Publications

The following list of publications represents scientific output that has benefitted from the support of the COSINE innovative training network (ITN):

  1. Zilvinas Rinkevicius, Xin Li, Olav Vahtras, Karan Ahmadzadeh, Manuel Brand, Magnus Ringholm, Nanna Holmgaard List, Maximilian Scheurer, Mikael Scott, Andreas Dreuw, and Patrick Norman. VeloxChem: a Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments, WIREs Computational Molecular Science, 2019, https://doi.org/10.1002/wcms.1457

  2. C. Steinmann, P. Reinholdt, M.S. Nørby, J. Kongsted and J.M.H. Olsen, Response properties of embedded molecules through the polarizable embedding model, IJQC, 2019, 119, e25717

  3. L. D. M. Peters, J. Kussmann, and C. Ochsenfeld, Non-adiabatic molecular dynamics on graphics processing units: performance and application to rotary molecular motors, JCTC, 2019, 15, 6647

  4. P. Norman and A. Dreuw, Simulating X-ray Spectroscopies and Calculating Core-Excited States of Molecules, Chem. Rev., 2018, 118, 7208

  5. P. Reinholdt, M.S. Nørby and J. Kongsted, Modeling of magnetic circular dichroism and UV/Vis absorption spectra using fluctuating charges or polarizable embedding within a resonant-convergent response theory formalism, JCTC, 2018, 14, 6391

  6. M. Scheurer, M.F. Herbst, P. Reinholdt, J.M.H. Olsen, A. Dreuw and J. Kongsted, Polarizable embedding combined with the algebraic diagrammatic construction: Tackling excited states in biomolecular systems, JCTC, 2018, 14, 4870

  7. M. S. Nørby, S. Coriani and J. Kongsted, Modeling magnetic circular dichroism within the polarizable embedding approach, TCA, 2018, 137, 49

  8. B. N. C. Tenorio, T. Moitra, M. A. C. Nascimento, A. Braga Rocha, and S. Coriani, Molecular inner-shell photoabsorption/photoionization cross sections at corevalence-separated coupled cluster level: Theory and examples, JCP, 2019, 150, 224104

  9. R. H. Myhre, S. Coriani, and H. Koch, X‑ray and UV Spectra of Glycine within Coupled Cluster Linear Response Theory, JPCA 2019, 123, 9701−9711

  10. M. L. Vidal, A. I. Krylov and S. Coriani, Dyson orbitals within the fc-CVS-EOM-CCSD framework: theory and application to X-ray photoelectron spectroscopy of ground and excited states, PCCP, 2020, 22, 2693

  11. S. Prioli, P. Reinholdt, M. Hornum, J, Kongsted, Rational Design of Nile Red Analogs for Sensing in Membranes, JPCB, 2019, 123, 10424-10432

  12. S. Tsuru, M. L. Vidal, M. Papai, A. I. Krylov, K. B. Møller, and S. Coriani, Time-resolved near-edge X-ray absorption fine structure of pyrazine from electronic structure and nuclear wave packet dynamics simulations, JCP 2019, 151, 124114

  13. R. Faber, E. F. Kjønstad, H. Koch, and S. Coriani, Spin adapted implementation of EOM CCSD for triplet excited states: Probing intersystem crossings of acetylacetone at the carbon and oxygen K-edges, JCP 2019, 151, 144107.

  14. A. Battisti, M. Ambrosetti, G. Ruggeri, C. Cappelli, A . Pucci, “4,4’-bis(2-benzoxazolyl)stilbene luminescent probe: assessment of aggregates formation through photo physics experiments and quantum-chemical calculations”, Phys. Chem. Chem. Phys., 2018, DOI: 10.1039/C8CP04450C

  15. F. Egidi, T. Giovannini, G. Del Frate, P. M. Lemler,P. H. Vaccaro, C. Cappelli “A Combined Experimental and Theoretical Study of Optical Rotatory Dispersion for (R)-Glycidyl Methyl Ether in Aqueous Solution”, Phys. Chem. Chem. Phys., 2018, DOI:10.1039/C8CP04445G

  16. T. Giovannini, M. Rosa, S. Corni, C. Cappelli “A Classical Picture of Subnanometer Junctions: an Atomistic Drude Approach to Nanoplasmonics”, Nanoscale, 2019, 11, 6004-6015,DOI: 10.1039/C8NR09134J

