Publications
Preprints:

      OS100: A Benchmark Set of 100 Digitized UV-Visible Spectra and Derived Experimental Oscillator Strengths.
      Tarleton AS, Garcia-Alvarez JC, Wynn A, Awbrey CM, Roberts TP, Gozem S.
      Submitted. 2021. [Preprint]

Published work:

40. The Ionic Atmosphere Effect on the Absorption Spectrum of a Flavoprotein: A Reminder to Consider Solution Ions.
      Dratch BD, Orozco-Gonzalez Y, Gadda G, Gozem S.
      J. Phys. Chem. Lett. 12(34), 8384–8396. 2021. [html]

39. Tuning Protein Dynamics to Sense Rapid Endoplasmic Reticulum Calcium Dynamics.
      Deng X, Yao X, Berglund K, Dong B, Ouedraogo D, Ghane MA, Zhuo Y, McBean C, Wei ZZ, Gozem S, Yu SP,
      Wei L, Fang N, Mabb AM, Gadda G, Hamelberg D, Yang JJ.
      Angew. Chem. Int. Ed. 133(43), 23477–23486. 2021. [html]

38. Free Energy Computation for an Isomerizing Chromophore in a Cavity via the Average Solvent Electrostatic
Configuration Model: Application to Rhodopsin and Rhodopsin-mimicking Systems.
      Nikolaev D, Madushanka M, Orozco-Gonzalez Y, Shtyrov A, Guerrero-Martinez Y, Gozem S, Ryazantsev M,
      Coutinho K, Canuto S, Olivucci M.
      J. Chem. Theory Comput. 17(9), 5885–5895. 2021. [html]

37. The Effect of Hydrogen-Bonding on Flavin's Infrared Absorption Spectrum.
      Kabir MP, Orozco-Gonzalez Y, Hastings G, Gozem S.
      Spectrochim. Acta A. 911, 120110, 2021. [html]

36. The ezSpectra suite: An easy-to-use toolkit for spectroscopy modeling.
      Gozem S, Krylov AI.
      WIREs Comput. Mol. Sci. e1546. 2021. [html]

35. Cyclopropenone (c-C3H2O) as a Tracer of the Non-Equilibrium Chemistry Mediated by Galactic Cosmic Rays in
Interstellar Ices.
      Kleimeier NF, Abplanalp MJ, Johnson RN, Gozem S, Wandishin J, Shingledecker CN, Kaiser RI.
      Astrophys. J. 911(1) 24. 2021. [html]

34. A Single Point Mutation in D-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in
Altered Cofactor Reactivity.
      Iyer I, Reis RAG, Gannavaram S, Momin M, Spring-Connell AM, Orozco-Gonzalez Y, Agniswamy J, Hamelberg D,
      Weber IT, Gozem S, Wang S, Germann MW, Gadda G.
      Biochemistry. 60(9) 711–724. 2021. [html]

33. QM/MM Investigation of the Spectroscopic Properties of the Fluorophore of Bacterial Luciferase
      Giuliani G, Melaccio F, Gozem S, Cappeli A, Olivucci M.
      J. Chem. Theory Comput. 17(2) 605–613. 2021. [html]

32. Probing the Electronic Structure of Bulk Water at the Molecular Length Scale with Angle-Resolved Photoelectron
Spectroscopy
      Gozem S, Seidel R, Hergenhahn U, Lugovoy E, Abel B, Winter B, Krylov AI, Bradforth SE.
      J. Phys. Chem. Lett. 11(13) 5162–5170. 2020. [html]

31. Excited-State Vibronic Dynamics of Bacteriorhodopsin from Two-Dimensional Electronic Photon Echo
Spectroscopy and Multiconfigurational Quantum Chemistry
      Gozem S, Johnson PJM, Halpin A, Luk HL, Morizumi T, Prokhrenko VI, Ernst OP, Olivucci M, Miller RJD.
      J. Phys. Chem. Lett. 11(10) 3889–3896. 2020. [html]

30.  Spectra of Flavin in Different Redox and Protonation States: A Computational Perspective on the Effect of the
Electrostatic Environment
      Kabir MP, Orozco-Gonzalez Y, Gozem S.
      Phys. Chem. Chem. Phys. 21, 16526–16537. 2019. [html]

