{ "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": "MP-06-079", "title": "Hybrid Quantum Mechanics-Molecular Mechanics study of the Bleomycin Activity", "funding_scheme_id": 2265, "funding_scheme": "Rekentijd nationale computersystemen Rekentijd nationale computersystemen 2006 EW", "department": "Exacte en Natuurwetenschappen", "sub_department": "Exacte Wetenschappen", "start_date": "2006-08-16T00:00:00", "end_date": "2008-03-03T00:00:00", "reporting_year": 2006, "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 research project is to analyze the light-driven electron transfer (ET) and to study the response of the protein in which the BRC is embedded, stabilizing the charge separation process in photosynthesis. We make use of several computational tools including Density Functional Theory (DFT), Car-Parrinello molecular dynamics simulations, hybrid QM/MM approaches, and topological analysis of the electron density based on the \"Atoms in Molecule (AIM)\" theory. These methods enable us to calculate the electronic structure, absorption energies, NMR chemical shifts, and dynamical properties of the model system within the same framework. The long term goal is not only to complement and interpret available spectroscopic data, but also to predict properties of artificial p!\n\n hotosynthetic systems. This project is interrelated with the ongoing experimental activity on photosynthetic systems in our group and is part of a NWO-CW Top Grant. \n\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 research project is to analyze the light-driven electron transfer (ET) and to study the response of the protein in which the BRC is embedded, stabilizing the charge separation process in photosynthesis. We make use of several computational tools including Density Functional Theory (DFT), Car-Parrinello molecular dynamics simulations, hybrid QM/MM approaches, and topological analysis of the electron density based on the \"Atoms in Molecule (AIM)\" theory. These methods enable us to calculate the electronic structure, absorption energies, NMR chemical shifts, and dynamical properties of the model system within the same framework. The long term goal is not only to complement and interpret available spectroscopic data, but also to predict properties of artificial p!\n\n hotosynthetic systems. This project is interrelated with the ongoing experimental activity on photosynthetic systems in our group and is part of a NWO-CW Top Grant. \n\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": "Electronic structure of axial histidines in photosynthetic reaction centres of Rhodobacter sphaeroides ", "year": 2008, "type": "Wetenschappelijk artikel", "authors": [ { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Auteur", "index_number": 2 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "first_name": "Piotr", "role": "Auteur", "index_number": 3 }, { "last_name": "Alia", "initials": "A.", "role": "Auteur", "index_number": 1 } ] }, { "title": "A DFT Study of the BChl-His Complex", "year": 2006, "type": "Overige Output", "authors": [ { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Maker", "index_number": 3 }, { "last_name": "Groot", "initials": "H.J.M.", "first_name": "Huub", "prefix": "de", "role": "Maker", "index_number": 2 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "first_name": "Piotr", "role": "Maker", "index_number": 1 } ] }, { "title": "Electronic structure of axial histidines in photosynthetic reaction centres of Rhodobacter sphaeroides", "year": 2007, "type": "Overige Output", "authors": [ { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Maker", "index_number": 3 }, { "last_name": "Groot", "initials": "H.J.M.", "first_name": "Huub", "prefix": "de", "role": "Maker", "index_number": 5 }, { "last_name": "Matysik", "initials": "J.", "first_name": "Jörg", "role": "Maker", "index_number": 4 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "first_name": "Piotr", "role": "Maker", "index_number": 2 }, { "last_name": "Alia", "initials": "A.", "role": "Maker", "index_number": 1 } ] }, { "title": "Assignment of histidines protonation states in Rhodobacter Sphaeroides reaction center: DFT calculations of NMR chemical shifts", "year": 2007, "type": "Overige Output", "authors": [ { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Maker", "index_number": 4 }, { "last_name": "Groot", "initials": "H.J.M.", "first_name": "Huub", "prefix": "de", "role": "Maker", "index_number": 3 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "first_name": "Piotr", "role": "Maker", "index_number": 1 }, { "last_name": "Alia", "initials": "A.", "role": "Maker", "index_number": 2 } ] }, { "title": "A DFT Study of the Special Pair in Bacterial Reaction Center: \nEffect of Histidine Protonation on the Chemical Shifts \n", "year": 2006, "type": "Overige Output", "authors": [ { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Maker", "index_number": 4 }, { "last_name": "Groot", "initials": "H.J.M.", "first_name": "Huub", "prefix": "de", "role": "Maker", "index_number": 3 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "first_name": "Piotr", "role": "Maker", "index_number": 1 }, { "last_name": "Heemskerk", "initials": "M.", "role": "Maker", "index_number": 2 } ] }, { "title": "Why formally neutral histidines behave as positive in light-harvesting system II?", "year": 2008, "type": "Overige Output", "authors": [ { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Maker", "index_number": 6 }, { "last_name": "Groot", "initials": "H.J.M.", "first_name": "Huub", "prefix": "de", "role": "Maker", "index_number": 5 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "first_name": "Piotr", "role": "Maker", "index_number": 1 }, { "last_name": "Alia", "initials": "A.", "role": "Maker", "index_number": 2 }, { "last_name": "Schaap", "initials": "R.G.", "role": "Maker", "index_number": 3 }, { "last_name": "Heemskerk", "initials": "M.M.", "role": "Maker", "index_number": 4 } ] }, { "title": "Pressure-dependent charge transfer in histidine coordinating Mg in Chlorophylls ", "year": 2007, "type": "Overige Output", "authors": [ { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Maker", "index_number": 6 }, { "last_name": "Wawrzyniak", "initials": "P.K.", "first_name": "Piotr", "role": "Maker", "index_number": 1 }, { "last_name": "Alia", "initials": "A.", "role": "Maker", "index_number": 2 }, { "last_name": "Schaap", "initials": "R.G.", "role": "Maker", "index_number": 3 }, { "last_name": "Heemskerk", "initials": "M.M.", "role": "Maker", "index_number": 4 }, { "last_name": "Groot", "initials": "H.J.M. ", "prefix": "de", "role": "Maker", "index_number": 5 } ] } ] } ] }