
Francesco Buda
Assistant professor
- Name
- Dr. F. Buda
- Telephone
- +31 71 527 5723
- f.buda@chem.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 physics and chemistry tools to investigate molecular mechanisms in protein and protein aggregates.
Computational modeling is nowadays an important tool complementary to experiment in characterizing complex systems at a microscopic level. Our research is focused on the application and development of state-of-the-art computational physics and chemistry tools to investigate molecular mechanisms in protein and protein aggregates. A long-term goal is to employ biological principles in producing synthetic devices on the nanometer scale. We are also interested in enzyme catalyzed oxidation reactions that are industrially and pharmacologically relevant. The Computational methods mainly used in our group include: Density Functional Theory, Car-Parrinello ab-initio molecular dynamics, Classical force-field Molecular Dynamics, and Hybrid Quantum-Mechanics Molecular-Mechanics (QM-MM) methods.
PhD candidates
Assistant professor
- Science
- Leiden Institute of Chemistry
- LIC/Energy & Sustainability
- 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, Journal of Physical Chemistry C 124(51): 27965−27976.
- 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 .
- Belić J., Beek B. van, Menzel J.P., Buda F. & Visscher L. (2020), Systematic Computational Design and Optimization of Light Absorbing Dyes, Journal of Physical Chemistry A 124: 6380-6388.
- 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.
- 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.
- 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.
- 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.
- 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., Ruiter J.M. de, Groot H.J.M. de, Buda F. , Jessica M. de Ruiter Orcid , Huub J. M. de Groot Shao Y., Ruiter J.M. de, Groot JH.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 C 123(35): 21403-21414.
- 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 C 123(26): 16462−16478.
- 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 and Environmental Science 11(10): 2768-2783.
- 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, Journal of Physical Chemistry C 122(26): 14877-14888.
- 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.
- 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.
- 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.
- 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, Phys.Chem.Chem.Phys. 19: 4204215.
- 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 C 120(40): 23074-23082.
- 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.
- 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.
- 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.
- Monti A., Groot H.J.M. de & Buda F. (2014), In-Silico Design of a Donor–Antenna–Acceptor Supramolecular Complex for Photoinduced Charge Separation, : 15600-15609.
- Eisenmayer T.J. & Buda F. (2014), Real-time Simulations of Photoinduced Coherent Charge Transfer and Proton-Coupled Electron Transfer, CHEMPHYSCHEM 15(15).
- 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., 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, 117(38): 11162-11168.
- Pandit A., Ocakoglu K., Buda F., Marle Th. 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, 117: 11292-11298.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Pandit A., Buda F., van Gammeren A.J., 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.
- 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.
- Ganapathy S., Oostergetel G.T., Wawrzyniak P.K., Reus M., Chew A.G.M., Buda F., Boekema E.J., Bryant D., Holzwarth A.R. & de Groot H.J.M. de (2009), Alternating syn-anti bacteriochlorophylls form concentric helical nanotubes in chlorosomes, Proceedings of the National Academy of Sciences of the United States of America 106(21): 8525-8530.
- Alia A., Wawrzyniak P.K., Janssen G., 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.
- 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., 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 of the United States of America 106(28): 11472-11477.
- Zaccheddu M., Filippi C. & Buda F. (2008), Anion-pi and pi-pi cooperative interactions regulating the self-assembly of nitrate-triazine-triazine complexes, 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 : PCCP 10(46): 6971-6978.
- 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. In: Photosynthesis Research. Photosynthesis Research no. 91: Kluwer Academic Publishers. 146-147.
- 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.
- Rodziewicz P., Rutkowski K.S., Melikova S.M., Koll A. & Buda F. (2006), Car-Parrinello molecular dynamics study of the blue-shifted F3CH center dot center dot center dot FCD3 system in liquid N-2, CHEMPHYSCHEM 7(6): 1221-1228.
- 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.
- Karawaijczyk A. & Buda F. (2006), The anticancer drug bleomycin investigated by density functional theory, Molecular Simulation 32(15): 1233-1239.
- 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.
- 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.
- 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.
- 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.
- 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.
- Filippi C. & Buda F. (2005), Response to a "Comment on excitations in photo-active molecules from quantum Monte Carlo", Journal of Chemical Physics 122(8): 087102.
- 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.
- 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.
- 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.
- 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.
- Ensing B., Buda F., Gribnau M.C. & 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.
- Schautz F., Buda F. & Filippi C. (2004), Excitations in photoactive molecules from quantum Monte Carlo, Journal of Chemical Physics 121(12): 5836.
- Ensing B., Buda F. & Baerends E.J. (2003), Fenton-like chemistry in water: Oxidation catalysis by Fe(III) and H2O2, Journal of Physical Chemistry A 107(30): 5722-5731.
- 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., 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 : PCCP 4(4): 3619-3627.
- 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.
- 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.
- 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.
- 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.
- 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.
No relevant ancillary activities