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Polypeptide formation in clusters of β-alanine amino acids by single ion impact

The formation of peptide bonds by energetic processing of amino acids is an important step towards the formation of biologically relevant molecules. As amino acids are present in space, scenarios have been developed to identify the roots of life on Earth, either by processes occurring in outer space or on Earth itself. We study the formation of peptide bonds in single collisions of low-energy He2+ ions (α-particles) with loosely bound clusters of β-alanine molecules at impact energies typical for solar wind. Experimental fragmentation mass spectra produced by collisions are compared with results of molecular dynamics simulations and an exhaustive exploration of potential energy surfaces. We show that peptide bonds are efficiently formed by water molecule emission, leading to the formation of up to tetrapeptide. The present results show that a plausible route to polypeptides formation in space is the collision of energetic ions with small clusters of amino acids.See full text here:

  • Rousseau*, D.G. Piekarski, M. Capron, A. Domaracka, L. Adoui, F. Martín, M. Alcamí, S. Díaz-Tendero* and B.A. Huber
    Polypeptide formation in clusters of β-alanine amino acids by single ion impact
    Nature Communications 11, 3818 (2020)
    https://doi.org/10.1038/s41467-020-17653-z
 

IDEAS project is awarded with an ERC Advanced Grant

The UAM professor Fernando Martín, from the Department of Chemistry of the Faculty of Sciences has obtained funding from the European Research Council to develop the IDEAS project (Imaging, Decoherence and AttoSecond probing of ionization-induced charge migration in molecules)

The European Research Council (ERC) has selected the “Imaging, Decoherence and AttoSecond probing of ionization-induced charge migration in molecules” (IDEAS) project, led by the Professor of Physical Chemistry at the Autonomous University of Madrid ( UAM), Fernando Martín, to be financed by the ERC Advanced Grant program. It is the second time that the CampuS group receives one of these grants.

This project is one of the 82 projects in the category of Physical Sciences and Engineering that the ERC is going to finance this year 2020. According to the leading researcher its objective is to understand, and eventually predict, the first stages of charge migration processes in complex molecules, occurring in the time range of attoseconds (10-18 seconds). To do this, the team will have to develop and validate the theoretical methodology necessary to describe the effects that such migration produces experimentally, with the additional complication that existing techniques for simple atoms and simple molecules are not trivially extensible for complex ones.

The computational codes to be developed within the IDEAS project will provide a description of ionization and charge migration in relatively complex molecules, with a level of detail unprecedented to date. This is an essential step for the establishment and consolidation of attosecond science as a discipline that, beyond revolutionizing our basic knowledge of the electronic processes that occur in matter, allows addressing problems of practical interest in physics and chemistry.

Obtaining this ERC grant will boost the research that we have been developing in our group in recent years and, in particular, will allow us to continue advancing in the development of new attosecond experiments aimed at understanding and controlling chemical processes in a time scale inaccessible to date. This could allow us to generate more efficient charge transfer processes than those currently used in, for example, optoelectronic and photovoltaic devices. In addition, the project will reinforce the investigations carried out within the framework of the European CA18222 Action (AttoChem) that we coordinate from the Autonomous University of Madrid ”, explained Professor Martín.

