Schweinfurth D, Krzystek J, Schapiro I, Demeshko S, Klein J, Telser J, Ozarowski A, Su C-Y, Meyer F, Atanasov M, et al. Electronic structures of octahedral Ni(II) complexes with "click" derived triazole ligands: A combined structural, magnetometric, spectroscopic, and theoretical study. Inorganic Chemistry [Internet]. 2013;52 (12) :6880 - 6892. Publisher's Version
Huntress MM, Gozem S, Malley KR, Jailaubekov AE, Vasileiou C, Vengris M, Geiger JH, Borhan B, Schapiro I, Larsen DS, et al. Toward an understanding of the retinal chromophore in rhodopsin mimics. Journal of Physical Chemistry B [Internet]. 2013;117 (35) :10053 - 10070. Publisher's Version
El-Khoury PZ, Joseph S, Schapiro I, Gozem S, Olivucci M, Tarnovsky AN. Probing vibrationally mediated ultrafast excited-state reaction dynamics with multireference (CASPT2) trajectories. Journal of Physical Chemistry A [Internet]. 2013;117 (44) :11271 - 11275. Publisher's Version
Schapiro I, El-Khoury P, Olivucci M. Ab Initio Investigation of Photochemical Reaction Mechanisms: From Isolated Molecules to Complex Environments. In: Handbook of Computational Chemistry. Amsterdam: Springer Netherlands ; 2012. pp. 1359-1404. Publisher's VersionAbstract

This chapter focuses on the computational investigations of light-induced chemical reactions in different systems ranging from organic molecules in vacuo to chromophores in complex protein environments. The aim is to show how the methods of computational photochemistry can be used to attain a molecular-level understanding of the mechanisms of photochemical and photophysical transformations. Following a brief introduction to the field, the most frequently used quantum chemical methods for mapping excited state potential energy surfaces and for studying the mechanism of photochemical reactions in isolated molecules are outlined. In the following sections, such methods and concepts are further developed to allow the investigation of photo-induced reactions in solution and in the protein environment.

El-Khoury PZ, Schaprio I, Huntress M, Melaccio F, Gozem S, Frutos LM, Olivucci M. Computational Photochemistry and Photobiology. In: CRC Handbook of Organic Photochemistry and Photobiology. Vol. 1. 3rd ed. Boca Raton: CRC Press ; 2012. pp. 1029-1056. Publisher's Version
Gozem S, Huntress M, Schapiro I, Lindh R, Granovsky AA, Angeli C, Olivucci M. Dynamic electron correlation effects on the ground state potential energy surface of a retinal chromophore model. Journal of Chemical Theory and Computation [Internet]. 2012;8 (11) :4069 - 4080. Publisher's Version
Gozem S, Schapiro I, Ferré N, Olivucci M. The molecular mechanism of thermal noise in rod photoreceptors. Science [Internet]. 2012;337 (6099) :1225 - 1228. Publisher's Version
Mechanistic origin of the vibrational coherence accompanying the photoreaction of biomimetic molecular switches
Léonard J, Schapiro I, Briand J, Fusi S, Paccani RR, Olivucci M, Haacke S. Mechanistic origin of the vibrational coherence accompanying the photoreaction of biomimetic molecular switches. Chemistry - A European Journal [Internet]. 2012;18 (48) :15296 - 15304. Publisher's VersionAbstract

The coherent photoisomerization of a chromophore in condensed phase is a rare process in which light energy is funneled into specific molecular vibrations during electronic relaxation from the excited to the ground state. In this work, we employed ultrafast spectroscopy and computational methods to investigate the molecular origin of the coherent motion accompanying the photoisomerization of indanylidene–pyrroline (IP) molecular switches. UV/Vis femtosecond transient absorption gave evidence for an excited- and ground-state vibrational wave packet, which appears as a general feature of the IP compounds investigated. In close resemblance to the coherent photoisomerization of rhodopsin, the sudden onset of a far-red-detuned and rapidly blue-shifting photoproduct signature indicated that the population arriving on the electronic ground state after nonadiabatic decay through the conical intersection (CI) is still very focused in the form of a vibrational wave packet. Semiclassical trajectories were employed to investigate the reaction mechanism. Their analysis showed that coupled double-bond twisting and ring inversions, already populated during the excited-state reactive motion, induced periodic changes in π-conjugation that modulate the ground-state absorption after the non-adiabatic decay. This prediction further supports that the observed ground-state oscillation results from the reactive motion, which is in line with a biomimetic, coherent photoisomerization scenario. The IP compounds thus appear as a model system to investigate the mechanism of mode-selective photomechanical energy transduction. The presented mechanism opens new perspectives for energy transduction at the molecular level, with applications to the design of efficient molecular devices.

Schapiro I, Ryazantsev MN, Frutos LM, Ferré N, Lindh R, Olivucci M. The ultrafast photoisomerizations of rhodopsin and bathorhodopsin are modulated by bond length alternation and HOOP driven electronic effects. Journal of the American Chemical Society [Internet]. 2011;133 (10) :3354 - 3364. Publisher's Version
Zhou D, Mirzakulova E, Khatmullin R, Schapiro I, Olivucci M, Glusac KD. Fast excited-state deactivation in N(5)-ethyl-4a-hydroxyflavin pseudobase. Journal of Physical Chemistry B [Internet]. 2011;115 (21) :7136 - 7143. Publisher's Version
Schapiro I, Melaccio F, Laricheva EN, Olivucci M. Using the computer to understand the chemistry of conical intersections. Photochemical and Photobiological Sciences [Internet]. 2011;10 (6) :867 - 886. Publisher's Version
Lim JS, Kim SK. Experimental probing of conical intersection dynamics in the photodissociation of thioanisole. [Internet]. 2010;2. Publisher's Version
Schapiro I, Ryazantsev MN, Ding WJ, Huntress MM, Melaccio F, Andruniow T, Olivucci M. Computational photobiology and beyond. Australian Journal of Chemistry [Internet]. 2010;63 (3) :413 - 429. Publisher's Version
El-Khoury PZ, George L, Kalume A, Schapiro I, Olivucci M, Tarnovsky AN, Reid SA. Matrix isolation and computational studies of the CF2I radical. Chemical Physics Letters [Internet]. 2010;496 (1-3) :68 - 73. Publisher's Version
Schapiro I, Weingart O, Buss V. Bicycle-pedal isomerization in a rhodopsin chromophore model. Journal of the American Chemical Society [Internet]. 2009;131 (1) :16 - 17. Publisher's Version
El-Khoury PZ, Tarnovsky AN, Schapiro I, Ryazantsev MN, Olivucci M. Structure of the photochemical reaction path populated via promotion of CF2i2 into its first excited state. Journal of Physical Chemistry A [Internet]. 2009;113 (40) :10767 - 10771. Publisher's Version
Weingart O, Schapiro I, Buss V. Photochemistry of visual pigment chromophore models by ab initio molecular dynamics. Journal of Physical Chemistry B [Internet]. 2007;111 (14) :3782 - 3788. Publisher's Version
Weingart O, Schapiro I, Buss V. Bond torsion affects the product distribution in the photoreaction of retinal model chromophores. Journal of Molecular Modeling [Internet]. 2006;12 (5) :713 - 721. Publisher's Version