Archive for the ‘Funded STSMs’ Category

STSM by Mark Stockett, Aarhus University (DK) with Henrik Cederquist, Stockholm Universty (SE)
On October 25, 2015 (8 days)

Relaxation dynamics of laser-excited clusters at DESIREE

The purpose of this Short Term Scientific Mission (STSM) was to perform the first experiments with laser-excited cluster ions at the DESIREE (Double ElectroStatic Ion Storage Ring ExpEriments) infrastructure at Stockholm University. This project was motivated by one of the most exciting developments in recent years within the electrostatic storage device community, namely the observation of fast radiative cooling of hot, stored ions by Poincaré fluorescence, also called recurrent fluorescence [1, 2]. In this process, highly vibrationally excited ions initially in their electronic ground state undergo inverse internal conversion (IIC) to a low-lying electronic excited state. Once in the electronic excited state, emission of a single optical or UV photon rapidly decreases the internal energy of the molecule/cluster. The rate of radiative cooling by Poincaré fluorescence is much faster than the slow process of sequential emission of multiple IR photons corresponding to vibrational quanta of the hot electronic ground state.

We measured the delayed neutralization of C4 ions (a species for which Poincaré fluorescence has been observed before [3]) which survived one half-turn around the ring (about 20 µs) after being excited by 355 nm light from a ns pulsed Nd:YAG laser. This delayed signal probes the population of ions whose internal energy prior to excitation was such that the addition of one 3.5 eV photon placed them just at the threshold for electron detachment (3.9 eV), which is too low for Poincaré fluorescence to be active. The measured time constant with 355 nm excitation is consistent with infrared (vibrational) radiative cooling rates, but it is important to keep in mind that there is also a contribution to the population we probe due to cascade processes from above. Excitation at additional UV wavelengths will give a more complete picture of population dynamics of these cold ions.


During the course of this STSM, a pulsed laser was interfaced to the DESIREE electrostatic storage ring for the first time. We succeeded in observing laser-induced decay of C4 ions and measured the vibrational radiative lifetime for clusters of very low internal energy which had not been studied previously. We also established a number of protocols and techniques for performing further systematic studies in the future. This effort has enabled a new class of experiments at DESIREE for studying the de-excitation dynamics of colder ions over longer timescales than is possible at non-cryogenic storage rings.

[1] S Martin et al. Phys Rev Lett 110 063003 (2013)
[2] G Ito et al.  Phys Rev Lett 112 183001 (2014)
[3] Kono et al. Phys Chem Chem Phys 17 24732 (2015)


STSM by Violaine VIZCAINO, CIMAP, Caen (FR) withThomas Schlatholter, Zernike Institute for Advanced Materials (NL)VVIZ_logos
On September 26, 2015 (10 days)

Radiation damage to human type II collagen fragments on the single molecule level

The purpose of the STSM was to study the radiation-induced molecular degradation of human type II collagen. We looked at the photo-fragmentation induced by both soft X-ray and XUV of two peptides: PK26-P [PGGPPGPKGNSGEPGAPGSKGDTGAK] which is made of a repetition of the amino acids sequence X-Y-Gly specific to collagen protein, and PK26-HyP [PGGP-HyP-GPKGNSGE-HyP-GA-HyP-GSKGDTGAK] which contains the unnatural hydroxyproline (HyP) residue.

Fragmentation of both peptides, in two different protonated states (M+3H)3+ and (M+4H)4+, were measured at different photon energies in order to highlight the main fragmentation channels, their threshold and the influence of hydroxyproline (HyP) residue in these processes. Figure 1 shows typical fragmentation spectra of (PK26-Hyp +4H)4+ at three different energies (14, 18 and 21 eV).

We expect to submit our results in a peer-reviewed scientific journal at the beginning of 2016. Moreover, this STSM has also allowed strengthening the collaboration between the CIMAP (Caen, France) and the University of Groningen (Netherlands).


Figure 1 : Fragmentation spectra of (PK26-Hyp +4H)4+. All spectra are normalized to the parent depletion.

