Probing the protein electronic structure by soft X-ray action spectroscopy
The motivation of this study is to see if the electronic structure of the protein can be correlated with its charge state, which defines the protein tertiary structure. Due to the Coulomb repulsion, protein precursors with higher charge states tend to unfold, or have elongated structures. Therefore, by roughly controlling the protein tertiary structure in the gas phase, we are able to investigate the influence on the protein electronic structure and give more insights into protein fundamental properties.
We used the near edge X-ray absorption fine structure (NEXAFS) method to obtain the absorption spectra from the trapped Ubiquitin and bovine pancreatic trypsin inhibitor (BPTI) protein ions, produced by an electrospray ion source (ESI). Several precursor ion charge states of these two proteins were isolated and subjected to the soft X-ray photons from PLEIADES beamline at SOLEIL synchrotron near Paris. Single ionization yields were obtained for different precursor charge states in C- and N-edge photon energy ranges. In the obtained spectra, we could clearly resolve the features corresponding to the Carbon 1s and Nitrogen 1s electron excitation into higher molecular orbitals. An example of our preliminary results obtained for BPTI protein in the C-edge energy range is presented in Figure 1.
Figure 1 – Single ionization yields for the precursor charge state 5+ of the BPTI protein in the C-edge. Two peaks at about 284.5 eV and 288 eV correspond to the C 1s electron excitation into π*aromatic and π*amide molecular orbitals. The yield is normalized to the unity area under the curve.
The main goals of this STSM were successfully accomplished and we expect to publish the results in peer review journal as soon as possible. We plan to continue the collaboration with the new studies involving NEXAFS of other biologically relevant samples in the gas phase.
A collaboration project between the Synchrotron SOLEIL ( http://www.synchrotron-soleil.fr ), France and the University of Turku (http://www.utu.fi/en ), Finland, is looking for candidates to apply for a 4 year funded PhD position. The collaboration involves the PLEIADES beamline of SOLEIL and the Materials Research Laboratory in the Department of Physics and Astronomy of the University of Turku, and is aimed at developing and applying novel methods for gas-phase spectroscopy of fragile organic molecules.
While several fragmentation studies of soft x-ray irradiation of DNA bases or peptides exist, there is a lack of studies on neutral polypeptides or medium sized neutral biomolecules. Indeed, this is mainly due to their tendency to decompose during the heating phase, leading to their sublimation. The new technique, based on generation followed by flash vaporization of nano-droplets of a solution containing a specific molecules, will be combined with studies on the influence of electronic excited states after an excitation with soft x-ray synchrotron radiation. This targeted energy deposition can also lead to selective fragmentation of these floppy molecular edifices. The PhD student will be closely involved in instrumental development using electrospray and molecular cluster sources and will participate in experiments at SOLEIL, but also at other international synchrotron radiation facilities such as MAX-IV or at free electron lasers. The experimental methods consist mainly of electron spectroscopy, and electron-ion coincidence techniques. In addition, the student will participate in the general study programs of the graduate schools.
The successful candidate will enroll in both the Doctoral Program in Physical and Chemical Sciences of the University of Turku and the wave and matter doctoral school of the Physics of light and matter of the University Paris-Saclay, under a COTUTELLE double degree agreement. The student will spend time at both partner institutions for courses and research, although the scheduling will be flexible.
After successful completion of the studies and the defence of the thesis, the PhD student will be granted a Doctor of Philosophy degree by both the Finnish and French universities.
To qualify, the candidates must have a recent Master of Science or equivalent degree in a relevant field. The application deadlines are announced at the graduate school websites:
The nearest deadline is September 19th, 2016.
Contacts: Prof. Edwin Kukk (email@example.com)
Dr Christophe Nicolas (firstname.lastname@example.org)
The 3rd XLIC WG2 Expert meeting (July 22-28, 2016) was focused on Delocalized Electrons in Atomic and Molecular Nanoclusters. It was organized by Klavs Hansen and took place at the Ettore Majorana Center for Scientific Culture, Erice, Sicily, Italy.