  17. T. Giovannini, P. Lafiosca, B. Chandramouli, V. Barone, C. Cappelli, “Effective yet Reliable Computation of EPR Spectra in Solution by a QM/MM Approach: Interplay between Electrostatics and Non-electrostatic Effects”, J. Chem. Phys, 2019, 150, 124102, DOI: 10.1063/1.5080810

  18. T. Giovannini, M. Ambrosetti, A. Puglisi, C. Cappelli, “Polarizable QM/MM Approach with Fluctuating Charges and Fluctuating Dipoles: the QM/FQFμ Model”, J. Chem. Theory Comput., 2019, 13, 4854-4870, DOI: 10.1021/acs.jctc.8b01149

  19. R. Di Remigio, T. Giovannini, M. Ambrosetti, C. Cappelli, L. Frediani “Fully Polarizable QM/Fluctuating Charge Approach to Two-Photon Absorption of Aqueous Solutions”, J. Chem. Theory Comput., 2019, DOI: 10.1021/acs.jctc.9b00305.

  20. A. Puglisi, T. Giovannini, L. Antonov, C. Cappelli “Interplay between Conformational and Solvent Effects in UV-Visible Absorption Spectra: Curcumin Tautomers as Case Study”, Phys. Chem. Chem. Phys, 2019, DOI: 10.1039/C9CP00907H.

  21. T. Giovannini, R. R. Riso, A. Puglisi C. Cappelli “Electronic Transitions for a Fully Polarizable QM/MM Approach Based on Fluctuating Charges and Fluctuating Dipoles: Linear and Corrected Linear Response Regimes” J. Chem. Phys. 2019, 151, 174104.DOI: 10.1063/1.5121396.

  22. I. Tosi, B. Bardi, M. Ambrosetti, E. Domenichini, A. Iagatti, L. Baldini, C. Cappelli, M. Di Donato, F. Sansone, C. Sissa, F. Terenziani “Investigation of electronic energy transfer in BODIPY-decorated calixarenes”, Dyes and Pigments, 2019, DOI:10.1016/j.dyepig.2019.107652.

  23. N. Rojas-Valencia, S. Gomez, S. Montillo, M. Manrique-Moreno, C. Cappelli, C. Zilahy Hadad, A. Restrepo Evolution of Bonding During the Insertion of Anionic Ibuprofen Into Model Cell Membranes J. Phys. Chem. B 2019, DOI:10.1021/acs.jpcb.9b09705 .

  24. S. Gomez, T. Giovannini, C. Cappelli, Absorption spectra of xanthines in aqueous solution: a computational study, Phys. Chem. Chem. Phys. 2020, 22, 5929-5941.

  25. S. A. Gomez, N. Rojas-Valencia, S. Gomez , F. Egidi , C Cappelli, A. Restrepo, Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution, ChemBioChem 2020, DOI: 10.1002/cbic.202000618 .

  26. L. D. M. Peters, J. Kussmann, C. Ochsenfeld, A Fermi Smearing Variant of the Tamm-Dancoff Approximation for Nonadiabatic Dynamics Involving S1-S0 Transitions: Validation and Application to Azobenzene, J. Chem. Phys. 2020 , 153 094104.

  27. List, N. H., Dempwolff, A. L., Dreuw, A., Norman, P., Martínez, T. J. (2020). Probing competing relaxation pathways in malonaldehyde with transient X-ray absorption spectroscopy. Chemical Science, 11(16), 4180–4193. https://doi.org/10.1039/D0SC00840K

  28. Scheurer, M., Fransson, T., Norman, P., Dreuw, A., Rehn, D. R. (2020). Complex excited state polarizabilities in the ADC/ISR framework. The Journal of Chemical Physics, 153(7), 074112. https://doi.org/10.1063/5.0012120

  29. L. D. M. Peters, J. Kussmann, and C. Ochsenfeld, Combining Graphics Processing Units, Simplified Time-Dependent Density Functional Theory, and Finite-Difference Couplings to Accelerate Nonadiabatic Molecular Dynamics, JPC Lett., 2020, 11, 3955-3961.

  30. D. B. Konrad, G. Savasci, L. Allmendinger, D. Trauner, C. Ochsenfeld, and A. M. Ali, Computational Design and Synthesis of a Deeply Red-Shifted and Bistable Azobenzene, JACS, 2020, 142, 6538−6547.