STSM by Christina Kjaer Soerensen, Aarhus University (DK) with Yoni Toker, Bar Ilan University (IL)
On September 5, 2015 (6 days)

Mass spectrometric analysis of chlorophyll cluster ions produced by electrospray ionization

The purpose of the STSM was to study which chlorophyll dimers or larger clusters that can be formed with electrospray ionisation using the high resolution Agilent q-TOF Mass Spectrometer located at Bar Ilan University in Israel.Chlorophyll_a_R1_ach
Chlorophyll (Chl) a and b are the light-absorbers of plants and are composed of a porphyrin macrocycle with a divalent magnesium ion in the center. The pi − pi* transitions in the porphyrin are responsible for the strong UV/Vis absorption by these molecules. It is non-trivial to predict the absorption spectra of Chl a and b, and what effect the in vivo protein environment has. Accordingly, it is interesting to study absorption by isolated chlorophylls in vacuo, which was previously obtained indirectly from action spectroscopy.
Exciton coupling between two or more chlorophylls is expected to have a significant effect on the absorption spectrum, and by comparing the absorption by the dimers to that of the monomers, the strength of these couplings can be identified through band splitting / broadening or shifts. In order to obtain the absorption spectra of the dimers, it is necessary to determine which dimer or cluster complexes can be made with electrospray ionisation.
During the STSM, different solvents, temperatures and other settings of the system were tested in the attempt of producing dimers or larger cluster complexes with a quaternary ammonium cation (tetramethylammonium and acetylcholine), as these are used for charge tagging the neutral Chl molecule in order to perform gas-phase action spectroscopy.
One out of many obtained mass spectra is shown in Figure 1. This is the mass spectrum of Chl a and the charge tag acetylcholine (ACh) in the mass to charge ratio range 1740-1815. The highest yield in this range is from the protonated dimer consisting of two Chl a with one magnesium ion replaced by two hydrogen atoms (m/z 1764.1). The shape of the peak distribution arise from isotopic species. Two other interesting dimers are produced with weak intensities: the protonated Chl a dimer (m/z 1786.1) and protonated dimer of two Chls with both magnesium ions replaced (m/z 1742.1). However, the dimer-tag complex with both magnesium ions was not present in any of the obtained spectra.
The process of replacing the magnesium center in Chl also occurs in nature and is the reason why leaves lose the green color in the fall. From the obtained spectra it can be concluded that complexes of Chl a without the magnesium ion are easily produced with high intensity. This gives the opportunity of studying the absorption by the “fall-Chl” in Aarhus.
Additionally, the spectra show that the protonated dimers are possible to produce and this gives hope for producing dimers tagged with the cations. These complexes are more fragile, and more work is required in optimising the conditions in order to produce these. This work continues after the STSM and hopefully brings the desired results and more knowledge and experience with producing such fragile biomolecules in gas-phase.
If the desired mass spectra are achieved, they will be applicable for a publication on the subject of absorption by Chl-dimer complexes. The already obtained spectra will be relevant in a future experimental study of the absorption by fall-Chls which hopefully also will deliver results to a
Furthermore, the collaboration between Bar Ilan University (Israel) and Aarhus University (Denmark) has been strengthened through this STSM.

CHRISK_imgFigure 1: Mass spectrum revealing the presence of more dimer-complexes. The highest signal is seen from a protonated Chl a dimer with one magnesium center replaced by two hydrogen atoms (m/z 1764). The signal at m/z 1786 is from a protonated Chl a dimer and at m/z 1742 the dimer with both magnesium replaced is observed.


STSM by Sylwia Stefanowska, Gdansk University of Technology (PL) with Alicja Domaracka, Center of Research on Ions Materials And Photonics (FR)
On August 1, 2015 (20 days)


