Archive for the ‘Funded STSMs’ Category

STSM by Zdenek Masin, The Open University (UK) with Olga Smirnova, Max Born Institute, Berlin (DE)
On October 19th, 2014 (15 days)

High Harmonic Generation from pyrazine

Irradiation of an atom or a molecule by an intense laser pulse leads to the emission of photons with frequency that is an integer multiple of the frequency of the laser field. This is the high harmonic radiation. The spectrum of the radiation depends sensitively on the sub-cycle dynamics in the ion and can be used as a sensitive probe of the electronic and nuclear dynamics. The aim of our collaboration is to construct a theoretical model for the High Harmonic Generation (HHG) for the biological molecule pyrazine.

Our theoretical description is based on the well-known three-step model of HHG. This STSM has allowed us to complete the set of data required to construct the model: transition dipole matrix elements, ionization amplitudes for the low-lying states of the pyrazine cation (carried out by Serguei Patchkovskii, MBI) and the sub-cycle laser-induced dynamics in the cation.

The transition dipole matrix elements were obtained using the UKRmol suite, the UK implementation of the molecular R-matrix method. We have benchmarked our calculations against the known photoionization cross sections for pyrazine. Our results show the strong role of correlation in the photoionization dynamics involving the deeper lying valence states: the scattering model using ~5000 configurations significantly underestimates the partial photoionization cross sections for these states. In order to obtain accurate cross sections for these states a much larger set of ~135000 configurations was needed.

Combining all the obtained data our preliminary analysis has identified several interesting channels that may play role in the process of HHG: ionization into the cationic ground state with recombination into the second excited single-hole state (B1u) and vice versa. However, the potentially most interesting dynamics involves a low-lying satellite state of B2u symmetry: ionization into the satellite state with recombination into the cationic ground state.

Finally, we have developed routines for the UKRmol suite that allow us to visualize the Dyson orbitals produced by the CDENPROP module, see Figure 1.

Further collaboration will focus on analysis of the role of the different cross channels and on generation of the harmonic yields.


Figure 1: Dyson orbitals for ground state of pyrazine cation, 1 Ag, and its two lowest-lying excited single-hole states: 1 B1g, 1 B1u. For each cationic state the label in the parentheses corresponds to the singly occupied molecular orbital in the most dominant configuration in the CAS-CI expansion of the wavefunction.

STSM by Sandra Gomez,  Complutense University of Madrid (ES) with Volker Engel Institut für Physikalische und Theoretische Chemie der Universität Würzburg (DE)
On November 23rd, 2014 (5 days)logo

Strong field decoupling of nuclear dynamics

The interaction of molecules with strong laser fields produces molecular dynamics much more complicated than in the presence of weak fields. The solution for structureless two-level systems in a single frequency field is known as Rabi solution and the population of states oscillates at the Rabi frequency, known as Rabi oscillations or Rabi floppings.
When this system is replaced by two electronic states with dependance on nuclear coordinates, the Rabi oscillations decay on time while the nuclei are moving due to a dephasing that damps electronic coherences.
The goal of our collaboration is to minimize these effects by decoupling as much as possible the nuclear motion.

During the short visit we discussed possible models where these effects could be observed, we generated the potential energy curves of some diatomic molecules (Na2 and NaI) and we started to study how to analyze the dynamics using hamiltonians of coupled electron-nuclear motion (beyond Born-Oppenheimer approximation).
Due to the short time availiable, only the transition between ground and first excited state of Na2 molecule was studied at different amplitudes of the laser field (continuous wave laser).
We plan to extend these results to systems with other decoherence processes, as the NaI predissociation and to control of coupled nuclear and electronic degrees of freedom.

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 Michael Gatchell, Stockholm University (SE) with Yang Wang, Manuel Alcamí, and Fernando Martín, Universidad Autónoma de Madrid (ES)
On November 9th, 2014 (6 days)

Studying ion induced reactions in Pyrene clusters

Fusion of Polycyclic Aromatic Hydrocarbon (PAH) molecules inside clusters when irradiated by ions is a process that could play a crucial role in the evolution of PAHs in the interstellar medium when stellar winds collide with carbonaceous grains. This processes has recently been discovered in experiments performed in Caen, France, with support from classical molecular dynamics (MD) simulations developed at Stockholm University.

