2012

Filippi, C., Buda, F., Guidoni, L., Sinicropi, A. , Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches, Journal of Chemical Theory and Computation, vol. 8.

2011

Hartl, F., Maheswari, P.U., Quesada, M., Buda, F., Lutz, M., Spek, A.L., Gamez, P., Reedijk, J. , Spectro-electrochemical and DFT studies of a planar Cu(II)-phenolate complex active in the aerobic oxidation of primary alcohols, Inorganica Chimica Acta, vol. 374, no. 1, pp. 406-414.

Wawrzyniak, P.K., Beerepoot, M.T., de Groot, H.J., Buda, F. , Acetyl group orientation modulates the electronic ground-state asymmetry of the special pair in purple bacterial reaction centers, Phys. Chem. Chem. Phys, vol. 13, no. 21, pp. 10270-9.

Neugebauer, J., Veldstra, J., Buda, F. , Theoretical Spectroscopy of Astaxanthin in Crustacyanin Proteins:Absorption, Circular Dichroism, and Nuclear Magnetic Resonance, The journal of Physical Chemsitry, vol. 115, pp. 3216.

2010

Pandit, A., Buda, F., van Gammeren, A.J., Ganapathy, S., de Groot, H.J.M. , 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, vol. 114, no. 18, pp. 6207-6215.

Pandit, A., Wawrzyniak, P.K., van Gammeren, A.J., Buda, F., Ganapathy, S., de Groot, H.J.M. , Nuclear Magnetic Resonance Secondary Shifts of a Light-Harvesting 2 Complex Reveal Local Backbone Perturbations Induced by Its Higher-Order Interactions, Biochemistry, vol. 49, no. 3, pp. 478-486.

2009

Roy, S., Westmaas, J.A., Buda, F., Reedijk, J. , Platinum(II) compounds with chelating ligands based on pyridine and pyrimidine: synthesis, characterizations, DFT calculations, cytotoxic assays and binding to a DNA model base, J Inorg Biochem, vol. 103, no. 9, pp. 1278-87.

Ganapathy, S., Oostergetel, G.T., Wawrzyniak, P.K., Reus, M., Chew, A.G.M., Buda, F., Boekema, E.J., Bryant, D.A., Holzwarth, A.R., de Groot, H.J.M. , Alternating syn-anti bacteriochlorophylls form concentric helical nanotubes in chlorosomes, Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 21, pp. 8525-8530.

Buda, F. , Introduction to theory/modeling methods in photosynthesis, Photosynth Res.

Buda, F. , Introduction to theory/modeling methods in photosynthesis, Photosynth Res.

Alia, A., Wawrzyniak, P.K., Janssen, G.J., Buda, F., Matysik, J., de Groot, H.J.M. , Differential Charge Polarization of Axial Histidines in Bacterial Reaction Centers Balances the Asymmetry of the Special Pair, Journal of the American Chemical Society, vol. 131, no. 28, pp. 9626-9627.

Ganapathy, S., Sengupta, S., Wawrzyniak, P.K., Huber, V., Buda, F., Baumeister, U., Wurthner, F., de Groot, H.J.M. , 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, vol. 106, no. 28, pp. 11472-11477.

Filippi, C., Ziccheddu, M., Buda, F. , Absorption Spectrum of the Green Fluorescent Protein Chromophore: A Difficult Case for ab Initio Methods?, Journal of Chemical Theory and Computation, vol. 5, no. 8, pp. 2074-2087.

2008

Zaccheddu, M., Filippi, C., Buda, F. , Anion-pi and pi-pi cooperative interactions regulating the self-assembly of nitrate-triazine-triazine complexes, Journal of Physical Chemistry A, vol. 112, no. 7, pp. 1627-1632.

Wawrzyniak, P.K., Alia, A., Schaap, R.G., Heemskerk, M.M., de Groot, H.J.M., Buda, F. , Protein-induced geometric constraints and charge transfer in bacteriochlorophyll-histidine complexes in LH2, Physical Chemistry Chemical Physics, vol. 10, no. 46, pp. 6971-6978.

2007

Ratnala, V.R.P., Kiihne, S.R., Buda, F., Leurs, R., de Groot, H.J.M., DeGrip, W.J. , 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, vol. 129, no. 4, pp. 867-872.

Alia,, Wawrzyniak, P., Buda, F., Matysik, J., de Groot, H.J.M. , Electronic structure of axial histidines in photosynthetic reaction centres of Rhodobacter sphaeroides, International congress of photosynthesis, 22-27 July 2007, vol. 91, Glasgow, Photosynth. Res. , pp. 146.

2006

Karawajczyk, A., Gossens, C., Roethlisberger, U., Buda, F. , Mechanism of bleomycin suicide: a Car-Parrinello molecular dynamics investigation, J Phys Chem B, vol. 110, no. 42, pp. 21245-50.

Amat, P., Granucci, G., Buda, F., Persico, M., Tozzini, V. , The chromophore of asFP595: A theoretical study, Journal of Physical Chemistry B, vol. 110, no. 18, pp. 9348-9353.

Rodziewicz, P., Rutkowski, K.S., Melikova, S.M., Koll, A., Buda, F. , Car-Parrinello molecular dynamics study of the blue-shifted F3CH center dot center dot center dot FCD3 system in liquid N-2, Chemphyschem, vol. 7, no. 6, pp. 1221-1228.

Karawajczyk, A., Buda, F. , The anticancer drug bleomycin investigated by density functional theory, Molecular Simulation, vol. 32, no. 15, pp. 1233-1239.

Casellas, H., Massera, C., Buda, F., Gamez, P., Reedijk, J. , Crystallographic evidence of theoretically novel anion-pi interactions, New Journal of Chemistry, vol. 30, no. 11, pp. 1561-1566.

2005

Rodziewicz, P., Melikova, S.M., Rutkowski, K.S., Buda, F. , Car-Parrinello molecular dynamics study of a blue-shifted intermolecular weak-hydrogen-bond system, Chemphyschem, vol. 6, no. 9, pp. 1719-1724.

van Gammeren, A.J., Buda, F., Hulsbergen, F.B., Kiihne, S., Hollander, J.G., Egorova-Zachernyuk, T.A., Fraser, N.J., Cogdell, R.J., de Groot, H.J.M. , 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, vol. 127, no. 9, pp. 3213-3219.

Karawajczyk, A., Buda, F. , The metal bonding domain of the antitumor drug Fe(II)-bleomycin: a DFT investigation (vol 10, pg 33, 2005), Journal of Biological Inorganic Chemistry, vol. 10, no. 2, pp. 208-208.

Francesco Buda teaches or supervises the following courses:

• Molecular Quantum Mechanics and Molecular Modeling (MQM)
• Modern Quantum Chemistry (MQC)
• Theoretical Chemistry 1 (TC1)

Francesco currently supervises the following students:

• Adriano Monti
• Thomas Eisenmayer

Towards artificial photosynthetic devices

In the photosynthetic reaction centers of plants, light energy is converted into chemically useful energy and oxygen is produced. This photochemical reaction is initiated by a charge separation process in the reaction center complex. Our goal is to analyze the light-driven electron transfer occuring in bacterial reaction center and to study the response of the protein in which the reaction center is embedded, stabilizing the charge separation process in photosynthesis. We make use of several computational tools including DFT, CPMD, hybrid QM/MM approaches, and topological analysis of the electron density based on the 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 photosynthetic systems. This project is interrelated with the ongoing experimental activity on photosynthetic systems in our group.