Ion induced reactivity in molecular clusters

The aim of this Short Term Scientific Mission was to study collisions of 1-5keV Ar+ ions with PAH neutral clusters. The research was extended to acridine. This experiment has been performed to compare with anthracene (C14H10) and phenazine (C12H8N2) results and to understand how the presence of the nitrogen in a benzene ring can modify the molecular fragmentation and the reactivity of these kinds of molecules.
In the COLIMACON experiment pulsed beam of positive atomic ions collide with neutral particles in the interaction region of a linear time-of-flight mass spectrometer. Cationic products from individual collision events were detected in coincidence by microchannel plate detector. The Ar+ ions were produced by an ion gun, accelerated to 1.2 keV and pulsed into 1.5 μs bunches. The effusive jet of neutral particles of Acridine (C13H9N, 179 amu) was prepared using an isolated oven.
Measurements were carried out as a function of extraction delay, the extraction of cationic products is made a few μs after the interaction. Figure 1 presents the mass spectra for different delays of extraction, from 17.1 μs to 22.1 μs. It clearly appears that, with the increase of delay, the probability to lose one hydrogen atom from acridine molecule also increases. The analysis of the obtained data is still in progress.


STSM by Sandor Borbely, Babes-Bolyai University (RO) with Joachim Burgdörfer, Vienna University of Technology (AT)logo_ubb_albastru TU_logo
On August 9, 2015 (14 days)

Ionization and excitation of He by antiproton impact

During the interaction of high energy charged particles and atomic, molecular or solid targets the projectile loses parts of its energy. This energy is deposited in the target system via non-elastic processes like single or multiple ionization, excitations, etc. The relative importance of these energy deposition channels as a function of the projectile’s impact energy is a fundamental question is collision physics. This is also a key question during the assessment of the damage created by such high energy projectiles in biological tissues, since in biological systems after a charged projectile impact the most damage is caused by the residual charged targets created during the primary collision event. The chosen antiproton impact ionization and excitation of He is an ideal benchmark system for the investigation of the above mentioned energy loss processes.

For the antiproton-helium collision we have solved the electronic time-dependent Schrödinger equation numerically in the framework of the semiclassical impact parameter approach. From the obtained fully-correlated two-electron wave functions we have extracted the ionization and excitation probabilities, which were used to calculate the stopping power for each energy dissipation channel (single ionization, double ionization and single excitations). From these stopping powers the stopping cross sections were calculated by performing the impact parameter integrations. The obtained partial stopping cross sections are shown on the attached figure as a function of antiproton impact energy. On the figure one can observe that the dominant energy dissipation channel is single ionization followed by single excitations and double ionization. Since the present results are based on fully-correlated two-electron ab initio calculations, they can provide a reference for approximate calculations. After further analysis and comparison with the results of existing calculations and measurements the present results will be prepared for dissemination in the form of an article.


STSM by Inés Corral, Universidad Autonoma de Madrid (ES)  with Maurizio Persico, Universita di Pisa (IT)
On June 3rd, 2015 (63 days)

Competing ultrafast internal conversion and intersystem crossing in DNA and RNA modified nucleobases

The particular topology of the excited state potential energy surfaces (PES) of natural DNA monomers is the cornerstone of the photostability of our genetic material. [1] In fact, for these species the steeply descending nature of the spectroscopic state PES at the region connecting the Franck Condon geometry with the internal conversion funnel to the ground state prevents the retention of the wavepacket at interstate crossings, minimizing at the same time the transfer of population to lower lying excited states and other competing radiative emission processes, and therefore facilitates the relaxation of the population to the ground sate, Figure 1a. [2] This topology can be modified by altering the substitution pattern of the heterocyclic purine and pyrimidine skeleton, changing, thus, the intrinsic photophysical properties of natural nucleobases, Figure 1b.

This context frames the present STSM, along which we have explored the excited state deactivation dynamics of two modified nucleobases where one (4-thiothymine) or the two exocyclic oxygens (2,4-dithiothymine) of the natural nucleobase thymine have been substituted with sulfur atoms. To this purpose we have used the semiclassical surface-hopping algorithm developed in the group of Profs. Persico and Granucci, incorporating both non adiabatic and spin orbit couplings in the adiabatic representation. [3] These simulations were based on semiempirical PESs and couplings calculated from a reparameterized Hamiltonian with CASPT2 calculations. On the basis of these simulations we propose the following kinetic model for the deactivation of both systems: S2->S1->T2/T1. However, we also conclude, in agreement with previous experimental findings, [4] that the degree of substitution has a significant impact in the total triplet rise time, due to the very different excited state PESs topology predicted for both systems.