FERNANDO MARTÍN GARCÍA graduated in Chemical Sciences (Quantum Chemistry specialty) in 1984 and in Physical Sciences (Theoretical Physics specialty) in 1986 at the Autonomous University of Madrid. He obtained his doctorate at that university in 1986 and obtained the extraordinary doctorate award. Subsequently, he completed postdoctoral stays at the Université de Bordeaux I (1988), the Université de Paris VI (1989-1990) and the University of Chicago (1995-1996). He has been Full Professor at the Autonomous University of Madrid from 1993 to 2005 and, since then, Professor of the same in the area of ​​Physical Chemistry.
His research work has focused mainly on the theoretical and computational modeling of photoexcitation and photoionization processes in atomic and molecular systems induced by synchrotron radiation and ultrashort laser pulses with femto- and atosecond durations, as well as in the theoretical study and prediction of properties of materials and nano-objects, of complex molecular systems, aggregates and fullerenes, isolated or deposited on metallic and non-metallic surfaces. All of this, in close collaboration with prestigious Spanish and European experimental groups.
He has directed 24 doctoral theses, is co-author of several scientific codes (XChem, FullFun, M3C), and has published nearly 500 articles, among which several stand out in the journals Science, Nature, Chemical Reviews, Nature Chemistry, Nature Physics, Nature Photonics, Nature Communications, Proceedings of the National Academy of Science, Physical Review Letters, Angewandte Chemie, Journal of the American Chemical Society, ACS Nano, Advanced Materials, Small, Nano Letters, as well as various reviews and book chapters.
He has also received numerous awards, including the Rey Juan Carlos I National Research Prize (2000); the prize from the Royal Spanish Society of Chemistry in Physical Chemistry (2010), the Advanced Grant XCHEM from the European Research Council (2011), and the Rey Jamie I Prize in Basic Research (2017). He has been the coordinator of two COST Actions for European cooperation, the first between 2008 and 2012 (CUPSFEL, CM0702) and the second, mentioned above, in attosecond chemistry, from 2019 to 2023 (AttoChem, CA18222).

The European Research Council (ERC) is the main European funding organization for excellent frontier research and is part of the Horizon 2020 research and innovation program. Each year, it selects and funds the best creative researchers of any nationality and age to execute projects carried out in Europe. In this year’s call, researchers and teachers from 26 nationalities have been selected. Germany, the United Kingdom and France are the countries with the highest number of projects in a classification in which Spain ranks sixth, with 14 selected. In total, 450 million euros will be allocated to finance the 185 researchers who have won some of the grants from this call.

As explained in a statement by the promoters of this European initiative, these research projects will not only help to strengthen the European knowledge base, but will also allow the creation of 1,800 new jobs for postdoctoral researchers, doctoral students and other related jobs.

For more information, we refer you to:
ERC press release: https://erc.europa.eu/news/erc-2019-advanced-grants-results
H2020 in Spain, official website: https://eshorizonte2020.es/ciencia-excelente/consejo-europeo-de-investigacion-erc/noticias/resultados-convocatoria-advanced-grants-2019
UAM press release: See here 

 

INPhiNIT fellowship programme – 2020 call

The 2020 call of INPhiNIT doctoral fellowship programme, funded by “la Caixa”, is now open. Campus theoretical group is willing to host students who get a fellowship in any of its modalities:

  • INPhINIT-Incoming: There are 35 phd fellowships directed to students NOT having resided in Spain for more than 12 months in the last 3 years. Deadline: 4/02/2020.
    Research topic offered by Campus group (If selected, the student should join the IFIMAC – UAM Condensed Matter Physics Center, accredited with the Spanish Seal of Excellence María de Maeztu):

  • INPhINIT-Retaining: 30 phd fellowships to develop the doctorate in any field and any center. Requirements: have resided in Spain for more than 12 months in the last 3 years. Deadline: 26/02/2020.
    Campus group is active in several research lines. If selected, the student can join either the IFIMAC – UAM Condensed Matter Physics Center (with the María de Maeztu Seal of Excellence), the Universidad Autonoma de Madrid (UAM+CSIC Campus of Excellece), or IMDEA-Nanoscience (Severo Ochoa Seal of Excellence):

 INPhINIT fellowships have a duration of 3 years and are foreseen to start by October 2020; they offer a competitive salary, interdisciplinary training activities, short stays, a mentoring programme and dissemination and socialization activities.

If interested, you may contact us at campus.theorygroup@uam.es to widen information on the research project.

 

Time-resolved Molecular Dynamics of Single and Double Hydrogen Migration in Ethanol

Molecular movie snapshots. Movie frames representing the evolution of the ethanol dication along typical trajectories leading to the three precursor channels: a) H+ + C2H5O+, b) H2O+ + C2H4+ and c) H3O+ + C2H3+ for the triple coincidence channel H+ + H2O+ + C2H3+.

Molecular movie snapshots. Movie frames representing the evolution of the ethanol dication along typical trajectories leading to the three precursor channels: a) H+ + C2H5O+, b) H2O+ + C2H4+ and c) H3O+ + C2H3+ for the triple coincidence channel H+ + H2O+ + C2H3+.

