Archive for the ‘Funded STSMs’ Category
Training in Attosecond Technology and Ultrafast Electron Dynamics Experiments
Working at the ELYCHE laboratory, Politecnico di Milano, for two months enabled me to become procient in the operation and application of ultrafast technology and attosecond science experimental techniques. This mission has been an opportunity to strengthen our collaboration on the study of ultrafast charge motions in complex molecules such as amino acids.
The most interesting results carried out during my STSM has been the study of charge dynamics in the Tryptophan amino acid at attosecond time resolution by means of an attosecond XUV pump-IR probe experiment. A clear charge oscillation has been observed along the excitation and the consequent exponential decay trend (Figure 1, green line) of the ion yield of the double
charge immonium fragment. Fourier analysis of the oscillating signal and the best fit of the experimental data (Figure 1, red curve) confirm the presence of two predominant modes with frequencies 0,23 PHz and 0,35 PHz. These results represents the shortest charge dynamics (order of few femtoseconds) observed in complex biomolecule, opening the path to a deeper understanding of electronic dynamics within complex molecules and the potential to control it in the future.
The present work complements previous experiments realised by the same collaborating group, who has recently studied a similar ultrafast charge motion in the Phenylalanine amino acid [Belshaw et al. (2012),Calegari et al. (2014)]. Future work will focus on the improved signal stability and statistics by upgrading the experimental pump-probe setup and the biomolecule source.
Figure 1: Evolution of the normalised yield of the doubly-charged immonium ion as a function the attosecond XUV pump-IR probe delay, measured with 0,5 fs temporal steps. (a) The green line is the fitting curve that gives a rise-time of trise = 8 +/- 2 fs an exponential decay of tau = 24 +/- 3 fs. The
red line is the best fit of the resulting curve obtained by summing the green line with two sinusoidal functions with frequencies nu1 = 0,23 +/- 1 PHz and nu2 = 0,35 +/- 1 PHz, respectively. (b) The dierence between the experimental data and the fitted green line is shown. The red line represents the sum of the sinusoidal functions only.
STSM by Daniel Jose Arismendi Arrieta, Institute of Fundamental Physics (IFF-CSIC), Madrid (ES) with Graham Worth, University of Birmingham (UK)
On February 3rd, 2014 (90 days)
From SPAIN to UNITED KINGDOM
Confining molecules inside a nanoscale cavity: the case of clathrate hydrates
In order to provide insights into the water-trapped gas interactions, active research using simulations for hydrates continues to make progress in quantifying spectroscopic values, growth rates, thermodynamic stability, and other physical properties. They have been found to occur naturally in large quantities, and have important industrial applications. The interest in CO2 hydrate is driven in part by the possibility of its storage replacing and extracting of methane trapped in deep ocean clathrates, as well as due to its interest in astrophysics and its formation conditions at Mars, satellites, comets and dense interstellar clouds.
From the perspective of quantum dynamics, by confining a molecule into a cage leads to the quantization of the translational (T) degrees of freedom of its center of mass, and well as to its rotational (R) and vibrational (V) states. This allows the investigation of the dynamics of the guest molecule, and the effect of the size, shape and composition of the host cavity, as well as the occupancy and identity of the trapped molecules, and finally the validation of model interactions. Between several methods to describe the time-evolution of a chemical system at the atomic level by directly solving the Schrödinger equation, the most versatile and efficient is probably the multi-configuration time-dependent Hartree (MCTDH) method.
In this STSM, most of the work was invested on deriving the Hamiltonian setup for treating efficiently the full-dimensional system (e.g. triatomic molecule inside of hydrate cavity types) within the MCTDH program. The next step is to conclude and prepare the analysis of results for a publication. We stablish a new collaboration with the MCTDH developers in Birmingham and for future collaborations such system will be used as a benchmark calculation for direct dynamic methods.
The VCO2−cavity interaction potential as a function of distance R between the center of mass of the cavity and the center of mass of the CO2 molecule. Zero point energies are with their corresponding geometries are shown for the small (512) and large (51262 ) cavities of SI clathrate structure. The small cavity (512) is common to all structures clathrate structures.