  31. Rehn, D. R. et al. (2021). Gator: A Python-driven program for spectroscopy simulations using correlated wave functions. WIREs Computational Molecular Science, 11(6), e1528. https://doi.org/10.1002/wcms.1528

  32. Scott, M., Rehn, D. R., Norman, P., Dreuw, A. (2021). Ab Initio Excited-State Electronic Circular Dichroism Spectra Exploiting the Third-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator. The Journal of Physical Chemistry Letters, 12(21), 5132–5137. https://doi.org/10.1021/acs.jpclett.1c00839

  33. Todarwal, Y. et al. (2021). Tau Protein Binding Modes in Alzheimer’s Disease for Cationic Luminescent Ligands. The Journal of Physical Chemistry B, 125(42), 11628–11636. https://doi.org/10.1021/acs.jpcb.1c06019

  34. Brand, M., Ahmadzadeh, K., Li, X., Rinkevicius, Z., Saidi, W. A., Norman, P. (2021). Size-dependent polarizabilities and van der Waals dispersion coefficients of fullerenes from large-scale complex polarization propagator calculations. The Journal of Chemical Physics, 154(7), 074304. https://doi.org/10.1063/5.0040009

  35. Ahmadzadeh, K., Scott, M., Brand, M., Vahtras, O., Li, X., Rinkevicius, Z., Norman, P. (2021). Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation. The Journal of Chemical Physics, 154(2), 024111. https://doi.org/10.1063/5.0031851

  36. Scott, M., Rehn, D. R., Coriani, S., Norman, P., & Dreuw, A. (2021). Electronic circular dichroism spectra using the algebraic diagrammatic construction schemes of the polarization propagator up to third order. The Journal of Chemical Physics, 154(6), 064107. https://doi.org/10.1063/5.0038315

  37. C.S. Kofod, S.Prioli S, M. Hornum, J. Kongsted, P. Reinholdt, ”Computational Characterization of Novel Malononitrile Variants of Laurdan with Improved Photophysical Properties for Sensing in Membranes” Journal of Physical Chemistry B, 2020, 124, 9526, DOI: 10.1039/D1CP00831E

  38. S. Prioli, J. Kongsted, “Modelling environmental effects in two-photon circular dichroism calculations”, Theoretical Chemistry Accounts, 2021, 140, 138, DOI:10.1007/s00214-021-02838-6

  39. S. Prioli, J. Kongsted, “Computational analysis of altered one- and two-photon circular dichroism of sterol ligands inside protein binding pockets” Theoretical Chemistry Accounts, 2022, 141, 5, DOI:10.1007/s00214-022-02866-w

  40. Torsha Moitra, Sonia Coriani & Bruno Nunes Cabral Tenorio (2021) Inner-shell photoabsorption and photoionisation cross-sections of valence excited states from asymmetric-Lanczos equation-of-motion coupled cluster singles and doubles theory, Molecular Physics, 119:21-22, DOI: 10.1080/00268976.2021.1980235

  41. Torsha Moitra, Sonia Coriani, and Piero Decleva, Capturing Correlation Effects on Photoionization Dynamics, Journal of Chemical Theory and Computation 2021 17 (8), 5064-5079 DOI: 10.1021/acs.jctc.1c00303

  42. Torsha Moitra, Aurora Ponzi, Henrik Koch, Sonia Coriani, and Piero Decleva, Accurate Description of Photoionization Dynamical Parameters, The Journal of Physical Chemistry Letters 2020 11 (13), 5330-5337, DOI: 10.1021/acs.jpclett.0c01337

  43. Bruno Nunes Cabral Tenorio, Torsha Moitra, Marco Antonio Chaer Nascimento, Alexandre Braga Rocha, and Sonia Coriani, "Molecular inner-shell photoabsorption/photoionization cross sections at core-valence-separated coupled cluster level: Theory and examples",
    J. Chem. Phys. 150, 224104 (2019) https://doi.org/10.1063/1.5096777

  44. Torsha Moitra, Diana Madsen, Ove Christiansen, and Sonia Coriani "Vibrationally resolved coupled-cluster x-ray absorption spectra from vibrational configuration interaction anharmonic calculations", J. Chem. Phys. 153, 234111 (2020) https://doi.org/10.1063/5.0030202

