@article {27311,
	title = {Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation},
	journal = {Photosensory Receptors-Mechanisms and Effects},
	volume = {436},
	number = {5},
	year = {2024},
	month = {2024},
	pages = {168356},
	abstract = {The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.},
	keywords = {LOV, molecular mechanism, Optogenetics, photoreceptor, Signal Transduction},
	isbn = {0022-2836},
	url = {https://www.sciencedirect.com/science/article/pii/S0022283623004679},
	author = {Flores-Ibarra, Andrea and Maia, Raiza N.A. and Olasz, Bence and Church, Jonathan R. and Gotthard, Guillaume and Schapiro, Igor and Heberle, Joachim and Nogly, Przemyslaw}
}
@article {27310,
	title = {Merocyanines form bacteriorhodopsins with strongly bathochromic absorption maxima},
	volume = {23},
	number = {1},
	year = {2024},
	month = {2024},
	pages = {31 - 53},
	abstract = {There is a need to shift the absorbance of biomolecules to the optical transparency window of tissue for applications in optogenetics and photo-pharmacology. There are a few strategies to achieve the so-called red shift of the absorption maxima. Herein, a series of 11 merocyanine dyes were synthesized and employed as chromophores in place of retinal in bacteriorhodopsin (bR) to achieve a bathochromic shift of the absorption maxima relative to bR{\textquoteright}s \({\lambda }_{\mathrm{max}}^{a}\) of 568\&nbsp;nm. Assembly with the apoprotein bacterioopsin (bO) led to stable, covalently bound chromoproteins with strongly bathochromic absorbance bands, except for three compounds. Maximal red shifts were observed for molecules 9, 2, and 8 in bR where the \({\lambda }_{\mathrm{max}}^{a}\)\&nbsp;was 766, 755, and 736\&nbsp;nm, respectively. While these three merocyanines have different end groups, they share a similar structural feature, namely, a methyl group which is located at the retinal equivalent position 13 of the polyene chain. The absorption and fluorescence data are also presented for the retinal derivatives in their aldehyde, Schiff base (SB), and protonated SB (PSB) forms in solution. According to their hemicyanine character, the PSBs and their analogue bRs exhibited fluorescence quantum yields (Φf) several orders of magnitude greater than native bR (Φf 0.02 to 0.18 versus 1.5 {\texttimes} 10{\textendash}5 in bR) while also exhibiting much smaller Stokes shifts than bR (400 to 1000\&nbsp;cm-1 versus 4030\&nbsp;cm-1 in bR). The experimental results are complemented by quantum chemical calculations where excellent agreement between the experimental \({\lambda }_{\mathrm{max}}^{a}\)and the calculated \({\lambda }_{\mathrm{max}}^{a}\) was achieved with the second-order algebraic-diagrammatic construction [ADC(2)] method. In addition, quantum mechanics/molecular mechanics (QM/MM) calculations were employed to shed light on the origin of the bathochromic shift of merocyanine 2 in bR compared with native bR.},
	isbn = {1474-9092},
	url = {https://doi.org/10.1007/s43630-023-00496-0},
	author = {Mackintosh, Megan J. and Hoischen, Dorothee and Martin, Hans-Dieter and Schapiro, Igor and Wolfgang G{\"a}rtner}
}
@article {27320,
	title = {Tuning the Emission Behaviour of Halogenated Bridged Ethers in Solution, as Solids and as Aggregates by Chalcogen Substitution},
	journal = {ChemPhotoChem},
	volume = {7},
	number = {1},
	year = {2023},
	month = {2023},
	pages = {e202200169},
	publisher = {John Wiley \& Sons, Ltd},
	abstract = {Abstract In this contribution, we describe a set of three chlorinated bridged ethers with varying numbers of sulfur and oxygen atoms. The substitution leads to highly emissive compounds with tunable photophysical properties in relationship to their state of aggregation, i.?e. in solution, as aggregates and in the solid state. Additionally, an in-depth X-ray diffractometric analysis supported by a Hirshfeld study of non-covalent interactions and quantum chemical simulations was carried out. As the outcome, it was found that the content of sulfur in the compounds regulates the tuning of emission in solution as well as in the aggregated states as a consequence of their variation of planarity.},
	keywords = {aggregation, aggregation-induced emission, chalcogens, computational chemistry, solid-state structures},
	isbn = {2367-0932},
	url = {https://doi.org/10.1002/cptc.202200169},
	author = {Dubbert, Justin and Valtolina, Marco and Huber, Alexander and Scherz, Tim D. and W{\"o}lper, Christoph and Daniliuc, Constantin G. and Filiba, Ofer and Sen, Saumik and Schapiro, Igor and Rizzo, Fabio and Voskuhl, Jens}
}
@article {27319,
	title = {Optical Activity and Spin Polarization: The Surface Effect},
	journal = {Journal of the American Chemical Society},
	volume = {145},
	number = {7},
	year = {2023},
	note = {doi: 10.1021/jacs.2c10456},
	month = {2023},
	pages = {3972 - 3977},
	publisher = {American Chemical Society},
	abstract = {Chirality ({\textquoteleft}handedness{\textquoteright}) is a property that underlies a broad variety of phenomena in nature. Chiral molecules appear in two forms, and each is a mirror image of the other, the two enantiomers. The chirality of molecules is associated with their optical activity, and circular dichroism is commonly applied to identify the handedness of chiral molecules. Recently, the chiral induced spin selectivity (CISS) effect was established, according to which transfer of electrons within chiral molecules depends on the electron{\textquoteright}s spin. Which spin is preferred depends on the handedness of the chiral molecule and the direction of motion of the electron. Several experiments in the past indicated that there may be a relation between the optical activity of the molecules and their spin selectivity. Here, we show that for a molecule containing several stereogenic axes, when adsorbed on a metal substrate, the peaks in the CD spectra have the same signs for the two enantiomers. This is not the case when the molecules are adsorbed on a nonmetallic substrate or dissolved in solution. Quantum chemical simulations are able to explain the change in the CD spectra upon adsorption of the molecules on conductive and nonconductive surfaces. Surprisingly, the CISS properties are similar for the two enantiomers when adsorbed on the metal substrate, while when the molecules are adsorbed on nonmetallic surface, the preferred spin depends on the molecule handedness. This correlation between the optical activity and the CISS effect indicates that the CISS effect relates to the global polarizability of the molecule.Chirality ({\textquoteleft}handedness{\textquoteright}) is a property that underlies a broad variety of phenomena in nature. Chiral molecules appear in two forms, and each is a mirror image of the other, the two enantiomers. The chirality of molecules is associated with their optical activity, and circular dichroism is commonly applied to identify the handedness of chiral molecules. Recently, the chiral induced spin selectivity (CISS) effect was established, according to which transfer of electrons within chiral molecules depends on the electron{\textquoteright}s spin. Which spin is preferred depends on the handedness of the chiral molecule and the direction of motion of the electron. Several experiments in the past indicated that there may be a relation between the optical activity of the molecules and their spin selectivity. Here, we show that for a molecule containing several stereogenic axes, when adsorbed on a metal substrate, the peaks in the CD spectra have the same signs for the two enantiomers. This is not the case when the molecules are adsorbed on a nonmetallic substrate or dissolved in solution. Quantum chemical simulations are able to explain the change in the CD spectra upon adsorption of the molecules on conductive and nonconductive surfaces. Surprisingly, the CISS properties are similar for the two enantiomers when adsorbed on the metal substrate, while when the molecules are adsorbed on nonmetallic surface, the preferred spin depends on the molecule handedness. This correlation between the optical activity and the CISS effect indicates that the CISS effect relates to the global polarizability of the molecule.},
	isbn = {0002-7863},
	url = {https://doi.org/10.1021/jacs.2c10456},
	author = {Metzger, Tzuriel S. and Batchu, Harikrishna and Kumar, Anil and Fedotov, Daniil A. and Goren, Naama and Bhowmick, Deb Kumar and Israa Shioukhi and Yochelis, Shira and Schapiro, Igor and Ron Naaman and Gidron, Ori and Paltiel, Yossi}
}
@article {27318,
	title = {Induction effects on the absorption maxima of photoreceptor proteins},
	volume = {20},
	year = {2023},
	month = {2023},
	pages = { - },
	abstract = {Multiscale simulations have been established as a powerful tool to calculate and predict excitation energies in complex systems such as photoreceptor proteins. In these simulations the chromophore is typically treated using quantum mechanical (QM) methods while the protein and surrounding environment are described by a classical molecular mechanics (MM) force field. The electrostatic interactions between these regions are often treated using electrostatic embedding where the point charges in the MM region polarize the QM region. A more sophisticated treatment accounts also for the polarization of the MM region. In this work, the effect of such a polarizable embedding on excitation energies was benchmarked and compared to electrostatic embedding. This was done for two different proteins, the lipid membrane-embedded jumping spider rhodopsin and the soluble cyanobacteriochrome Slr1393g3. It was found that the polarizable embedding scheme produces absorption maxima closer to experimental values. The polarizable embedding scheme was also benchmarked against expanded QM regions and found to be in qualitative agreement. Treating individual residues as polarizable recovered between 50\% and 71\% of the QM improvement in the excitation energies, depending on the system. A detailed analysis of each amino acid residue in the chromophore binding pocket revealed that aromatic residues result in the largest change in excitation energy compared to the electrostatic embedding. Furthermore, the computational efficiency of polarizable embedding allowed it to go beyond the binding pocket and describe a larger portion of the environment, further improving the results.},
