Tanszéki szemináriumok

30. October 2012

Dr. Sophie LECOMTE

Chimie et Biologie des Membranes et des Nanoobjets, L'Unité Mixte de Recherche (UMR) 5248, Le Centre National de la Recherche Scientifique (CNRS) - Université Bordeaux 1, Pessac, France


Probing oligonucleotides by microfluidic and Surface-Enhanced Raman Spectroscopy detection

Detection of specific DNA/RNA sequence is a major challenge for molecular biology and diagnosis, where probing of a particular disease is based on nucleic acid identification. Our strategy is to use Surface Enhanced Raman Scattering (SERS) to detect label free RNA. SERS takes advantage of the strongly increased Raman signals of molecules when adsorbed on adapted silver nanoparticles. We defined conditions to characterize the four bases of RNA, in single strands of polyadenosine (pA), polyuridine (pU), polycytosine (pC) and polyguanosine (pG). Creighton silver colloid [1] was used to enhance Raman scattering and MgCl2 was added, as aggregating agent [2]. We were able to obtain specific spectral signature of pA, pC, pG and pU until limit concentration of 1 µM to pA and 10µM to pC, pG and pU. We recently established a procedure allowing to a quantitative analysis of SERS spectra recorded for various RNA single strand mixtures [3]. Then, we determined the percentage of each base free in the mixture. A standard deviation of 10% was calculated between the percentage obtained after quantitative analysis and percentage introduced in the sample. To improve the SERS detection we need a precise control of adsorption and aggregation processes, which could be achieve by using microfluidic chips. The use of microfluidic platforms allows better control of spatial and temporal resolution, in comparison with classical bulk analysis. We have implemented two different microfluidic chips, one based on single-phase flows and one other based on droplets generation. We demonstrated that in the single-phase flows configuration a large aggregation of silver colloids was observed in the bottom of the channel. Then, we performed the detection of oligonucleotide in a microfluidic chips based on droplet generation. Recently, we obtained SERS specific signature of pA and pG and pC in nano-dropplet. On the long range, this methodology will allow us to detect special structures, like free bases in stem-loop, or mismatching, characteristic of diseases or pathogen agents.




28. August 2012

Prof. Dr. Koichi IWATA

Department of Chemistry, Gakushuin University, Tokyo, Japan


Lipid bilayer membranes and ionic liquids observed with fast time-resolved spectroscopy

Structure and dynamics of lipid bilayer membranes or room-temperature ionic liquids are closely related to their functions. We study the lipid bilayer membranes and ionic liquids with time-resolved spectroscopic methods including picosecond time-resolved Raman spectroscopy, picosecond time-resolved fluorescence spectroscopy and femtosecond time-resolved near-infrared spectroscopy. Local heat transfer, rotational reorientation, or solvation dynamics is observed with these spectroscopic methods. We examine the solvation environments and try to characterize the heterogeneous structures from the results of the experiments.




12. April 2012

Mihaela CĂLUGĂREANU

Politechnica University of Bucharest

Study of chemical speciation in aqueous carbonate systems. Accumulation and sequestration of carbon dioxide from environment

Detection of specific DNA/RNA sequence is a major challenge for molecular biology and diagnosis, where probing of a particular disease is based on nucleic acid identification. Our strategy is to use Surface Enhanced Raman Scattering (SERS) to detect label free RNA. SERS takes advantage of the strongly increased Raman signals of molecules when adsorbed on adapted silver nanoparticles. We defined conditions to characterize the four bases of RNA, in single strands of polyadenosine (pA), polyuridine (pU), polycytosine (pC) and polyguanosine (pG). Creighton silver colloid [1] was used to enhance Raman scattering and MgCl2 was added, as aggregating agent [2]. We were able to obtain specific spectral signature of pA, pC, pG and pU until limit concentration of 1 µM to pA and 10µM to pC, pG and pU. We recently established a procedure allowing to a quantitative analysis of SERS spectra recorded for various RNA single strand mixtures [3]. Then, we determined the percentage of each base free in the mixture. A standard deviation of 10% was calculated between the percentage obtained after quantitative analysis and percentage introduced in the sample. To improve the SERS detection we need a precise control of adsorption and aggregation processes, which could be achieve by using microfluidic chips. The use of microfluidic platforms allows better control of spatial and temporal resolution, in comparison with classical bulk analysis. We have implemented two different microfluidic chips, one based on single-phase flows and one other based on droplets generation. We demonstrated that in the single-phase flows configuration a large aggregation of silver colloids was observed in the bottom of the channel. Then, we performed the detection of oligonucleotide in a microfluidic chips based on droplet generation. Recently, we obtained SERS specific signature of pA and pG and pC in nano-dropplet. On the long range, this methodology will allow us to detect special structures, like free bases in stem-loop, or mismatching, characteristic of diseases or pathogen agents.




6. September 2011.

Dr. Djemel HAMDANE

Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 avenue de la Terrasse, 91198, France

Exploring Conformational Changes during catalysis, Energy Landscape and Protein thermodynamics

It is widely accepted that the biological function of many proteins and enzymes is controlled by conformational changes of different magnitudes. If proteins were rigid objects they would be essentially “dead”. These crucial structural changes are rarely characterized since they are transiently populated. I am going to illustrate this concept by presenting two kinds of protein system. In the first part of my talk, I will present the nature of the conformational changes along the catalytic cycle in the NADPH-cytochrome P450 reductase, a diflavin reductase that transfers two electrons to the heme of the cytochrome P450 enzymes at two precise steps of the catalysis. Based on site directed mutagenesis, crystal structure and fast kinetics, we have recently shown that spectacular conformational changes of this protein must occur during the intra and inter-molecular electron transfers. The second example will concern the myoglobin. This latter displays a dynamic behavior during ligand binding of considerable complexity and hence has been referred to as “paradigm of complexity”. I will illustrate how cutting edge biophysical techniques such as flash photolysis coupled to high-pressure system can unravel the dynamic nature of ligand binding to ferrous myoglobin.