  45. Li, T.; Ma, X.; Fedotov, D.; Kjaerulff, L.; Frydenvang, K.; Coriani, S.; Hansen, P.R.; Kongstad, K.T.; Staerk, D. Structure Elucidation of Prenyl- and Geranyl-Substituted Coumarins in Gerbera piloselloides by NMR Spectroscopy, Electronic Circular Dichroism Calculations, and Single Crystal X-ray Crystallography. Molecules 2020, 25, 1706. https://doi.org/10.3390/molecules25071706

  46. Sarai D. Folkestad, Eirik F. Kjønstad, Rolf H. Myhre, Josefine H. Andersen, Alice Balbi, Sonia Coriani, Tommaso Giovannini, Linda Goletto, Tor S. Haugland, Anders Hutcheson, Ida-Marie Høyvik, Torsha Moitra, Alexander C. Paul, Marco Scavino, Andreas S. Skeidsvoll, Åsmund H. Tveten, and Henrik Koch, "eT 1.0: An open source electronic structure program with emphasis on coupled cluster and multilevel methods",
    J. Chem. Phys. 152, 184103 (2020) https://doi.org/10.1063/5.0004713

  47. D.A. Fedotov, A. C. Paul, P. Posocco, F. Santoro, M. Garavelli, H. Koch, S. Coriani, and R. Improta,

Excited-State Absorption of Uracil in the Gas Phase: Mapping the Main Decay Paths by Different Electronic Structure Methods
Journal of Chemical Theory and Computation 2021 17 (3), 1638-1652 - DOI: 10.1021/acs.jctc.0c0115

  1. D. A. Fedotov, A.C. Paul, H. Koch, F. Santoro, S. Coriani and R. Improta, Phys. Chem. Chem. Phys., 2022, DOI: 10.1039/D1CP04340D

  2. L. Uribe, S. Gómez, T. Giovannini, F. Egidi, A. Restrepo, “An efficient and robust procedure to calculate absorption spectra of aqueous charged species applied to NO2-”, Phys. Chem. Chem. Phys., 2021,23, 14857-14872, DOI: 10.1039/d1cp00652e

  3. S. Gómez; N. Rojas-Valencia; S. A. Gómez; C. Cappelli; G. Merino; Albeiro Restrepo, “A molecular twist on hydrophobicity”, Chem. Sci., 2021,12, 9233-9245, DOI: 10.1039/d1sc02673a

  4. S. Gómez, F. Egidi; A. Puglisi; T. Giovannini; B. Rossi; C. Cappelli, “Unlocking the Power of Resonance Raman Spectroscopy: the Case of Amides in Aqueous Solution”, J. Mol. Liq., 346 (2022), 117841, DOI: 10.1016/j.molliq.2021.117841

  5. G. Marrazzini; T. Giovannini; M. Scavino; F. Egidi; C. Cappelli; H. Koch, “Multilevel Density Functional Theory”. J. Chem. Theory Comput. 2021, 17, 2, 791-803, DOI: 10.1021/acs.jctc.0c00940

  6. T. Giovannini; L. Grazioli; M. Ambrosetti; C. Cappelli, “Calculation of IR Spectra with a Fully Polarizable QM/MM Approach Based on Fluctuating Charges and Fluctuating Dipoles”, J. Chem. Theory Comput. 2019, 15, 10, 5495-5507, DOI: 10.1021/acs.jctc.9b00574

  7. N. Rojas-Valencia, S. Gómez, F. Núñez-Zarur, C. Cappelli, C. Hadad, A. Restrepo, “Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes”, J. Phys. Chem. B 2021, 125, 36, 1038-10391, DOI: 10.1021/acs.jpcb.1c06766

  8. S. A. Gómez, N. Rojas-Valencia, S. Gómez, C. Cappelli, A. Restrepo “The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective”, ChemBioChem, 2022, DOI: 10.1002/cbic.202100393

  9. S. Skoko, M. Ambrosetti, T. Giovannini, C. Cappelli, “Simulating Absorption Spectra of Flavonoids in Aqueous Solution: A Polarizable QM/MM Study”, Molecules, 2020, 25(24), 5853, DOI: 10.3390/molecules25245853

  10. S. Gómez, N. Rojas-Valencia, T. Giovannini, A. Restrepo, C. Cappelli, “Ring Vibrations to Sense Anionic Ibuprofen in Aqueous Solution as Revealed by Resonance Raman”, Molecules, 2022, 27(2), 442, DOI: 10.3390/molecules27020442