For this STSM, carried out at the Universidad Autónoma de Madrid, we studied the reactions between PAH molecules and PAH fragments using Density Function Tight Binding (DFTB) MD simulations. This allowed us to study the reactions with greater accuracy regarding molecular structures than the classical simulations and to include effects of for instance molecular charge states. These new simulations have allowed us to benchmark the simpler classical simulations.

With the DFTB simulations we found that molecular fusion processes indeed can occur in PAH clusters after collisions with ions as predicted by the classical MD. Low charge states do not significantly affect the reactivity of the fragments and intact molecules, or the stability of the new molecules that are formed. We found that the newly formed molecules are more sensitive to high internal temperatures than predicted by the classical simulations. The results of this STSM are included in a manuscript that is being written at the present time.


Figure: Example of simulation where a keV atom or ion (red) collides with a loosely bound PAH cluster, in this case a cluster of 36 pyrene molecules. Fragments formed in the collisions can easily form covalent bonds with neighboring molecules in the cluster. Within a few picoseconds the hot clusters dissociate.


STSM by Jan Zabka, J. Heyrovsky Institute of Physical Chemistry of the ASCR, v. v. i., Prague (CZ), with Christian Alcaraz, Laboratoire de Chimie Physique, Orsay (FR)
On October 7th, 2014 (7 days)

State-selected reactivity of CO2+ with CH4 of relevance for the modelling of plasma systems and the Earth atmosphere.

The purpose of the STSM was to perform a study the reactivity of CO2+ ions, generated in the electronic ground state with a known amount of vibrational excitation, with CH4. These reactions are of relevance for the modelling of plasma based dry reforming of methane and the chemistry of the Earth atmosphere.

The experiments was performed with the CERISES apparatus, (Collisions Et Réactions d’Ions Sélectionnés par Electrons de Seuil) an associated experiment to synchrotron SOLEIL. Vibrational state selection of CO2+ was performed via the Threshold Photoelectron Photoion Coincidence (TPEPICO) method using the cell ion source of CERISES and the DESIRS beamline. The photon energies were in the range from about 13.7 to 17.3 eV to produce the parent ion by photoionization.

JAZAB-exp-1 JAZAB-exp-2

Fig.1.: CERISES: Experimental setup

For the reactive systems described above, were obtaining an absolute cross sections (and hence branching ratios) and product velocity distributions for the various reaction pathways as a function of the vibrational excitation of CO2+ and at selected values of the collision energy within the 0.1 – 10 eV range.

From the dependences on the collision energy were get some insights onto the reaction dynamics, e.g. reaction mechanism or presence of energy barriers. The obtained cross sections and branching ratios will be useful to improve the predictability of chemical models for plasma based reforming of hydrocarbons and atmospheric chemistry.


Fig.2.: Exp. results: a) States of CO2+


Fig.2.: Exp. results: b) Product velocity distributions

Fig.2.: Exp. results:  c) Collision energy dependences


STSM by Andrea Cernuto, University of Trento (IT)  with Christian Alcaraz, Université Paris-Sud, Orsay (FR)
On May 21st, 2014 (7 days)

Effect of internal and kinetic energy on the reactions of methyl cations with hydrocarbons

The purpose of the STSM to the Soleil Synchrotron (Paris) was to study the reactivity of CH3+ with a varying degree of internal excitation with CH4, allene (C3H4) and 2-butyne (C4H6). These reactions are of relevance for the modelling of high energy environments such as planetary atmospheres and plasma systems. In fact the methyl carbocation has been detected in the atmosphere of Titan and in laboratory plasmas, e.g. those used for the conversion of methane (in some cases mixed with CO2) into higher hydrocarbons.
The experiments have been performed, at the DESIRS beamline of the Soleil Synchrotron, with a multipole QOOQ mass spectrometer set-up, that is optimized to study ion-molecule reactions as a function of the collision energy. The CH3+ cation is produced by VUV photoionization of CH3 radicals generated in a molecular beam seeded in Ar and coupled to a flash pyrolysis source using CH3NO2 as precursor. The internal excitation of the parent cation can be varied by changing the photon energy from the threshold ionization of CH3 (about 9.8 eV) to 12.5 eV.
For the reaction of CH3+ with methane we expected two products, C2H3+ (m/z 27) and C2H5+ (m/z 29): the results about this system clearly show the change in the branching ratios of the two products at different photon energies and a huge effect of the internal energy on the cation reactivity. The last system studied is the reaction between CH3+ and 2-butyne. The reactivity can be summarized by the following energy scheme.


