Francesco Buda
Associate professor
- Name
- Dr. F. Buda
- Telephone
- +31 71 527 5723
- f.buda@lic.leidenuniv.nl
- ORCID iD
- 0000-0002-7157-7654
The research of Francesco Buda is focused on the application and development of state-of-the-art computational tools to simulate key processes in photosynthesis by modelling, providing a novel theoretical interpretation for the efficient photo-induced charge separation in proteins and artificial mimics based on the coherent coupling between the electronic excitation and specific nuclear vibrational modes. He has translated the acquired understanding of the natural photosynthesis machinery into the design of artificial molecular and heterogeneous complexes able to combine the light-absorption, charge separation, and catalytic functionalities for solar to fuel conversion.
More information about Francesco Buda
PhD candidates
Teaching
-
Energy Transition: Photon Power (Minor Sustainable Chemistry and Biotechnology)
-
Computational Chemistry and Molecular Simulations (MSc Chemistry/MSc LST)
-
Computational Techniques for Chemical Biology (MSc Chemistry/MSc LST)
-
Photochemistry (MSc Chemistry)
-
Theory of Spectroscopy and Molecular Properties (MSc Chemistry)
Curriculum Vitae
Personal information
Nationality: Italian
Date of birth: 22 January 1961
Place of birth: Messina, Italy
Education
1989 Ph.D. in Condensed Matter Physics (approved cum laude), International School for Advanced Studies, Trieste, Italy. Thesis title: Hydrogen in Silicon: a First Principles Molecular Dynamics Study;
Supervisors: Roberto Car and Michele Parrinello
1984 MSc in Physics cum laude, University of Messina, Messina, Italy. Thesis title: Order-disorder transitions in lattice-gas models for adsorbed systems;
Supervisor: Paolo Giaquinta
Current and previous professional employments
2022 – now Associate Professor, Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University, The Netherlands
2001 – 2022 Assistant Professor, Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University, The Netherlands
1999 – 2001 Research assistant, Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, The Netherlands (group of Prof. Evert Jan Baerends)
1994 – 1999 Researcher of the National Institute for Matter Physics (INFM), Scuola Normale Superiore, Pisa, Italy (group of Prof. M. Tosi)
1993 – 1994 Scientific Consultant, IBM ECSEC Scientific Center, Rome, Italy
1992 – 1993 Postdoctoral researcher, IBM Zurich Research Laboratory, Switzerland (group of Prof. Michele Parrinello)
1990 – 1991 Postdoctoral researcher, Physics Department, Ohio State University, Columbus, Ohio, USA (group of Prof J.W. Wilkins and Prof K. Wilson)
Grants, awards
NWO Computing Time on National Computer Facilities: As my research is mostly computational, each year I secured computational resources for my group via NWO (NWO project numbers: MP-079, MP-083, MP-104, SG-227, SH-082-08, SH-171-11, SH-221-12, SH-221-13, SH-221-14, 15308, 16161, 17212, 2019.038, 2021.057)
2016 NWO Solar to Products grant: Design and optimization of a photoanode for solar fuel production (project number: 733.000.007)
2017 Supervisor for Top Sector Chemistry Student Competition 2017 CW, An Interdisciplinary Screening Of Proteorhodopsin Mutants For Near Infrared Proton Pumping Systems (project number: 700.001.516.56.16)
2011 NWO-ECHO grant. Project title: Bio-inspired molecular rectifier for artificial photosynthesis (project number: 713.011.002)
2010 BioSolarCells program: C1.9 project “Characterization and predictive modeling of nanodevice components”
2010 BioSolarCells program: C4.3 project “Honours class ‘From Solar to Fuel with Bio”
2003 Co-applicant CW-TOP-grant project (main applicant Prof. HJM de Groot) on “Natural and Artificial Photosynthesis”
1998 DSM Research award for the best scientific publication for the paper entitled Structure and Stability of Aluminum-Alkyl Cocatalysts in Ziegler-Natta Catalysis, by A. Tarazona, E. Koglin, F. Buda, B. B. Coussens, J. Renkema, S. van Heel, and R. J. Meier published in the Journal of Physical Chemistry B 101, 4370-4378 (1997)
Contribution to teaching and supervision
Bachelor level
- Energy Transition: Photon Power (PP), Minor SCB (2021-present)
- Theoretical Chemistry (TC), BSc MST (2008-2023)
- Molecular Quantum-mechanics and Molecular Modeling (QM&MM), BSc LST (2002-2008)
- Molecular Quantum-mechanics Life (MQL), BSc Chemistry (2003-2005)
- Molecular Quantum-mechanics 1 (MQM1), BSc Chemistry (2006)
- Molecular Quantum-mechanics (MQM), BSc LST & BSc MST (2008-2014)
Master level
- Computational Chemistry and Molecular Simulations (CCMS), MSc Chemistry & MSc LST (2020-present)
- Computational Techniques for Chemical Biology (CTCB), MSc Chemistry & MSc LST (2020-present)
- Photochemistry (PC), MSc Chemistry (2013-present)
- Theory of Spectroscopy and Molecular Properties (TSMP), MSc Chemistry (2012-present)
