Project acronym XRAYonACTIVE
Project An X-ray spectroscopy view on active sites: removing the obscuring silent majority
Researcher (PI) Franciscus Martinus Frederikus De Groot
Host Institution (HI) UNIVERSITEIT UTRECHT
Call Details Advanced Grant (AdG), PE4, ERC-2013-ADG
Summary One of the holy grails in catalytic research is the determination of the structure of the active site. Information on the catalytically active site is notoriously difficult to obtain as it concerns a small minority of states in a sea of other silent states. This silent majority of states obscures the action that takes place on the active states. Because the core hole localizes the final state, X-ray absorption spectroscopy (XAS) is a powerful local probe of the electronic structure and XAS provides detailed information on catalysts under working conditions. A major limitation in the present experiments is the fact that the signal from the majority of non-active sites overwhelms the details from the active sites.
In this proposal I will develop a new idea to solve this problem and allow x-ray spectroscopy to unveil the nature of active sites. The idea is based on a detailed knowledge of the resonant x-ray emission (RXES) process that allows the detection of RXES spectra that are specific for the active state only. Model calculations predict an enhancement of the active sites over the silent sites of approximately a factor 50, allowing the clear detection of active sites above 1 % presence.
This method will be suitable to study active sites in heterogeneous catalysts based on transition metal ions. However, the approach is also suitable to study transition metal active sites in homogeneous catalysis and biocatalysis. In addition, the proposed research will have an impact on first principles x-ray spectroscopy calculations in theoretical chemistry and theoretical physics.
Summary
One of the holy grails in catalytic research is the determination of the structure of the active site. Information on the catalytically active site is notoriously difficult to obtain as it concerns a small minority of states in a sea of other silent states. This silent majority of states obscures the action that takes place on the active states. Because the core hole localizes the final state, X-ray absorption spectroscopy (XAS) is a powerful local probe of the electronic structure and XAS provides detailed information on catalysts under working conditions. A major limitation in the present experiments is the fact that the signal from the majority of non-active sites overwhelms the details from the active sites.
In this proposal I will develop a new idea to solve this problem and allow x-ray spectroscopy to unveil the nature of active sites. The idea is based on a detailed knowledge of the resonant x-ray emission (RXES) process that allows the detection of RXES spectra that are specific for the active state only. Model calculations predict an enhancement of the active sites over the silent sites of approximately a factor 50, allowing the clear detection of active sites above 1 % presence.
This method will be suitable to study active sites in heterogeneous catalysts based on transition metal ions. However, the approach is also suitable to study transition metal active sites in homogeneous catalysis and biocatalysis. In addition, the proposed research will have an impact on first principles x-ray spectroscopy calculations in theoretical chemistry and theoretical physics.
Max ERC Funding
2 500 000 €
Duration
Start date: 2014-04-01, End date: 2019-03-31
Project acronym XRayProton
Project Ultrafast Structural Dynamics of Elementary Water-Mediated Proton Transport Processes
Researcher (PI) Erik Theodorus Johannes NIBBERING
Host Institution (HI) FORSCHUNGSVERBUND BERLIN EV
Call Details Advanced Grant (AdG), PE4, ERC-2017-ADG
Summary How acids and bases react in water is a question raised since the pioneering days of modern chemistry. Recent decades have witnessed an increased effort in elucidating the microscopic mechanisms of proton exchange between acids and bases and the important mediating role of water in this. With ultrafast spectroscopy it has been shown that the elementary steps in aqueous proton transfer occur on femtosecond to picosecond time scales. Aqueous acid-base neutralization predominantly proceeds in a sequential way via water bridging acid and base molecules. These ultrafast experiments probing molecular transitions in the ultraviolet, visible and mid-infrared spectral ranges, though, only provide limited insight into the electronic structure of acids, bases and the water molecules accommodating the transfer of protons in the condensed phase. Soft-x-ray absorption spectroscopy (XAS), probing transitions from inner-shell levels to unoccupied molecular orbitals, is a tool to monitor electronic structure with chemical element specificity. The aim is now to develop steady-state and time-resolved soft-x-ray spectroscopy of acids and bases in water-poor and water-rich solutions. Here novel liquid flatjet technology is utilized with soft-x-ray sources at synchrotrons as well as table-top laser-based high-order harmonic systems, to elucidate the electronic structural evolution of proton transfer pathways. Questions to be solved are electronic structural changes upon hydrogen bond formation, the nature of hydrated proton species, and the impact of conversion from acid to conjugate base (or base to conjugate acid) in aromatic alcohols, carboxylic and amine compounds, and ultimately the oxygen oxidation state in hydrated protons. Resolving the electronic structural dynamics of elementary steps of aqueous proton transport will furthermore elucidate the role of mediating water in bulk solution, and in specific conditions such as hydrogen fuel cells or trans-membrane proteins.
