Posts Tagged ‘biomolecules’

The 2nd meeting organized in the framework of Working Group 2 of COST Action CM1204 (XUV/X-ray light and fast ions for ultrafast chemistry) took place in Fruska gora (Serbia) from April 27th to April 30th, 2015. It was an expert meeting centered on Biomolecules.

EWG2M_RS-Biomolecules-pictureThis meeting gathered experts from different disciplines (physics, chemistry), experiments and theory to discuss aspects on photon, ion and electron interaction with biomolecules, as well as properties of biomolecules, stability of highly excited and highly charged biological molecules in the gas phase and their reactivity. The aim of the meeting was to initiate new projects and collaborations, inspire new scientific achievements and help promotion of young researchers.
The “WG2 expert meeting on biomolecules” was organized by Aleksandar Milosavljević (Institute of Physics Belgrade, University of Belgrade, Serbia) and Paola Bolognesi (CNR-ISM, Rome, Italy) in the “CePTOR congress center” located in Fruška gora (Serbia) from 27th to 30th April 2015.
The meeting format was based on 20 talks (20’) with long discussion time (10’), 1 poster section (with 9 posters) and free time for discussion. Seven talks were given by young researchers.
The total number of participants was 38 (ranged from MSc and PhD students, postdoctoral researchers to experienced leading researchers and full professors).

The detailed program of the meeting, the book of abstracts and the full list of attendees can be found following the links below.

Aleksandar Milosavljević (IPB, University of Belgrade, Serbia)
The Local Organiser

Related links:

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 Zdenek Masin, The Open University (London), with Olga Smirnova, Max-Born-Institute (Berlin)
On February 2nd, 2014 (14 days)

High Harmonic Generation from biological molecules

High Harmonic molecular spectra provide insights into attosecond electronic dynamics in the target molecule. Accurate values of the dipole matrix elements between bound and continuum molecular states are required to generate the spectra. This STSM has allowed Zdeněk Mašín to learn to use the codes developed at Max Born Institute to generate the dipole matrix elements from the results of the R-matrix calculations and to apply them to calculations of photoionization cross sections.

The calculations were performed using the UKRmol suite of codes implementing the molecular R-matrix method. In order to benchmark the quality of our calculated dipole matrix elements for pyrazine we calculated the photoionization cross sections and photoelectron angular distributions (shown in the Figure). The results, performed using a simple Close-Coupling model including the lowest-lying 40 electronic states, show an encouraging agreement with previous experiments and theory. However, the description of the correlation/polarization interaction was limited in this model and therefore the shape resonances, such as the broad resonance in the 6ag cross section, appear too high in energy. This deficiency will be removed in more sophisticated models which we are developing.

This STMS has allowed us to obtain the first photoelectron angular distributions for pyrazine and to identify directions for further improvement of our calculations so that accurate High Harmonic spectra can be obtained. The next steps in the collaboration will include:

  1. Improving on the target CI description in the scattering calculations by including dynamical correlation.
  2. Calculating the population transfer in the target cation induced by the laser field.
  3. Analyzing the Dyson orbitals generated using the R-matrix codes.
  4. Generating the High Harmonic spectra.