Molecular Beam Mass Spectrometry With Tunable Vacuum Ultraviolet (VUV) Synchrotron Radiation

Summary

A molecular beam coupled to tunable vacuum ultraviolet photoionization mass spectrometer at a synchrotron provides a convenient tool to explore the electronic structure of isolated gas phase molecules and clusters. Proton transfer mechanisms in DNA base dimers were elucidated with this technique.

Abstract

Tunable soft ionization coupled to mass spectroscopy is a powerful method to investigate isolated molecules, complexes and clusters and their spectroscopy and dynamics^1-4. Fundamental studies of photoionization processes of biomolecules provide information about the electronic structure of these systems. Furthermore determinations of ionization energies and other properties of biomolecules in the gas phase are not trivial, and these experiments provide a platform to generate these data. We have developed a thermal vaporization technique coupled with supersonic molecular beams that provides a gentle way to transport these species into the gas phase. Judicious combination of source gas and temperature allows for formation of dimers and higher clusters of the DNA bases. The focus of this particular work is on the effects of non-covalent interactions, i.e., hydrogen bonding, stacking, and electrostatic interactions, on the ionization energies and proton transfer of individual biomolecules, their complexes and upon micro-hydration by water^{1, 5-9}.

We have performed experimental and theoretical characterization of the photoionization dynamics of gas-phase uracil and 1,3-dimethyluracil dimers using molecular beams coupled with synchrotron radiation at the Chemical Dynamics Beamline¹⁰ located at the Advanced Light Source and the experimental details are visualized here. This allowed us to observe the proton transfer in 1,3-dimethyluracil dimers, a system with pi stacking geometry and with no hydrogen bonds¹. Molecular beams provide a very convenient and efficient way to isolate the sample of interest from environmental perturbations which in return allows accurate comparison with electronic structure calculations^{11, 12}. By tuning the photon energy from the synchrotron, a photoionization efficiency (PIE) curve can be plotted which informs us about the cationic electronic states. These values can then be compared to theoretical models and calculations and in turn, explain in detail the electronic structure and dynamics of the investigated species ^{1, 3}.

Protocol

1. Sample Loading

1. Remove the back flange and disassemble the 3/8" stainless nozzle tube from the apparatus (See Figure 1 and Figure 2) and make sure it is clean and the 100 mm orifice is clear (This can be done by looking at a light source through it). For cleaning, fill the tube with ~1 ml ethanol and scrub the inside using cotton tips. Alternatively, place the nozzle in an ultrasonic bath filled with soap and water or ethanol for about 20 min. Then dry with compressed air.
2. Using a small, clean spatula, place about 250 mg of sample in the front part of the nozzle, close to the orifice but not blocking it. A g....

Results

Figure 7 shows a typical mass spectrum of the supersonic expansion of 1,3-dimethyluracil vapors (A) and the PIE curves of the three main features (the monomer at m/z 140, protonated monomer at m/z 141, and the 1,3-dimethyluracil dimer at m/z 280) as extracted from a VUV scan between 8 eV and 10 eV (B). The gray shadow is the standard deviation from three consecutive scans.

Discussion

The monomers and dimers are generated in a supersonic jet expansion which gives rise to a molecular beam. A small sample of the DNA base is placed in a thermal vaporization source and heated to generate sufficient vapor pressure. Argon gas carries the vapors through a 100 μm orifice and passes a 2 mm skimmer to produce a cold molecular beam¹⁴. Alternatively, an effusive beam source can be used, where the sample is placed in a heated oven attached to the repeller plate (ion optics) of the mass spectrometer.<.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Uracil	Sigma	U0750
1,3-Dimethyluracil	Aldrich	349801