Fig. 1. Guess of energy values referred to NIST.

The main reactions are the charge transfer (C4H6+), the extraction of H- (C4H5+) and the condensation (C5H7+) path. Very interesting to study are the channels leading to the formation of C3H3+ and C2H3+: in fact, these clearly show the effect of the internal excitation of CH3+, because they are either endothermic or thermoneutral processes. In addition, we can confirm that the other pathways are exothermic and in general insensitive to the effect of the internal excitation of the primary ion.

The obtained results are encouraging because they show the effect of the internal excitation on the reaction of CH3+ with unsatured hydrocarbons.The results hereby obtained are a successful proof of principle demonstrating the feasibility of studying state-selected reactivity of CH3+ cations using the photon energy.
Future collaboration with the host institution can be foreseen in the form of further synchrotron campaigns to complete and quantify the study initiated. The experimental results will need to be carefully analyzed but we can predict that at least one publication (in the form of Communication or Letter) will result from the STSM.

STSM by Raluca Cireasa, CNRS, Orsay (FR) with Francesca Calegari, National Research Council of Italy CNR-IFN (IT)
On April 14th, 2014 (20 days)

RACI-logosUltrafast Dynamics of Biomolecules Induced by XUV Attosecond Pulses

Exposing biomolecules, including those of the human body, to high energy photons (from VUV to X-ray) leads to radiation damage. The objective of this project is to use XUV ultrashort pulses (hundreds of attosecond, 1as=10-18 s) to investigate the modifications induced in biomolecules at the level of the electrons and the first stages of the chemical (nuclear) changes. We have investigated several molecules belonging to different classes: aminoacids (Glycine), nucleobasis (Uracil), radiosensitizers=molecules that increase the effect of the radiotherapies (5-Halouracils).

The charge dynamics (electron and hole motions) launched by the photoionisation process are expected to be extremely important in triggering subsequent nuclear dynamics and the associated chemical change and therefore, it plays an essential role in many chemical and biological processes. We have performed pump-probe experiments to study the ultrafast dynamics occurring in some benchmarks biomolecules upon excitation with XUV attosecond pulses. The ensuing dynamics was detected by recording Time-of-Flight (TOF) spectra of the singly ionised fragments as a function of the delay between the XUV pump (~300 as) and a broad VIS-IR probe pulses (~4 fs) and as a function of the XUV energy spectrum. For all systems, we have recorded ultrafast dynamics (<10 fs) manifested as delayed signal appearances and/or sharp rising/decaying signals. An important objective of the experiments on halogenated uracil (FU and BrU) and uracil (U) was to measure the H/H+ transfer dynamics underlying the formation of some fragments. An ultrafast decay of 30-40 fs was observed on the signal from the fragment 43 (HNCO or FCCH) and the complementary rising behaviour on the same timescale was observed for fragment 44, which can be only formed by H/H+ transfer, most probably via tautomerisation (see Fig.). Similar behaviours, although slower, were also measured for the fragments 31 (FC) and 32. These dynamics may be associated with H or proton transfer processes where the difference in timescale is determined by the initial and final sites of the H/proton transfer and, in particular, to the involvement of the halogen atom. Similar dynamics were observed for the corresponding fragments of BrU and U.

The analysis of the results obtained during this campaign is underway. Some preliminary results were already presented as talks at IPW&RIXS2014 conference and at departmental seminars and when finalised, this work will also be the object of joint publications. The STSM has given us the opportunity of setting up a longer term collaboration for designing a gas-phase biomolecular source for the Milano setup – based on the ISMO source that was used for the STSM experiments, for testing the performances of this source at ISMO using energy resolved spectroscopy techniques (beginning of 2015) and for undertaking other common projects to investigate the ultrafast dynamics induced by XUV attosecond pulses in biomolecules (Spring 2015).

