List of Publications

list of the publications with results that have been computed with COBRAMM

  1. Segarra-Martí, J.; Segatta, F.; Mackenzie, T. A.; Nenov, A.; Rivalta, I.; Bearpark, M.; Garavelli, M.
    Modeling Multidimensional Spectral Lineshapes from First Principles: Application to Water-Solvated Adenine.
    Faraday Discuss. 2019. https://doi.org/10.1039/C9FD00072K.
  2. Bracker, M.; Dinkelbach, F.; Weingart, O.; Kleinschmidt, M.
    Impact of Fluorination on the Photophysics of the Flavin Chromophore: A Quantum Chemical Perspective.
    Phys. Chem. Chem. Phys. 2019, 21 (19), 9912–9923. https://doi.org/10.1039/C9CP00805E.
  3. Nenov, A.; Conti, I.; Borrego-Varillas, R.; Cerullo, G.; Garavelli, M.
    Linear Absorption Spectra of Solvated Thiouracils Resolved at the Hybrid RASPT2/MM Level.
    Chem. Phys. 2018, 515, 643–653. https://doi.org/10.1016/j.chemphys.2018.07.025.
  4. Borrego-Varillas, R.; Teles-Ferreira, D. C.; Nenov, A.; Conti, I.; Ganzer, L.; Manzoni, C.; Garavelli, M.; Maria de Paula, A.; Cerullo, G.
    Observation of the Sub-100 Femtosecond Population of a Dark State in a Thiobase Mediating Intersystem Crossing.
    J. Am. Chem. Soc. 2018, 140 (47), 16087–16093. https://doi.org/10.1021/jacs.8b07057.
  5. Zvereva, E.; Segarra-Martí, J.; Marazzi, M.; Brazard, J.; Nenov, A.; Weingart, O.; Léonard, J.; Garavelli, M.; Rivalta, I.; Dumont, E.; et al.
    The Effect of Solvent Relaxation in the Ultrafast Time-Resolved Spectroscopy of Solvated Benzophenone.
    Photochem. Photobiol. Sci. 2018, 17 (3), 323–331. https://doi.org/10.1039/C7PP00439G.
  6. Pepino, A. J.; Segarra-Martí, J.; Nenov, A.; Rivalta, I.; Improta, R.; Garavelli, M.
    UV-Induced Long-Lived Decays in Solvated Pyrimidine Nucleosides Resolved at the MS-CASPT2/MM Level.
    Phys. Chem. Chem. Phys. 2018, 20 (10), 6877–6890. https://doi.org/10.1039/C7CP08235E.
  7. Martínez-Fernández, L.; Pepino, A. J.; Segarra-Martí, J.; Jovaišaitė, J.; Vaya, I.; Nenov, A.; Markovitsi, D.; Gustavsson, T.; Banyasz, A.; Garavelli, M.; et al.
    Photophysics of Deoxycytidine and 5-Methyldeoxycytidine in Solution: A Comprehensive Picture by Quantum Mechanical Calculations and Femtosecond Fluorescence Spectroscopy.
    J. Am. Chem. Soc. 2017, 139 (23), 7780–7791. https://doi.org/10.1021/jacs.7b01145.
  8. Segatta, F.; Cupellini, L.; Jurinovich, S.; Mukamel, S.; Dapor, M.; Taioli, S.; Garavelli, M.; Mennucci, B.
    A Quantum Chemical Interpretation of Two-Dimensional Electronic Spectroscopy of Light-Harvesting Complexes.
    J. Am. Chem. Soc. 2017, 139 (22), 7558–7567. https://doi.org/10.1021/jacs.7b02130.
  9. Demoulin, B.; Altavilla, S. F.; Rivalta, I.; Garavelli, M.
    Fine Tuning of Retinal Photoinduced Decay in Solution.
    J. Phys. Chem. Lett. 2017, 8 (18), 4407–4412. https://doi.org/10.1021/acs.jpclett.7b01780.
  10. Pepino, A. J.; Segarra-Martí, J.; Nenov, A.; Improta, R.; Garavelli, M.
    Resolving Ultrafast Photoinduced Deactivations in Water-Solvated Pyrimidine Nucleosides.