	url = {https://www.jstage.jst.go.jp/article/biophysico/20/Supplemental/20_e201007/_article},
	author = {Church, Jonathan R. and Olsen,J{\'o}gvan Magnus Haugaard and Schapiro, Igor}
}
@article {27317,
	title = {Unexpected Nucleophile Masking in Acyl Transfer to Sterically Crowded and Conformationally Restricted Galactosides},
	journal = {The Journal of Organic Chemistry},
	volume = {88},
	number = {13},
	year = {2023},
	note = {doi: 10.1021/acs.joc.3c00878},
	month = {2023},
	pages = {9313 - 9320},
	publisher = {American Chemical Society},
	abstract = {Design and synthesis of orthogonally protected monosaccharide building blocks are crucial for the preparation of well-defined oligosaccharides in a stereo- and regiocontrolled manner. Selective introduction of protecting groups to partially protected monosaccharides is nontrivial due to the often unpredictable electronic, steric, and conformational effects of the substituents. Abolished reactivity toward a commonly used Lewis base-catalyzed acylation of O-2 was observed in conformationally restricted 4,6-O-benzylidene-3-O-Nap galactoside. Investigation of analogous systems, crystallographic characterization, and quantum chemical calculations highlighted the overlooked conformational and steric considerations, the combination of which produces a unique passivity of the 2-OH nucleophile. Evaluating the role of electrophile counterion and auxiliary base in the acylation of the sterically crowded and conformationally restricted galactoside system revealed an alternative Br{\o}nsted base-driven reaction pathway via nucleophilic activation. Insights gained from this model system were utilized to access the target galactoside intermediate within the envisioned synthetic route. The acylation strategy described herein can be implemented in future syntheses of key monomeric building blocks with unique protecting group hierarchies.Design and synthesis of orthogonally protected monosaccharide building blocks are crucial for the preparation of well-defined oligosaccharides in a stereo- and regiocontrolled manner. Selective introduction of protecting groups to partially protected monosaccharides is nontrivial due to the often unpredictable electronic, steric, and conformational effects of the substituents. Abolished reactivity toward a commonly used Lewis base-catalyzed acylation of O-2 was observed in conformationally restricted 4,6-O-benzylidene-3-O-Nap galactoside. Investigation of analogous systems, crystallographic characterization, and quantum chemical calculations highlighted the overlooked conformational and steric considerations, the combination of which produces a unique passivity of the 2-OH nucleophile. Evaluating the role of electrophile counterion and auxiliary base in the acylation of the sterically crowded and conformationally restricted galactoside system revealed an alternative Br{\o}nsted base-driven reaction pathway via nucleophilic activation. Insights gained from this model system were utilized to access the target galactoside intermediate within the envisioned synthetic route. The acylation strategy described herein can be implemented in future syntheses of key monomeric building blocks with unique protecting group hierarchies.},
	isbn = {0022-3263},
	url = {https://doi.org/10.1021/acs.joc.3c00878},
	author = {Sukhran, Yonatan and Alshanski, Israel and Filiba, Ofer and Mackintosh, Megan J. and Schapiro, Igor and Hurevich, Mattan}
}
@article {27316,
	title = {Transient 2D IR Spectroscopy and Multiscale Simulations Reveal Vibrational Couplings in the Cyanobacteriochrome Slr1393-g3},
	journal = {Journal of the American Chemical Society},
	volume = {145},
	number = {29},
	year = {2023},
	note = {doi: 10.1021/jacs.3c00896},
	month = {2023},
	pages = {15766 - 15775},
	publisher = {American Chemical Society},
	abstract = {Cyanobacteriochromes are bistable photoreceptor proteins with desirable photochemical properties for biotechnological applications, such as optogenetics or fluorescence microscopy. Here, we investigate Slr1393-g3, a cyanobacteriochrome that reversibly photoswitches between a red-absorbing (Pr) and green-absorbing (Pg) form. We applied advanced IR spectroscopic methods to track the sequence of intermediates during the photocycle over many orders of magnitude in time. In the conversion from Pg to Pr, we have revealed a new intermediate with distinct spectroscopic features in the IR, which precedes Pr formation using transient IR spectroscopy. In addition, stationary and transient 2D IR experiments measured the vibrational couplings between different groups of the chromophore and the protein in these intermediate states, as well as their structural disorder. Anharmonic QM/MM calculations predict spectra in good agreement with experimental 2D IR spectra of the initial and final states of the photocycle. They facilitate the assignment of the IR spectra that serve as a basis for the interpretation of the spectroscopic results and suggest structural changes of the intermediates along the photocycle.Cyanobacteriochromes are bistable photoreceptor proteins with desirable photochemical properties for biotechnological applications, such as optogenetics or fluorescence microscopy. Here, we investigate Slr1393-g3, a cyanobacteriochrome that reversibly photoswitches between a red-absorbing (Pr) and green-absorbing (Pg) form. We applied advanced IR spectroscopic methods to track the sequence of intermediates during the photocycle over many orders of magnitude in time. In the conversion from Pg to Pr, we have revealed a new intermediate with distinct spectroscopic features in the IR, which precedes Pr formation using transient IR spectroscopy. In addition, stationary and transient 2D IR experiments measured the vibrational couplings between different groups of the chromophore and the protein in these intermediate states, as well as their structural disorder. Anharmonic QM/MM calculations predict spectra in good agreement with experimental 2D IR spectra of the initial and final states of the photocycle. They facilitate the assignment of the IR spectra that serve as a basis for the interpretation of the spectroscopic results and suggest structural changes of the intermediates along the photocycle.},
	isbn = {0002-7863},
	url = {https://doi.org/10.1021/jacs.3c00896},
	author = {Buhrke, David and Yigal Lahav and Rao, Aditya and Ruf, Jeannette and Schapiro, Igor and Hamm, Peter}
}
@article {27315,
	title = {Embedding Nonrigid Solutes in an Averaged Environment: A Case Study on Rhodopsins},
	journal = {Journal of Chemical Theory and Computation},
	volume = {19},
	number = {15},
	year = {2023},
	note = {doi: 10.1021/acs.jctc.3c00285},
	month = {2023},
	pages = {5289 - 5302},
	publisher = {American Chemical Society},
	abstract = {Many simulation methods concerning solvated molecules are based on the assumption that the solvated species and the solvent can be characterized by some representative structures of the solute and some embedding potential corresponding to this structure. While the averaging of the solvent configurations to obtain an embedding potential has been studied in great detail, this hinges on a single solute structure representation. This assumption is re-examined and generalized for conformationally flexible solutes and tested on 4 nonrigid systems. In this generalized approach, the solute is characterized by a set of representative structures and the corresponding embedding potentials. The representative structures are identified by means of subdividing the statistical ensemble, which in this work is generated by a constant-temperature molecular dynamics simulation. The embedding potential defined in the Frozen-Density Embedding Theory is used to characterize the average effect of the solvent in each subensemble. The numerical examples concern the vertical excitation energies of protonated retinal Schiff bases in protein environments. It is comprehensively shown that subensemble averaging leads to huge computational savings compared with explicit averaging of the excitation energies in the whole ensemble while introducing only minor errors in the case of the systems examined.Many simulation methods concerning solvated molecules are based on the assumption that the solvated species and the solvent can be characterized by some representative structures of the solute and some embedding potential corresponding to this structure. While the averaging of the solvent configurations to obtain an embedding potential has been studied in great detail, this hinges on a single solute structure representation. This assumption is re-examined and generalized for conformationally flexible solutes and tested on 4 nonrigid systems. In this generalized approach, the solute is characterized by a set of representative structures and the corresponding embedding potentials. The representative structures are identified by means of subdividing the statistical ensemble, which in this work is generated by a constant-temperature molecular dynamics simulation. The embedding potential defined in the Frozen-Density Embedding Theory is used to characterize the average effect of the solvent in each subensemble. The numerical examples concern the vertical excitation energies of protonated retinal Schiff bases in protein environments. It is comprehensively shown that subensemble averaging leads to huge computational savings compared with explicit averaging of the excitation energies in the whole ensemble while introducing only minor errors in the case of the systems examined.},