RACI-imgTautomerisation dynamics for 5-FluoroUracil from the di-keto isomer to keto-enol isomer

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 Judith Dura Diez, Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy (DE) with Luis Bañares, Universidad Complutense de Madrid (ES)SmallFigures_logos
On October 6th, 2014 (14 days)

Structural determination of methyl iodide complexes by femtosecond Coulomb repulsion

The main purpose of the STSM was to continue with the research line established in the past at the host institution on the ultrafast dynamics of Van der Waals complexes. These types of aggregates are interesting media for studying molecular dynamics under the influence of a weakly bound environment. The ‘‘solvent’’ effect does not necessarily involve subtle changes, even though the typical inter-molecular distances in Van der Waals clusters are large [1]. Reactions that take place in the isolated molecules can witness important differences when the molecule is immersed in such an environment [2]. Clusters being the precursors of condensed media, is the goal of this research to establish the connection between the original geometry of the aggregate and the observed dynamics.

Upon dimer molecular jet expansion, where monomers and dimers can be found in the interaction region in approximately equal proportions, the A-band photodissociation dynamics of CH3I/(CH3I)2 were investigated. Series of kinetic energy (K.E.) distributions were obtained upon irradiation of the molecular jet for different pump (267 nm) and probe (333.5 nm) time delays. The CH3 moiety is detected resonantly at lambda_probe = 333.5 nm. These center of mass (C.M.) K.E. distributions are displayed in Fig 1. Five K.E. contributions can be distinguished. Components (1) and (2) correspond to the A-band photodissociation channel of CH3I in correlation with I*(2P1/2). We detect simultaneous contributions from dimers (1) and monomers (2). Analogously, contributions (3) and (4) correspond to the photodissociation channel in correlation with I(2P3/2). A new component for the A-band dissociation is observed only upon dimer expansion: component (5). This component shows a time-dependent KE dynamics; and it is tentatively assigned to the observation a Coulomb repulsion channel.

The evaluation of the data and further theoretical simulations will shed some light into the origin of the Coulomb repulsion channels upon neutral dissociation in small aggregates  and the relation of the Coulomb trajectories with different geometries of the dimers present in the molecular jet.


Figure 1. Center of mass kinetic energy distributions of the CH3 fragment upon A-band excitation of CH3I/(CH3I)2 (Lambda_prump = 266 nm) for different pump-probe time delays, obtained through Abel inversion of recorded images for ground state CH3 fragment resonantly ionized at Lambda_probe = 333.5 nm.



1. K. V. Vidma,, J. Chem. Phys. 125, 133303 (2006).
2. R. de Nalda, et. al., Phys. Chem. Chem. Phys. 13, 13295 (2011).

STSM by David Ayuso, Universidad Autónoma de Madrid, Madrid (ES) with Piero Decleva, Trieste University (IT)
On July 14th, 2014 (12days)DavidAyuso_logoUAM

Light-induced electron dynamics in molecules

The purpose of this 2-week STSM was to move forward in a project with the final goal of simulating multiphoton absorption situations (such as pump-probe schemes) in large molecules. Having this long-term purpose in mind, we started by calculating and analyzing the photoionization channels of the simplest molecule, H2+, which has permitted to check the validity of the approach.

We have evaluated the electronic (bound and continuum) states of H2+ using the codes that have been implemented in the group of Prof. Decleva during the last years [1,2]. As an illustration, fig. 1 shows cuts of continuum orbitals with σu symmetry for four selected photoelectron energies along the plane which is perpendicular to the molecular axis and contains the center of mass. The corresponding dipole-transition matrix elements (DME) between all (bound-bound, bound-continuum and continuum-continuum) electronic states were then evaluated.

After checking the values of the DME in H2+ we are ready to apply the present method to larger systems. We will combine these tools with those developed in our group in Madrid in the last few years (see, for instance [3]) to simulate pump-probe schemes. Our plan is to start with diatomic molecules, such as N2 or CO, and then move towards biologically relevant systems.


Footnote in fig. 1: Cuts of the real part of S-normalized continuum orbitals of H2+ with σu symmetry and different values of quantum angular momentum number l (1 and 3) and photoelectron energy (0.1, 0.2, 1 and 5 a.u.) along the XY axis. The molecular axis is located along the Z axis.


[1] D. Toffoli et al. Chem. Phys. 276, 25 (2002)
[2] H. Bachau et al. Rep. Prog. Phys. 64, 1601-1728 (2001)
[3] A. Palacios et al. Phys. Rev. A 75, 013408 (2007)