- Modern Quantum Chemistry (MQC), MSc Chemistry & MSc LST (2008-2019)
Graduate level (schools)
- HRSMC course on Photophysics, Photochemistry and Photobiology, Amsterdam (2007, 2010, 2014, 2017, 2019, 2021)
- HRSMC course on Molecular Modeling, Amsterdam (2005, 2008)
- Winter School for Theoretical Chemistry and Spectroscopy, Han-sur-Lesse, BE (2005, 2010)
- BioSolarCells Winter School – The Artificial Leaf, Twente University (2012)
- Summer School Energy & Sustainability: Artificial Photosynthesis, Leiden (2015)
- Summer School in Multi-Scale Modelling, Lorentz Center, Leiden (2019)
Supervision of PhD students, postdoctoral fellow, exchange students
PhD students
- Dario Calvani (started 16-10-2018)
- Titus de Haas (started 1-11-2020)
- Matthijs Hakkennes (started 1-9-2021)
- Emiel Koridon (started 1-10-2020; external co-promotor, VU Amsterdam)
- Bas Kreupeling (started 1-05-2022)
Former PhD students
- Anna Karawajczyk (thesis defense 31 October 2007)
- Piotr Wawrzyniak (thesis defense 26 January 2011)
- Jose Luis Valles Pardo (thesis defense 19 December 2012)
- Thomas Eisenmayer (thesis defense 15 December 2014)
- Adriano Monti (thesis defense 21 December 2015)
- Jessica de Ruiter (thesis defense 30 October 2018)
- Yang Shao (thesis defense 24 February 2021)
- Jan Paul Menzel (thesis defense 3 March 2022) (cum laude)
- Jelena Belic (thesis defense 23-11-2022; external co-promotor, VU Amsterdam)
Postdoctoral fellows and exchange students
- Jorge Lasave (postdoctoral fellow: August 2011 – August 2012)
- Pawel Rodziewicz (exchange PhD student: March - May 2004. University of Wroclaw, Wroclaw, Poland)
- Emiliano de Santis (exchange PhD student: March - June 2017. University of Rome Tor Vergata)
Other activities/responsibilities
- External member for PhD committees in Switzerland, Italy, Spain, and The Netherlands
- Reviewer for ACS journals (JPC, JACS, JCTC, ACS-Catalysis, ACS Energy Letters, Inorganic Chem.), APS journals (PRB), RSC journals (PCCP), Elsevier journals (Chem.Phys.Lett., Comp.Theor.Chem.), and Wiley journals (ChemPhysChem, ChemPhotoChem, ChemSusChem, IJQC).
- Reviewer for ERC projects
- Reviewer for Danish Council for Independent Research
- Member of the European Psi-k network for electronic structure calculations and ab initio simulations.
- Member of the Board of Examiners for MSc Chemistry and MSc LST (2021-present)
- Member of the HRSMC education committee (2009 – 2010)
- Member of the HRSMC research committee (2010 – 2017)
- Member of the education committee for MSc Chemistry and MSc LST (2013 to 2018; co-Chaired the committee in 2015 and 2016).
- Member of the Board of Examiners for BSc MST (2007-2016)
Conference organisation
- Organizer of the Focus session entitled “Quantum computing for quantum chemistry”, for NWO CHAINS 2022, 21-22 September 2022, Veldhoven (co-organizers: Ariana Torres-Knoop, Lucas Visscher)
- Organizer of a Colloquium Session at the CMD26 Meeting (4-9 September 2016, Groningen). Title: “Experimental and Computational techniques to investigate Proteins: folding, aggregation and Chaperons” (co-organizers: Silvia Morante)
- Organizer of computational chemistry session “Classical and Quantum Dynamics” at CHAINS 2014, Veldhoven 17-18 November 2014
- Organizer of FOM – Focus session for FOM Physics Meeting entitled “Charge transfer and coherent dynamics”, 21-22 January 2014, Veldhoven
- Member of the organizing committee for the European School on Photochemistry (15-19 September 2012, Wijk aan Zee)
- Lorentz workshop on “Modeling natural and artificial photosynthesis”, Leiden, March 2011 (co-organizers: Lucas Visscher and Markus Reiher)
- Member of the organizing committee (with F. Brouwer, L. De Cola, G. van der Zwan) for the European Photochemistry School “Photochemistry 2008: Fundamentals and Applications”, Maastricht 31 May – 4 June 2008
- Lorentz center Workshop on Progress in ab initio modelling of biomolecules: methods and applications, 3-7 July 2006, Leiden (co-organizers: P. Carloni and U. Röthlisberger). Sponsored by Lorentz Center and Psi-k European network
- Forum-INFM Workshop on Computer simulations of systems of biological interest; Scuola Normale Superiore of Pisa, May 12-14, 1997
Publication record including five recent representative publications
130 refereed journals; 17 book chapters, conference proceedings and other publications
Number of citations 4550; H-index 36 (Web of Science)
Full publication record: Leiden University
- Titus de Haas, Hannah van Overeem, Huub J.M. de Groot, and Francesco Buda: Strategies to Enhance the Rate of Proton-Coupled Electron Transfer Reactions in Dye-Water Oxidation Catalyst Complexes, ChemPhotoChem (2023), 7, e202200274. DOI: 10.1002/cptc.202200274