	isbn = {1549-9618},
	url = {https://doi.org/10.1021/acs.jctc.3c00285},
	author = {Ricardi, Niccol{\`o} and Gonz{\'a}lez-Espinoza, Cristina E. and Adam, Suliman and Church, Jonathan R. and Schapiro, Igor and Weso{\l}owski, Tomasz Adam}
}
@article {27314,
	title = {Disequilibrating azobenzenes by visible-light sensitization under confinement},
	journal = {Science},
	volume = {381},
	number = {6664},
	year = {2023},
	note = {doi: 10.1126/science.adh9059},
	month = {2023},
	pages = {1357 - 1363},
	publisher = {American Association for the Advancement of Science},
	abstract = {Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host?photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation. Chemists often strive to push reactions metaphorically uphill toward less energetically favorable products. The challenge is to keep those products from rolling right back down. Gemen et al. report a clever tactic for twisting azobenzene into its higher-energy Z conformation. Specifically, they lured the more stable E isomer into a supramolecular host, along with a photosensitizer. When visible light injects energy to induce the twist, the Z isomer no longer fits in the cavity, so it gets pushed out before more light can twist it back. ?Jake S. Yeston Spatial constraints in a supramolecular host selectively convert azobenzenes to their metastable state under visible light.Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host?photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation. Chemists often strive to push reactions metaphorically uphill toward less energetically favorable products. The challenge is to keep those products from rolling right back down. Gemen et al. report a clever tactic for twisting azobenzene into its higher-energy Z conformation. Specifically, they lured the more stable E isomer into a supramolecular host, along with a photosensitizer. When visible light injects energy to induce the twist, the Z isomer no longer fits in the cavity, so it gets pushed out before more light can twist it back. ?Jake S. Yeston Spatial constraints in a supramolecular host selectively convert azobenzenes to their metastable state under visible light.},
	url = {https://doi.org/10.1126/science.adh9059},
	author = {Gemen, Julius and Church, Jonathan R. and Ruoko, Tero-Petri and Durandin, Nikita and Bia{\l}ek, Micha{\l} J. and Wei{\ss}enfels, Maren and Feller, Moran and Kazes, Miri and Odaybat, Magdalena and Borin, Veniamin A. and Kalepu, Rishir and Diskin-Posner, Yael and Oron, Dan and Fuchter, Matthew J. and Priimagi, Arri and Schapiro, Igor and Klajn, Rafal}
}
@article {27313,
	title = {The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry},
	journal = {Journal of Chemical Theory and Computation},
	volume = {19},
	number = {20},
	year = {2023},
	note = {doi: 10.1021/acs.jctc.3c00182},
	month = {2023},
	pages = {6933 - 6991},
	publisher = {American Chemical Society},
	abstract = {The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.},
	isbn = {1549-9618},
	url = {https://doi.org/10.1021/acs.jctc.3c00182},
	author = {Li Manni, Giovanni and Fdez. Galv{\'a}n, Ignacio and Alavi, Ali and Aleotti, Flavia and Aquilante, Francesco and Autschbach, Jochen and Avagliano, Davide and Alberto Baiardi and Bao, Jie J. and Stefano Battaglia and Birnoschi, Letitia and Blanco-Gonz{\'a}lez, Alejandro and Bokarev, Sergey I. and Broer, Ria and Cacciari, Roberto and Calio, Paul B. and Carlson, Rebecca K. and Carvalho Couto, Rafael and Cerd{\'a}n, Luis and Chibotaru, Liviu F. and Chilton, Nicholas F. and Church, Jonathan Richard and Irene Conti and Coriani, Sonia and Cu{\'e}llar-Zuquin, Juliana and Daoud, Razan E. and Dattani, Nike and Decleva, Piero and de Graaf, Coen and Delcey, Micka{\"e}l G. and De Vico, Luca and Dobrautz, Werner and Dong, Sijia S. and Feng, Rulin and Ferr{\'e}, Nicolas and Filatov(Gulak), Michael and Gagliardi, Laura and Garavelli, Marco and Gonz{\'a}lez, Leticia and Guan, Yafu and Guo, Meiyuan and Hennefarth, Matthew R. and Hermes, Matthew R. and Hoyer, Chad E. and Huix-Rotllant, Miquel and Jaiswal, Vishal Kumar and Kaiser, Andy and Kaliakin, Danil S. and Khamesian, Marjan and King, Daniel S. and Kochetov, Vladislav and Kro{\'s}nicki, Marek and Kumaar, Arpit Arun and Ernst D. Larsson and Lehtola, Susi and Lepetit, Marie-Bernadette and Lischka, Hans and L{\'o}pez R{\'\i}os, Pablo and Lundberg, Marcus and Ma, Dongxia and Mai, Sebastian and Marquetand, Philipp and Merritt, Isabella C. D. and Montorsi, Francesco and M{\"o}rchen, Maximilian and Nenov, Artur and Nguyen, Vu Ha Anh and Nishimoto, Yoshio and Oakley, Meagan S. and Olivucci, Massimo and Oppel, Markus and Padula, Daniele and Pandharkar, Riddhish and Phung, Quan Manh and Plasser, Felix and Raggi, Gerardo and Rebolini, Elisa and Reiher, Markus and Rivalta, Ivan and Roca-Sanju{\'a}n, Daniel and Romig, Thies and Safari, Arta Anushirwan and S{\'a}nchez-Mansilla, Aitor and Sand, Andrew M. and Schapiro, Igor and Scott, Thais R. and Segarra-Mart{\'\i}, Javier and Francesco Segatta and Dumitru-Claudiu Sergentu and Sharma, Prachi and Shepard, Ron and Shu, Yinan and Staab, Jakob K. and Straatsma, Tjerk P. and S{\o}rensen, Lasse Kragh and Tenorio, Bruno Nunes Cabral and Donald G. Truhlar and Ungur, Liviu and Vacher, Morgane and Veryazov, Valera and Vo{\ss}, Torben Arne and Weser, Oskar and Wu, Dihua and Yang, Xuchun and Yarkony, David and Zhou, Chen and Zobel, J. Patrick and Lindh, Roland}
}
@article {27312,
	title = {Short-Range Effects in the Special Pair of Photosystem II Reaction Centers: The Nonconservative Nature of Circular Dichroism},
	journal = {The Journal of Physical Chemistry Letters},
	volume = {14},
	number = {51},
	year = {2023},
	note = {doi: 10.1021/acs.jpclett.3c02693},
	month = {2023},
	pages = {11758 - 11767},
	publisher = {American Chemical Society},
	abstract = {Photosystem II reaction centers extract electrons from water, providing the basis of oxygenic life on earth. Among the light-sensitive pigments of the reaction center, a central chlorophyll a dimer, known as the special pair, so far has escaped a complete theoretical characterization of its excited state properties. The close proximity of the special pair pigments gives rise to short-range effects that comprise a coupling between local and charge transfer (CT) excited states as well as other intermolecular quantum effects. Using a multiscale simulation and a diabatization technique, we show that the coupling to CT states is responsible for 45\% of the excitonic coupling in the special pair. The other short-range effects cause a nonconservative nature of the circular dichroism spectrum of the reaction center by effectively rotating the electric transition dipole moments of the special pair pigments inverting and strongly enhancing their intrinsic rotational strength.Photosystem II reaction centers extract electrons from water, providing the basis of oxygenic life on earth. Among the light-sensitive pigments of the reaction center, a central chlorophyll a dimer, known as the special pair, so far has escaped a complete theoretical characterization of its excited state properties. The close proximity of the special pair pigments gives rise to short-range effects that comprise a coupling between local and charge transfer (CT) excited states as well as other intermolecular quantum effects. Using a multiscale simulation and a diabatization technique, we show that the coupling to CT states is responsible for 45\% of the excitonic coupling in the special pair. The other short-range effects cause a nonconservative nature of the circular dichroism spectrum of the reaction center by effectively rotating the electric transition dipole moments of the special pair pigments inverting and strongly enhancing their intrinsic rotational strength.},
	url = {https://doi.org/10.1021/acs.jpclett.3c02693},
	author = {Gemeinhardt, Felix G. and Yigal Lahav and Schapiro, Igor and Noy, Dror and M{\"u}h, Frank and Lindorfer, Dominik and Renger, Thomas}
}
@article {27333,
	title = {The impact of retinal configuration on the protein{\textendash}chromophore interactions in bistable jumping spider rhodopsin-1},
	journal = {Molecules},
	volume = {27},
	number = {1},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 8},
	month = {2022},
	abstract = {Bistable rhodopsins have two stable forms that can be interconverted by light. Due to their ability to act as photoswitches, these proteins are considered as ideal candidates for applications such as optogenetics. In this work, we analyze a recently crystalized bistable rhodopsin, namely the jumping spider rhodopsin-1 (JSR1). This rhodopsin exhibits identical absorption maxima for the parent and the photoproduct form, which impedes its broad application. We performed hybrid QM/MM simulations to study three isomers of the retinal chromophore: the 9-cis, 11-cis and all-trans configurations. The main aim was to gain insight into the specific interactions of each isomer and their impact on the absorption maximum in JSR1. The absorption spectra were computed using sampled snapshots from QM/MM molecular dynamics trajectories and compared to their experimental counterparts. The chromophore{\textendash}protein interactions were analyzed by visualizing the electrostatic potential of the protein and projecting it onto the chromophore. It was found that the distance between a nearby tyrosine (Y126) residue plays a larger role in the predicted absorption maximum than the primary counterion (E194). Geometric differences between the isomers were also noted, including a structural change in the polyene chain of the chromophore, as well as changes in the nearby hydrogen bonding network. {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85121700915\&doi=10.3390\%2fmolecules27010071\&partnerID=40\&md5=5704eaa5d752b3e92319fc79f4d0917d},
