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In its 85-year story, the mission of our institute has been to carry out excellence research in fundamental and applied physical chemistry, contributing to the scientific training of several generations of researchers at the highest level. Our vision is to be an international reference in multidisciplinary research focused on the resolution of the present challenges of our society in the fields of health, biotechnology, new materials, and environment.

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December 2017
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GFCThe Final Conference of the GLYCOPHARM project  will take place at the Institute of Physical Chemistry  Rocasolano (IQFR, CSICa) from Wednesday 27 to Friday 29, July 2016, in Madrid.

GLYCOPHARM is a Marie Curie Initial Training Network devised to offer training to young researchers in the interdisciplinary field of glycosciences. The research programme of this project is aimed at the development of innovative therapeutic agents and strategies, new diagnostic/prognostic tests and new methodologies, e.g., for drug screening. GLYCOPHARM focuses on a family of endogenous lectins, the galectins, which play key roles in many clinically relevant processes, including cancer and the immune and inflammatory processes. 

The conference will be also open to external participants.

Detailed information is available on the program.

Contact details: bmorales@iqfr.csic.es

 

GPDH

Galactitol-1-phosphate 5-dehydrogenase (GPDH) is a polyol dehydrogenase that catalyses the Zn2+ and NAD+-dependent stereoselective dehydrogenation of L-galactitol-1-phosphate to D-tagatose-6-phosphate. J.M. Mancheño (Dept. of Crystallography) in collaboration with Gert W. Kohring, Federico Gago and Rosario Muñoz, have reported three crystal structures of GPDH from Escherichia coli: the open state with Zn2+ in the catalytic site and also those of the closed state in complex with the polyols Tris and glycerol, respectively, but with no cofactor bound, which contrast with the behaviour of the prototypical mammalian liver alcohol dehydrogenase. Unexpectedly, a large internal cavity was found at the main contacting interface between GPDH subunits (GPDH is a dimer) that probably facilitates their relative movement. The binding mode of the substrate analogue glycerol reveals, for the first time in the polyol dehydrogenases, a penta-coordinated zinc ion in complex with a polyol and also a strong hydrogen bond with the conserved Glu144, an interaction originally proposed more than thirty years ago that supports a catalytic role for this acidic residue.

 

Rocío Benavente, María Esteban-Torres, Gert-Wieland Kohring, Álvaro Cortés-Cabrera, Pedro A. Sánchez-Murcia, Federico Gago, Iván Acebrón, Blanca De Las Rivas, Rosario Muñoz, José M. Mancheño. “Enantioselective oxidation of galactitol-1-phosphate by galactitol-1-phosphate 5-dehydrogenase from Escherichia coli”. Acta Crystallographica (2015) D71, 1540-1554. 
(doi: 10.1107/S1399004715009281)

 

rnalda

Many dynamical processes in molecules occur in extraordinarily short timescales, of the order of femtoseconds (1 fs = 10-15 s). In order to follow these processes in real time it is necessary to use the fastest stopwatches available, which are made of ultrashort laser light pulses. In the Center for Ultrashort Lasers (CLUR), in the Complutense University, Madrid, a research team with the participation of Rebeca de Nalda, from IQFR (CSIC), has been taking snapshots of some of these ultrafast processes in molecular systems, while trying to understand the details of the underlying light-matter interaction phenomena.

The new ingredient that has been recently added to these studies is an additional laser pulse that goes beyond the observation of the reaction, and is capable of modifying its course. This pulse is sufficiently intense to alter the molecular potentials, and thus, it causes changes in the products of the reaction and the speeds they acquire in reactions where bonds are broken. This work has been published in Nature Chemistry, and it is a demonstration that the fine control of the properties of this "control" laser pulse turns it into a true "photonic scalpel" capable of manipulating chemical reactions, as well as shedding new light into the dynamics of complex molecular dynamical processes.

M. E. Corrales, J. González-Vázquez, G. Balerdi, I. R. Solá, R. de Nalda, L. Bañares, Control of ultrafast molecular photodissociation by laser field induced potentials, Nature Chemistry (2014), doi:10.1038/nchem.2006

 

Matteo Monti
Instituto de Química Física "Rocasolano"
calle Serrano 119, Madrid
viernes 11 de julio, 11:30, Salón de actos
Supervisors: J.F. Marco, J. de la Figuera
 

Iron oxides are common compounds which are widespread in nature and constitute an important class of materials. Thinking about the importance of iron oxides for the humankind, magnetite, one of the most abundant magnetic minerals in earth's crust, comes to mind as a clear example. For many years, magnetite found a wide technological application range from navigation (compasses) to modern high density magnetic recording media. Moreover, iron oxides prepared in several nanostructure forms are also involved in environmental science, catalysis, biology, electronics, and other fields.