Summary
How acids and bases react in water is a question raised since the pioneering days of modern chemistry. Recent decades have witnessed an increased effort in elucidating the microscopic mechanisms of proton exchange between acids and bases and the important mediating role of water in this. With ultrafast spectroscopy it has been shown that the elementary steps in aqueous proton transfer occur on femtosecond to picosecond time scales. Aqueous acid-base neutralization predominantly proceeds in a sequential way via water bridging acid and base molecules. These ultrafast experiments probing molecular transitions in the ultraviolet, visible and mid-infrared spectral ranges, though, only provide limited insight into the electronic structure of acids, bases and the water molecules accommodating the transfer of protons in the condensed phase. Soft-x-ray absorption spectroscopy (XAS), probing transitions from inner-shell levels to unoccupied molecular orbitals, is a tool to monitor electronic structure with chemical element specificity. The aim is now to develop steady-state and time-resolved soft-x-ray spectroscopy of acids and bases in water-poor and water-rich solutions. Here novel liquid flatjet technology is utilized with soft-x-ray sources at synchrotrons as well as table-top laser-based high-order harmonic systems, to elucidate the electronic structural evolution of proton transfer pathways. Questions to be solved are electronic structural changes upon hydrogen bond formation, the nature of hydrated proton species, and the impact of conversion from acid to conjugate base (or base to conjugate acid) in aromatic alcohols, carboxylic and amine compounds, and ultimately the oxygen oxidation state in hydrated protons. Resolving the electronic structural dynamics of elementary steps of aqueous proton transport will furthermore elucidate the role of mediating water in bulk solution, and in specific conditions such as hydrogen fuel cells or trans-membrane proteins.
Max ERC Funding
2 482 500 €
Duration
Start date: 2018-09-01, End date: 2023-08-31
Project acronym YEAST-TRANS
Project Deciphering the transport mechanisms of small xenobiotic molecules in synthetic yeast cell factories
Researcher (PI) Irina BORODINA
Host Institution (HI) DANMARKS TEKNISKE UNIVERSITET
Call Details Starting Grant (StG), LS9, ERC-2017-STG
Summary Industrial biotechnology employs synthetic cell factories to create bulk and fine chemicals and fuels from renewable resources, laying the basis for the future bio-based economy. The major part of the wanted bio-based chemicals are not native to the host cell, such as yeast, i.e. they are xenobiotic. Some xenobiotic compounds are readily secreted by synthetic cells, some are poorly secreted and some are not secreted at all, but how does this transport occur? Or why does it not occur? These fundamental questions remain to be answered and this will have great implications on industrial biotechnology, because improved secretion would bring down the production costs and enable the emergence of novel bio-based products.
YEAST-TRANS will fill in this knowledge gap by carrying out the first systematic genome-scale transporter study to uncover the transport mechanisms of small xenobiotic molecules by synthetic yeast cells and to apply this knowledge for engineering more efficient cell factories for bio-based production of fuels and chemicals.
