{ "meta": { "api_type": "NWO Projects API", "version": "1.0.2", "licence": { "name": "CC0 1.0 Universal", "url": "https://creativecommons.org/publicdomain/zero/1.0", "description": "To the extent possible under law, all copyright and related or neighbouring rights have been waived worldwide to the data made available through this API." }, "documentation": "https://doi.org/10.5281/zenodo.14918287", "release_date": "2025-08-20T00:00:00", "funder": "https://doi.org/10.13039/501100003246", "ror_id": "https://ror.org/04jsz6e67", "date": "2026-11-05T00:00:00", "count": 1, "per_page": 100, "pages": 1, "page": 1 }, "projects": [ { "project_id": "SH-082-08", "title": "Quantum chemical modeling of natural and artificial photosynthetic systems", "funding_scheme_id": 2267, "funding_scheme": "Rekentijd nationale computersystemen Rekentijd nationale computersystemen 2008 EW", "department": "Exacte en Natuurwetenschappen", "sub_department": "Exacte Wetenschappen", "start_date": "2008-03-20T00:00:00", "end_date": "2010-06-21T00:00:00", "reporting_year": 2008, "summary_nl": "In the photosynthetic bacterial reaction center (BRC) light energy is converted into chemically useful energy. This photochemical reaction is initiated by a charge separation process in the BRC complex. Our goal in this project is to analyze the first steps in this light-driven electron transfer (ET) process and the role played by the protein environment on the geometrical and electronic structure of the Bacteriochlorophyll (BChl) special pair. By using Density Functional Theory (DFT) we have already computed the NMR chemical shifts of BChl-His complexes, which enabled us to characterize how the protein is able to tune the charge transfer between the BChl and the coordinated histidine. Moreover, we have proposed a model for the observed asymmetry in NMR data for the BChl-His complexes.\nIn the following part of the project we will focus on the dynamical properties of our model of the special pair using Car-Parrinello molecular dynamics simulations. The main goal is to calculate the free-energy profile along putative proton transfer paths with the metadynamics approach. The models used in this project are quite large, comprising up to approximately 200 atoms, and we need to investigate trajectories of a few picoseconds for each hypothetical reaction path. Thus, the use of a parallel computing architecture is crucial for our project. The long term goal is not only to complement and interpret available spectroscopic data, but also to predict properties of artificial photosynthetic systems. This project is interrelated with the ongoing experimental activity in our group on natural and artificial photosynthetis.\n", "summary_en": "In the photosynthetic bacterial reaction center (BRC) light energy is converted into chemically useful energy. This photochemical reaction is initiated by a charge separation process in the BRC complex. Our goal in this project is to analyze the first steps in this light-driven electron transfer (ET) process and the role played by the protein environment on the geometrical and electronic structure of the Bacteriochlorophyll (BChl) special pair. By using Density Functional Theory (DFT) we have already computed the NMR chemical shifts of BChl-His complexes, which enabled us to characterize how the protein is able to tune the charge transfer between the BChl and the coordinated histidine. Moreover, we have proposed a model for the observed asymmetry in NMR data for the BChl-His complexes.\nIn the following part of the project we will focus on the dynamical properties of our model of the special pair using Car-Parrinello molecular dynamics simulations. The main goal is to calculate the free-energy profile along putative proton transfer paths with the metadynamics approach. The models used in this project are quite large, comprising up to approximately 200 atoms, and we need to investigate trajectories of a few picoseconds for each hypothetical reaction path. Thus, the use of a parallel computing architecture is crucial for our project. The long term goal is not only to complement and interpret available spectroscopic data, but also to predict properties of artificial photosynthetic systems. This project is interrelated with the ongoing experimental activity in our group on natural and artificial photosynthetis.