This dissertation studies several aspects of iron oxide grown on Ru(0001) and the modification of their properties when one dimension is reduced at the nanoscale limit. Since the preparation of iron oxides with defined structure and stoichiometry turned out to be not trivial, the basic understanding about the chemical and physical properties of ultrathin films becomes fundamental in order to tailor desired applications.
 
PDF of the PhD thesis: 
 

Matteo Monti
Instituto de Química Física "Rocasolano"
calle Serrano 119, Madrid
viernes 11 de julio, 11:30, Salón de actos
Supervisors: J.F. Marco, J. de la Figuera

Atomic-ensemble effects and non-covalent interactions at the electrode-electrolyte interface

Jueves 10 de julio a las 10:30 en el Salón de actos.

ampdh2-verybigThe zinc protease AmpDh2 is a virulence determinant of Pseudomonas aeruginosa, a problematic human pathogen. The mechanism of how the protease manifests virulence is not known, but it is known that it turns over the bacterial cell wall. A research conducted by the Instituto de Química-Física Rocasolano and the University of Notre Dame (Indiana, USA) provided insights into the mechanism of action of AmpDh2. The reaction of AmpDh2 with the cell wall was investigated and nine distinct turnover products were characterized by LC/MS/MS. The enzyme turns over both the crosslinked and non-crosslinked cell wall. Three high-resolution X-ray structures, of the apo enzyme and of two complexes with turnover products, were solved. The X-ray structures show how the dimeric protein interacts with the inner leaflet of the bacterial outer membrane and that the two monomers provide a more expansive surface for recognition of the cell wall. This binding surface can accommodate the three-dimensional solution structure of the crosslinked cell wall. We have disclosed in this report the nature of the reactions of AmpDh2 with the bacterial sacculus and have determined the structure of the protein, which reveals the importance of the dimeric nature in accommodating larger segments of the cell wall. The present study reveals at atomic detail the structural attributes of this important virulence factor of P. areruginosa in the reactions that it performs, which are at the roots of the manifestation of the virulence.

 Reference:

Siseth Martínez-Caballero, Mijoon Lee, Cecilia Artola-Recolons, César Carrasco-López, Dusan Hesek, Edward Spink, Elena Lastochkin, Weilie Zhang, Lance M. Hellman, Bill Boggess, Shahriar Mobashery* and Juan A. Hermoso*

Reaction products and the X-ray structure of AmpDh2, a virulence determinant of Pseudomonas aeruginosa.

Journal of the American Chemical Society (2013) 135, - (in press)  (doi:10.1021/ja405464b)

Generación, caracterización y control de plasmas de ablación láser

Wednesday, July 3rd 2013

12:00 Salón de Actos

Oxide surfaces are usually considered to be static, even when they are catalyzing chemical reactions. But researchers at Instituto de Química-Física “Rocasolano” and the Sandia National Labs showed that this view is incorrect for magnetite (Fe3O4), an important industrial catalyst. Real-time microscopy reveals that magnetite’s surface steps advance continuously during oxygen exposure. The iron needed for this growth of new magnetite comes from the material’s interior. The first step of oxidation, dissociative oxygen adsorption, occurs uniformly over magnetite’s terraces. The common assumption in heterogeneous catalysis, in contrast, is that redox reactions occur at surface steps. Furthermore, this research establishes that catalytic redox cycles on magnetite do not involve creating and destroying oxygen vacancies, as usually assumed. Instead, catalytic cycles grow and etch the crystal through a different defect, iron vacancies.

1(a-d) Low-energy electron microscopy images from Fe3O4(100) exposed to O2. Surface steps are at the boundaries between the bright/dark bands. The red lines show one step advancing. Field of view = 20 m. (e) Spiral step topography. (f) Model of Fe3O4 growth at the surface. e un escalón. Campo de visión = 20 µm. (e) Topografía de escalón espiral. (f) Modelo de crecimiento de Fe3O4 (100) en la superficie.

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Shu Nie,1 Elena Starodub,1 Matteo Monti,2 David Siegel,1 Lucía Vergara,2 Farid El Gabaly,1 Norman Bartelt,1 Juan de la Figuera,2 and Kevin McCarty1, Insight into magnetite’s redox catalysis from observing surface morphology during oxidation, J. Am. Chem. Soc., in press (2013). 1 = SNL, 2 = IQFR