29. Electrostatic Spectral Tuning Maps for Biological Chromophores
      Orozco-Gonzalez Y, Kabir MP, Gozem S.
      J. Phys. Chem. B. 123, 4813–4824. 2019. [html]

28. Fluorescence Properties of Flavin Semiquinone Radicals in Nitronate Monooxygenase
      Su D, Kabir MP, Orozco-Gonzalez Y, Gozem S, Gadda G.
      ChemBioChem. 20, 1646–1652. 2019. [html]

27. Vacuum ultraviolet photoionization cross section of the hydroxyl radical
      Dodson LG, Savee JD, Gozem S, Shen L, Krylov AI, Taatjes CA, Osborn DL, Okumura M.
      J. Chem. Phys. 148, 184302. 2018. [html]

26. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores
      Gozem S, Luk HL, Schapiro I, Olivucci M.
      Chem. Rev.  117, 13502–13565. 2017. [html]

25. Supramolecular Sensors for Opiates and Their Metabolites
      Shcherbakova E, Zhang B, Gozem S, Minami T, Zavalij P, Pushina M, Isaacs L, Anzenbacher P.
      J. Am. Chem. Soc. 139, 14954–14960. 2017. [html]

24. Photoelectron Spectroscopy Study of Quinonimides
      Hossain E, Deng SM, Gozem S, Krylov AI, Wang XB, Wenthold PG
      J. Am. Chem. Soc. 139, 11138–11148. 2017. [html]

23. Electronic Spectra of Tris(2,2'-bipyridine)-M(II) Complex Ions in Vacuo (M = Fe and Os)
       Xu S, Smith J, Gozem S, Krylov AI, Weber JM
       Inorg. Chem. 56, 7029–7037. 2017. [html]

22. Fluorescence-Based Assay for Carbonic Anhydrase Inhibitors
      Koutnik P, Shcherbakova EG, Cagayan MG, Gozem S, Minami T, Anzenbacher P
      Chem. 2, 271–282. 2017. [html]

21. A Study of Interstellar Aldehydes and Enols as Tracers of a Cosmic Ray-Driven Nonequilibrium Synthesis
      of Complex Organic Molecules
      Abplanalp MJ, Gozem S, Krylov AI, Shingledecker CN, Herbst E, Kaiser RI
      Proc. Natl. Acad. Sci. U.S.A. 113, 7727–7732. 2016. [html]

20. Probing the Photodynamics of Rhodopsins with Reduced Retinal Chromophores
      Manathunga M,  Yang X, Luk HL, Gozem S, Frutos LM, Valentini A, Ferré N, Olivucci M
      J. Chem. Theory Comput. 12, 839–850. 2016. [html]

19. Ligand Influence on the Electronic Spectra of Monocationic Copper–Bipyridine Complexes
      Xu S, Gozem S, Krylov AI, Christopher CR, Weber JM
      Phys. Chem. Chem. Phys. 17, 31938–31946. 2015. [html]

18. Photoelectron Wave Function in Photoionization: Plane wave or Coulomb wave?
      Gozem S, Gunina AO, Ichino T, Osborn DL, Stanton JF, Krylov AI
      J. Phys. Chem. Lett. 6, 4532–4540. 2015. [html]

17. Molecular Bases for the Selection of the Chromophore of Animal Rhodopsins
      Luk HL, Melaccio F, Rinaldi S, Gozem S, Olivucci M
      Proc. Natl. Acad. Sci. U.S.A. 112, 15297–15302. 2015. [html]

16. Assessment of Approximate Coupled-Cluster and Algebraic-Diagrammatic-Construction Methods for
      Ground- and Excited-State Reaction Paths and the Conical-Intersection Seam of a Retinal-Chromophore
      Model
      Tuna D, Lefrancois D, Wolański Ł, Gozem S, Schapiro I, Andruniów T, Dreuw A, Olivucci M
      J. Chem. Theory Comput. 11, 5758–5781. 2015. [html]

15. Quantum Monte Carlo Treatment of the Charge Transfer and Diradical Electronic Character in a Retinal
      Chromophore Minimal Model
      Zen A, Coccia E, Gozem S, Olivucci M, Guidoni L
      J. Chem. Theory Comput. 11, 992–1005. 2015. [html]