Article: published in Nature Communications by Sergio Díaz-Tendero and Fernando Martín, IFIMAC researchers, in collaboration with the group of Nora Berrah, Univ. Connecticut, USA.

Being the lightest, most mobile atom that exists, hydrogen plays an important role in the chemistry of hydrocarbons, proteins and peptides and most biomolecules. Hydrogen can undergo transfer, exchange and migration processes, having considerable impact on the chemical behavior of these molecules. Although much has been learned about reaction dynamics involving one hydrogen atom, less is known about those processes where two or more hydrogen atoms participate. Here we show that single and double hydrogen migrations occurring in ethanol cations and dications take place within a few hundred fs to ps, using a 3D imaging and laser pump-probe technique. For double hydrogen migration, the hydrogens are not correlated, with the second hydrogen migration promoting the breakup of the C–O bond. The probability of double hydrogen migration is quite significant, suggesting that double hydrogen migration plays a more important role than generally assumed. The conclusions are supported by state-of-the-art molecular dynamics calculations.

This work was funded by the National Science Foundation under award No. 1700551, the MINECO projects FIS2016-77889-R and CTQ2016- 76061-P, ‘Severo Ochoa’ Programme for Centres of Excellence in R&D (SEV-2016-0686) and ‘María de Maeztu’ Programme for Units of Excellence in R&D (MDM-2014-0377). We acknowledge the generous allocation of computer time at the Centro de Computación Científica at the Universidad Autónoma de Madrid (CCC-UAM). S.D.-T. gratefully acknowledges the “Ramón y Cajal” program (RYC-2010-07019) of the Spanish Ministerio de Educación y Ciencia. We thank Todd Martinez and Daniel Rolles for helpful discussions. [Full article]

References

  1. Time-resolved molecular dynamics of single and double hydrogen migration in ethanol, Nora G. Kling, S. Díaz-Tendero, R. Obaid, M. R. Disla, H. Xiong, M. Sundberg, S. D. Khosravi, M. Davino, P. Drach, A. M. Carroll, T. Osipov, F. Martín & N. Berrah, Nature Communicationsvolume 10, Article number: 2813 (2019). [URL]

 

 

INPhiNIT fellowship programme – 2019 call

The 2019 call of INPhiNIT doctoral fellowship programme, funded by “la Caixa”, has been just launched: https://obrasociallacaixa.org/en/investigacion-y-becas/programa-de-becas-de-posgrado/inphinit/incoming

Campus theoretical group is willing to host students who get a fellowship in any of its modalities:

  • INPhINIT-Incoming: There are 35 phd fellowships directed to students NOT having resided in the country of the host institution for more than 12 months in the last 3 years.  Focused on STEM disciplines. If selected, students should join a Research Centre accredited with a Spanish or Portuguese Seal of Excellence (as Severo Ochoa, María de Maeztu, etc). Deadline: 6/02/2019.
    Research topics offered by Campus group are (https://hosts.lacaixafellowships.org/finder#1):

    • Ultrafast molecular dynamics induced by attosecond pulses (Prof. Fernando Martín García)
    • Theoretical Attosecond Electron Dynamics: from biomolecules to solids (Prof. Fernando Martín García)
    • Graphene-based materials: Exploring new physical properties based on theoretical simulations (Dr. Cristina Diaz Blanco)
    • Chemical-physics properties of new 2D materials (Prof. Fernando Martín García)
  • INPhINIT-Retaining: 30 phd fellowships to develop the doctorate in any field and any center in Spain or Portugal. Requirements: have resided in the country of the host institution for more than 12 months in the last 3 years. Deadline: 27/02/2019.

 INPhINIT fellowships have a duration of 3 years and are foreseen to start by October 2019; they offer a competitive salary, interdisciplinary training activities, short stays, a mentoring programme and dissemination and socialization activities.

If interested, you may contact us at campus.theorygroup@uam.es to widen information on the research projects offered.

 

Curso sobre Programación paralela con OpenMP y MPI

Ya está abierto el plazo de inscripción en la edición 2017 del curso sobre “Programación paralela con OpenMP y MPI”, organizado por el Centro de Computación Científica de la UAM y el Centro Nacional de Supercomputación (BSC-CNS), y patrocinado por la Cátedra UAM-Fujitsu.