    J. Phys. Chem. Lett. 2017, 8 (8), 1777–1783. https://doi.org/10.1021/acs.jpclett.7b00316.
  11. Li, Q.; Giussani, A.; Segarra-Martí, J.; Nenov, A.; Rivalta, I.; Voityuk, A. A.; Mukamel, S.; Roca-Sanjuán, D.; Garavelli, M.; Blancafort, L.
    Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate.
    Chem. - A Eur. J. 2016, 22 (22), 7497–7507. https://doi.org/10.1002/chem.201505086.
  12. Martínez-Fernández, L.; Pepino, A. J.; Segarra-Martí, J.; Banyasz, A.; Garavelli, M.; Improta, R.
    Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.
    J. Chem. Theory Comput. 2016, 12 (9), 4430–4439. https://doi.org/10.1021/acs.jctc.6b00518.
  13. Aquilante, F.; Autschbach, J.; Carlson, R. K.; Chibotaru, L. F.; Delcey, M. G.; De Vico, L.; Fdez. Galván, I.; Ferré, N.; Frutos, L. M.; Gagliardi, L.; et al.
    Molcas 8: New Capabilities for Multiconfigurational Quantum Chemical Calculations across the Periodic Table.
    J. Comput. Chem. 2016, 37 (5), 506–541. https://doi.org/10.1002/jcc.24221.
  14. Bonvicini, A.; Demoulin, B.; Altavilla, S. F.; Nenov, A.; El-Tahawy, M. M. T.; Segarra-Martí, J.; Giussani, A.; Batista, V. S.; Garavelli, M.; Rivalta, I.
    Ultraviolet Vision: Photophysical Properties of the Unprotonated Retinyl Schiff Base in the Siberian Hamster Cone Pigment.
    Theor. Chem. Acc. 2016, 135 (4), 110. https://doi.org/10.1007/s00214-016-1869-x.
  15. Giussani, A.; Segarra-Martí, J.; Nenov, A.; Rivalta, I.; Tolomelli, A.; Mukamel, S.; Garavelli, M.
    Spectroscopic Fingerprints of DNA/RNA Pyrimidine Nucleobases in Third-Order Nonlinear Electronic Spectra.
    Theor. Chem. Acc. 2016, 135 (5), 121. https://doi.org/10.1007/s00214-016-1867-z.
  16. Nenov, A.; Segarra-Martí, J.; Giussani, A.; Conti, I.; Rivalta, I.; Dumont, E.; Jaiswal, V. K.; Altavilla, S. F.; Mukamel, S.; Garavelli, M.
    Probing Deactivation Pathways of DNA Nucleobases by Two-Dimensional Electronic Spectroscopy: First Principles Simulations.
    Faraday Discuss. 2015, 177, 345–362. https://doi.org/10.1039/C4FD00175C.
  17. Altavilla, S. F.; Segarra-Martí, J.; Nenov, A.; Conti, I.; Rivalta, I.; Garavelli, M.
    Deciphering the Photochemical Mechanisms Describing the UV-Induced Processes Occurring in Solvated Guanine Monophosphate.
    Front. Chem. 2015, 3 (APR). https://doi.org/10.3389/fchem.2015.00029.
  18. Polli, D.; Rivalta, I.; Nenov, A.; Weingart, O.; Garavelli, M.; Cerullo, G.
    Tracking the Primary Photoconversion Events in Rhodopsins by Ultrafast Optical Spectroscopy.
    Photochem. Photobiol. Sci. 2015, 14 (2), 213–228. https://doi.org/10.1039/C4PP00370E.
  19. Conti, I.; Nenov, A.; Höfinger, S.; Flavio Altavilla, S.; Rivalta, I.; Dumont, E.; Orlandi, G.; Garavelli, M.
    Excited State Evolution of DNA Stacked Adenines Resolved at the CASPT2//CASSCF/Amber Level: From the Bright to the Excimer State and Back.
    Phys. Chem. Chem. Phys. 2015, 17 (11), 7291–7302. https://doi.org/10.1039/C4CP05546B.
  20. Dokukina, I.; Weingart, O.
    Spectral Properties and Isomerisation Path of Retinal in C1C2 Channelrhodopsin.
    Phys. Chem. Chem. Phys. 2015, 17 (38), 25142–25150. https://doi.org/10.1039/C5CP02650D.