	author = {Church, J.R. and Olsen, J.M.H. and Schapiro, I.}
}
@article {27332,
	title = {The impact of twisting on the intersystem crossing in acenes: An experimental and computational study},
	journal = {Physical Chemistry Chemical Physics},
	volume = {24},
	number = {4},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 7},
	month = {2022},
	pages = {2357 - 2362},
	abstract = {Due to their unique excited state dynamics, acenes play a dominant role in optoelectronic and light-harvesting applications. Their optical and electronic properties are typically tailored by side-group engineering, which often result in distortion of the acene core from planarity. However, the effect of such distortion on their excited state dynamics is not clear. In this work, we investigate the effect of twisting on the photophysics of acenes, which are helically locked to a defined twist angle by tethers of different lengths. Ultrafast transient absorption and time resolved fluorescence show a clear dependence of the rate of intersystem crossing with twisting. This trend is explained using quantum chemical calculations, showing an increase of spin-orbit coupling (SOC). At much earlier times, structural reorganization in S1, including coherent vibrational wave packet motions, is reflected in transient spectral changes. As predicted by theory, decreasing the length of diagonal tether induces enhanced activity and frequency blue-shifting of a normal vibration consisting of anthracene twisting against restraint of the tethering chain. Overall, these results serve as design principles for tuning photophysical properties of acenes via controlled twisting of their aromatic core. {\textcopyright} 2022 the Owner Societies.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85123856563\&doi=10.1039\%2fd1cp05728f\&partnerID=40\&md5=55b5777daef2b6979ae3f511423961aa},
	author = {Malakar, P. and Borin, V. and Bedi, A. and Schapiro, I. and Gidron, O. and Ruhman, S.}
}
@article {27331,
	title = {Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine},
	journal = {Nature Communications},
	volume = {13},
	number = {1},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 15},
	month = {2022},
	abstract = {In nature as in biotechnology, light-oxygen-voltage photoreceptors perceive blue light to elicit spatiotemporally defined cellular responses. Photon absorption drives thioadduct formation between a conserved cysteine and the flavin chromophore. An equally conserved, proximal glutamine processes the resultant flavin protonation into downstream hydrogen-bond rearrangements. Here, we report that this glutamine, long deemed essential, is generally dispensable. In its absence, several light-oxygen-voltage receptors invariably retained productive, if often attenuated, signaling responses. Structures of a light-oxygen-voltage paradigm at around 1 {\r A} resolution revealed highly similar light-induced conformational changes, irrespective of whether the glutamine is present. Naturally occurring, glutamine-deficient light-oxygen-voltage receptors likely serve as bona fide photoreceptors, as we showcase for a diguanylate cyclase. We propose that without the glutamine, water molecules transiently approach the chromophore and thus propagate flavin protonation downstream. Signaling without glutamine appears intrinsic to light-oxygen-voltage receptors, which pertains to biotechnological applications and suggests evolutionary descendance from redox-active flavoproteins. {\textcopyright} 2022, The Author(s).},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85130041158\&doi=10.1038\%2fs41467-022-30252-4\&partnerID=40\&md5=187f392dfa79e54afd6fa10e1e35f9ec},
	author = {Dietler, J. and Gelfert, R. and Kaiser, J. and Borin, V. and Renzl, C. and Pilsl, S. and Ranzani, A.T. and Garc{\'\i}a de Fuentes, A. and Gleichmann, T. and Diensthuber, R.P. and Weyand, M. and Mayer, G. and Schapiro, I. and M{\"o}glich, A.}
}
@article {27325,
	title = {Control of a far-red/near-infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin},
	journal = {Protein Science},
	volume = {31},
	number = {9},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 1},
	month = {2022},
	abstract = {The molecular structure of mBDFP, a far-red fluorescent protein (FPs) derived from an allophycocyanin homolog was resolved to 2.52 {\r A}. Its biliverdin chromophore was found to be attached to the protein in an unusual way that was never observed in natural phycobiliproteins, and only once in a sub-population of artificial bacteriophytochrome-derived FPs. One of the biliverdin{\textquoteright}s vinyl groups had two cysteine residues covalently bound to its two carbon atoms. This reduces the conjugation length of the biliverdin π-electron system, which shifts the absorption and emission spectra by about 40 nm, from the near-infrared to the far-red region of the spectrum. By spectrally characterizing a set of mBDFP mutants, we show that such spectral shifts can be induced by modifying a single residue in either one of two critical positions in the vicinity of the binding cysteines. This changes the reactivity of biliverdin and the cysteine{\textquoteright}s thiols towards forming one, or two thioether bonds to the vinyl group. The ability to control the spectral properties of BDFP by specific point mutations opens many possibilities for rational design of far-red and near-infrared FPs that are of great interest to the development of fluorescence markers for bioimaging since most biological tissues are transparent in this spectral window. {\textcopyright} 2022 The Protein Society.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85137662517\&doi=10.1002\%2fpro.4412\&partnerID=40\&md5=7ed59a5141a416721e1c7eaff0de7ad3},
	author = {Hou, Y.-N. and H{\"o}ppner, A. and Rao, A.G. and Lahav, Y. and Kumar Das, P. and Ding, W.-L. and Jiang, X.-X. and Hu, J.-L. and Schapiro, I. and Noy, D. and Zhao, K.-H.}
}
@article {27324,
	title = {Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry},
	journal = {Chemistry - A European Journal},
	volume = {28},
	number = {28},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 4},
	month = {2022},
	abstract = {Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. There are two phenotypes of PR exhibiting an environmental adaptation to the ocean{\textquoteright}s depth which tunes their maximum absorption: blue-absorbing proteorhodopsin (BPR) and green-absorbing proteorhodopsin (GPR). This blue/green color-shift is controlled by a glutamine to leucine substitution at position 105 which accounts for a 20 nm shift. Typically, spectral tuning in rhodopsins is rationalized by the external point charge model but the Q105L mutation is charge neutral. To study this tuning mechanism, we employed the hybrid QM/MM method with sampling from molecular dynamics. Our results reveal that the positive partial charge of glutamine near the C14-C15 bond of retinal shortens the effective conjugation length of the chromophore compared to the leucine residue. The derived mechanism can be applied to explain the color regulation in other retinal proteins and can serve as a guideline for rational design of spectral shifts. {\textcopyright} 2022 The Authors. Chemistry~-~A European Journal published by Wiley-VCH GmbH.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85127557708\&doi=10.1002\%2fchem.202200139\&partnerID=40\&md5=04f1997054c6c2c90457baa381f8c906},
	author = {Church, J.R. and Amoyal, G.S. and Borin, V.A. and Adam, S. and Olsen, J.M.H. and Schapiro, I.}
}
@article {27323,
	title = {Dynamics and mechanism of a light-driven chloride pump},
	journal = {Science},
	volume = {375},
	number = {6583},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 34},
	month = {2022},
	pages = {845 - 851},
	abstract = {Chloride transport by microbial rhodopsins is an essential process for which molecular details such as the mechanisms that convert light energy to drive ion pumping and ensure the unidirectionality of the transport have remained elusive. We combined time-resolved serial crystallography with time-resolved spectroscopy and multiscale simulations to elucidate the molecular mechanism of a chloride-pumping rhodopsin and the structural dynamics throughout the transport cycle. We traced transient anion-binding sites, obtained evidence for how light energy is used in the pumping mechanism, and identified steric and electrostatic molecular gates ensuring unidirectional transport. An interaction with the p-electron system of the retinal supports transient chloride ion binding across a major bottleneck in the transport pathway. These results allow us to propose key mechanistic features enabling finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump. {\textcopyright} 2022 American Association for the Advancement of Science. All rights reserved.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85125289281\&doi=10.1126\%2fscience.abj6663\&partnerID=40\&md5=8052b5e432c0efd7cc2911c690261ff6},
	author = {Mous, S. and Gotthard, G. and Ehrenberg, D. and Sen, S. and Weinert, T. and Johnson, P. J. M. and James, D. and Nass, K. and Furrer, A. and Kekilli, D. and Ma, P. and Br{\"u}nle, S. and Maria Casadei, C. and Martiel, I. and Dworkowski, F. and Gashi, D. and Skopintsev, P. and Wranik, M. and Knopp, G. and Panepucci, E. and Panneels, V. and Cirelli, C. and Ozerov, D. and Schertler, G. F. X. and Wang, M. and Milne, C. and Standfuss, J. and Schapiro, I. and Heberle, J. and Nogly, P.}
}
@article {27327,
	title = {Insight into the isomerization mechanism of retinal proteins from hybrid quantum mechanics/molecular mechanics simulations},
	journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
	volume = {12},
	number = {1},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 6},
	month = {2022},
