Research Projects and Grants

Research Projects

eTRANSFER – Decomposition of biological molecular targets by electron transfer experiments
PTDC/FIS-AQM/31281/2017, Fundação para a Ciência e a Tecnologia, Portugal (2018 – 2021);

We aim at investigating the molecular mechanisms of biological molecular targets decomposition upon electron transfer in atom-molecule collision experiments. The fragmentation pattern will be analysed in a high-resolution time-of-flight mass reflectron. Such charge transfer processes are prevalent in a wide variety of environments (e.g. biological, chemical, atmospheric, combustion) in particular within the biological medium, where at the molecular level, electron induced decomposition plays a relevant role in chemical reactions. These experiments will be performed in the gas-phase, yet detailed knowledge of the underlying processes are essential to obtain key relevant molecular aspects of the targets which may be quenched in a liquid and/or condensed phases. The present proposal opens up an opportunity to contribute to the current need of exploring charge transfer collisions in biomolecular targets which are unknown as to their structure and behaviour in presence of an extra electron.

Biologic building blocks and relevant electron transfer processes: an atom-collision study
PTDC/FIS-ATO/1832/2012, Fundação para a Ciência e a Tecnologia, Portugal (2013 – 2015);

In this project we propose to study for the first time the interaction of neutral potassium atoms with purines (DNA/RNA subunits) and some amino acids. These studies will make use of a cross molecular beam technique in the low/intermediate energy range in atom-molecule collisions. Both studies and the experimental setup are unique in Europe. In this process, an electron is transferred from the donor to the acceptor molecule. Alkali atoms (e.g., potassium, K) have very low ionisation energies and are therefore excellent electron donors. In such an alkali-molecule interaction a positive ion K+ and a temporary negative molecular (TNI) ion are formed. The TNI is formed with an excess of internal energy that may lead to dissociation. In such dissociative process, an anion is formed together with neutral species. The relevance of these neutral molecules in physiological environment as secondary species formed along the ionisation tracks is potentially damaging if they are reactive species (e.g., H∙, O∙, OH∙). Though and in order to assess the damaging effect of such radicals, we also propose for the first time a side detection method, in which the diffusing radicals will be stabilized in a substrate (covered with a spin trap) for further spectroscopic analysis (e.g., EPR-Electron Paramagnetic Resonance). Such radicals formation upon collision, will allow assessing the risk of damage of biological structures (such as some DNA/RNA base pairs) with the ultimate goal extended to the cellular environment.

Nanoscale radiation interactions and their applications in radiotherapy and radiodiagnostics
SPID201200X031248IVO – Ministerio de Economia y Competitividad, Spain (2012 – 2015);

Electron Transfer to Biomolecules
2005/R4, The Royal Society, UK (2006-2008);

It is generally recognized that a DNA molecule in equilibrium state does not have any free charge carriers so it would be useful to probe alternative routes by which electrons might form anions without the initial electron being ‘free’ since such a process may be a more realistic analogue for DNA damage under physiological conditions. Alkali atoms have very low ionization potentials and are therefore excellent electron donors. Accordingly in Lisbon a new experiment is being developed to study for the first time, electron transfer processes with constituent molecules of DNA using potassium – molecule collisions. In these experiments a positive ion K+ and a molecular anion are formed, allowing access to parent molecular states which are not accessible by free electron attachment experiments. In particular states with a positive electron affinity can be formed, and the role of vibrational excitation of the parent neutral molecule can be studied. Even if the free negative molecular ion is unstable in the gas phase, in the atom/molecule collision complex it can be stabilized. The negative molecular ion lifetime will depend upon both the collision time and the autodetachment time. If the lifetime of the parent negative ion is longer than the fragmentation time energy can be distributed over the available vibrational degrees of freedom and so change the fragmentation pathways. If the collision time is shorter than the dissociation time collision induced dissociation is likely to take place and produce fragment ions with finite kinetic energies. Comparison of electron transfer in atom-molecule experiments and free electron molecule interactions and in particular comparison of the fragmentation patterns will therefore allow us to develop a more detailed model of electron induced damage in DNA. Developing a project comparing biomolecular fragmentation by free electrons and by atom-molecule transfer is the purpose of this project.

Electron Transfer in Biomolecules: A mechanism for damage and repair?
POCT/FIS/58845/2004, Fundação para a Ciência e a Tecnologia, Portugal (2006 – 2009);

The interaction of high energy radiation (alpha, beta, gamma rays or heavy ions) with living cells does not in general lead directly to DNA (desoxyribonucleic acid) strand breaks. However, the primary interaction can remove some electrons from the components of the nanosize complex molecular network, i.e., electrons from valence states of the chemical bonds, as well as electrons from localised inner shells of the individual atoms. With subsequent charge transfer and energy dissipation, chemical bonds can be broken generating neutral and/or ionic radicals as additional secondary species. Electrons are the major species formed (~ 5×104 electrons per 1 MeV primary radiation), with kinetic energies up to 20 eV, and therefore can induce single and double strand breaks. In electron attachment experiments, low energy electrons destroy deoxyribose more easily than the nucleobases. Most fragments of deoxyribose, formed by (dissociative) electron attachment show a resonance peak close or at about 0 eV. Under isolated conditions the RNA (ribonucleic acid) bases are also effectively damaged by very low energy free electrons (below the threshold for electronic excitation (< 3eV)). In the proposed present experiments (vd. attachments), the electron affinity (EA) will be investigated by a crossed molecular beam technique by atom (potassium) molecule collisions. In this type of processes na electron jump occurs and a positive ion K+ and a molecular anion are formed, allowing access to states which are not accessible by electron attachment experiments. In particular, states with a positive electron affinity can be formed, and the role of vibrational excitation of the parent neutral molecule can be studied. So far as we are aware, no one has investigated such transitions. These biomolecules to be studied will be prepared in na effusive molecular beam and include: single isolated components of the DNA bases (adenine, guanine, cytosine and thymine), deoxyribose and RNA (uracil). The proposed experiment will therefore form a core part of larger European projects to investigate DNA damage and irradiation of biomolecules and cellular material. The co-ordinators of these projects have indicated that they are willing (and keen) to integrate the proposed project within the European programme and invite staff employed on the project to conferences and to other laboratories in the network for collaboration.