  21. Nenov, A.; Giussani, A.; Fingerhut, B. P.; Rivalta, I.; Dumont, E.; Mukamel, S.; Garavelli, M.
    Spectral Lineshapes in Nonlinear Electronic Spectroscopy.
    Phys. Chem. Chem. Phys. 2015, 17 (46), 30925–30936. https://doi.org/10.1039/C5CP01167A.
  22. Taioli, S.; Simonucci, S.; a Beccara, S.; Garavelli, M.
    Tetrapeptide Unfolding Dynamics Followed by Core-Level Spectroscopy: A First-Principles Approach.
    Phys. Chem. Chem. Phys. 2015, 17 (17), 11269–11276. https://doi.org/10.1039/C4CP05902F.
  23. Dumont, E.; Wibowo, M.; Roca-Sanjuán, D.; Garavelli, M.; Assfeld, X.; Monari, A.
    Resolving the Benzophenone DNA-Photosensitization Mechanism at QM/MM Level.
    J. Phys. Chem. Lett. 2015, 6 (4), 576–580. https://doi.org/10.1021/jz502562d.
  24. Polli, D.; Weingart, O.; Brida, D.; Poli, E.; Maiuri, M.; Spillane, K. M.; Bottoni, A.; Kukura, P.; Mathies, R. A.; Cerullo, G.; et al.
    Wavepacket Splitting and Two-Pathway Deactivation in the Photoexcited Visual Pigment Isorhodopsin.
    Angew. Chemie Int. Ed. 2014, 53 (9), 2504–2507. https://doi.org/10.1002/anie.201309867.
  25. Nenov, A.; a Beccara, S.; Rivalta, I.; Cerullo, G.; Mukamel, S.; Garavelli, M.
    Tracking Conformational Dynamics of Polypeptides by Nonlinear Electronic Spectroscopy of Aromatic Residues: A First-Principles Simulation Study.
    ChemPhysChem 2014, 15 (15), 3282–3290. https://doi.org/10.1002/cphc.201402374.
  26. Nenov, A.; Rivalta, I.; Mukamel, S.; Garavelli, M.
    Bidimensional Electronic Spectroscopy on Indole in Gas Phase and in Water from First Principles.
    Comput. Theor. Chem. 2014, 1040–1041, 295–303. https://doi.org/10.1016/j.comptc.2014.03.031.
  27. Rivalta, I.; Nenov, A.; Garavelli, M.
    Modelling Retinal Chromophores Photoisomerization: From Minimal Models in Vacuo to Ultimate Bidimensional Spectroscopy in Rhodopsins.
    Phys. Chem. Chem. Phys. 2014, 16 (32), 16865–16879. https://doi.org/10.1039/C3CP55211J.
  28. Rivalta, I.; Nenov, A.; Weingart, O.; Cerullo, G.; Garavelli, M.; Mukamel, S.
    Modelling Time-Resolved Two-Dimensional Electronic Spectroscopy of the Primary Photoisomerization Event in Rhodopsin.
    J. Phys. Chem. B 2014, 118 (28), 8396–8405. https://doi.org/10.1021/jp502538m.
  29. Nenov, A.; Rivalta, I.; Cerullo, G.; Mukamel, S.; Garavelli, M.
    Disentangling Peptide Configurations via Two-Dimensional Electronic Spectroscopy: Ab Initio Simulations Beyond the Frenkel Exciton Hamiltonian.
    J. Phys. Chem. Lett. 2014, 5 (4), 767–771. https://doi.org/10.1021/jz5002314.
  30. Calvaresi, M.; Stenta, M.; Garavelli, M.; Altoé, P.; Bottoni, A.
    Computational Evidence for the Catalytic Mechanism of Human Glutathione S-Transferase A3-3: A QM/MM Investigation.
    ACS Catal. 2012, 2 (2), 280–286. https://doi.org/10.1021/cs200369b.
  31. Klaffki, N.; Weingart, O.; Garavelli, M.; Spohr, E.
    Sampling Excited State Dynamics: Influence of HOOP Mode Excitations in a Retinal Model.
    Phys. Chem. Chem. Phys. 2012, 14 (41), 14299. https://doi.org/10.1039/c2cp41994g.
  32. Weingart, O.; Garavelli, M.
    Modelling Vibrational Coherence in the Primary Rhodopsin Photoproduct.
