CHENG GIUSEPPE CHEN

Dottore di ricerca

ciclo: XXXVI


co-supervisore: Marco D'Abramo

Titolo della tesi: Modeling the Spectroscopic Properties of Complex Systems of Biological Interest

The aim of this thesis was the development and application of novel theoretical and computational methods to model the photochemical properties of systems of biological interest in solution. This was achieved by using classical Molecular Dynamics (MD) and the Molecular Dynamics-Perturbed Matrix Method (MD-PMM), a mixed quantum/classical approach. New methodologies were implemented in the MD-PMM framework, including the calculation of the magnetic properties and the Circular Dichroism of molecules in solution, a simplified and cost-effective approach to model the vibrational overlaps, and a general approach to model the kinetics of slow processes where the proper sampling of the reactive events is not feasible. Moreover, an open-source program written in Python3 was developed to run MD-PMM simulations and to serve as the basis to implement existing and new methodologies to make them easily accessible. These approaches were applied to challenging and meaningful molecular systems to test their accuracy and gain important chemical insight. The spectroscopic behavior of Indole, the model for the sidechain of the amino acid Tryptophan (Trp), was reproduced in solution, including UV-Vis absorption and emission along an isobar. A model for the overall relaxation mechanism of excited Indole was also proposed. These results could serve as the starting point for understanding the complex fluorescence properties of Trp. The UV-Vis absorption properties of the anti-cancer drug Doxorubicin (DX) were calculated in different environments. The complex shape of its signal and its changes due to the polarity of the solvent were interpreted by identifying the contributions arising from two conformers of DX. The complexation of DX on polystyrene sulfonate chains was described using classical MD, providing a structural interpretation of the experimental data. Finally, the Circular Dichroism (CD) spectrum of L-Alanine in solution was reproduced by explicitly accounting for the most relevant degrees of freedom, providing the basis to expand the implemented methodology to larger systems such as peptides.

Produzione scientifica

11573/1706162 - 2024 - Modeling the temperature dependence of the fluorescence properties of Indole in aqueous solution
Chen, Cheng Giuseppe; Amadei, Andrea; D’Abramo, Marco - 01a Articolo in rivista
rivista: SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY (Elsevier Science Limited:Oxford Fulfillment Center, PO Box 800, Kidlington Oxford OX5 1DX United Kingdom:011 44 1865 843000, 011 44 1865 843699, EMAIL: asianfo@elsevier.com, tcb@elsevier.co.UK, INTERNET: http://www.elsevier.com, http://www.elsevier.com/locate/shpsa/, Fax: 011 44 1865 843010) pp. 1-9 - issn: 1386-1425 - wos: WOS:001208353100001 (0) - scopus: 2-s2.0-85186699403 (0)

11573/1688686 - 2023 - Unveiling the excited state dynamics of Indole in solution
Chen, C. G.; Giustini, M.; D'abramo, M.; Amadei, A. - 01a Articolo in rivista
rivista: JOURNAL OF CHEMICAL THEORY AND COMPUTATION (Washington, D.C. : American Chemical Society, 2005-) pp. 4114-4124 - issn: 1549-9618 - wos: WOS:001011505600001 (2) - scopus: 2-s2.0-85164285445 (2)

11573/1684343 - 2023 - A study of cyanidin/alginate complexation: influence of pH in assembly and chiral properties
Chotechuang, Nattida; Di Gianvincenzo, Paolo; Chen, Cheng Giuseppe; Nardi, Alessandro Nicola; Padró, Daniel; Boonla, Chanchai; Ortore, Maria Grazia; D' Abramo, Marco; Moya, Sergio E - 01a Articolo in rivista
rivista: CARBOHYDRATE POLYMERS (Elsevier Science Limited:Oxford Fulfillment Center, PO Box 800, Kidlington Oxford OX5 1DX United Kingdom:011 44 1865 843000, 011 44 1865 843699, EMAIL: asianfo@elsevier.com, tcb@elsevier.co.UK, INTERNET: http://www.elsevier.com, http://www.elsevier.com/locate/shpsa/, Fax: 011 44 1865 843010) pp. 1-9 - issn: 0144-8617 - wos: WOS:001001292200001 (2) - scopus: 2-s2.0-85158845434 (2)

11573/1678126 - 2023 - P1 push-pull dye as a case study in QM/MM theoretical characterization for dye-sensitized solar cell organic chromophores**
D'annibale, V.; Chen, C. G.; Bonomo, M.; Dini, D.; D'abramo, M. - 01a Articolo in rivista
rivista: CHEMISTRYSELECT (John Wiley & Sons, Inc) pp. - - issn: 2365-6549 - wos: WOS:000962465000001 (2) - scopus: 2-s2.0-85152012814 (3)