We expect to publish these results, together with the outcome of femtosecond broadband transient absorption experiments performed in the group of Prof. Crespo-Hernández from the Case Western Reserve University in Cleveland (Ohio), in a near future.

Fig-largeFigure 1. Schematic representation of potential energy surfaces characteristic of photostable (a) and photoreactive (b) chromophores.

[1] Photoinduced processses in nucleic acids Vols I, II, M. Barbatti, A.C. Borin, S. Ullrich (Eds.), Springer 2015.
[2] L. Serrano-Andrés, M. Merchán. J. Photochem. Photobiol. C 2009, 10, 21-32.
[3] G. Granucci, M. Persico, G. Spighi, J. Chem. Phys., 2012, 
137, 22A501.
[4] M. Pollum, S. Jockusch, C.E Crespo-Hernández, J. Am. Chem. Soc. 2014, 136, 17930.


STSM by Attila Toth, University of Debrecen (HU) with Benjamin Lasorne, Institut Charles Gerhardt Montpellier, Universite de Montpellier (FR)
On June 29th, 2015 (6 days)

Exploring the potential energy surfaces of NO2

In polyatomic molecules there are many energetically close-lying electronic states, which may cross at particular nuclear arrangements. In the vicinity of these degeneracy points, also known as conical intersections (CIs), the electronic and nuclear motions are strongly coupled, and nonadiabatic e ects play a crucial role. Our long term goal is to provide a fully quantum mechanical treatment of such coupled electronic-nuclear dynamics induced by laser radiation in the NO2 molecule. For this reason, the purpose of the present STSM was the investigation of the involved potential energy surfaces.
First, we explored the number and nature of electronic states lying within the energy range of our interest. This scan was performed at the state-averaged complete active space self-consistent eld (SA-CASSCF) level of theory. The state averaging was performed over three states, employing correlation consistent polarized quadruple zeta (cc-pVQZ) basis set and an active space of 13 electrons in 10 orbitals. Based on these result, we decided to focus thereafter only on the calculation of the ground and rst excited state. Due to the CI between these two states (see Figure 1), the kinetic energy coupling diverges in the adiabatic representation, which makes the dynamical calculations numerically dicult. For this reason, an essential part of the present STSM was the diabatization of the PESs. This was achieved by a quasidiabatization procedure based on the linear vibronic coupling (LVC) model.PESs_DV_seam

Figure 1: a) PES of the ground (1 2A1) and rst excited (1 2B2) electronic states of NO2. The black curve represents the seam of conical intersections. b) The three lowest lying PES of NO2 in C2v symmetry at Rs = 2.2 a.u.
The next step of our collaborative project will consist in the re nement of the results ob-
tained during the STSM. This will be achieved by recomputing the PESs at the multireference con guration interaction (MRCI) level of theory. These surfaces will serve as input for our quantum dynamical calculations, which are expected to produce interesting results over the next few months.

STSM by Carlos Marante, Universidad Autónoma de Madrid (ES)  with Eva Lindroth, Alba Nova University Center (SE)Small_Fig
On June 2nd, 2015 (29 days)

Calculation of multi-channel ionization state properties in complex

The main purpose of the STSM, was to establish a benchmark for the scattering observables of neon. This would be very helpful to validate the new code, XCHEM, under development in the Fernando Martn’s group in Madrid, which is intended to describe the ionization continuum of complex atoms and molecules.
The comparisons consisted in three test cases: i) only one parent ion with 1s2 2s2 p6 con g-
uration (2s-1), ii) only one parent ion with 1s22s22p5 con guration (2p-1) and iii) both 2s-1 and 2p-1 parent ions. The energies obtained for these cations were in good agreement, and using our close-coupling approach, the eigenphases were obtained above and between the previous thresholds, which compared well with the reference.
The results obtained so far, contributed to the improvement of the XCHEM suite. At least one article will be prepared in the mid term, adding more correlated Ne neutral and cations, as well as a higher number of parent ions in the close-coupling expansion.