X-ray induced fragmentation of nucleic acids building blocks and their halogenated analogues
The purpose of this short term scientific mission hosted by Dr Paola Bolognesi was to study the ionisation/fragmentation of nucleic acids building blocks. Particularly, using photoelectron/photoion coincidence technique (PEPICO) and tunable synchrotron light, we can obtain site/state selective mass spectrum giving insights into the fragmentation dynamics following the ionisation. The systems under study were halogenated analogues of the pyrimidine molecule, namely the 2-Cl-pyrimidine, the 2-Br-pyrimidine, and the 5-Br-pyrimidine (see the molecular structures in Figure).
We perform several PEPICO measurements where, at a fixed photon energy, the photoion mass spectrum is recorded in coincidence with an electron of a given kinetic energy. As an example, the direct photoionisation of 2-Cl-pyrimidine at 100 eV photon energy is given in Figure where the mass spectrum associated to electronic states of increasing binding energies are shown. A marked selectivity in the fragmentation of these different ionic states is clearly visible. In the case of the X-ray photoabsorption, the PEPICO technique is applied by setting the photon energy for the resonant excitation of the 1s ® p* transition of a specific atomic site in the molecule and recording the mass spectrum in coincidence with the resonant Auger electron emitted.
The analysis of the different sets of results is in progress. Their presentation in international conferences as well as the publication in peer-reviewed journal is foreseen. In the near future, we expect to further the collaboration between our two groups in order to apply coincidence techniques (PEPICO, ion-ion coincidence after ionisation by ion-impact  or X-ray) to study the fragmentation dynamics of complex molecular systems.
STSM by Sylvain Maclot, CIMAP, Caen (FR) with Paola Bolognesi, CNR, IMIP (IT)
On March 26th, 2014 (12 days)
From FRANCE to ITALY
Study of stability of nucleosides and their radiosensitising analogues after interaction with X-Rays
This work is part of a combined effort of the groups at CIMAP in Caen and CNR/IMIP in Rome aiming to study the radiation damage of biomolecules at the molecular scale using X-ray absorption and multiply-charged ion impact.
The aim of the experiments performed in Elettra Synchrotron was to investigate the basic processes at molecular level occurring in nucleosides after interaction with X-Rays. Nucleosides are building blocks of DNA/RNA and are composed of a sugar and a nucleic base. This study was mainly focused on valence photoionization using photoemission spectroscopy (PES) and photo-electron-photo-ion coincidence (PEPICO) measurements in order to probe the fragmentation dynamics of ionised molecules. We obtained results for nucleosides 2’-deoxythymidine and 2’-deoxycytidine.
This work should lead to publication and especially marks the consolidation of collaboration between the two teams on nucleoside studies in the gas phase.
Fragmentation dynamics of N-methyl substituted glycine
The purpose of the STSM was to study the fragmentation dynamics of methyl derivatives of amino acid, namely N,N,N-trimethylglycine (glycine-betaine) and its fully deuterated analogue, with respect to low-energy ion collisions. The molecule exists in the zwitterionic form thus carry two opposite formal charges located at the clearly separated molecular sites. Since in a real biological environment amino acids exist as zwitterionic (twin-ion molecules) therefore the investigation of the glycine-betaine is of particular interest in order to understand the physico-chemical stage of radiation damage.
The experiments were performed by using COLIMACON set-up within ARIBE facility. Briefly, we obtain molecules in the gas phase by evaporation of powders in the ovens. The collimated molecular beam interacts with a pulsed ion beam of O6+. The cationic products are analysed by linear TOF mass spectrometer.
We have performed the experiments with isolated molecules of glycine-betaine and its labelled analogue, which allow us to precisely determine from which side of the molecule a projectile captures the electrons.
