Publications
50. Solvent-Dependent Emissions Properties of a Model Aurone Enable Use in Biological Applications
Anderson B, Bryant DL, Gozem S, Brambley C, Handy ST, Farone A, Miller JM
J. Fluoresc., In press. 2024. [html]
49. How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The
Quest for a Suitable Solvent Model.
Le DPN, Hastings G, Gozem S.
Molecules, 29(2), 520. 2024. [html]
48. Solvatochromic and aggregation-induced emission active nitrophenyl-substituted pyrrolidinone-fused-1,
2-azaborine with a pre-twisted molecular geometry
Campbell AD, Ellis K, Gordon LK, Riley JE, Le VV, Hollister KK, Ajagbe SO, Gozem S, Hughley RB, Boswell AM,
Adjei-sah O, Baruah PD, Whitt LM, Gilliard RJ, Saint-Louis CJ.
J. Mater. Chem. C. 11, 13740–13751. 2023. [html]
47. Synthesis and Evaluation of Cereblon‐Recruiting HaloPROTACs
Ody BK, Zhang J, Nelson SE,Xie Y, Liu R, Dodd CJ, Jacobs SE, Whitzel SL, Williams LA, Gozem S, Turlington M,
Yin J.
ChemBioChem e202300498. 2023. [html]
46. Photoelectron Spectroscopy of Oppositely Charged Molecular Switches in the Aqueous Phase:
Theory and Experiment
Ikonnikov E, Paolino M, Garcia-Alvarez JC, Orozco-Gonzalez Y, Granados C, Röder A, Léonard J,
Olivucci M, Haacke S, Kornilov O, Gozem S.
J. Phys. Chem. Lett. 14(26), 6061–6070. 2023. [html]
45. Alternative Strategy for Spectral Tuning of Flavin-Binding Fluorescent Proteins.
Kabir MP, Ouedraogo D, Orozco-Gonzalez Y, Gadda G, Gozem S.
J. Phys. Chem. B. 127(6), 1301–1311. 2023. [html]
44. Dipole Effects in the Photoelectron Angular Distributions of the Sulfur Monoxide Anion.
Ru B, Hart CA, Mabbs R, Gozem S, Krylov AI, Sanov A.
Phys. Chem. Chem. Phys. 24, 23367–23381. 2022. [html]
43. Photochemically Triggered Cheletropic Formation of Cyclopropenone (c-C3H2O) from Carbon Monoxide and
Electronically Excited Acetylene.
Wang J, Kleimeier NF, Johnson RN, Gozem S, Abplanalp MJ,Turner AM, Marks JH, Kaiser RI.
Phys. Chem. Chem. Phys. 24. 17449–17461. 2022. [html]
42. Quantum–classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum
efficiency.
Yang X, Manathunga M, Gozem S, Léonard J, Andruniów T, Olivucci M.
Nat. Chem. 14. 441–449. 2022. [html]
41. 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.
J. Phys. Chem. A. 126(3), 435–443. 2022. [html]
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. 12(2), 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]