Tendrá lugar en la Facultad de Ciencias, ente el 2 y el 8 de noviembre de 2017. Aunque el curso es gratuito, es necesario inscribirse siguiendo las instrucciones indicadas en esta página , donde podrá encontrarse además el programa completo del curso. La fecha límite para inscribirse es el 16 de Octubre de 2017.
Dado el carácter eminentemente práctico del curso, se espera que los asistentes tengan conocimientos previos en el uso de OpenMP y MPI.

Para aquellos interesados que no cumplan este requisito se ofrece, como novedad, la posibilidad de acceder a un curso de “Introducción a la programación paralela con OpenMP y MPI” que tendrá lugar entre el 2 y 6 de octubre de 2017 en el CCC-UAM (más información aquí).

ATENCIÓN. La fecha límite para inscribirse en el curso de iniciación a la programación paralela es el 21 de septiembre de 2017.

 

Fernando Martín, King Jaime I Prize in Basic Research

Fernando Martín, Full Professor at the Chemistry Department of the Universidad Autónoma de Madrid and researcher at IMDEA-Nanociencia, has been awarded the King Jaime I Prize in Basic Research in its 2017 edition. The jury has recognized his role in the establishment of the theoretical foundations of attochemistry. This emerging scientific field aims at observing and manipulating the electronic motion in atoms and molecules in their natural time scale, the attosecond (10-18 seconds), so as to control the chemical properties of substances and modify their natural behaviour. Although the first steps in this new scientific field date back only a decade ago, it is expected to become a multidisciplinary tool with numerous applications in chemistry, physics or biology, for example, to control the evolution of a chemical reaction, obtain images of charge transfer processes in individual molecules or influence the biological response to radiation, whether desired or undesired.

The demonstration that attosecond science can have a large impact in chemistry came in 2014, when, with the help of sophisticated computational modelling, it was shown (Science 346, 336) that experiments in which the amino acid phenylalanine is irradiated with attosecond laser pulses are indeed able to monitor the movement of electrons, and hence to modify the properties and chemical behaviour of the molecule.

According to the award-winning, the next steps in this field point to the use of attosecond techniques to prevent undesired chemical reactions, as those biological processes leading to adverse effects or, conversely, to induce chemical reactions that are currently impossible, which could lead to the production of new substances or materials. According to a recent article (Chemical Reviews, DOI: 10.1021/acs.chemrev.6b00453), the measurement and control of electronic motion in complex molecular structures is a formidable challenge that must be tackled in a multidisciplinary way, including intensive theoretical modelling in supercomputers, and may have a strong impact In chemistry for years to come.

King Jaime I Prizes

The Rey Jaime I Award recognizes researchers whose work is highly significant and has been developed for the most part in Spain. Throughout its 28 editions, it has been awarded to more than 100 researchers, the most important figures of the scientific, technological and entrepreneurial world of Spain. Many of the winners have received, during their careers, other relevant national and international awards.

Fernando Martín

Fernando Martín was born in Madrid, Spain, in 1961. He graduated in Chemistry in 1984 and Physics in 1986 at the Universidad Autónoma de Madrid. He received his Ph.D. at the same university in 1986. He completed his postdoctoral studies at the University of Bordeaux (1988), the Université de Paris VI (1989–1990), and the Univesity of Chicago (1995–1996). He has been Full Profesor at the Universidad Autónoma de Madrid since 2005. He obtained the national research price Rey Juan Carlos I on 2000 and the prize of the Spanish Royal Society of Chemistry in 2010. He is currently Chair of the “Cátedra UAM-Fujitsu” on Scientific Computing and Big Data.

His research focuses on the theoretical modelling of photoexcitation and photoionization of atomic and molecular systems induced by synchrotron radiation and ultrashort laser pulses, as well as that of complex molecular systems, isolated or deposited on surfaces. He has published almost 400 articles, and since 2011, he has been the recipient of an Advanced Grant of the European Research Council to lead a project focused on the development of computational tools for the study of processes that occur in the femto- and atto-second timescales (XCHEM).