It was aimed at scientists, postdocs and graduate students who work with the effects of delocalized electrons with focus on free nanoclusters. Subjects such as quantum size effects, novel materials, and reaction pathways exhibit a range of phenomena which are highly sensitive to delocalized electrons’ mobility, screening, response, direct and exchange interactions, correlations, etc. The aim of the workshop was to bring together researchers in adjacent fields to examine recent and future developments.
The structure was workshop format of a week’s duration and included invited talks, selected oral presentations, a poster session, as well as time for individual discussions, as can be seen in the program below. The number of participants was 58.
The workshop was organized locally by the Ettore Majorana Center for Scientific Culture. The center, with the president Prof. Antonino Zichichiby, has a long and illustrious history of organizing such types of meetings. The workshop was in the framework of the International School of Solid State Physics, directed by Prof. Giorgio Benedek.Klavs Hansen (Gothenburg, Sweden)
The Local Organiser
STSM by Armin Scrinzi, Ludwig Maximilians University (DE) with Fernando Martin, Universidad Autonoma de Madrid (ES)
On April 11, 2016 (19 days)
From GERMANY to SPAIN
Absorption and electron spectra for small chemical systems
The momentum spectra of fragments emitted in laser-matter interaction are a main source of information about the internal dynamics. With tSurff a new and powerful theoretical tool was developed. The STSM was to introduce and implement the method in the group at UAM.
Implementations were designed and partially finished for emission from single- and multi-particle systems. This will, in certain applications, allow substantial speedup of calculations at UAM. Use with the XChem code was laid out and implementation is in progress. In turn, the for LMU’s tRecX code, structural adaptions for a new interface to standard quantum chemistry structure were intiated. In a third line of development, adopting tSurff for breakup was discussed.
Outcome: the expertise for using tSurff has been successfully transferred to the UAM group. A collaboration for breakup has been agreed on. A new strategy for a quantum chemistry interface for tRecX has been adopted.
Figure: tSurff for break up: partitioning of configuration space (from an internal report)
STSM by Manuel Yáñez, Universidad Autonoma de Madrid (ES) with Jean-Yves Salpin, LAMBE – Université d’Evry Val d’Essonne (FR)
On April 9, 2016 (22 days)
From SPAIN to FRANCE
Reactions of peptides and aminoacids with multiply charged ions. A theoretical and experimental perspective
The main goal was trying to gain insight on the toxicity of organomercury compounds and on the anticancer activity of cisplatin, by investigating their complexes with nucleobases through the use of InfraRed Multiple Photon Dissociation (IRMPD) experiments and high-level density functional theory (DFT) methods.
In the first case it has been found that the interaction of uracil, thymine and cytosine with RHgCl (R=CH3, n-Bu) results in the alkylation of the nucleobase, and the most stable structures have been characterized through IRMPD and high-level DFT calculations. In the second case, the interaction of cisplatin with uracil. and its thio and dithio derivatives was investigated using similar experimental and theoretical techniques, showing that several adducts are stable and contribute to the IRMPD spectra.
A poster, under the title “Alkylation of nucleobases by organomercuric compounds: a gas-phase study” was presented in the Biennial conference on isolated biomolecules and bimolecular interactions. Mass spectrometry, spectroscopy, and theory, and we expect to submit one paper to Int. J. Mass Spectrom. along this year and at least a second, and probably a third one, in another peer reviewed journals.