	abstract = {The photoisomerization of retinal is a unifying primary event in the rhodopsin protein family. In vertebrate rhodopsins it is the first step in the vision process, while in the microbial rhodopsins it activates the transport of ions across the cell-membrane. This reaction is highly optimized in the protein, which is ultrafast, selective, and efficient. A great effort was directed to elucidate the mechanism due to the overall complexity of the process inside the protein. The classical one-bond-flip is too demanding in space for the confined protein cavity. Therefore, various space saving mechanisms based on the rotation of multiple double bonds have been proposed. The hybrid quantum mechanics/molecular mechanics (QM/MM) method played an important role in the elucidation of the mechanism inside the tight protein environment. It allows to take the entire protein into account while describing the ground and excited states of retinal. The predicted mechanisms include full isomerization of two or three double bonds, a simultaneous isomerization of a single and a double bond as well as the partial rotation of bonds adjacent to the central isomerization. This review summarizes mechanistic studies in the literature and compares them. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Software > Molecular Modeling. {\textcopyright} 2021 Wiley Periodicals LLC.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85111156914\&doi=10.1002\%2fwcms.1562\&partnerID=40\&md5=3bc69366a1075afea33a81b7a6737acd},
	author = {Sen, S. and Kar, R.K. and Borin, V.A. and Schapiro, I.}
}
@article {27328,
	title = {The involvement of triplet states in the isomerization of retinaloids},
	journal = {Physical Chemistry Chemical Physics},
	volume = {114},
	number = {1},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 3},
	month = {2022},
	abstract = {Rhodopsins form a family of photoreceptor proteins which utilize the retinal chromophore for light energy conversion. Upon light absorption the retinal chromophore undergoes a photoisomerization. This reaction involves a non-radiative relaxation through a conical intersection between the singlet excited state and the ground state. In this work we studied the possible involvement of triplet states in the photoisomerization of retinaloids using the extended multistate (XMS) version of CASPT2. To this end, truncated models of three retinaloids were considered: protonated Schiff base, deprotonated Schiff base and the aldehyde form. The optimized geometries of the reactant, the product and the conical intersection were connected by a linear interpolation of internal coordinates to describe the isomerization. The energetic position of the low-lying singlet and triplet states as well as their spin-orbit coupling matrix elements (SOCME) were calculated along the isomerization profile. The SOCME values peaked in vicinity of the conical intersection for all the retinaloids. Furthermore, the magnitude of SOCME is invariant to the number of double bonds in the model. The SOCME for the protonated Schiff base is negligible (1.5 cm-1) which renders the involvement of the triplet state as improbable. However, the largest SOCME value of 30 cm-1 was found for the aldehyde form, followed by 15 cm-1 for the deprotonated Schiff base. {\textcopyright} 2022 The Royal Society of Chemistry.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141840255\&doi=10.1039\%2fd2cp03791b\&partnerID=40\&md5=e08c3a787b782d9bc8b5f1deade7f122},
	author = {Filiba, O. and Borin, V.A. and Schapiro, I.}
}
@booklet {27321,
	title = {Photoisomerization of phytochrome chromophore models: an XMS-CASPT2 study},
	journal = {Physical Chemistry Chemical Physics},
	volume = {24},
	number = {48},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 2},
	month = {2022},
	pages = {29393 - 29405},
	abstract = {Phytochromes are a superfamily of photoreceptors that harbor linear tetrapyrroles as chromophores. Upon light illumination, the linear tetrapyrrole chromophore undergoes a double bond isomerization which starts a photocycle. In this work, we studied the photoisomerization of chromophore models designed based on the C- and D-rings of the phycocyanobilin (PCB) chromophore. In total, five different models with varying substitutions were investigated. Firstly, the vertical excitation energies were benchmarked using different computational methods to establish the relative order of the excited states. Based on these calculations, we computed the photoisomerization profiles using the extended multi-state (XMS) version of the CASPT2 method. The profiles were obtained for both the clockwise and counterclockwise rotations of the C15 = C16 bond in the Z and E isomers using a linear interpolation of internal coordinates between the Franck-Condon and MECI geometries. In the minimal chromophore model that lacks the substitutions at the pyrrole rings, the isomerization involves both C14-C15 and C15 C16 bonds of the methine bridge between the C- and D-rings, resembling the hula-twist motion. The MECIs are characterized by a partial charge transfer between the two pyrrole rings pointing towards a twisted intramolecular charge transfer. Systematic introduction of substituents leads to an increase in the steric repulsion between the two pyrrole rings causing a pretwist of the dihedral around the C15 C16 bond, which creates a preference for the counterclockwise isomerization. An introduction of the carbonyl group at the D-ring increases the extent of charge transfer which changes the isomerization mechanism from hula-twist to one-bond flip. {\textcopyright} 2022 The Royal Society of Chemistry.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85143988319\&doi=10.1039\%2fd2cp04249e\&partnerID=40\&md5=4b2ba8324eea1bc2a2f961f03576b28f},
	author = {Rao, A.G. and Schapiro, I.}
}
@article {27322,
	title = {Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin},
	journal = {Nature Communications},
	volume = {13},
	number = {1},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 14},
	month = {2022},
	abstract = {The understanding of how the rhodopsin sequence can be modified to exactly modulate the spectroscopic properties of its retinal chromophore, is a prerequisite for the rational design of more effective optogenetic tools. One key problem is that of establishing the rules to be satisfied for achieving highly fluorescent rhodopsins with a near infrared absorption. In the present paper we use multi-configurational quantum chemistry to construct a computer model of a recently discovered natural rhodopsin, Neorhodopsin, displaying exactly such properties. We show that the model, that successfully replicates the relevant experimental observables, unveils a geometrical and electronic structure of the chromophore featuring a highly diffuse charge distribution along its conjugated chain. The same model reveals that a charge confinement process occurring along the chromophore excited state isomerization coordinate, is the primary cause of the observed fluorescence enhancement. {\textcopyright} 2022, The Author(s).},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141370303\&doi=10.1038\%2fs41467-022-33953-y\&partnerID=40\&md5=b278003b0651f2ca7d71225cf740f10d},
	author = {Palombo, R. and Barneschi, L. and Pedraza-Gonz{\'a}lez, L. and Padula, D. and Schapiro, I. and Olivucci, M.}
}
@article {27330,
	title = {Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels},
	journal = {Nature Structural and Molecular Biology},
	volume = {29},
	number = {6},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 18},
	month = {2022},
	pages = {592 - 603},
	abstract = {Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a microbial rhodopsin subfamily from marine unicellular algae, in which one rhodopsin domain of eight transmembrane helices or, more often, two such domains in tandem, are C-terminally fused to a bestrophin channel. Cryo-EM analysis of a rhodopsin-rhodopsin-bestrophin fusion revealed that it forms a pentameric megacomplex (~700 kDa) with five rhodopsin pseudodimers surrounding the channel in the center. Bestrhodopsins are metastable and undergo photoconversion between red- and green-absorbing or green- and UVA-absorbing forms in the different variants. The retinal chromophore, in a unique binding pocket, photoisomerizes from all-trans to 11-cis form. Heterologously expressed bestrhodopsin behaves as a light-modulated anion channel. {\textcopyright} 2022, The Author(s), under exclusive licence to Springer Nature America, Inc.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85132206207\&doi=10.1038\%2fs41594-022-00783-x\&partnerID=40\&md5=7b9998167b0641662705b948ee69156d},
	author = {Rozenberg, A. and Kaczmarczyk, I. and Matzov, D. and Vierock, J. and Nagata, T. and Sugiura, M. and Katayama, K. and Kawasaki, Y. and Konno, M. and Nagasaka, Y. and Aoyama, M. and Das, I. and Pahima, E. and Church, J. and Adam, S. and Borin, V.A. and Chazan, A. and Augustin, S. and Wietek, J. and Dine, J. and Peleg, Y. and Kawanabe, A. and Fujiwara, Y. and Yizhar, O. and Sheves, M. and Schapiro, I. and Furutani, Y. and Kandori, H. and Inoue, K. and Hegemann, P. and B{\'e}j{\`a}, O. and Shalev-Benami, M.}
}
@article {27326,
	title = {Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme},
	journal = {Nature Chemistry},
	volume = {14},
	number = {6},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 21},
	month = {2022},
	pages = {677 - 685},