This paper provides strategies for accelerating the Photocatalytic Water Splitting in solar energy conversion devices. - Yang Shao, Huub J. M. de Groot, and Francesco Buda: Tuning the Proton-Coupled Electron Transfer Rate by Ligand Modification in Catalyst-Dye Supramolecular Complexes for Photocatalytic Water Splitting, ChemSusChem (2021), 14, 479–486. DOI: 10.1002/cssc.202001863
This publication proposes a new way of improving the water splitting catalytic activity by rational molecular design. - Jan Paul Menzel, Anastasios Papadopoulos, Jelena Belić, Huub de Groot, Lucas Visscher, Francesco Buda: Photoinduced Electron Injection in a fully solvated Dye-Sensitized Photoanode: A dynamical semi-empirical study, The Journal of Physical Chemistry C (2020), 124, 27965−27976. DOI: 10.1021/acs.jpcc.0c09551
This paper moves forward the frontier of quantum-classical, semi-empirical simulations and provides a novel example of computational studies on Dye-Sensitized Solar Cells components. - Thomas E. O'Brien, Bruno Senjean, Ramiro Sagastizabal, Xavier Bonet-Monroig, Alicja Dutkiewicz, Francesco Buda, Leonardo DiCarlo, and Lucas Visscher: Calculating energy derivatives for quantum chemistry on a quantum computer, npj Quantum Information (2019) 5, 113. DOI: 10.1038/s41534-019-0213-4
This contribution paves the way to ab initio MD simulations within quantum computing platforms. - Jan Paul Menzel, Huub J. M. de Groot, and Francesco Buda: Photoinduced Electron Transfer in Donor−Acceptor Complexes: Isotope Effect and Dynamic Symmetry Breaking, J. Phys. Chem. Lett. (2019), 10, 6504−6511. DOI: 10.1021/acs.jpclett.9b02408
This publication provides a clear understanding on how vibronic coupling affects photoinduced electron transfer and is important both from a fundamental as well as applied perspective.
Presentations including five recent invited talks at national/international meetings
~75 invited talks at universities and at conferences
- Lorentz workshop “Accelerating theoretical spectroscopy for complex multiscale materials”, Lorentz Center, Leiden, 20-24 March 2023; Title: Microscopic origin of the efficient exciton transport in chlorosomes
- Invited Talk at NWO-NERA Energy Symposium ‘Promoting Interdisciplinary Research towards a successful Energy Transition’, Eindhoven, 11 November 2022; Title: Computational design and optimization of a photoanode for solar to fuel conversion
- Invited talk at Queen’s University Belfast, 8 May 2019. Title: Photocatalytic Water Splitting: Quantum-classical Simulations
- Invited talk at KNCV-CTC symposium, 26 March 2019, Amsterdam. Title: Photocatalytic water splitting for artificial photosynthesis devices
- Invited talk at the International Conference “Photoinduced Processes in Embedded Systems”, Pisa, ltaly, 24-27 June 2018. Title: Mechanism and Design Strategy in Photocatalytic Water Splitting
Associate professor
- Science
- Leiden Institute of Chemistry
- LIC/Energy & Sustainability
- Calvani D., Kreupeling B.A., Sevink G.J.A., Groot H.J.M. de, Schneider G.F. & Buda F. (2024), Covalent benzenesulfonic functionalization of a graphene nanopore for enhanced and selective proton transport, Journal of Physical Chemistry C 128(8): 3514-3524.
- Dsouza L.A., Li X., Erić V., Huijser A., Jansen T.L.C., Holzwarth A.R., Buda F., Bryant D.A., Bahri S., Sai Sankar Gupta K.B., Sevink G.J.A. & Groot H.J.M. de (2024), An integrated approach towards extracting structural characteristics of chlorosomes from a bchQ mutant of Chlorobaculum tepidum, Physical Chemistry Chemical Physics 26(22): 15856–15867.
- Erić V., Li X., Dsouza L.A., Huijser A., Holzwarth A.R., Buda F., Sevink G.J.A., Groot H.J.M. de & Jansen T.L.C. (2024), Observation of dark states in two-dimensional electronic spectra of chlorosomes, The Journal of Physical Chemistry B 128(15): 3575-3584.
- Calvani D., Louwersheimer R. & Buda F. (2024), Effect of anchoring dynamics on proton-coupled electron transfer in the Ru(bda) coordination oligomer on a graphitic surface, ChemPlusChem 89(8): e202400082.
- Zhu K., Rodríguez Paradelo A., Brands M.B., Haas T. de, Buda F., Reek J.N.H., Mul G. & Huijser A. (2024), Limiting molecular twisting: upgrading a donor–acceptor dye to drive H2 evolution, Advanced Science 11(40): 2403454.
- Zhou X., Wang P., Vadde R., Zhang L., Jiang S., Li X., Abyar S., Papadopoulou P., Shao Y., Bretin L.R., Siegler M.A., Buda F., Kros A., Fan J., Peng X., Sun W. & Bonnet S.A. (2023), In vivo metallophilic self-assembly of a light-activated anticancer drug, Nature Chemistry 15: 980-987 (980-987).
- Hakkennes M.L.A., Meijer M.S., Menzel J.P., Goetz A.C., Duijn R. van, Siegler M.A., Buda F. & Bonnet S.A. (2023), Ligand rigidity steers the selectivity and efficiency of the photosubstitution reaction of strained ruthenium polypyridyl complexes, Journal of the American Chemical Society 145(24): 13420-13434.
- Langevelde P.H. van, Engbers S., Buda F. & Hetterscheid D.G.H. (2023), Elucidation of the electrocatalytic nitrite reduction mechanism by bio-inspired copper complexes, ACS Catalysis 13(15): 10094-10103.