The most abundant ionic fragment is observed at m/z 44 and can unambiguously be assigned to COO+. This type of fragmentation has been previously reported from canonical amino acids, however, the fragment has been attributed to N-containing cationic species. Further prominent fragments appear at m/z 58 and 59 from non-labelled molecule and at m/z 66 and 68 from its deuterated analogue. These observations indicate that the fragments are generated from the cleavage of the Ca-Cb bond with the charge localised at the N-terminal group. In addition we observe that for zwitterionic amino acid the probability of nondissociative ionization is negligible (see Figure). The future experiments are planned as a continuation of this project, which will concern the different projectiles and different charge states.
Figure: Mass spectrum of product ions from 48 keV O6+ collisions with fully deuterated N,N,N-trimethylglycine.
Studies of multiply charged clusters of fullerenes
The purpose of this STSM was to establish a collaboration between the working group at Stockholm University and at the University of Innsbruck. Experimental studies of the Stockholm group have revealed the appearance size for multiply charged fullerene clusters. In case of doubly charged aggregates, the pentamer is the first cluster to be stable against Coulomb-explosion on the experimental timescale. Here we want to approach these findings with computational chemistry.
We investigated vertical ionisation processes of various sizes of fullerene clusters, starting from the monomer up to the pentamer using density functional theory and a moderately-sized basis set. In addition we calculated the changes in polarisation due to the presence of a point charge to get a first estimation of the interaction energy of a singly charged fullerene leaving the cluster (see Figure 1).
Since these calculations are computational quite demanding, the work is still continued. We plan to publish our results in a respective journal.
Figure 1 – Neutral C60 dimer and a point charge. Distance R is given from the centre of mass.
Spin-orbit effects on the two-electron continuum states following photoionization
It is well known that transitions to two-electron continuum states are restricted by a set of selection rules presented in detail in the work of Maulbetsch and Briggs some time ago . In this work it was claimed that these rules apply for an arbitrary ionization process. The purpose of the present STSM was to explore further this later claim.
More specifically, in the work by Maulbetsch and Briggs the formulation has been based on a LS uncoupled representation of the atomic states. As such it is questionable as to whether the selection rules should apply generally.
One notable example that is of relevance is the case of two-photon sequential double ionization of neon . In this case, there are two different theoretical predictions for the two-electron angular patterns for the Ne+2 3P residual ion. S. Fritzche et al follow an LSJMJ representation of the atomic states while A. Kheifets in his work assumes an LSMLMS representation . The resolution to this difference is that since the process is sequential the two-electron angular distributions are affected from the pulse properties (strength,duration) and the strength of the SO coupling in the intermediate singly-ionized neon doublet .
Motivated from the findings in ref  and the theoretical contradictions in refs  the main outcome of the STSM was that it is desirable to check the Maulbetsch and Briggs rules by following a formulation based on LSJMJ representation. Based on this formulation we hope that we’ll obtain a better understanding of the validity of the Maulbetsch and Briggs rules.
 F. Maulbetsch and J. S. Briggs “Selection rules for transitions to two-electron continuum”, J. Phys. B, 28, 551, (1995)
 S. Fritzsche et al, “Angular distributions and angular correlations in sequential two-photon double ionization of atoms”;J. Phys. B, 41, 165601, (2008) A. S. Kheifets, “Photoelectron angular correlation pattern in sequential two-photon double ionization of neon”J. Phys. B, 134016, (2009)
 Time-dependent Theory of Angular Correlations in Sequential Double Ionization, Phys. Rev. Lett. 111, 093001, (2013)
STSM by Rolf Heilemann Myhre, University of Science and Technology, Trondheim (NO), with Sonia Coriani, Dipartimento di Scienze Chimiche, Università di Trieste (IT)
On March 22nd, 2014 (8days)
From NORWAY to ITALY
Multi-level Lanczos-based Coupled Cluster Linear Response Methods for X-ray Absorption, Ionization and Emission Spectroscopies
Today, spectroscopy is experiencing a rapid development providing a wealth of information about molecules and their properties. To take full advantage of these experimental techniques, it is desireable to be able to replicate the results with computational modelling. With a good model, experiments that may take days or even weeks can be performed virtually over night on a computer.