24. August 2011

Prof. Ruifen DOU

Department of Physics, Functionalized Nano-material Film and Device Physics Laboratory, Beijing Normal University, Beijing 100875, P. R. China, E-mail: rfdou [k] bnu [p] edu [p] cn


Modulated Structural Diversity of Self-assembly of Anthryl-Based Molecule on Ag (100) and Ag (111)

Self-assembly of organic molecules into suprastructures has been an extensive research area because of the potential application in surface chemical functionalization and molecular electronics. Today, understanding how competing between inter-molecule and molecule-surface interactions is fundamental to precisely control molecular self-organization on surface. Herein, we present our novel experimental results about self-assembly of 3(5)-(9-anthryl) pyrazole (ANP) on Ag (100) and Ag (111) surfaces investigated by scanning tunneling microscopy (STM) under ultrahigh vacuum. Structural diversities are found on the ANP adsorption on above substrates. In the case of ANP on Ag (100), two suprastructures, the majority a and the minority b, form at monolayer coverage, in which suprastructure b evolves from a and exists in the boundary area. The superstructures a and b exhibit a primitive rectangular lattice with the molecular orientation tilted related to the substrate surface. In contrast, only one suprastructure composed of two trimers is present on Ag (111). In this case, three molecules are connected into a trimer through three hydrogen bonds (HBs). All suprastructures on Ag (100) and Ag (111) are commensurate with the substrates because of the specific molecular-adsorption orientation related to the surface. Based on the experiments, the molecule-substrate and the inter-molecule interactions, which control the ANP molecular adsorption states and energetically stable structures on the different metals, are discussed in details.




30. June 2011

Wesley D. ALLEN

Department of Chemistry and Center for Computational Chemistry University of Georgia, Athens, GA 30602-5016 USA

PROPYL + O2: DEFINITIVE THEORY, ON A PROTOTYPE OF HYDROCARBON OXIDATION

Reactions of alkyl radicals (R•) with O2 are ubiquitous in combustion, atmospheric chemistry, and biological processes. As the size of the alkyl radical grows, R + O2 reactions rapidly become more complex, and isomerizations to hydroperoxyalkyl radicals (QOOH) can increase in importance relative to concerted elimination of HO2. The need for definitive ab initio theoretical research on propyl + O2 is demonstrated by the disparity between the reaction energetics from the best existing electronic structure computations and parameters derived from master equation kinetic models that best reproduce the available body of experimental measurements. In this work, fully optimized geometries were obtained at the CCSD(T)/cc-pVTZ level of theory for all chemically relevant minima and transition states of the n-propyl and i-propyl + O2 systems. Final energetics were derived from explicit computations with basis sets as large as cc-pV5Z and correlation treatments as extensive as coupled cluster through full triples with perturbative inclusion of quadruple excitations [CCSDT(Q)]. Focal point analyses (FPA) targeting the complete basis set (CBS) limit of CCSDT(Q) theory were executed with inclusion of auxiliary corrections for core correlation, relativistic effects, and first-order non-Born-Oppenheimer terms. For the n-propyl + O2 system, we find the key transition state for concerted elimination of HO2 to lie 3.9 kcal mol–1 below the reactants and 3.1 kcal mol–1 lower than the isomerization barrier for hydroperoxypropyl radical formation. Even the robust CCSD(T)/cc-pVQZ method yields a concerted elimination barrier that is 1.8 kcal mol–1 too high, a striking result because such shifts of barrier heights in R + O2 reactions can change branching fractions by an order of magnitude. Our definitive energetics for minima and transition states provide benchmarks for assessing the accuracy of master equation kinetic models.




21. January 2011

Juan José Santana RODRÍGUEZ

Department of Process Engineering, University of Las Palmas de Gran Canaria, Campus Universitario de Tafira, E-35017 Las Palmas de Gran Canaria, Canary Islands, Spain.

Visualization of local degradation processes in coated metals by means of scanning electrochemical microscopy (SECM) and the scanning vibrating electrode technique (SVET)

Scanning electrochemical microscopy has been employed to obtain spatially-resolved information regarding surface topology, water uptake and blister formation at intact coatings, as well as the onset and progress of corrosion reactions within coating defects in different solutions (0,1 M Na2B4O7, 0,1 M Na2SO4 and 0,1 NaCl). Oxygen reduction was employed as redox mediator to monitor the intact polymer system and the reactive metal-polymer system, though the onset of a redox competition for this redox species between the SECM tip and the bare metal inside the holiday could be found in certain conditions. Whether attack predominated inside the holiday or the system became non reactive depended on the composition of the test electrolyte, with borate ions acting as corrosion inhibitor.
Application of scanning vibrating electrode technique (SVET) for corrosion studies of organic coatings on reactive metals is also presented. SVET was used too to monitor the electrochemical processes at painted steel immersed in either 10 mM Na2SO4 or 10 mM NaCl aqueous solutions. The coated samples were investigated after a scratch was operated through the polymer matrix down to the metal-substrate surface in order to simulate a defect across the coating. SVET imaging probes that the electrochemical behaviour of the system is different depending on the electrolyte employed. Enhanced coating delamination originating from the defect is observed when chloride ions are present in the environment.