- Vesna E., Castro J.L., Li X., Dsouza L.A., Frehan S.K., Huijser A., Holzwarth A.R., Buda F., Sevink G.J.A., Groot H.J.M. de & Jansen T.L.C. (2023), Ultrafast anisotropy decay reveals structure and energy transfer in supramolecular aggregates, The Journal of Physical Chemistry B 127(34): 7487-7496.
- Frehan S.K., D'Souza L.A., Li X., Eríc V., Jansen T.L.C., Mul G., Holzwarth A.R., Buda F., Sevink G.J.A., Groot H.J.M. de & Huijser A. (2023), Photon energy-dependent ultrafast exciton transfer in chlorosomes of Chlorobium tepidum and the role of supramolecular dynamics, The Journal of Physical Chemistry B 127(35): 7581-7589.
- Belić J., Förster A., Menzel J.P., Buda F. & Visscher L. (2023), Correction: automated assessment of redox potentials for dyes in dye-sensitized photoelectrochemical cells, Physical Chemistry Chemical Physics 25(28): 19266-19268.
- Hakkennes M.L.A., Buda F. & Bonnet S.A. (2023), MetalDock: An Open Access Docking Tool for Easy and Reproducible Docking of Metal Complexes, Journal of Chemical Information and Modeling 63(24): 7816-7825.
- Haas T. de, Overeem H. van, Groot H.J.M. de & Buda F. (2023), Strategies to enhance the rate of proton-coupled electron transfer reactions in dye-water oxidation catalyst complexes, ChemPhotoChem 7(3): e202200274.
- Eric V., Li X., D'souza L., Frehan S.K., Huijser A., Holzwarth A.R., Buda F., Sevink G.J.A., Groot H.J.M. de & Jansen T.L.C. (2023), Manifestation of hydrogen bonding and exciton delocalization on the absorption and two-dimensional electronic spectra of chlorosomes, The Journal of Physical Chemistry B 127(5): 1097-1109.
- Belic J., Förster A., Menzel J.P., Buda F. & Visscher L. (2022), Automated assessment of redox potentials for dyes in dye-sensitized photoelectrochemical cells, Physical Chemistry Chemical Physics 24(1): 197-210.
- Li X., Buda F., Groot H.J.M. de & Sevink G.J.A. (2022), The role of chirality and plastic crystallinity in the optical and mechanical properties of chlorosomes, iScience 25(1): 103618.
- Yalouz S., Koridon E., Senjean B., Lasorne B., Buda F. & Visscher L. (2022), Analytical nonadiabatic couplings and gradients within the state-averaged orbital-optimized variational quantum eigensolver, Journal of Chemical Theory and Computation 18(2): 776-794.
- Ham A. van der, Liu X., Calvani D., Melcrová A., Kozdra M., Buda F., Overkleeft H.S., Roos W.H., Filippov D.V. & Schneider G.F. (2022), Freestanding non-covalent thin films of the propeller-shaped polycyclic aromatic hydrocarbon decacyclene, Nature Communications 13(1): 1920.
- Menzel J.P., Boeije Y., Bakker T.M.A., Belic J., Reek J.N.H., Groot H.J.M. de, Visscher L. & Buda F. (2022), In silico optimization of charge separating dyes for solar energy conversion, ChemSusChem 15(15): e202200594.
- Boer D. den, Heer H.C. de, Buda F. & Hetterscheid D.G.H. (2022), Challenges in elucidating the free energy scheme of the laccase catalyzed reduction of oxygen, ChemCatChem 15(1): e202200878.
- Yalouz S., Senjean B., Günther J., Buda F., O'Brien T.E. & Visscher L. (2021), A state-averaged orbital-optimized hybrid quantum–classical algorithm for a democratic description of ground and excited states, Quantum Science and Technology 6(2): 024004.
- Menzel J.P., Kloppenburg M., Belić J., Groot H.J.M. de, Visscher L. & Buda F. (2021), Efficient workflow for the investigation of the catalytic cycle of water oxidation catalysts: combining GFN-xTB and density functional theory, Journal of Computational Chemistry 42(26): 1885–1894.
- Shao Y., Groot H.J.M. de & Buda F. (2021), Two-channel model for electron transfer in a dye-catalyst-dye supramolecular complex for photocatalytic water splitting, ChemSusChem 14(15): 3155-3162.
- Koridon E., Yalouz S., Senjean B., Buda F., O’Brien T. E. & Visscher L. (2021), Orbital transformations to reduce the 1-norm of the electronic structure Hamiltonian for quantum computing applications, Physical Review Research 3(3): 033127.
- Zhou X.Q., Mytiliniou M., Hilgendorf J., Zeng Y., Papadopoulou P., Shao Y., Dominguez Maximilian P., Zhang L., Hesselberth M.B.S., Bos E., Siegler M.A., Buda F., Brouwer A.M., Kros A., Koning R.I., Heinrich D. & Bonnet S. (2021), Intracellular dynamic assembly of deep‐red emitting supramolecular nanostructures based on the Pt…Pt metallophilic interaction, Advanced Materials 33(37): 2008613.