STSM by Samuel Jenkins, Royal Holloway University of London (UK)  with Bernard Piraux, Université Catholique de Louvain (BE)
On June 15th, 2015 (13 days)

Mixed basis set approach to ionization of atoms and molecules in strong fields

The Coulomb-Sturmian functions work extremely well when treating hydrogen in a strong laser field, but to treat other argon and other systems we propose a mixed basis to deal with the first few angular momenta where the potential is particularly non-hydrogenic and to use Sturmian functions for the angular momenta that remain.

Recently, in a collaboration between the group at Royal Holloway, the Bauer group in Poland and Professor Piraux’s group Louvain-la-Neuve, the excitation and ionization rates for the excited hydrogen atom were calculated using a Sturmian basis for all sub bound states pertaining to n = 2 when subject to a ten cycle, circularly polarized pulse with intensities ranging from 1011 – 1015 W/cm2 at a frequency of 800nm1. To compare with tunneling-type theories2, which predict the ratio of ionization rates for initially co-rotating and counter-rotating electrons, we are looking to extend the calculations performed on hydrogen with a circularly polarized pulse to argon from its ground state within the single active electron approximation. To do this, we propose to expand the first few angular momenta (up to and including l = 2) of the time dependent wavefunction as B-splines3 to cope with the non-hydrogenic potential, given here by Muller4, near the nucleus and the higher angular momenta as Coulomb-Sturmian functions. The mixed basis will produce sub-blocks of the Hamiltonian matrix with the laser interaction term involving both Sturmians and B-splines which will be dealt with numerically. The mixed basis will also result in a Hamiltonian with a bandwidth slightly larger than that of hydrogen. After the wavefunction has been propagated, ionization rates shall be calculated.

Thanks to the STSM, I was allowed to practice adapting Professor Piraux’s very successful Sturmian code by calculating the momentum maps for initially co-rotating and counter-rotating electrons in H to compare with results given in an earlier paper by Huens and Piraux5 (see Figures 1 and 2).


Figure 1: Photoelectron momentum distribution in the x-y plane for the ionization of a hydrogen atom in the excited state n = 2, l = 1, m = -1 subject to a 20 cycle circularly polarized laser pulse of frequency w = 0.25 (a.u.) and peak intensity I = 5.48351 x 1014 W/cm2 propagating along the z-axis.


Figure 2: Photoelectron momentum distribution in the x-y plane for the ionization of a hydrogen atom in the excited state n = 2, l = 1, m = 1 subject to a 20 cycle circularly polarized laser pulse of frequency w = 0.25 (a.u.) and peak intensity I = 5.48351 x 1014 W/cm2 propagating along the z-axis. Note the reduced probability to ionize relative to Figure 1.

STSM by Aurora Ponzi, University of Trieste (IT)  with Nadja Doslic, Ruder Boškovic Institute (HR)
On June 2nd, 2015 (60 days)

Time resolved photoelectron spectroscopy as a probe for ultrafast excited state dynamics

This project aims at a high level theoretical description of Time-Resolved Photoelectron Spectroscopy (TRPES) observables obtained from pump-probe experiments. TRPES permits one to probe electronic states and nuclear dynamics with femtosecond time resolution. Our goal is the combination of photoionization observables calculation (using Dyson orbitals) with semiclassical non-adiabatic dynamics calculation. During this short term scientific mission, initial calculations have addressed photoionization from ground and excited electronic states of furan.
The development of a theoretical framework for simulating the ultrafast dynamics of complex molecular systems and computation of spectroscopic observables is a goal of current and general importance. We have performed a comparative study of photoionization observables computed using the Dyson orbitals as initial states and an accurate solution of the continuum one particle wavefunctions, at the DFT and TDDFT levels. The Dyson orbitals were computed at the CASSCF, ADC(2) and TDDFT levels.
The results obtained during this mission will be collected in a manuscript in preparation. This preliminary study constitutes the first step of a more ambitious project which joins the know-how of two theoretical groups.
In parallel with the main project, I also performed multireference quantum chemistry calculations for two systems: pyrrole and adenine-water. The results of my contribution are included in an already published paper (Phys. Chem. Chem. Phys. 2015, 17,19012) and in a recently submitted paper to J. Phys. Chem. A.