In the last years, his research group (https://campusys.qui.uam.es/) has attracted significant funding from the European Union (projects ERC-AdG- 290853 XCHEM, COST Action CM0702, MCA-ITN- 264951 CORINF y MSCA-EJD-642294 TCCM, MCA-RIG- 268284 ATTOTREND) and national programs funded through MICINN, MINECO and the AEI (projects FIS-2016-77889-R, FIS-2013-42002-R, FIS-2010-15127 and PIM2010EEC-00751-ERA-Chemistry), which has allowed him to establish what is perhaps the reference research group in Europe in the area of “Theoretical Attochemistry”.

 

Post-doc position at CampuS theoretical group

A two-years postdoc position is available in the group of Prof. Fernando Martin. The position shall be co-financed by the European Social Fund[1] under the 2016 call for the recruitment of post-doctoral researchers of the Madrid region (more details here).

The successful applicant shall develop an open project which aims to develop computational tools either for the description of ionization processes (for complex molecules, surfaces or nanostructures), the description of heterogeneous catalysis or materials synthesis.

The CAMPUS  group at the Chemistry Department of the Universidad Autónoma de Madrid is focused on the theoretical study of the dynamics in isolated quantum systems (from the smallest to medium-sized systems, or extended ones) and the development of state-of-the-art theoretical tools which can help us to understand their properties and predict their behavior.

We seek for a post-doctoral researcher with a strong background in any of the group research lines  (laser-matter interaction, surfaces or clusters) who complies with the set of restrictions listed below.

Starting date: Expected start date is March 01, 2017. The position should normally start within one month from the publication of the resolution of the call here: http://www.madrimasd.org/madrid-ciencia-tecnologia/convocatorias-dgui/convocatorias-2016.

Remuneration: Gross annual salary (before applying national income taxes and social security contributions) amounts to roughly 26.500 €. Researchers may receive additional funding to support the expenses derived from research missions and the attendance to international conferences.

Eligibility criteria: According to the specific call restrictions, applicants must:

  • hold a PhD in Theoretical/Computational Physics, Chemistry or Informatics (for degrees obtained in a foreign university, homologation is required)
  • be registered in any locality within the Madrid Community from September 14th, 2016
  • be registered in the National Youth Guarantee system or be in a position to be a beneficiary of the system. Please, check the specific nationality, unemployment and age requirements here: http://www.empleo.gob.es/es/garantiajuvenil/accesoJovenes.html. As a general rule, the requirements are:
    1. be a national of the EU, EEA or Switzerland or meet the conditions to work in Spain (or have a valid residence permit being a national of another country)
    2. have less than 30 years
    3. be unemployed

Selection Criteria: The selection will be made on the basis of demonstrated knowledge in the following fields:

  1. Computational physics/chemistry methodologies and techniques,
  2. Theoretical atomic and molecular physics / Quantum Chemistry,
  3. Programming skills and code development (Fortran, C/C++, python, scripting languages, Linux/Unix, etc),
  4. Knowledge on parallelization and optimization of codes (MPI, openMP, etc),
  5. Handling of codes which are commonly used in the area of interest,
  6. Previous experience in any of the areas of interest.

Application procedure: Applicants should send, within 15 days from the date of publication of the resoluction (by January 31st):

  • a motivation letter explaining the research line(s) in which you are interested and why,
  • a detailed CV and contact information of two referees,
  • a copy of the doctoral degree (and, where applicable, homologation credential), and
  • a proof of meeting all the elegibility requirements
  • a proof of being registered in the National Youth Guarantee system or proofs of being  in a position to be a beneficiary of the said system.

All the documents must be sent in a single pdf file named as the candidate plus the research line he/she is interested in (e.g. SURNAME_NAME-reserach_line.pdf). Applications not following this procedure will be disregarded.

Upon evaluation of the applications received, selected candidates shall be contacted for an interview. Recommendation letters could be requested to referees during the selection process.

—————–
[1] This call is co-financed by the European Social Fund through the Youth Employment Operational Program for the 2014-2020 programming period, as well as the Youth Employment Initiative (YEI).