- Liu X., He M., Calvani D., Qi H., Sai Sankar Gupta K.B., Groot H.J.M. de, Sevink G.J.A., Buda F., Kaiser U. & Schneider G.F. (2020), Power generation by reverse electrodialysis in a single-layer nanoporous membrane made from core–rim polycyclic aromatic hydrocarbons, Nature Nanotechnology 15: 307-312.
- Li X., Buda F., Groot H.J.M. de & Sevink G.J.A. (2020), Dynamic Disorder Drives Exciton Transfer in Tubular Chlorosomal Assemblies, Journal of Physical Chemistry B 124(20): 4026-4035.
- Belić J. Beek B. van Menzel J.P. Buda F. Visscher L. (2020), Systematic Computational Design and Optimization of Light Absorbing Dyes, The Journal of Physical Chemistry A 124(1): 6380-6388.
- Shao Y., Groot H.J.M. de & Buda F. (2020), Tuning the Proton-Coupled Electron Transfer Rate by Ligand Modification in Catalyst-Dye Supramolecular Complexes for Photocatalytic Water Splitting, ChemSusChem 14(1): 479-486.
- Menzel J.P., Papadopoulos A., Belić J., Groot H.J.M. de, Visscher L. & Buda F. (2020), Photoinduced electron injection in a fully solvated dye sensitized photoanode: a dynamical semi-empirical study, The Journal of Physical Chemistry Part C 124(51): 27965−27976.
- Li X., Buda F., Groot H.J.M. de & Sevink G.J.A. (2019), Molecular Insight in the Optical Response of Tubular Chlorosomal Assemblies, The Journal of Physical Chemistry Part C 123(26): 16462−16478.
- Shao Y., Ruiter J.M. de, Groot H.J.M. de, Buda F., Ruiter Jessica M. de, Groot Huub J.M. de, Shao Y., Ruiter J.M. de, Groot J.H.J.N. de & Buda F. (2019), Photocatalytic Water Splitting Cycle in a Dye-Catalyst Supramolecular Complex: Ab Initio Molecular Dynamics Simulations, The Journal of Physical Chemistry Part C 123(35): 21403-21414.
- Menzel J.P., Groot H.J.M. de & Buda F. (2019), Photoinduced Electron Transfer in Donor-Acceptor Complexes: Isotope Effect and Dynamic Symmetry Breaking, Journal of Physical Chemistry Letters 10: 6504-6511.
- Shao Y., Groot H.J.M. de & Buda F. (2019), Proton Acceptor near the Active Site Lowers Dramatically the O-O Bond Formation Energy Barrier in Photocatalytic Water Splitting, Journal of Physical Chemistry Letters 10: 7690-7697.
- O'Brien T.E., Senjean B., Sagastizabal R., Bonet-Monroig X., Dutkiewicz A., Buda F., DiCarlo L. & Visscher L. (2019), Calculating energy derivatives for quantum chemistry on a quantum computer, npj Quantum Information 5: 113.
- Loco D., Buda F., Lugtenburg J. & Mennucci B. (2018), The dynamic origin of color tuning in proteins revealed by a carotenoid pigment, Journal of Physical Chemistry Letters 9(9): 2404-2410.
- Li X., Buda F., Groot H.J.M. de & Sevink G.J.A. (2018), Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum, The Journal of Physical Chemistry Part C 122(26): 14877-14888.
- Ardo S., Fernandez Rivas D., Modestino M., Schulze Greiving V., Abdi F.W., Alarcon Llado E., Artero V., Ayers K., Battaglia C., Becker J.-P., Bederak D., Berger A., Buda F., Chinello E., Dam B., Di Palma V., Edvinssson T., Fujii K., Gardeniers H., Geerling H., Hasherni S.M.H., Hausseener S., Houle F., Huskens J., James B.D., Konrad K., Kudo A., Kunturu P.P., Lohse D., Mei B., Miller E.L., Moore G.F., Muller J., Orchard K.L., Rosser T.E., Saai F.H., Schüttauf J.W., Seger B., Sheehan S.W., Smith W.A., Spurgeon J., Tang M.H., Krol R. van de, Vesborg P.C.K. & Westerik P. (2018), Pathways to Electrochemical Solar-Hydrogen Technologies, Energy & Environmental Science 11(10): 2768-2783.
- Ruiter J.M. de, Groot H.J.M. de & Buda F. (2018), Energetic Effects of a Closed System Approach Including Explicit Proton and Electron Acceptors as Demonstrated by a Mononuclear Ruthenium Water Oxidation Catalyst, ChemCatChem 10(20): 4594-4601.
- Thomas B., Rombouts J.A., Oostergetel G.T., Sai Sankar Gupta K.B., Buda F., Lammertsma K., Orru R. & Groot H.J.M. de (2017), A Hybrid Solid State NMR and Electron Microscopy Structure Determination Protocol for Engineering Advanced Paracrystalline Optical Materials, Chemistry: a European Journal 23: 3280-3284.
- Ruiter J.M. de & Buda F. (2017), Introducing a closed system approach for the investigation of chemical steps involving proton and electron transfer; as illustrated by a copper-based water oxidation catalyst, Physical Chemistry Chemical Physics 19(6): 4204215.
- Buda F., Keijer T., Ganapathy S. & Grip W.J. de (2017), A Quantum-mechanical Study of the Binding Pocket of Proteorhodopsin: Absorption and Vibrational Spectra Modulated by Analogue Chromophores, Photochemistry and Photobiology 93(6): 1399-1406.
