer (C(6)H(6))(C(6)D(6)) in a molecular beam, with various carrier gases. These two T-shaped conformers have a subtle zero-point energy difference of only a few cm(-1), and a transition state barrier of about 64 cm(-1). Nevertheless, depending on the carrier gas, the lowest energy conformer can exclusively be prepared in the molecular beam. Low-energy two-body collisions of the benzene-dimers with the carrier gas atoms are concluded to be responsible for this.

An experimental value for the B(1u) C-H stretch mode in benzene.

We here present experimental infrared spectra on two (C(6)H(6))(C(6)D(6)) benzene dimer isomers in the gas phase. The spectra show that the two benzene molecules in the dimer are symmetrically inequivalent and have distinct IR signatures. One of the two molecules is in a site of low symmetry, which leads to the IR activation of fundamental modes that are IR forbidden by symmetry in the monomer. In the spectra, all four fundamental C-H stretch modes of benzene are observed. Modes in the dimer are shifted up to 3 cm(-1) to the red, compared to the modes that are known for the monomer. For the nu(13) B(1u) C-H stretch fundamental mode of benzene, a first experimental value of 3015(+2) (-5) cm(-1) is determined, in excellent agreement with anharmonic frequency calculations presented here.