STSM by Judith Dura, MBI – Nonlinear optics and Short Pulse Spectroscopy (DE) with Luis Bañares, Universidad Complutense de Madrid (ES)
On April 13, 2016 (10 days)
From GERMANY to SPAIN
New energy transfer mechanisms in methyl iodide complexes unravel by femtosecond Coulomb repulsion
Multiphoton processes in atoms and molecules are highly probable upon ultrashort laser pulses irradiation. When the molecule is a Van der Waals cluster, there is a certain probability that within the same aggregate, one monomer experiences a neutral fragmentation channel, and a different monomer suffers an ionizing process. Within this particular situation, if a second laser pulse arrives it will ionize the fragment under neutral dissociation, which will experience a Coulomb repulsive force with the charge neighbour. Thus, the kinetic energy of the dissociated fragment will be modified as a function of the distance between the charge fragments. The kinetic energy trace of the Coulomb repulsed particles can be followed in time, i.e. charge particles distance, using the combination of ultrashort laser pump-probe techniques together with Velocity Map Imaging detection systems.
Figures 1 show 2D contour maps of the Centre of Mass (CM) kinetic energy (KE) of CH3 as a function of the time delay for λpump = 266 nm and λprobe = 333.5 nm a. Three time-dependent KE contributions can be distinguished.
Figure 1. Time-dependent ionization yield and Centre of Mass (CM) kinetic energy (KE) of photodissociation CH3 fragments at λpump = 266 nm and λprobe = 333.5 nm. Letters indicate time-dependent Coulomb repulsion trajectories.
Coulomb repulsion trajectories for the CH3 fragment in repulsion with the other CH3I of the dimer were simulated for the most stable dimer geometries (details of the calculations not given here) and compared with the experimental Coulomb repulsion trajectories.
The comparison suggest that trajectories A and B converge asymptotically to the neutral dissociation channels of the CH3I in the A-band.
An article with the outcome of this STSM has been writing at the moment to be send to Phys. Chem. Chem. Phys. in the next incoming months.
Photoelectron spectra for REMPI processes in (chiral) molecules
Chirality (the distinction of left and right mirror images) is one of the fascinating aspects of biology, since enzymes possess a 100% selectivity with respect to the stereochemistry of molecules. While the left-handed version of some molecule may be a very powerful pain reliever, its right-handed counterpart may be fully ignored by the human body, or, even worse, it may have fatal consequences.
Therefore, analytical tools for a very efficient and sensitive detection of the absolute configuration of a molecule is of great practical importance.
Some years ago the research group of Th. Baumert (Hassel, Germany) reported an asymmetry in the photoelectron angular distributions between two enantiomers of camphor as well as fenchone in (2+1) resonantly-enhanced multiphoton ionization. The similarity of the asymmetry may indicate some universal pattern which may pave a path to a sensitive detection tool for the absolute configuration of different enantiomers. In order to investigate this even further, it is of great interest to set up an approach that allows for the calculation of photoelectron angular distributions in resonant multiphoton ionization.
Within this STSM in Trieste a numerical approach for treating (2+1) resonantly enhanced multiphoton ionization, especially for extracting photoelectron spectra, was formulated and implemented. Two data sets for testing (hydrogen atom and the chiral molecule BrClFCH) were generated. During the STSM first tests for hydrogen atoms were performed by comparing the results with the ones of full solutions of the time-dependent Schroedinger equation. Furthermore, the STSM was used to clarify the strategy for extracting photoelectron distributions from the common Trieste/Berlin single-determinant time-dependent Schroedinger equation solver for arbitrary molecules and to prepare the resubmission of a joint publication.
Preparation work for studying ionization and dissociation dynamics of complex biomolecules or solvated biomolecules
If several fragmentation studies of soft x-ray irradiation of DNA bases or peptides exist; there is a paucity of studies on neutral polypeptides or medium sized neutral biomolecules. Indeed, this is mainly due to their tendency to decompose during the heating phase, leading to their sublimation. A new approach is needed, which should be compatible with low sample consumption and a high density of the neutral biomolecules transferred into vacuum.
Based on the flash vaporization of nano-bioparticles coming from the atomization of a solution of the biomolecule under study, developed by Wilson et al. , we tried to couple a modified electrospray source with an electron spectrometer chamber. In our case, the highly charged droplets are neutralized in order to stop their fragmentation prior to introduce them into vacuum through a few micrometers nozzle. During the present STSM, we succeeded to detect nanodroplets signal, introduced under vacuum, via electron spectroscopy (see figure 1).