- Ruiter J.M. de, Purchase R.L., Monti A., Ham C.J.M. van der, Gullo M.P., Joya K.S., D'Angelantonio M., Barbieri A., Hetterscheid D.G.H., Groot H.J.M. de & Buda F. (2016), Electrochemical and Spectroscopic Study of Mononuclear Ruthenium Water Oxidation Catalysts: A Combined Experimental and Theoretical Investigation, ACS Catalysis 6(11): 7340-7349.
- Monti A., Ruiter J.M. de, Groot H.J.M. de & Buda F. (2016), A Dynamic View of Proton-Coupled Electron Transfer in Photocatalytic Water Splitting, The Journal of Physical Chemistry Part C 120(40): 23074-23082.
- Monti A., Negre C.F.A., Batista V.S., Rego L.G.C., Groot H.J.M. de & Buda F. (2015), Crucial role of nuclear dynamics for electron injection in a dye-semiconductor Complex, Journal of Physical Chemistry Letters 6(12): 2393-2398.
- Faez S., Verhart N.R., Markoulides M., Buda F., Gourdon A. & Orrit M.A.G.J. (2015), Design and synthesis of aromatic molecules for probing electric fields at the nanoscale, Faraday Discussions 184: 251-262.
- Eisenmayer T.J. & Buda F. (2014), Real-time simulations of photoinduced coherent charge transfer and proton-coupled electron transfer, ChemPhysChem 15(15): 3258-3263.
- Monti A., Groot H.J.M. de & Buda F. (2014), In-silico design of a donor–antenna–acceptor supramolecular complex for photoinduced charge separation, The Journal of Physical Chemistry Part C 118(29): 15600-15609.
- Alia A., Buda F., Groot H.J.M. de & Matysik J. (2013), Solid-state NMR of nanomachines involved in photosynthetic energy conversion, Annual Review of Biophysics 42: 675-699.
- Sai Sankar Gupta K.B., Alia A., Buda F., Groot H.J.M. de & Matysik J. (2013), Bacteriopheophytin a in the active branch of the reaction center of Rhodobacter sphaeroides is not disturbed by the protein matrix as shown by C-13 photo-CIDNP MAS NMR, Journal of Physical Chemistry B 117(12): 3287-3297.
- Joya K.S., Valles-Pardo J.L., Joya Y.F., Eisenmayer T.J., Thomas B., Buda F. & Groot H.J.M. de (2013), Molecular catalytic assemblies for electrodriven water splitting, ChemPlusChem 78(1): 35-47.
- Eisenmayer T.J., Lasave J.A., Monti A., Groot H.J.M. de & Buda F. (2013), Proton displacements coupled to primary electron transfer in the Rhodobacter sphaeroides reaction center, Journal of Physical Chemistry B 117(38): 11162-11168.
- Pandit A., Ocakoglu K., Buda F., Marle T. van, Holzwarth A.R. & Groot H.J.M. de (2013), Structure determination of a bio-inspired self-assembled light-harvesting antenna by solid-state NMR and molecular modeling, Journal of Physical Chemistry B 117(38): 11292-11298.
- Filippi C., Buda F., Guidoni L. & Sinicropi A. (2012), Bathochromic shift in green fluorescent protein: a puzzle for QM/MM approaches, Journal of Chemical Theory and Computation 8(1): 112-124.
- Valles-Pardo J.L., Guijt M.C., Iannuzzi M., Joya K.S., Groot H.J.M. de & Buda F. (2012), Ab initio molecular dynamics study of water oxidation reaction pathways in mono-ru catalysts, ChemPhysChem 13(1): 140-146.
- Eisenmayer T.J., Groot H.J.M. de, Wetering E. van de, Neugebauer J. & Buda F. (2012), Mechanism and reaction coordinate of directional charge separation in bacterial reaction centers, Journal of Physical Chemistry Letters 3(6): 694-697.
- Valles-Pardo J.L., Groot H.J.M. de & Buda F. (2012), Structural rearrangements and reaction intermediates in a di-Mn water oxidation catalyst, Physical Chemistry Chemical Physics 14(44): 15502-15508.
- Ganapathy S., Oostergetel G.T., Reus M., Tsukatani Y., Chew A.G.M., Buda F., Bryant D.A., Holzwarth A.R. & Groot H.J.M. de (2012), Structural variability in wild-type and bchQ bchR mutant chlorosomes of the green sulfur bacterium Chlorobaculum tepidum, Biochemistry 51(22): 4488-4498.
- Neugebauer J., Veldstra J. & Buda F. (2011), Theoretical spectroscopy of astaxanthin in crustacyanin proteins: absorption, circular dichroism, and nuclear magnetic resonance, Journal of Physical Chemistry B 115(12): 3216-3225.
- Maheswari P.U., Hartl F., Quesada M., Buda F., Lutz M., Spek A.L., Gamez P. & Reedijk J. (2011), Spectro-electrochemical and DFT studies of a planar Cu(II)-phenolate complex active in the aerobic oxidation of primary alcohols, Inorganica Chimica Acta 374(1): 406-414.
- Wawrzyniak P.K., Beerepoot M.T.P., Groot H.J.M. de & Buda F. (2011), Acetyl group orientation modulates the electronic ground-state asymmetry of the special pair in purple bacterial reaction centers, Physical Chemistry Chemical Physics 13(21): 10270-10279.