\n", "project_members": [ { "role": "Project leader", "member_id": 104490, "last_name": "Buda", "degree_pre_nominal": "dr.", "initials": "F.", "first_name": "Francesco", "organisation": "Universiteit Leiden||Faculteit der Wiskunde en Natuurwetenschappen||Leiden Institute of Chemistry (LIC)", "organisation_id": 73960, "ror": "https://ror.org/027bh9e22", "active": false }, { "role": "Main Applicant", "member_id": 104490, "last_name": "Buda", "degree_pre_nominal": "dr.", "initials": "F.", "first_name": "Francesco", "organisation": "Universiteit Leiden||Faculteit der Wiskunde en Natuurwetenschappen||Leiden Institute of Chemistry (LIC)||Biofysische organische chemie", "organisation_id": 80475, "ror": "https://ror.org/027bh9e22", "active": true } ], "products": [ { "title": "Differential charge polarization of Axial Histidines in Bacterial Reaction Centres Balances the Asymmetry of the Special Pair", "year": 2009, "start": 9626, "end": 9627, "type": "Wetenschappelijk artikel", "journal_title": "J. Am. Chem. Soc.", "authors": [ { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Auteur", "index_number": 0 }, { "last_name": "Janssen", "initials": "G.J.", "first_name": "Geertje", "role": "Auteur", "index_number": 0 }, { "last_name": "Matysik", "initials": "J.", "first_name": "Jörg", "role": "Auteur", "index_number": 0 }, { "last_name": "Alia", "initials": "A.", "role": "Auteur", "index_number": 0 }, { "last_name": "de Groot", "initials": "H.J.M.", "role": "Auteur", "index_number": 0 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "role": "Auteur", "index_number": 0 } ] }, { "title": "Protein-induced geometric constraints and charge transfer in Bacteriochlorophyll-histidine complexes in LH2", "year": 2008, "start": 6971, "end": 6978, "type": "Wetenschappelijk artikel", "journal_title": "Phys. Chem. Chem. Phys.", "authors": [ { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Auteur", "index_number": 0 }, { "last_name": "Groot", "initials": "H.J.M.", "first_name": "Huub", "prefix": "de", "role": "Auteur", "index_number": 0 }, { "last_name": "Alia", "initials": "A.", "role": "Auteur", "index_number": 0 }, { "last_name": "Heemskerk", "initials": "M.M.", "role": "Auteur", "index_number": 0 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "role": "Auteur", "index_number": 0 }, { "last_name": "Schaap", "initials": "R.G.", "role": "Auteur", "index_number": 0 } ] }, { "title": "Zinc chlorins for artificial light-harvesting self-assemble into antiparallel stacks forming a microcrystalline solid-state material", "year": 2009, "start": 11472, "end": 11477, "type": "Wetenschappelijk artikel", "journal_title": "PNAS", "authors": [ { "last_name": "Würthner", "initials": "F.", "first_name": "Frank", "role": "Auteur", "index_number": 0 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "first_name": "Piotr", "role": "Auteur", "index_number": 0 }, { "last_name": "Buda", "initials": "F.", "role": "Auteur", "index_number": 0 }, { "last_name": "de Groot", "initials": "H.J.M.", "role": "Auteur", "index_number": 0 }, { "last_name": "Ganapathy", "initials": "S.", "role": "Auteur", "index_number": 0 }, { "last_name": "Sengupta", "initials": "S.", "role": "Auteur", "index_number": 0 }, { "last_name": "Baumeister", "initials": "U.", "role": "Auteur", "index_number": 0 }, { "last_name": "Huber", "initials": "V.", "role": "Auteur", "index_number": 0 } ] }, { "title": "Selective Chemical Shift Assignment of Bacteriochlorophyll a in Uniformly [13C-15N]-Labeled Light-Harvesting 1 Complexes by Solid-State NMR in Ultrahigh Magnetic Field", "year": 2010, "start": 6207, "end": 6215, "type": "Wetenschappelijk artikel", "journal_title": "Journal of Physical Chemistry B", "authors": [ { "last_name": "Ganapathy", "initials": "S.", "first_name": "Swapna", "role": "Auteur", "index_number": 0 }, { "last_name": "Pandit", "initials": "A.", "role": "Auteur", "index_number": 0 }, { "last_name": "van Gammeren", "initials": "A.J.", "role": "Auteur", "index_number": 0 }, { "last_name": "Buda", "initials": "F.", "role": "Auteur", "index_number": 0 }, { "last_name": "de Groot", "initials": "H.J.M.", "role": "Auteur", "index_number": 0 } ] }, { "title": "Nuclear Magnetic Resonance Secondary Shifts of a Light-Harvesting 2 Complex Reveal Local Backbone Perturbations Induced by Its Higher-Order Interactions", "year": 2010, "start": 478, "end": 486, "type": "Wetenschappelijk artikel", "journal_title": "Biochemistry", "authors": [ { "last_name": "Pandit", "initials": "A.", "role": "Auteur", "index_number": 0 }, { "last_name": "Gammeren", "initials": "A.J.", "prefix": "van", "role": "Auteur", "index_number": 0 }, { "last_name": "Buda", "initials": "F.", "role": "Auteur", "index_number": 0 }, { "last_name": "de Groot", "initials": "H.J.M.", "role": "Auteur", "index_number": 0 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "role": "Auteur", "index_number": 0 }, { "last_name": "Ganapathy", "initials": "S.", "role": "Auteur", "index_number": 0 } ] } ] } ] }