	abstract = {Flavin coenzymes are universally found in biological redox reactions. DNA photolyases, with their flavin chromophore (FAD), utilize blue light for DNA repair and photoreduction. The latter process involves two single-electron transfers to FAD with an intermittent protonation step to prime the enzyme active for DNA repair. Here we use time-resolved serial femtosecond X-ray crystallography to describe how light-driven electron transfers trigger subsequent nanosecond-to-microsecond entanglement between FAD and its Asn/Arg-Asp redox sensor triad. We found that this key feature within the photolyase-cryptochrome family regulates FAD re-hybridization and protonation. After first electron transfer, the FAD{\textbullet}- isoalloxazine ring twists strongly when the arginine closes in to stabilize the negative charge. Subsequent breakage of the arginine{\textendash}aspartate salt bridge allows proton transfer from arginine to FAD{\textbullet}-. Our molecular videos demonstrate how the protein environment of redox cofactors organizes multiple electron/proton transfer events in an ordered fashion, which could be applicable to other redox systems such as photosynthesis. [Figure not available: see fulltext.] {\textcopyright} 2022, The Author(s), under exclusive licence to Springer Nature Limited.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85127648859\&doi=10.1038\%2fs41557-022-00922-3\&partnerID=40\&md5=65afb613e670bbbcb95aa5e0e2d5c5a5},
	author = {Maestre-Reyna, M. and Yang, C.-H. and Nango, E. and Huang, W.-C. and Ngurah Putu, E.P.G. and Wu, W.-J. and Wang, P.-H. and Franz-Badur, S. and Saft, M. and Emmerich, H.-J. and Wu, H.-Y. and Lee, C.-C. and Huang, K.-F. and Chang, Y.-K. and Liao, J.-H. and Weng, J.-H. and Gad, W. and Chang, C.-W. and Pang, A.H. and Sugahara, M. and Owada, S. and Hosokawa, Y. and Joti, Y. and Yamashita, A. and Tanaka, R. and Tanaka, T. and Luo, F. and Tono, K. and Hsu, K.-C. and Kiontke, S. and Schapiro, I. and Spadaccini, R. and Royant, A. and Yamamoto, J. and Iwata, S. and Essen, L.-O. and Bessho, Y. and Tsai, M.-D.}
}
@article {27329,
	title = {Ultrafast proton-coupled isomerization in the phototransformation of phytochrome},
	journal = {Nature Chemistry},
	volume = {14},
	number = {7},
	year = {2022},
	note = {Export Date: 06 April 2024; Cited By: 11},
	month = {2022},
	pages = {823 - 830},
	abstract = {The biological function of phytochromes is triggered by an ultrafast photoisomerization of the tetrapyrrole chromophore biliverdin between two rings denoted C and D. The mechanism by which this process induces extended structural changes of the protein is unclear. Here we report ultrafast proton-coupled photoisomerization upon excitation of the parent state (Pfr) of bacteriophytochrome Agp2. Transient deprotonation of the chromophore{\textquoteright}s pyrrole ring D or ring C into a hydrogen-bonded water cluster, revealed by a broad continuum infrared band, is triggered by electronic excitation, coherent oscillations and the sudden electric-field change in the excited state. Subsequently, a dominant fraction of the excited population relaxes back to the Pfr state, while ~35\% follows the forward reaction to the photoproduct. A combination of quantum mechanics/molecular mechanics calculations and ultrafast visible and infrared spectroscopies demonstrates how proton-coupled dynamics in the excited state of Pfr leads to a restructured hydrogen-bond environment of early Lumi-F, which is interpreted as a trigger for downstream protein structural changes. [Figure not available: see fulltext.]. {\textcopyright} 2022, The Author(s).},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85130154686\&doi=10.1038\%2fs41557-022-00944-x\&partnerID=40\&md5=bb99275888487c75b68825eac1a6a9dd},
	author = {Yang, Y. and Stensitzki, T. and Sauthof, L. and Schmidt, A. and Piwowarski, P. and Velazquez Escobar, F. and Michael, N. and Nguyen, A.D. and Szczepek, M. and Br{\"u}nig, F.N. and Netz, R.R. and Mroginski, M.A. and Adam, S. and Bartl, F. and Schapiro, I. and Hildebrandt, P. and Scheerer, P. and Heyne, K.}
}
@article {26375,
	title = {Bending versus Twisting Acenes {\textendash} A Computational Study},
	journal = {European Journal of Organic Chemistry},
	volume = {2021},
	number = {39},
	year = {2021},
	note = {Export Date: 30 January 2022},
	month = {2021},
	pages = {5424 - 5429},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85117518611\&doi=10.1002\%2fejoc.202100865\&partnerID=40\&md5=9e6f97c30382cd93ff149ebe2c2aafb9},
	author = {Armon, A.M. and Bedi, A. and Borin, V. and Schapiro, I. and Gidron, O.}
}
@article {26377,
	title = {Bridged Aromatic Oxo- and Thioethers with Intense Emission in Solution and the Solid State},
	journal = {Chemistry - An Asian Journal},
	volume = {16},
	number = {16},
	year = {2021},
	note = {Export Date: 30 January 2022},
	month = {2021},
	pages = {2307 - 2313},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85112685629\&doi=10.1002\%2fasia.202100492\&partnerID=40\&md5=f8f33df0bcf6421e9ee47424daeeea9f},
	author = {Riebe, S. and Adam, S. and Roy, B. and Maisuls, I. and Daniliuc, C.G. and Dubbert, J. and Strassert, C.A. and Schapiro, I. and Voskuhl, J.}
}
@article {26380,
	title = {Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2},
	journal = {Physical Chemistry Chemical Physics},
	volume = {23},
	number = {12},
	year = {2021},
	note = {Cited By :2Export Date: 30 January 2022},
	month = {2021},
	pages = {7359 - 7367},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103692833\&doi=10.1039\%2fd0cp05314g\&partnerID=40\&md5=43be10161b20aec1064b7a95c13d6732},
	author = {Rao, A.G. and Wiebeler, C. and Sen, S. and Cerutti, D.S. and Schapiro, I.}
}
@article {26381,
	title = {Spectral tuning of chlorophylls in proteins - electrostaticsvs.ring deformation},
	journal = {Physical Chemistry Chemical Physics},
	volume = {23},
	number = {11},
	year = {2021},
	note = {Cited By :3Export Date: 30 January 2022},
	month = {2021},
	pages = {6544 - 6551},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103355595\&doi=10.1039\%2fd0cp06582j\&partnerID=40\&md5=448274a0c5cba9ef66f9ab684cf38a20},
	author = {Lahav, Y. and Noy, D. and Schapiro, I.}
}
@article {26376,
	title = {Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2},
	journal = {Journal of Chemical Theory and Computation},
	volume = {17},
	number = {10},
	year = {2021},
	note = {Cited By :3Export Date: 30 January 2022},
	month = {2021},
	pages = {6302 - 6313},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85111115742\&doi=10.1021\%2facs.jctc.1c00160\&partnerID=40\&md5=4877a47080db9d5d1006f4136f3e5f1d},
	author = {Adam, S. and Wiebeler, C. and Schapiro, I.}
}
@article {26374,
	title = {Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization},
	journal = {Nature Communications},
	volume = {12},
	number = {1},
	year = {2021},
	note = {Cited By :7Export Date: 30 January 2022},
	month = {2021},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099922560\&doi=10.1038\%2fs41467-020-20596-0\&partnerID=40\&md5=f37f843a312ca36ac8d57660bc1700cc},
	author = {Bada Juarez, J.F. and Judge, P.J. and Adam, S. and Axford, D. and Vinals, J. and Birch, J. and Kwan, T.O.C. and Hoi, K.K. and Yen, H.-Y. and Vial, A. and Milhiet, P.-E. and Robinson, C.V. and Schapiro, I. and Moraes, I. and Watts, A.}
}
@article {26378,
	title = {Transient Near-UV Absorption of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2: A Spectroscopic Marker for Retinal Configuration},
	journal = {Journal of Physical Chemistry Letters},
	volume = {12},
	number = {27},
	year = {2021},
	note = {Export Date: 30 January 2022},
	month = {2021},
	pages = {6284 - 6291},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85111337057\&doi=10.1021\%2facs.jpclett.1c01436\&partnerID=40\&md5=074f65ce4cde957d5eea023c184a3af3},
	author = {Asido, M. and Kar, R.K. and Kriebel, C.N. and Braun, M. and Glaubitz, C. and Schapiro, I. and Wachtveitl, J.}
}
@article {26382,
	title = {Two-photon conversion of a bacterial phytochrome},
	journal = {Biophysical Journal},
	volume = {120},
	number = {5},
	year = {2021},
	note = {Cited By :2Export Date: 30 January 2022},
	month = {2021},
	pages = {964 - 974},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85101243282\&doi=10.1016\%2fj.bpj.2021.01.028\&partnerID=40\&md5=7811a13010f602d500aadc6298874f4b},
	author = {Sokolovski, S.G. and Zherebtsov, E.A. and Kar, R.K. and Golonka, D. and Stabel, R. and Chichkov, N.B. and Gorodetsky, A. and Schapiro, I. and M{\"o}glich, A. and Rafailov, E.U.}
}
@article {26384,
	title = {Binding affinity and mechanisms of SARS-CoV-2 variants},
	journal = {Computational and Structural Biotechnology Journal},
	volume = {19},
	year = {2021},
	note = {Cited By :4Export Date: 30 January 2022},
	month = {2021},
	pages = {4184 - 4191},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85111766326\&doi=10.1016\%2fj.csbj.2021.07.026\&partnerID=40\&md5=949850a3591d42dc55fae16912c228b4},
	author = {Han, Y. and Wang, Z. and Wei, Z. and Schapiro, I. and Li, J.}
}
@book {26386,
	title = {Computational Studies of Photochemistry in Phytochrome Proteins},
	series = {Challenges and Advances in Computational Chemistry and Physics},
	volume = {31},
	year = {2021},
	note = {Export Date: 30 January 2022},
	month = {2021},
	pages = {197 - 226},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85094566081\&doi=10.1007\%2f978-3-030-57721-6_4\&partnerID=40\&md5=0a2a42f1ede5621cd41315575869d0b6},
	author = {Church, J.R. and Rao, A.G. and Barnoy, A. and Wiebeler, C. and Schapiro, I.}
}
@article {26383,
	title = {Frontiers in Multiscale Modeling of Photoreceptor Proteins},
	journal = {Photochemistry and Photobiology},
	volume = {97},
	number = {2},
	year = {2021},
	note = {Cited By :5Export Date: 30 January 2022},
	month = {2021},
	pages = {243 - 269},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85100850859\&doi=10.1111\%2fphp.13372\&partnerID=40\&md5=847931448b2107c679cb1c5c97aabb85},
	author = {Mroginski, M.-A. and Adam, S. and Amoyal, G.S. and Barnoy, A. and Bondar, A.-N. and Borin, V.A. and Church, J.R. and Domratcheva, T. and Ensing, B. and Fanelli, F. and Ferr{\'e}, N. and Filiba, O. and Pedraza-Gonz{\'a}lez, L. and Gonz{\'a}lez, R. and Gonz{\'a}lez-Espinoza, C.E. and Kar, R.K. and Kemmler, L. and Kim, S.S. and Kongsted, J. and Krylov, A.I. and Lahav, Y. and Lazaratos, M. and NasserEddin, Q. and Navizet, I. and Nemukhin, A. and Olivucci, M. and Olsen, J.M.H. and P{\'e}rez de Alba Ort{\'\i}z, A. and Pieri, E. and Rao, A.G. and Rhee, Y.M. and Ricardi, N. and Sen, S. and Solov{\textquoteright}yov, I.A. and De Vico, L. and Wesolowski, T.A. and Wiebeler, C. and Yang, X. and Schapiro, I.}