- Pandit A., Buda F., Gammeren A.J. van, Ganapathy S. & Groot H.J.M. de (2010), Selective chemical shift assignment of bacteriochlorophyll a in uniformly [C-13-N-15]-labeled light-harvesting 1 complexes by solid-state NMR in ultrahigh magnetic field, Journal of Physical Chemistry B 114(18): 6207-6215.
- Pandit A., Wawrzyniak P.K., Gammeren A.J. van, Buda F., Ganapathy S. & Groot H.J.M. de (2010), Nuclear magnetic resonance secondary shifts of a light-harvesting 2 complex reveal local backbone perturbations induced by its higher-order interactions, Biochemistry 49(3): 478-486.
- Ganapathy S., Sengupta S., Wawrzyniak P.K., Huber V., Buda F., Baumeister U., Wurthner F. & Groot H.J.M. de (2009), Zinc chlorins for artificial light-harvesting self-assemble into antiparallel stacks forming a microcrystalline solid-state material, Proceedings of the National Academy of Sciences 106(28): 11472-11477.
- Filippi C., Zaccheddu M. & Buda F. (2009), Absorption spectrum of the Green Florescent Protein chromophore: a difficult case for Ab Initio methods?, Journal of Chemical Theory and Computation 5(8): 2074-2087.
- Buda F. (2009), Introduction to theory/modeling methods in photosynthesis, Photosynthesis Research 102: 437-441.
- Roy S., Westmaas J.A., Buda F. & Reedijk J. (2009), Platinum(II) compounds with chelating ligands based on pyridine and pyrimidine: synthesis, characterizations, DFT calculations, cytotoxic assays and binding to a DNA model base, Journal of Inorganic Biochemistry 103(9): 1278-1287.
- Ganapathy S., Oostergetel G.T., Wawrzyniak P.K., Reus M., Chew A.G.M., Buda F., Boekema E.J., Bryant D., Holzwarth A.R. & Groot H.J.M. de (2009), Alternating syn-anti bacteriochlorophylls form concentric helical nanotubes in chlorosomes, Proceedings of the National Academy of Sciences 106(21): 8525-8530.
- Alia A., Wawrzyniak P.K., Janssen G.J., Buda F., Matysik J. & Groot H.J.M. de (2009), Differential charge polarization of axial histidines in bacterial reaction centers balances the asymmetry of the special pair, Journal of the American Chemical Society 131(28): 9626-9627.
- Zaccheddu M., Filippi C. & Buda F. (2008), Anion-pi and pi-pi cooperative interactions regulating the self-assembly of nitrate-triazine-triazine complexes, The Journal of Physical Chemistry A 112(7): 1627-1632.
- Wawrzyniak P.K., Alia A., Schaap R.G., Heemskerk M.M., Groot H.J.M. de & Buda F. (2008), Protein-induced geometric constraints and charge transfer in bacteriochlorophyll-histidine complexes in LH2, Physical Chemistry Chemical Physics 10(46): 6971-6978.
- Ratnala V.R.P., Kiihne S.R., Buda F., Leurs R., Groot H.J.M. de & Grip W.J. de (2007), Solid-state NMR Evidence for a protonation switch in the binding pocket of the H1 receptor upon binding of the agonist histamine, Journal of the American Chemical Society 129(4): 867-872.
- Alia A., Wawrzyniak P.K., Buda F., Matysik J. & Groot H.J.M. de (2007), Electronic structure of axial histidines in photosynthetic reaction centres of Rhodobacter sphaeroides, Photosynthesis Research 91(2-3): 146-147.
- Amat P., Granucci G., Buda F., Persico M. & Tozzini V. (2006), The chromophore of asFP595: a theoretical study, Journal of Physical Chemistry B 110(18): 9348-9353.
- Casellas H., Massera C., Buda F., Gamez P. & Reedijk J. (2006), Crystallographic evidence of theoretically novel anion- interactions, New Journal of Chemistry 30(11): 1561-1566.
- Karawajczyk A., Gossens C., Roethlisberger U. & Buda F. (2006), Mechanism of bleomycin suicide: a Car-Parrinello molecular dynamics investigation, Journal of Physical Chemistry B 110(42): 21245-21250.
- Buda F., Glaude P.A., Battin-Leclerc F., Porter R., Hughes K.J. & Griffiths J.F. (2006), Use of detailed kinetic mechanisms for the prediction of autoignitions, Journal of Loss Prevention in the Process Industries 19(2-3): 227-232.
- Karawaijczyk A. & Buda F. (2006), The anticancer drug bleomycin investigated by density functional theory, Molecular Simulation 32(15): 1233-1239.
- Rodziewicz P., Rutkowski K.S., Melikova S.M., Koll A. & Buda F. (2006), Car-Parrinello molecular dynamics study of the blue-shifted F3CHFCD3 system in liquid N2, ChemPhysChem 7(6): 1221-1228.
- Gorkum R. van, Buda F., Kooijman H., Spek A.L., Bouwman E. & Reedijk J. (2005), Trigonal-prismatic vs. octahedral geometry for MnII complexes with innocent didentate ligands: a subtle difference as shown by XRD and DFT on Mn(acac)2(bpy), European Journal of Inorganic Chemistry 2005(11): 2255-2261.