Summary
Industrial biotechnology employs synthetic cell factories to create bulk and fine chemicals and fuels from renewable resources, laying the basis for the future bio-based economy. The major part of the wanted bio-based chemicals are not native to the host cell, such as yeast, i.e. they are xenobiotic. Some xenobiotic compounds are readily secreted by synthetic cells, some are poorly secreted and some are not secreted at all, but how does this transport occur? Or why does it not occur? These fundamental questions remain to be answered and this will have great implications on industrial biotechnology, because improved secretion would bring down the production costs and enable the emergence of novel bio-based products.
YEAST-TRANS will fill in this knowledge gap by carrying out the first systematic genome-scale transporter study to uncover the transport mechanisms of small xenobiotic molecules by synthetic yeast cells and to apply this knowledge for engineering more efficient cell factories for bio-based production of fuels and chemicals.
Max ERC Funding
1 423 358 €
Duration
Start date: 2017-12-01, End date: 2022-11-30
Project acronym YIELD
Project Is there a limit to yield?
Researcher (PI) Daniel Zamir
Host Institution (HI) THE HEBREW UNIVERSITY OF JERUSALEM
Call Details Advanced Grant (AdG), LS9, ERC-2011-ADG_20110310
Summary Plant breeders are challenged with sustaining global crop improvements. Is there a limit to crop yield? This project will address this central question using processing tomatoes as a model for a mechanized crop. By integrating in a single web-based platform of ‘Phenom Networks’ a broad germplasm base, deep phenotypes, and multiple genome sequences of tomato species, we will identify the genes and mechanisms that dictate crop productivity and implement them in the creation of next generation F1 hybrids. Our work is founded on our years of efforts to establish the following integrated genetic pillars: 1) The tomato genome revealed SNPs for broader marker-assisted selection between cultivated parents and untapped diversity from closely-related red-fruited ancestors. We will develop new elite parental lines into which all discovered traits will be introduced. 2) We will enrich the narrow genetic base of modern processing tomato by pyramiding recessive, additive, dominant and overdominant QTL from six wild species introgression lines (ILs) and field-test them in diverse environments. 3) By producing hybrids with ‘recessive’ deleterious mutants we have identified heterosis genes that increase yield by ~50%; these will be combined with the IL QTL. 4) Finally, we will focus on newly discovered “stability QTL” that significantly improve the reproducibility of yield effects by canalizing this phenotype in spite of environmental perturbations. This multi-faceted integrated tomato breeding effort will unite classical and genomics assisted methods with statistical genetics to demonstrate that yield barriers of the leading commercial hybrids are only there to be broken. We will clone the genes responsible for yield, domestication, heterosis, epistasis and canalization and explore their molecular action. I expect that the breeding concepts and methods developed through this project will lead the way to increased productivity of crops that are important for global food security.
Summary
Plant breeders are challenged with sustaining global crop improvements. Is there a limit to crop yield? This project will address this central question using processing tomatoes as a model for a mechanized crop. By integrating in a single web-based platform of ‘Phenom Networks’ a broad germplasm base, deep phenotypes, and multiple genome sequences of tomato species, we will identify the genes and mechanisms that dictate crop productivity and implement them in the creation of next generation F1 hybrids. Our work is founded on our years of efforts to establish the following integrated genetic pillars: 1) The tomato genome revealed SNPs for broader marker-assisted selection between cultivated parents and untapped diversity from closely-related red-fruited ancestors. We will develop new elite parental lines into which all discovered traits will be introduced. 2) We will enrich the narrow genetic base of modern processing tomato by pyramiding recessive, additive, dominant and overdominant QTL from six wild species introgression lines (ILs) and field-test them in diverse environments. 3) By producing hybrids with ‘recessive’ deleterious mutants we have identified heterosis genes that increase yield by ~50%; these will be combined with the IL QTL. 4) Finally, we will focus on newly discovered “stability QTL” that significantly improve the reproducibility of yield effects by canalizing this phenotype in spite of environmental perturbations. This multi-faceted integrated tomato breeding effort will unite classical and genomics assisted methods with statistical genetics to demonstrate that yield barriers of the leading commercial hybrids are only there to be broken. We will clone the genes responsible for yield, domestication, heterosis, epistasis and canalization and explore their molecular action. I expect that the breeding concepts and methods developed through this project will lead the way to increased productivity of crops that are important for global food security.