 

Short term post-doc position on theoretical attosecond physics

A short term postdoc position for an experienced researcher is available to work on coupled electron and nuclear dynamics induced by attosecond laser pulses and strong electromagnetic fields on small and mid-size molecules .

The applicants should hold a PhD in Chemical Physics and at least 3 years of postdoctoral experience. A strong and demonstrable background in  atomic, molecular and optical physics, attosecond physics, scattering theory, numerical methods, and programming is also required. 

Remuneration: Gross salary per month shall be 2.085 € (before applying national taxes and social security contributions)

The two-months postdoc position should start as soon as possible and, in any case, not later than January 16, 2017

Application procedure: Interested researchers should send a detailed CV, motivation letter and contact information for 2 references (in a single pdf file named as the candidate) to xchem.positions (at) uam.es.
Recommendation letters and further information could be requested during the selection process. Applications shall be reviewed as they come. Selected candidates shall be contacted for an interview.

Deadline: December 21st, 2016

 

A study on charged fullerenes embedded in helium nanodroplets confirms their existence in interstellar space

Irradiation with pulses of infrared light of fullerene ions embedded in liquid helium nanodroplets has revealed transitions between the solid, liquid and superfluid phases of the helium layers surrounding the charged fullerene. The accuracy of these measurements, performed in an environment similar to that found in interstellar space, confirms the presence of fullerenes in space and opens the door to the characterization of diffuse interstellar clouds associated with other species rich in carbon.

Helium nanodroplets provide a unique tool for the study of properties of molecules under conditions similar to those found in interstellar space: low temperatures and almost total absence of interaction with the environment. The latter is the consequence of the superfluidity of liquid helium, which prevents embedded molecules to experience any friction when they move inside. However, the introduction of charged molecular species inside these nanodroplets produces substantial modifications in the latter, especially in the first layers of solvation around the charged molecule.

Using photoelectron spectroscopy techniques in combination with molecular dynamics calculations, the properties of the first helium layers that form around the C60+ fullerene have been studied in the framework of a wide international collaboration involving researchers from Universidad Autónoma de Madrid, IMDEA-Nanoscience and IFIMAC Condensed Matter Physics Center. The results demonstrate the appearance of phase transitions in the first helium layers as the number of helium atoms increases. In particular, it is observed a transition from a solid phase of helium (usually referred to as the “Atkins snowball”, see figure), to a liquid phase, when the second layer begins to form, and finally to the superfluidity phase. All this happens before reaching a hundred helium atoms. The precision required to reveal such changes is of the order of 0.05 nanometers, which explains why such phenomena have gone unnoticed to date.

Given the insulation and low temperature environment provided by helium nanodroplets, the method has confirmed the assignment of two diffuse interstellar bands (DIB) to the presence of the C60+ ion in space, which demonstrates the important role of fullerenes as a carbon reservoir in the universe. The work published in the journal Nature Communications shows that, with the accuracy achieved in this study, the absorption spectra of other astrophysically relevant species can be determined, such as smaller fullerenes, polycyclic aromatic hydrocarbons and their derivatives.

 

noticia-fulerenos

Figure 1. The measurement principle. Fullerene C60+ (whose carbon atoms are represented by black spheres), surrounded by an “Atkins snowball” formed by a layer of helium atoms (transparent spheres surrounding the C60+), is irradiated by a laser pulse of infrared light, which leads to the evaporation of helium atoms. The wavelength of the absorbed light depends on the number of helium atoms initially adsorbed on the C60+.

 

Reference:

Atomically resolved phase transition of fullerene cations solvated in helium droplets
M. Kuhn, M. Renzler, J. Postler, S. Ralser, S. Spieler, M. Simpson, H. Linnartz, A.G.G.M. Tielens, J. Cami, A. Mauracher, Y. Wang, M. Alcamí, F. Martín, M.K. Beyer, R. Wester, A. Lindinger & P. Scheier
Nat. Commun. 7, 13550 doi: 10.1038/ncomms13550 (2016)

 

 

XChem code

FullFun Code

M3C Code

AttoChem COST Action

XChem project

Attotrend project

Master

Our group belongs to the Erasmus Mundus European program, which offers opportunities to obtain a master to European and non-European students. More details in Jobs.

 

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