Accurate models are computationally expensive, limiting the size of molecules it is possible to study. The Lanczos algorithm reduces the cost of calculating excitation energies by calculating them all at ones, while multi-level coupled cluster uses an accurate model on the most interesting part of the molecule and a more approximate one on the rest.
In this STSM, we combined these methods in the Dalton software package. While we are still ironing out some bugs, we expect that we will be able to compute high energy spectra for molecules that have so far been too expensive. This will make it possible to explore in detail the new mechanisms behind the experimental results.
Figure: Electron density of decanal is divided into three different spaces for the multi-level method. The bottom right figure is the total electron density.
STSM by Aurelie Chenel, Université Paris-Sud, Orsay (France), with Octavio Roncero Villa, Consejo Superior de Investigaciones Científicas (CSIC), Madrid (ES)
On February 24th, 2014 (26 days)
From FRANCE to SPAIN
Control of the infrared photodissociation of LiHF
We numerically study the competitive dissociation of the Van der Waals complex LiHF into the LiF + H or the Li + HF products. The potential energy surface of the LiHF system has been calculated by Roncero and al. (JCP 107,23 (1997)). Our goal aims at controlling the dissociation of LiHF toward the formation of the Li + HF products, that are not the products predominantly formed. The dynamics will be studied in hyperspherical coordinates. For the control we will use the Local Control Theory (LCT) strategy with a time-dependent approach based on Møller-operators.
The program we want to use for the control is written in hyperspherical coordinates. Furthermore, to be feasible in terms of calculation costs, we achieve it in a reduced two-dimensional model, so that in fact we use polar coordinates. To get such polar coordinates, it is usual to start with the Jacobi coordinates (rjac , Rjac ), as shown in the ﬁgure, where the angle γ is set at a value of 73° .
We ﬁrst started with these coordinates. However, studying the energy potential curves we got, we then saw that they were not appropriate to describe our problem in two dimensions : we cannot have a good description of both rearrangement channels, leading to the LiF + H or the Li + HF products. To describe well both dissociation products, we are going to use bond coordinates, where r = rHF and R = rLiF . However, with these coordinates, we have to make some assumptions to be able to use our program for the control: in particular, we will neglect the cross-terms of the kinetic energy. These assumptions may be too strong, so that we will still have to think if these coordinates are suitable for the control.
STSM by Aleksandar Milosavljevic, Institute of Physics Belgrade, University of Belgrade (RS), with EAlexandre Giuliani, Synchrotron SOLEIL,Gif-sur-Yvette (FR)
On February 10th, 2014 (14 days)
From SERBIA to FRANCE
Study of ion collisions with protein poly-ions stored in a linear ion trap
The purpose of the STSM was to perform a study on highly charged ion (HCI) collisions with multiply charged protein ions stored in a linear ion trap. Particularly, the effect of Xe25+ ion collisions with protein poly-cations and poly-anions, as a function of the charge state was investigated, since in the gas phase the charge strongly influences the structure of the proteins.
The experimental system was based on a commercial linear quadrupole ion trap (“Thermo scientific LTQ XL”), equipped with the electrosprayed ions (ESI) probe, which has been coupled to the ARIBE beamline of the GANIL facility. The target protein ions were introduced from the front side into the trap and after isolation of the desired precursor, the HCI beam was introduced into the trap through the back lens. Xe25+ ions collisions with both positive and negative Cytochrome C (»12.5 kDa) proteins ions (charge states from 7 to 17) have been investigated.
The performed experiment proofed the concept of studying HCIs collisions with multiply charged proteins by coupling a linear ion trap setup to the ion beamline. Unprecedented results have been obtained on HCI interaction with multiply charged gas-phase protein cations (regarding the mass resolution, variety of charged states and charge of the projectile) and the first results on HCI interaction with protein anions. The future experiments are planned as a continuation of the present work, which should be performed for different target charge states and different projectiles. At least one publication in a leading international journal is expected as an outcome of the visit, as well as plethora of new interesting results to be obtained in the future.