Posts Tagged ‘fragmentation’

STSM by Jean-Christophe Poully, CIMAP, Caen (FR) with Samuel Eden, Open University, Milton Keynes (UK)JCPOUL2_logo
On December 8th, 2014 (6 days)

Multiphoton ionization with a tunable UV laser allows measuring excited state adiabatic energies of DNA bases

The group of Samuel Eden at the Open University Milton Keynes is expert in the field of irradiation of biomolecules and clusters by lasers and electrons. In particular, they probe the influence of nanohydration and clustering on the fragmentation of DNA and RNA bases in the gas phase. Recently, they discovered a microsecond-timescale dissociation channel from isolated uracil and thymine after UV-multiphoton ionization, with an unexplained wavelength threshold. The aim of this STSM was to investigate further this intriguing observation.

We measured the mass spectrum of thymine after UV multiphoton ionization as a function of wavelength, and obtained a threshold of 224 ± 0.5 nm (5.53 ± 0.02 eV) for the metastable dissociation channel (HCNO loss). Our hypothesis is that this threshold corresponds to accessing the S1 state with vibrational excitation matching the energy difference between the ionic ground state (8.82 ± 0.03 eV) and the dissociative ionic state leading to HNCO loss (10.70 ± 0.05 eV) 1, yielding an S1 adiabatic energy of 3.65 ± 0.07 eV. This value agrees with the most recent DFT calculation: 3.72 eV 2. Preliminary results on Adenine-Thymine clusters also suggest a stabilizing effect on the S1 state due to clustering.

Furthermore, we also carried out experiments on cytosine, and observed metastable dissociation, thus demonstrating that measurement of metastable channel wavelength threshold is a possible tool to measure S1 adiabatic energies. We will write a journal article in early 2015 including data from the STSM as well as the host group’s follow-up measurements. We will also arrange further collaborative experiments in the near future with the aim of probing electronic excitation and ionization induced processes in isolated and clustered amino acids.

JCPOUL2_imgMPI (220 nm, average fluence 8×109 mass spectrum of gas-phase thymine. The insert shows the wavelength threshold for metastable HNCO loss.

(1) Jochims, H. W.; Schwell, M.; Baumgärtel, H.; Leach, S. Chemical Physics 2005, 314, 263.
(2) Etinski, M.; Marian, C. M. Physical Chemistry Chemical Physics 2010, 12, 4915.

STSM by Helena Levola, Department of Physics and Astronomy, University of Turku (FI) with Fernando Martín, Universidad Autónoma de Madrid (ES)hele-logo
On October 20th, 2014 (5 days)

Theoretical and experimental studies on ionization induced fragmentation of thiophene and L-α-alanine

Radiation induced fragmentation of biomolecules is a widely studied subject due its importance to medical and industrial applications. In addition, these studies provide information about the properties of the molecules as well as quantum mechanical processes involved. Therefore, understanding the phenomena responsible for the radiation damage of biomolecules is of interdisciplinary interest for physicists, chemists, and materials scientists from the basic science point of view.

In this study, we used electron-ion-ion-coincidence measurements to investigate the fragmentation of two organic molecules – L-α-alanine and thiophene – after ionizing them with soft x-ray radiation. The results were compared with theoretical calculations. It was observed that alanine has many different fragmentation pathways, some of them involving multiple dissociation steps. Thiophene, on the other hand, dissociates mainly into two fragments (see figure below).

During this STSM, theoreticians from Universidad Autónoma de Madrid met with the experimentalists of University of Turku to compare their results on the fragmentation of these molecules. The primary purpose of this STSM was to develop a consistent interpretation of the molecular dynamics in medium-sized molecules such as thiophene and alanine that has a common foundation on both the experimental findings and the computational results. To this end, intensive discussions and reviews of both the experimental and theoretical results were held during the STSM, with intervening refinements of the analysis. The results will be published in a joint article about the fragmentation of thiophene, including analysis of the effect of internal energy on the fragmentation. The theoretical analysis of alanine is still to be continued and a joint article about alanine’s fragmentation will be written once the analysis is completed.

hele-imgPEPIPICO maps of alanine (left) and thiophene (right) with the main fragmentation pathways marked.

STSM by Antonella Cartoni, Università di Roma “Sapienza” (IT)  with Patrick Rousseau, Université de Caen Basse-Normandie (FR)
On June  15th, 2014 (6  days)

Study of the effect of the environment in the ion-induced fragmentation in uracil and halouracil

The halosubstituted analogues of DNA bases that can be efficiently incorporated in the DNA of fast replicating tumor cells to make them more sensitive to the lethal effect of radiation in radiotherapy are known as radiosensitisers. The 5-bromouracil (5BrU) as well as 5-fluorouracil (5FU, Figure 1), analogues of thymine, are considered good radiosensitisers even though the elementary mechanisms of their action is still not completely clear.

The main goal of the work performed at the ARIBE beamline in collaboration with Patrick Rousseau from CIMAP and Paola Bolognesi from CNR-ISM was to investigate the effect of the environment on the radiosensiting mechanisms of halouracil molecules, and  in particular on the properties and behavior of the selected target molecules by studying and comparing the 12C4+ ion induced fragmentation of uracil, 5BrU and 5FU considered as isolated targets and embedded in pure and hydrated clusters. The aggregation source shown in Figure 2 has been used to efficiently produce the clusters (see for example Figure 3).


The study demonstrates that the presence of water molecules in the environment surrounding the 5BrU increases the formation of 5BrU in its enol tautomers with respect to Uracil molecule. Moreover the molecular modifications probably explain the extensive and the very fast fragmentation processes taking place on the halosubstituted rather than on the natural uracil base and hence its radiosensitising effects. These results are the first experimental evidence of the hypothesized mechanism [2] for the mutagenic activity of halouracil: the existence of keto-enol tautomerization induced by the water environment.


This work will produced more than one publication and future experiments on thymine and other bases have been planned with the CIMAP, CNR-ISM and Dipartimento di Chimica (Università Sapienza di Roma) groups.

[1] Bergen et al. Rev. Sci. Instrum. 70 (1999) 3244
[2] X. Hu, H. Li, J. Ding, S. Han, Biochemistry 43, 6361–6369 (2004).