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

Published: October 30th, 2012



1Chemical Sciences Division, Lawrence Berkeley National Laboratory

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.

Tunable soft ionization coupled to mass spectroscopy is a powerful method to investigate isolated molecules, complexes and clusters and their spectroscopy and dynamics1-4. 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 water1, 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 calculations11, 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.

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.......

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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.

Figure 1

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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.<.......

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The experiments were carried out at the Chemical Dynamics Beamline at the Advanced Light Source, Lawrence Berkeley National Laboratory and supported by the Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under Contract No. DE-AC02-05CH11231, through the Chemical Sciences Division.


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Name of Reagent/Material Company Catalog Number Comments
Uracil Sigma U0750
1,3-Dimethyluracil Aldrich 349801

  1. Golan, A. Ionization of dimethyluracil dimers leads to facile proton transfer in the absence of hydrogen bonds. Nat. Chem. 4, 323-329 (2012).
  2. Belau, L. Vacuum-Ultraviolet Photoionization Studies of the Microhydration of DNA Bases (Guanine, Cytosine, Adenine, and Thymine). The Journal of Physical Chemistry A. 111, 7562-7568 (2007).
  3. Golan, A., Ahmed, M. Ionization of Water Clusters Mediated by Exciton Energy Transfer from Argon Clusters. The Journal of Physical Chemistry Letters. 3, 458-462 (2012).
  4. Nicolas, C. Vacuum Ultraviolet Photoionization of C3. Journal of the American Chemical Society. 128, 220-226 (2005).
  5. Kamarchik, E. Spectroscopic signatures of proton transfer dynamics in the water dimer cation. Journal of Chemical Physics. 132, (2010).
  6. Khistyaev, K. The effect of microhydration on ionization energies of thymine. Faraday Discussions. 150, 313-330 (2011).
  7. Bravaya, K. B. The effect of pi-stacking, H-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine-adenine, thymine-thymine and adenine-thymine dimers. Physical Chemistry Chemical Physics. 12, 2292-2307 (2010).
  8. Kostko, O. Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations. Physical Chemistry Chemical Physics. 12, 2860-2872 (2010).
  9. Bravaya, K. B. Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra. Journal of Physical Chemistry A. 114, 12305-12317 (2010).
  10. Leone, S. R., Ahmed, M., Wilson, K. R. Chemical dynamics, molecular energetics, and kinetics at the synchrotron. Physical Chemistry Chemical Physics. 12, 6564-6578 (2010).
  11. Scoles, G., Bassi, D., Buck, U. . Atomic and Molecular Beam Methods. 1, (1988).
  12. Pauly, H. . Atom, Molecule and Cluster Beams I. , (2000).
  13. Wiley, W. C., McLaren, I. H. Time-of-Flight Mass Spectrometer with Improved Resolution. Review of Scientific Instruments. 26, 1150-1157 (1955).
  14. Levy, D. H. The Spectroscopy of Very Cold Gases. Science. 214, 263-269 (1981).

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