14. A Conical Intersection Controls the Deactivation of the Bacterial Luciferase Fluorophore
      Gozem S, Mirzakulova E, Schapiro I, Melaccio F, Glusac KD, Olivucci M
      Angew. Chem. Int. Ed. 53, 9870–9875. 2014. [html]

13. Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential
      Energy Surfaces at a Conical Intersection
      Gozem S, Melaccio F, Valentini A, Filatov M, Huix-Rotllant M, Ferré N, Frutos LM, Angeli C, Krylov AI, 
      Granovsky AA, Lindh R, Olivucci M
      J. Chem. Theory Comput. 10, 3074–3084. 2014. [html]

12. Learning from Photobiology how to Design Molecular Devices Using a Computer
      Gozem S, Melaccio F, Luk HL, Rinaldi S, Olivucci M
      Chem. Soc. Rev. 43, 4019–4036. 2014. [html]

11. Comparison of the Isomerization Mechanisms of Human Melanopsin and Invertebrate and Vertebrate
     Rhodopsins
     Rinaldi S, Melaccio F, Gozem S, Fanelli F, Olivucci M
     Proc. Natl. Acad. Sci. U.S.A. 111, 1714–1719. 2014. [html]

10. Probing Vibrationally Mediated Ultrafast Excited-State Reaction Dynamics with Multireference (CASPT2)
      Trajectories
      El-Khoury PZ, Joseph S, Schapiro I, Gozem S, Olivucci M, Tarnovsky AN
      J. Phys. Chem. A. 117, 11271–11275. 2013. [html]

9. Mapping the Excited State Potential Energy Surface of a Retinal Chromophore Model with Multireference
    and Equation-of-Motion Coupled-Cluster Methods
    Gozem S, Melaccio F, Lindh R, Krylov AI, Granovsky AA, Angeli C, Olivucci M
    J. Chem. Theory Comput. 9, 4495–4506. 2013. [html]

8. Towards an Understanding of the Retinal Chromophore in Rhodopsin Mimics
     Huntress MM, Gozem S, Malley K, Jailaubekov A, Vasileiou C, Vengris M, Geiger J, Borhan B, Schapiro I, 
     Larsen D, Olivucci M
     J. Phys. Chem. B. 117, 10053–10070. 2013. [html]

7. Assessment of Density Functional Theory for Describing the Correlation Effects on the Ground and Excited
    State Potential Energy Surfaces of a Retinal Chromophore Model
    Huix-Rotllant M, Filatov M, Gozem S, Schapiro I, Olivucci M, Ferré N
    J. Chem. Theory Comput. 9, 3917–3932. 2013. [html]

6. Combined Self-Consistent-Field and Spin-Flip Tamm-Dancoff Density Functional Approach to Potential
    Energy Surfaces for Photochemistry
    Xu X, Gozem S, Olivucci M, Truhlar D
    J. Phys. Chem. Lett. 4, 253–258. 2013. [html]

5. Conical Intersection and Potential Energy Surface Features of a Model Retinal Chromophore: Comparison
    of EOM-CC and Multireference Methods
    Gozem S, Krylov AI, Olivucci M
    J. Chem. Theory Comput. 9, 284–292. 2013. [html]

4. Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal
     Chromophore Model
     Gozem S, Huntress M, Schapiro I, Lindh R, Granovsky AA, Angeli C, Olivucci M
     J. Chem. Theory Comput. 8, 4069–4080. 2012. [html]

3. The Molecular Mechanism of Thermal Noise in Rod Photoreceptors
     Gozem S, Schapiro I, Ferré N, Olivucci M
     Science. 137, 1225–1228. 2012. [html]

2. Origin of Fluorescence in 11-cis Locked Bovine Rhodopsin
    Laricheva EN, Gozem S, Rinaldi S, Melaccio F, Valentini A , Olivucci M
    J. Chem. Theory Comput. 8, 2559–2563. 2012. [html]

1. Calculations on the Kinetics, Thermodynamics, and Selectivity of Methyl Radical Addition to Olefins
    Coordinated to d8 and d0 Transition-Metal Fragments: Two Distinct and Opposite anti-Evans−Polanyi
    Effects with Potential Practical Implications
    Hasanayn F, Gozem S
    Organometallics. 27, 5426–5429. 2008. [html]
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