11573/1634223 - 2022 - Computational Modeling of the Thermodynamics of the Mesophilic and Thermophilic Mutants of Trp-Cage Miniprotein
Bo, L.; Milanetti, E.; Chen, C. G.; Ruocco, G.; Amadei, A.; D'abramo, M. - 01a Articolo in rivista
rivista: ACS OMEGA (Washington, D.C. : American Chemical Society, 2016-) pp. 13448-13454 - issn: 2470-1343 - wos: WOS:000812716500001 (4) - scopus: 2-s2.0-85129107149 (4)

11573/1610372 - 2022 - Theoretical-computational modelling of the L-alanine CD spectrum in water
Chen, C. G.; Giustini, M.; Scipioni, A.; Amadei, A.; D'abramo, M. - 01a Articolo in rivista
rivista: COMPUTATIONAL AND THEORETICAL CHEMISTRY (Amsterdam [u.a.] : Elsevier) pp. 1-7 - issn: 2210-271X - wos: WOS:000791286900005 (4) - scopus: 2-s2.0-85123010718 (4)

11573/1617322 - 2022 - Theoretical modeling of redox potentials of biomolecules
Chen, C. G.; Nardi, A. N.; Amadei, A.; D'abramo, M. - 01g Articolo di rassegna (Review)
rivista: MOLECULES (Basel: MDPI Berlin: Springer, 1996-) pp. 1-27 - issn: 1420-3049 - wos: WOS:000755042400001 (8) - scopus: 2-s2.0-85124216255 (10)

11573/1643770 - 2022 - Absorption behavior of doxorubicin hydrochloride in visible region in different environments: a combined experimental and computational study
Chen, C. G.; Nardi, A. N.; Giustini, M.; D'abramo, M. - 01a Articolo in rivista
rivista: PHYSICAL CHEMISTRY CHEMICAL PHYSICS (Thomas Graham House, Science Park, Cambridge: Royal Society of Chemistry) pp. 12027-12035 - issn: 1463-9076 - wos: WOS:000792835800001 (9) - scopus: 2-s2.0-85131252024 (9)

11573/1676449 - 2022 - A simplified treatment for efficiently modeling the spectral signal of vibronic transitions: application to aqueous Indole
Chen, Cheng Giuseppe; Massimiliano, Aschi; D’Abramo, Marco; Andrea, Amadei - 01a Articolo in rivista
rivista: MOLECULES (Basel: MDPI Berlin: Springer, 1996-) pp. 1-19 - issn: 1420-3049 - wos: WOS:000897336300001 (4) - scopus: 2-s2.0-85143659533 (4)

11573/1664893 - 2022 - PyMM: an open-source python program for QM/MM simulations based on the perturbed matrix method
Chen, Cheng Giuseppe; Nardi, Alessandro Nicola; Amadei, Andrea; D’Abramo, Marco - 01a Articolo in rivista
rivista: JOURNAL OF CHEMICAL THEORY AND COMPUTATION (Washington, D.C. : American Chemical Society, 2005-) pp. 33-41 - issn: 1549-9626 - wos: WOS:000886598100001 (9) - scopus: 2-s2.0-85142202691 (9)

11573/1657343 - 2022 - Complexation and organization of doxorubicin on polystyrene sulfonate chains: impacts on doxorubicin dimerization and quenching
Gjerde, Natalie Solfrid; Nardi, Alessandro Nicola; Chen, Cheng Giuseppe; Di Gianvincenzo, Paolo; D'abramo, Marco; Scipioni, Anita; Galantini, Luciano; Moya, Sergio E; Giustini, Mauro - 01a Articolo in rivista
rivista: PHYSICAL CHEMISTRY CHEMICAL PHYSICS ([London, England] : Royal Society of Chemistry, 1999-) pp. 25990-25998 - issn: 1463-9084 - wos: WOS:000870311900001 (4) - scopus: 2-s2.0-85141742847 (4)

11573/1607625 - 2022 - Point mutations at a key site alter the cytochrome P450 oleP structural dynamics
Montemiglio, L. C.; Gugole, E.; Freda, I.; Exertier, C.; D'auria, L.; Chen, C. G.; Nardi, A. N.; Cerutti, G.; Parisi, G.; D'abramo, M.; Savino, C.; Vallone, B. - 01a Articolo in rivista
rivista: BIOMOLECULES (Basel: MDPI) pp. 55- - issn: 2218-273X - wos: WOS:000747839400001 (7) - scopus: 2-s2.0-85122022030 (8)

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