- Wijk A.A.C. van, Spaans A.P., Uzunbajakava N., Otto C., Groot H.J.M. de, Lugtenburg J. & Buda F. (2005), Spectroscopy and quantum chemical modelling reveal a predominant contribution of excitonic interactions to the bathochromatic shift in alpha-crustacyanin, the blue carotenoprotein in the carapace of the lobster Homarus gammarus, Journal of the American Chemical Society 127(5): 1438-1445.
- Filippi C. & Buda F. (2005), Response to a "Comment on excitations in photo-active molecules from quantum Monte Carlo", The Journal of Chemical Physics 122(8): 087102.
- Gammeren A.J. van, Buda F., Hulsbergen F.B., Kiihne S., Hollander J.G., Egorova-Zachernyuk T.A., Fraser N.J., Cogdell R.J. & Groot H.J.M. de (2005), Selective chemical shift assignment of B800 and B850 bacteriochlorophylls in uniformly [C-13,N-15]-labeled light-harvesting complexes by solid-state NMR spectroscopy at ultra-high magnetic field, Journal of the American Chemical Society 127(9): 3213-3219.
- Rodziewicz P., Melikova S.M., Rutkowski K.S. & Buda F. (2005), Car-Parrinello molecular dynamics study of a blue-shifted intermolecular weak-hydrogen-bond system, ChemPhysChem 6(9): 1719-1724.
- Karawajczyk A. & Buda F. (2005), The metal bonding domain of the antitumor drug Fe(II)-bleomycin: a DFT investigation, Journal of Biological Inorganic Chemistry 10(1): 33-40.
- Schautz F., Buda F. & Filippi C. (2004), Excitations in photoactive molecules from quantum Monte Carlo, The Journal of Chemical Physics 121(12): 5836.
- Touw S.I.E., Groot H.J.M. de & Buda F. (2004), DFT calculations of the H-1 chemical shifts and C-13 chemical shift tensors of retinal isomers, Journal of Molecular Structure: Theochem 711(1-3): 141-147.
- Ensing B., Buda F., Gribnau M.C.M. & Baerends E.J. (2004), Methane-to-methanol oxidation by the hydrated iron(IV) oxo species in aqueous solution: a combined DFT and Car-Parrinello molecular dynamics study, Journal of the American Chemical Society 126(13): 4355-4365.
- Touw S.I.E., Groot H.J.M. de & Buda F. (2004), Ab initio modeling of the spatial, electronic, and vibrational structure of Schiff base models for visual photoreceptors, Journal of Physical Chemistry B 108(35): 13560-13572.
- Premvardhan L.L., Buda F., Horst M.A. van der, Luhrs D.C., Hellingwerf K.J. & Grondelle R. van (2004), Impact of photon absorption on the electronic properties of p-coumaric acid derivatives of the photoactive yellow protein chromophore, Journal of Physical Chemistry B 108(16): 5138-5148.
- Buda F., Ensing B., Gribnau M.C.M. & Baerends E.J. (2003), O-2 evolution in the Fenton reaction, Chemistry: a European Journal 9(14): 3436-3444.
- Ensing B., Buda F. & Baerends E.J. (2003), Fenton-like chemistry in water: oxidation catalysis by Fe(III) and H2O2, The Journal of Physical Chemistry A 107(30): 5722-5731.
- Bonapasta A.A., Buda F., Colombet P.C. & Guerrini G. (2002), Cross-linking of poly(vinyl alcohol) chains by CA ions in macro-defect-free cements, Chemistry of Materials 14(3): 1016-1022.
- Bonapasta A.A. & Buda F. (2002), Binding and Migration Paths of Au Adatoms on the GaAs (001) Surface, Physical Review B 65(4): 045308.
- Bonapasta A.A., Scavia G. & Buda F. (2002), Clustring Effects in a Low Coverage Deposition on the GaAs (001)-Beta 2(2x4)Surface: An STM-UHV and Theoretical Study, Surface Science 520(1-2): 53-64.
- Ensing B., Buda F., Blochl P.E. & Baerends E.J. (2002), A Car-Parinello Study of the Formation of Oxidizing Intermediates from the Fenton's Reagent in Aqueous Solution, Physical Chemistry Chemical Physics 4(4): 3619-3627.
- Buda F., Touw S.I.E. & Groot H.J.M. de (2001), An ab-initio molecular dynamics modeling of the primary photochemical event in vision. In: Kiihne S.R. & Groot H.J.M. (Eds.), Perspectives on Solid State NMR in Biology. Focus on Structural Biology no. 1. Dordrecht: Springer. 111-122.
- Tozzini V., Buda F. & Fasolino A. (2001), Fullerene-like III-V clusters: a density functional theory prediction, Journal of Physical Chemistry B 105(50): 12477-12480.
- La Penna G., Buda F., Bifone A. & Groot H.J.M. de (1998), The transition state in the isomerization of rhodopsin, Chemical Physics Letters 294(6): 447-453.
- Bifone A., Groot H.J.M. de & Buda F. (1997), Energy storage in the primary photoproduct of vision, Journal of Physical Chemistry B 101(15): 2954-2958.
- Bifone A., Groot H.J.M. de & Buda F. (1996), Ab initio molecular dynamics of retinals, Chemical Physics Letters 248(3-4): 165-172.
- Buda F., Groot H.J.M. de & Bifone A. (1996), Charge localization and dynamics in rhodopsin, Physical Review Letters 77(21): 4474-4477.