    J. Chem. Phys. 2012, 137 (22), 22A523. https://doi.org/10.1063/1.4742814.
  33. Weingart, O.; Altoè, P.; Stenta, M.; Bottoni, A.; Orlandi, G.; Garavelli, M.
    Product Formation in Rhodopsin by Fast Hydrogen Motions.
    Phys. Chem. Chem. Phys. 2011, 13 (9), 3645. https://doi.org/10.1039/c0cp02496a.
  34. Capdevila, M. G.; Benfatti, F.; Zoli, L.; Stenta, M.; Cozzi, P. G.
    Merging Organocatalysis with an Indium(III)-Mediated Process: A Stereoselective α-Alkylation of Aldehydes with Allylic Alcohols.
    Chem. - A Eur. J. 2010, 16 (37), 11237–11241. https://doi.org/10.1002/chem.201001693.
  35. Lupieri, P.; Ippoliti, E.; Altoè, P.; Garavelli, M.; Mwalaba, M.; Carloni, P.
    Spectroscopic Properties of Formaldehyde in Aqueous Solution: Insights from Car−Parrinello and TDDFT/CASPT2 Calculations.
    J. Chem. Theory Comput. 2010, 6 (11), 3403–3409. https://doi.org/10.1021/ct100384f.
  36. Polli, D.; Altoè, P.; Weingart, O.; Spillane, K. M.; Manzoni, C.; Brida, D.; Tomasello, G.; Orlandi, G.; Kukura, P.; Mathies, R. A.; et al.
    Conical Intersection Dynamics of the Primary Photoisomerization Event in Vision.
    Nature 2010, 467 (7314), 440–443. https://doi.org/10.1038/nature09346.
  37. Conti, I.; Altoè, P.; Stenta, M.; Garavelli, M.; Orlandi, G.
    Adenine Deactivation in DNA Resolved at the CASPT2//CASSCF/AMBER Level.
    Phys. Chem. Chem. Phys. 2010, 12 (19), 5016. https://doi.org/10.1039/b926608a.
  38. Tomasello, G.; Olaso-González, G.; Altoè, P.; Stenta, M.; Serrano-Andrés, L.; Merchán, M.; Orlandi, G.; Bottoni, A.; Garavelli, M.
    Electrostatic Control of the Photoisomerization Efficiency and Optical Properties in Visual Pigments: On the Role of Counterion Quenching.
    J. Am. Chem. Soc. 2009, 131 (14), 5172–5186. https://doi.org/10.1021/ja808424b.
  39. Altoè, P.; Climent, T.; De Fusco, G. C.; Stenta, M.; Bottoni, A.; Serrano-Andrés, L.; Merchán, M.; Orlandi, G.; Garavelli, M.
    Deciphering Intrinsic Deactivation/Isomerization Routes in a Phytochrome Chromophore Model.
    J. Phys. Chem. B 2009, 113 (45), 15067–15073. https://doi.org/10.1021/jp904669x.
  40. Benfatti, F.; Bottoni, A.; Cardillo, G.; Gentilucci, L.; Monari, M.; Mosconi, E.; Stenta, M.; Tolomelli, A.
    Synthesis of Ethyl 5-Hydroxyisoxazolidine-4-Carboxylates via Michael Addition/Intramolecular Hemiketalisation.
    European J. Org. Chem. 2008, 2008 (36), 6119–6127. https://doi.org/10.1002/ejoc.200800719.
  41. Stenta, M.; Calvaresi, M.; Altoè, P.; Spinelli, D.; Garavelli, M.; Bottoni, A.
    The Catalytic Activity of Proline Racemase: A Quantum Mechanical/Molecular Mechanical Study.
    J. Phys. Chem. B 2008, 112 (4), 1057–1059. https://doi.org/10.1021/jp7104105.
  42. Altoè, P.; Stenta, M.; Bottoni, A.; Garavelli, M.
    A Tunable QM/MM Approach to Chemical Reactivity, Structure and Physico-Chemical Properties Prediction.
    Theor. Chem. Acc. 2007, 118 (1), 219–240. https://doi.org/10.1007/s00214-007-0275-9.

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Marco Garavelli

Group leader of the Computational Photophysics and Photochemistry group

University of Bologna

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