}
@article {26385,
	title = {Insight into the isomerization mechanism of retinal proteins from hybrid quantum mechanics/molecular mechanics simulations},
	journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
	year = {2021},
	note = {Export Date: 30 January 2022},
	month = {2021},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85111156914\&doi=10.1002\%2fwcms.1562\&partnerID=40\&md5=3bc69366a1075afea33a81b7a6737acd},
	author = {Sen, S. and Kar, R.K. and Borin, V.A. and Schapiro, I.}
}
@article {26388,
	title = {Modulation of Light Energy Transfer from Chromophore to Protein in the Channelrhodopsin ReaChR},
	journal = {Biophysical Journal},
	volume = {119},
	number = {3},
	year = {2020},
	note = {Cited By :1Export Date: 30 January 2022},
	month = {2020},
	pages = {705 - 716},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85088223349\&doi=10.1016\%2fj.bpj.2020.06.031\&partnerID=40\&md5=eb1dd08eaac581eda4cbcceeefc25d95},
	author = {Kaufmann, J.C.D. and Krause, B.S. and Adam, S. and Ritter, E. and Schapiro, I. and Hegemann, P. and Bartl, F.J.}
}
@article {26387,
	title = {NeoR, a near-infrared absorbing rhodopsin},
	journal = {Nature Communications},
	volume = {11},
	number = {1},
	year = {2020},
	note = {Cited By :11Export Date: 30 January 2022},
	month = {2020},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85095766677\&doi=10.1038\%2fs41467-020-19375-8\&partnerID=40\&md5=3b0e15225ed6d978ab1d6f478f64e005},
	author = {Broser, M. and Spreen, A. and Konold, P.E. and Peter, E. and Adam, S. and Borin, V. and Schapiro, I. and Seifert, R. and Kennis, J.T.M. and Bernal Sierra, Y.A. and Hegemann, P.}
}
@article {26389,
	title = {Tuning Quantum Dots Coupling Using Organic Linkers with Different Vibrational Modes},
	journal = {Journal of Physical Chemistry C},
	volume = {124},
	number = {29},
	year = {2020},
	note = {Cited By :1Export Date: 30 January 2022},
	month = {2020},
	pages = {16159 - 16165},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85089818416\&doi=10.1021\%2facs.jpcc.0c03703\&partnerID=40\&md5=1cd1111443f3d9fce2f3bca66ab43ac1},
	author = {Kolodny, Y. and Fererra, S. and Borin, V. and Yochelis, S. and Dibenedetto, C.N. and Mor, M. and Dehnel, J. and Remmenik, S. and Fanizza, E. and Striccoli, M. and Schapiro, I. and E. Lifshitz and Paltiel, Y.}
}
@article {24766,
	title = {The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome},
	journal = {Proceedings of the National Academy of Sciences},
	year = {2020},
	month = {2020/06/26},
	pages = {201921706},
	abstract = {Bilin-binding photoreceptors are light-signaling proteins that mediate various processes from photomorphogenesis, phototaxis, chromatic acclimation, to photosynthesis. They are also promising tunable optical agents for use in optogenetics and superresolution microscopy. Using an integrated approach of crystallography, spectroscopy, and QM/MM calculations, this work examines the ultrafast dynamics of a photoactive single-domain phytochrome. Our work reveals in detail the critical role of the protein environment in defining the excited state lifetime and thereby the quantum efficiency of the bilin photoisomerization. This insight provides design principles for engineering of bilin-based photoreceptors for biotechnological and medical applications.Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z ⇄ E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. We have studied a single-domain bilin-binding photoreceptor All2699g1 (Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (Pr) and far red-absorbing (Pfr) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the Pr form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at \~{}300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.},
	url = {http://www.pnas.org/content/early/2020/06/25/1921706117.abstract},
	author = {Slavov, Chavdar and Fischer, Tobias and Barnoy, Avishai and Shin, Heewhan and Aditya G. Rao and Wiebeler, Christian and Zeng, Xiaoli and Sun, Yafang and Xu, Qianzhao and Gutt, Alexander and Zhao, Kai-Hong and Wolfgang G{\"a}rtner and Yang, Xiaojing and Schapiro, Igor and Wachtveitl, Josef}
}
@article {24685,
	title = {Spin-chemical effects on intramolecular photoinduced charge transfer reactions in bisphenanthroline copper(i)-viologen dyad assemblies},
	journal = {Chemical Science},
	volume = {11},
	number = {21},
	year = {2020},
	month = {2020},
	pages = {5511 - 5525},
	publisher = {The Royal Society of Chemistry},
	abstract = {Two covalently linked donor{\textendash}acceptor copper phenanthroline complexes (C{\textendash}A dyads) of interest for solar energy conversion/storage schemes, [Cu(i)(Rphen(OMV)24+)2]9+ = RC+A48+ with RC+ = [Cu(i)Rphen2]+ involving 2,9-methyl (R = Me) or 2,9-phenyl (R = Ph)-phenanthroline ligands that are 5,6-disubstituted by 4-(n-butoxy) linked methylviologen electron acceptor groups (A2+ = OMV2+), have been synthesized and investigated via quantum chemical calculations and nanosecond laser flash spectroscopy in 1,2-difluorobenzene/methanol (dfb/MeOH) mixtures. Upon photoexcitation, charge transfer (CT) states RC2+A+A36+ are formed in less than one ns and decay by charge recombination on a time scale of 6{\textendash}45 ns. The CT lifetime of RC2+A+A36+ has a strong dependence on MeOH solvent fraction when R = Me, but is unaffected if R = Ph. This solvent effect is due to coordination of MeOH solvent in MeC+A48+ (i.e. exciplex formation) allowed by conformational flattening of the ligand sphere, which cannot occur in PhC+A48+ having bulkier Phphen ligand framework. Interestingly, the decay time of the CT state increases for both species at low magnetic fields with a maximum increase of ca. 30\% at ca. 150 mT, then decreases as the field is increased up to 1500 mT, the highest field investigated. This magnetic field effect (MFE) is due to magnetic modulation of the spin dynamics interconverting 3CT and 1CT states. A quantitative modeling according to the radical pair mechanism involving ab initio multireference calculations of the complexes revealed that the spin process is dominated by the effect of Cu hyperfine coupling. The external magnetic field suppresses the hyperfine coupling induced spin state mixing thereby lengthening the CT decay time. This effect is counteracted by the field dependent processes of T0{\textendash}S mixing through the Δg-mechanism and by a local mode spin{\textendash}orbit mechanism. Further, the maximum MFE is limited by a finite rate of direct recombination of 3CT states and the spin-rotational mechanism of spin relaxation. This study provides a first comprehensive characterization of Cu(ii)-complex spin chemistry and highlights how spin chemistry can be used to manipulate solar energy harvesting and storage materials.},
	isbn = {2041-6520},
	url = {http://dx.doi.org/10.1039/D0SC00830C},
	author = {Lazorski, Megan S. and Schapiro, Igor and Gaddie, Ross S. and Lehnig, Ammon P. and Atanasov, Mihail and Neese, Frank and Steiner, Ulrich E. and Elliott, C. Michael}
}
@article {24684,
	title = {Modern quantum chemistry with [Open]Molcas},
	journal = {The Journal of Chemical Physics},
	volume = {152},
	number = {21},
	year = {2020},
	pages = {214117},
	doi = {10.1063/5.0004835},
	url = {https://aip.scitation.org/doi/abs/10.1063/5.0004835},
	author = {Aquilante, Francesco and Autschbach, Jochen and Alberto Baiardi and Stefano Battaglia and Borin, Veniamin A. and Chibotaru, Liviu F. and Irene Conti and De Vico, Luca and Micka{\"e}l Delcey and Fdez. Galv{\'a}n, Ignacio and Ferr{\'e}, Nicolas and Freitag, Leon and Garavelli, Marco and Xuejun Gong and Knecht, Stefan and Ernst D. Larsson and Lindh, Roland and Lundberg, Marcus and Malmqvist, Per {\r A}ke and Nenov, Artur and Norell, Jesper and Michael Odelius and Olivucci, Massimo and Thomas B. Pedersen and Laura Pedraza-Gonz{\'a}lez and Quan M. Phung and Pierloot, Kristine and Reiher, Markus and Schapiro, Igor and Segarra-Mart{\'\i}, Javier and Francesco Segatta and Luis Seijo and Sen, Saumik and Dumitru-Claudiu Sergentu and Stein, Christopher J. and Ungur, Liviu and Vacher, Morgane and Valentini, Alessio and Veryazov, Valera}
}
@article {24683,
	title = {Femtosecond-to-millisecond structural changes in a light-driven sodium pump},
	year = {2020},
	month = {2020},
	abstract = {Light-driven sodium pumps actively transport small cations across cellular membranes1. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience. Although the resting state structures of the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been solved2,3, it is unclear how structural alterations over time allow sodium to be translocated against a concentration gradient. Here, using the Swiss X-ray Free Electron Laser4, we have collected serial crystallographic data at ten pump{\textendash}probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds. Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds. Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond. In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit. These results provide direct molecular insight into the dynamics of active cation transport across biological membranes.},
	isbn = {1476-4687},
	url = {https://doi.org/10.1038/s41586-020-2307-8},
	author = {Skopintsev, Petr and Ehrenberg, David and Weinert, Tobias and James, Daniel and Kar, Rajiv K. and Johnson, Philip J. M. and Ozerov, Dmitry and Furrer, Antonia and Martiel, Isabelle and Dworkowski, Florian and Nass, Karol and Knopp, Gregor and Cirelli, Claudio and Arrell, Christopher and Gashi, Dardan and Mous, Sandra and Wranik, Maximilian and Gruhl, Thomas and Kekilli, Demet and Br{\"u}nle, Steffen and Deupi, Xavier and Schertler, Gebhard F. X. and Benoit, Roger M. and Panneels, Valerie and Nogly, Przemyslaw and Schapiro, Igor and Milne, Christopher and Heberle, Joachim and Standfuss, J{\"o}rg}