Max ERC Funding
2 500 000 €
Duration
Start date: 2012-01-01, End date: 2016-12-31
Project acronym YOUCITIZEN
Project Youth Citizenship in Divided Societies: Between Cosmpolitanism, Nation, and Civil Society
Researcher (PI) Lynn Staeheli
Host Institution (HI) UNIVERSITY OF DURHAM
Call Details Advanced Grant (AdG), SH3, ERC-2011-ADG_20110406
Summary YouCitizen is a comparative, multi-level ethnographic research project that examines the efforts of international organisations, civil society organisations, and states to foster citizenship for youth in divided societies. In their efforts, agents working in such organisations often engage in paradoxical, if not contradictory, acts to promote both cosmopolitanism within civil society and national identities, even when aspects of national identity have been a source of division. A central premise of the research is that the outcomes of these efforts are conditioned by the contexts in which programmes for youth are delivered and enacted. In these contexts – which include histories of division and marginalisation, societal and communal norms, family histories, and the spaces of daily life – youth interpret and experience citizenship. YouCitizen’s critical intervention is in extending the examination of citizenship formation to consider the ways in which youth interpret, experience, and potentially remake citizenship that is different to, and may actually challenge, the forms of citizenship that organisations and states attempt to instil.
The empirical foci of the study are the networks of organisations promoting citizenship and/or civic engagement, and youth, aged 15-24 in South Africa, Bosnia-Herzegovina and Lebanon who have been involved with those programmes. It explores the goals of those organisations, their funding sources and activities to understand both the vision of citizenship they promote and the traditions and influences from which they draw; particular attention is paid to ideals and values associated with cosmopolitanism vis-à-vis the nation and the ways in which they address social division. Interviews and participant observation with youth explore the ways in which their experiences and understanding of citizenship are influenced by those programmes, but are also entwined with daily life in their homes and communities.
Summary
YouCitizen is a comparative, multi-level ethnographic research project that examines the efforts of international organisations, civil society organisations, and states to foster citizenship for youth in divided societies. In their efforts, agents working in such organisations often engage in paradoxical, if not contradictory, acts to promote both cosmopolitanism within civil society and national identities, even when aspects of national identity have been a source of division. A central premise of the research is that the outcomes of these efforts are conditioned by the contexts in which programmes for youth are delivered and enacted. In these contexts – which include histories of division and marginalisation, societal and communal norms, family histories, and the spaces of daily life – youth interpret and experience citizenship. YouCitizen’s critical intervention is in extending the examination of citizenship formation to consider the ways in which youth interpret, experience, and potentially remake citizenship that is different to, and may actually challenge, the forms of citizenship that organisations and states attempt to instil.
The empirical foci of the study are the networks of organisations promoting citizenship and/or civic engagement, and youth, aged 15-24 in South Africa, Bosnia-Herzegovina and Lebanon who have been involved with those programmes. It explores the goals of those organisations, their funding sources and activities to understand both the vision of citizenship they promote and the traditions and influences from which they draw; particular attention is paid to ideals and values associated with cosmopolitanism vis-à-vis the nation and the ways in which they address social division. Interviews and participant observation with youth explore the ways in which their experiences and understanding of citizenship are influenced by those programmes, but are also entwined with daily life in their homes and communities.
Max ERC Funding
2 419 013 €
Duration
Start date: 2012-07-01, End date: 2017-06-30