Research Joint Collaborations

Investigating the effects of incident atoms and associated water molecules on electron capture and ionisation processes in DNA base molecules
British Council, Treaty of Windsor, UK, 2009-2010;

Intelligent DNA lesions and potential application to radiotherapy
GRICES-CNPq, Portugal-Brazil, 2007-2009; 

Electron and photon interactions with biomolecules
British Council, Treaty of Windsor, UK, 2007-2008;

Stopping power of electrons in based tissue equivalent materials
CSIC, Madrid, Spain, 2007-2009;

Secondary electron interactions and radiation damage in biomolecules systems
CSIC, Madrid, Spain, 2004-2006;

Molecular Fingerprinting for Atmospheric Sensing
British Council, Treaty of Windsor, UK, 2004-2005;

Electron and photon spectroscopy of molecules relevant to global warming and ozone depletion
University of Liège, Belgium, 2003-2006.


EU Networks

Molecular Dynamics in the GAS phase (MD-GAS)
EU COST Action – CA18212, 2019 – 2023;
Our Astro-Chemical History
EU COST Action – CM1401, 2014 – 2018;
Chemistry for ELectron-Induced NAnolithography (CELINA)
EU COST Action – CM1301, 2013 – 2017;
Nano-scale insights in ion beam cancer therapy (Nano-IBCT)
EU COST Action – MP1002, 2010 – 2014;
The Chemical Cosmos; Understanding Chemistry in Astronomical Environments
EU COST Action – CM0805, 2008 – 2012;
Electron Controlled Chemical Lithography with molecular resolution – ECCL
EU COST Action – CM0601, 2007 – 2011;
Ion Technology and Spectroscopy with Low Energy Ion beam Facilities – ITSLEIF
Transnational Access, Integrating Activities and Accompanying Measures, Integrated Infrastructure Initiative – I3, FP-VI, 2005 – ;
Radiation Damage in Bio-molecular Systems
EU COST – P9, 2003-2007;
Electron and Positron Induced Chemistry (EPIC)
FP-V, European Science Foundation (HPRN-CT-2002-00286), 2002-2005;
Electron Induced Processing at the Molecular Level (EIPAM)
FP-VI, European Science Foundation, 2004-2008;

Synchrotron Radiation

CALIPSOplus under the Grant Agreement 730872 from the EU Framework Programme for Research and Innovation HORIZON 2020:
Investigation of the valence and Rydberg electronic excitation of key selected thiophene derivatives (2019);
Exploring valence and Rydberg electronic states of indolequinone and derivatives (2018);

FP7 Transnational Access Programme, Integrated Activity Integrating Activity to the European Commission, CALIPSO:
Exploring the lowest-lying electronic states of cork TCA contaminant and its derivatives (2016);
The role of low-lying electronic states in aminophenol compounds (2016);
Exploring Focused Electron Beam Induced Deposition (FEBID) Precursors by VUV Photoabsorption (2015);
Valence shell electronic spectroscopy of nitrocompounds as studied by high-resolution VUV photoabsorption measurements (2014);

 I3 IA-SFS Integrated Activity on Synchrotron and Free Electron Laser Science (RII3-CT-2004-506008), Research Infrastructure Action of the FP6 EC:
Electronic excitation of model systems of non-polar liquids probed by VUV photoabsorption (2011);
VUV photoabsorption spectroscopic studies on commercial and food additives related molecules (2010);
Aeronomic relevant molecules studied by high resolution VUV photoabsorption: plasma processing and biogenic emission species (2009).
Electronic excitation of long chain fatty acids by high resolution VUV photoabsorption: fluorinated and chlorinated carboxylic acids derivatives (2009).
VUV photoabsorption studies of some atmospherically important molecules (2008).
VUV photoabsorption to biological relevant molecules: radiation damage studies at the molecular level (2008).
Electronic state spectroscopy of low vapour pressure molecules: VUV photoabsorption studies in a hot gas cell (2007).
Photon induced excitation of DNA nucleobases by VUV photoabsorption in a new hot gas cell oven (2007).
VUV spectroscopy of biomolecules and other biogenic molecular species (2006).
Electronic state spectroscopy of biomolecules studied by VUV photoabsorption (2005).
VUV spectroscopy of Volatile Organic Compounds (2005).
VUV photo-absorption studies in biomolecular systems (2004).
VUV photo-absorption of molecular species relevant to plasma etching (2004).