This STSM is the starting point of a collaboration between the two partners in order to improve the transfer efficiency of these nanobiodroplets into vacuum, as well as to design the vaporization stage. Wilson, Kevin R., et al. 2006. Journal of Physical Chemistry A 110 (6): 2106–13
Figure 1: Photoelectron spectra recorded with a helium lamp Green: just the gases running through the electrospray, Red with the buffer solution running in the electrospray and the neutralizer turned off and Blue: with the buffer solution running in the electrospray and the neutralizer turned on. The spectra show broad features, probably due to the nanodroplets of buffer transferred into the vacuum. The shifts of the broad structures could be due to a change of droplets size when the neutralizer is turned on (bigger size droplets are expected). These two broad structures are contrasting with the sharp photoelectron lines coming from the gases used in the electrospray
STSM by Ewa Erdmann, Gdansk University of Technology (PL) with Manuel Alcamí, Universidad Autonoma de Madrid (ES)
On February 15, 2016 (35 days)
From POLAND to SPAIN
Fragmentation dynamics of neutral and ionized furan molecule
The aim of this STSM within the XLIC COST Action was to continue investigation into the mechanism of fragmentation process of furan molecule. Furan is a five-membered heteroaromatic compound which plays a key role in many areas of chemistry such as polymer science, combustion chemistry and biologically active substances. A lot of theoretical and experimental studies have already focused on understanding this fundamental reaction. However, as the mechanism of the formation of the various products is still unclear, in this work we aim at extending and complementing previous studies.
During reported visit our efforts have focused on performing ab initio molecular dynamics calculations and analysis of the results for the case of singly- and doubly-ionized furan molecule. Singly-ionized furan displays similar fragmentation pattern to the fragmentation of the neutral molecule. Overall dynamics is dominated by unimolecular opening of the furan ring and hydrogen transfer to other carbon atoms. Doubly-ionized furan fragmentation follows a completely different dissociation path. One channel (Fig. 2) can be clearly distinguished with very high occurrence probability.
Moreover, our attention has been considerably focused on obtaining converged results using the statistical mechanics approach – Microcanonical Metropolis Monte Carlo (M3C) method for neutral and singly charged furan. Our present results can be directly compared with experimental data (mass spectrum) from NIST database.
During reported visit, the applicant had the opportunity to make significant progress with investigation of fragmentation process of ionized furan. Results obtained during the visit were already presented at the 2nd meeting of the XLIC Working Group 2 in Stockholm. The final results of this STSM are planned to be published in the near future.
STSM by Paula Pla Terrada, Universidad Autonoma de Madrid (ES) with Remco W. A. Havenith. University of Groningen (NL)
On January 10, 2016 (35 days)
From SPAIN to NETHERLANDS
Evaluation of Local Ring currents in fullerenes
Since their discovery, fullerenes have attracted a lot of interest due to its unique properties and applications and a huge effort has been done to predict their relative stabilities. However, there is still not a complete understanding of the importance of local effects. The aim of the mission was to understand better these effects using ring current calculations and to generate some plotting program that enables us to visualize ring current vector potential in 3-dimensions.
In this work we studied a family of exohedral fullerenes based on C64(1911) isomer with CTOCD-DZ method using Khon-Sham orbitals at BLYP/6-31G* level of theory. Important differences are found in the calculated ring current densities for C64(1911) and C64Cl4(1911) when the chlorine atoms are added in the 3-fused pentagons motif. While C64 presents a strong HOMOLUMO paratropic contribution, C64Cl4 presents several diatropic and paratropic contributions of lower intensity when the magnetic field is along the symmetry axis of the molecule. The plotting tools developed in the University of Groningen open the study in terms of ring currents to other fullerenes and 3-dimensional systems.
Collaboration between two groups has started thanks to this collaboration and once the work was finished it will be submitted to publication.