}
@article {24415,
	title = {Dynamic Properties of the Photosensory Domain of Deinococcus radiodurans Bacteriophytochrome},
	journal = {The Journal of Physical Chemistry BThe Journal of Physical Chemistry B},
	volume = {124},
	number = {9},
	year = {2020},
	month = {2020},
	pages = {1740 - 1750},
	publisher = {American Chemical Society},
	abstract = {Phytochromes are biological photoreceptors found in all kingdoms of life. Numerous physicochemical and spectroscopic studies of phytochromes have been carried out for many decades, both experimentally and computationally, with the main focus on the photoconversion mechanism involving a tetrapyrrole chromophore. In this computational work, we concentrate on the long-scale dynamic motion of the photosensory domain of Deinococcus radiodurans by means of classical all-atom molecular dynamics (MD) simulations. Conventional and accelerated MD methods in combination with two different force fields, CHARMM27 and AMBER ff14SB, are tested in long atomistic simulations to confront the dynamics of monomer and dimer forms. These calculations highlight dissimilar equilibrium conformations in aqueous solutions and, in turn, different large-scale dynamic behaviors of the monomer form vs the dimer form. While the phytochrome in a monomer form tends to close the cavity entailed between the GAF and PHY domains, the opposite trend is predicted for the phytochrome dimer, which opens up as a consequence of the formation of strong salt bridges between the PHY domains of two molecules in water.Phytochromes are biological photoreceptors found in all kingdoms of life. Numerous physicochemical and spectroscopic studies of phytochromes have been carried out for many decades, both experimentally and computationally, with the main focus on the photoconversion mechanism involving a tetrapyrrole chromophore. In this computational work, we concentrate on the long-scale dynamic motion of the photosensory domain of Deinococcus radiodurans by means of classical all-atom molecular dynamics (MD) simulations. Conventional and accelerated MD methods in combination with two different force fields, CHARMM27 and AMBER ff14SB, are tested in long atomistic simulations to confront the dynamics of monomer and dimer forms. These calculations highlight dissimilar equilibrium conformations in aqueous solutions and, in turn, different large-scale dynamic behaviors of the monomer form vs the dimer form. While the phytochrome in a monomer form tends to close the cavity entailed between the GAF and PHY domains, the opposite trend is predicted for the phytochrome dimer, which opens up as a consequence of the formation of strong salt bridges between the PHY domains of two molecules in water.},
	isbn = {1520-6106},
	url = {https://doi.org/10.1021/acs.jpcb.0c00612},
	author = {Battocchio, Giovanni and Gonz{\'a}lez, Ronald and Aditya G. Rao and Schapiro, Igor and Mroginski, Maria Andrea}
}
@article {24414,
	title = {Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein},
	year = {2020},
	month = {2020},
	abstract = {ABC importers are membrane proteins responsible for the transport of nutrients into the cells of prokaryotes. Although the structures of ABC importers vary, all contain four conserved domains: two nucleotide-binding domains (NBDs), which bind and hydrolyze ATP, and two transmembrane domains (TMDs), which help translocate the substrate. ABC importers are also dependent on an additional protein component, a high-affinity substrate-binding protein (SBP) that specifically binds the target ligand for delivery to the appropriate ABC transporter. AbnE is a SBP belonging to the ABC importer for arabino-oligosaccharides in the Gram-positive thermophilic bacterium Geobacillus stearothermophilus. Using isothermal titration calorimetry (ITC), purified AbnE was shown to bind medium-sized arabino-oligosaccharides, in the range of arabino-triose (A3) to arabino-octaose (A8), all with Kd values in the nanomolar range. We describe herein the 3D structure of AbnE in its closed conformation\&nbsp;in complex with a wide range of arabino-oligosaccharide substrates (A2-A8). These structures provide the basis for the detailed structural analysis of the AbnE-sugar complexes, and together with complementary quantum chemical calculations, site-specific mutagenesis, and isothermal titration calorimetry (ITC) experiments, provide detailed insights into the AbnE-substrate interactions involved. Small-angle X-ray scattering (SAXS) experiments and normal mode analysis (NMA) are used to study the conformational changes of AbnE, and these data, taken together, suggest clues regarding its binding mode to the full ABC importer.},
	keywords = {ABC transporter, Arabinan utilization system, arabinose, substrate-binding protein},
	isbn = {0022-2836},
	url = {http://www.sciencedirect.com/science/article/pii/S0022283620301078},
	author = {Lansky, Shifra and Salama, Rachel and Shulami, Smadar and Lavid, Noa and Sen, Saumik and Schapiro, Igor and Shoham, Yuval and Shoham, Gil}
}
@article {24413,
	title = {Ultrafast Backbone Protonation in Channelrhodopsin-1 Captured by Polarization Resolved Fs Vis-pump\&mdash;IR-Probe Spectroscopy and Computational Methods},
	journal = {Molecules},
	volume = {25},
	number = {4},
	year = {2020},
	abstract = {Channelrhodopsins (ChR) are light-gated ion-channels heavily used in optogenetics. Upon light excitation an ultrafast all-trans to 13-cis isomerization of the retinal chromophore takes place. It is still uncertain by what means this reaction leads to further protein changes and channel conductivity. Channelrhodopsin-1 in Chlamydomonas augustae exhibits a 100 fs photoisomerization and a protonated counterion complex. By polarization resolved ultrafast spectroscopy in the mid-IR we show that the initial reaction of the retinal is accompanied by changes in the protein backbone and ultrafast protonation changes at the counterion complex comprising Asp299 and Glu169. In combination with homology modelling and quantum mechanics/molecular mechanics (QM/MM) geometry optimization we assign the protonation dynamics to ultrafast deprotonation of Glu169, and transient protonation of the Glu169 backbone, followed by a proton transfer from the backbone to the carboxylate group of Asp299 on a timescale of tens of picoseconds. The second proton transfer is not related to retinal dynamics and reflects pure protein changes in the first photoproduct. We assume these protein dynamics to be the first steps in a cascade of protein-wide changes resulting in channel conductivity.\&nbsp;},
	author = {Stensitzki, Till and Adam, Suliman and Schlesinger, Ramona and Schapiro, Igor and Heyne, Karsten}
}
@article {24412,
	title = {Intramolecular Proton Transfer Controls Protein Structural Changes in Phytochrome},
	journal = {BiochemistryBiochemistry},
	volume = {59},
	number = {9},
	year = {2020},
	note = {doi: 10.1021/acs.biochem.0c00053},
	month = {2020},
	pages = {1023-1037},
	publisher = {American Chemical Society},
	abstract = {Phytochromes are biological photoswitches that interconvert between two parent states (Pr and Pfr). The transformation is initiated by photoisomerization of the tetrapyrrole chromophore, followed by a sequence of chromophore and protein structural changes. In the last step, a phytochrome-specific peptide segment (tongue) undergoes a secondary structure change, which in prokaryotic phytochromes is associated with the (de)activation of the output module. The focus of this work is the Pfr-to-Pr photoconversion of the bathy bacteriophytochrome Agp2 in which Pfr is the thermodynamically stable state. Using spectroscopic techniques, we studied the structural and functional consequences of substituting Arg211, Tyr165, His278, and Phe192 close to the biliverdin (BV) chromophore. In Pfr, substitutions of these residues do not affect the BV structure. The characteristic Pfr properties of bathy phytochromes, including the protonated propionic side chain of ring C (propC) of BV, are preserved. However, replacing Arg211 or Tyr165 blocks the photoconversion in the Meta-F state, prior to the secondary structure transition of the tongue and without deprotonation of propC. The Meta-F state of these variants displays low photochemical activity, but electronic excitation causes ultrafast alterations of the hydrogen bond network surrounding the chromophore. In all variants studied here, thermal back conversion from the photoproducts to Pfr is decelerated but substitution of His278 or Phe192 is not critical for the Pfr-to-Pr photoconversion. These variants do not impair deprotonation of propC or the α-helix/β-sheet transformation of the tongue during the Meta-F-to-Pr decay. Thus, we conclude that propC deprotonation is essential for restructuring of the tongue.Phytochromes are biological photoswitches that interconvert between two parent states (Pr and Pfr). The transformation is initiated by photoisomerization of the tetrapyrrole chromophore, followed by a sequence of chromophore and protein structural changes. In the last step, a phytochrome-specific peptide segment (tongue) undergoes a secondary structure change, which in prokaryotic phytochromes is associated with the (de)activation of the output module. The focus of this work is the Pfr-to-Pr photoconversion of the bathy bacteriophytochrome Agp2 in which Pfr is the thermodynamically stable state. Using spectroscopic techniques, we studied the structural and functional consequences of substituting Arg211, Tyr165, His278, and Phe192 close to the biliverdin (BV) chromophore. In Pfr, substitutions of these residues do not affect the BV structure. The characteristic Pfr properties of bathy phytochromes, including the protonated propionic side chain of ring C (propC) of BV, are preserved. However, replacing Arg211 or Tyr165 blocks the photoconversion in the Meta-F state, prior to the secondary structure transition of the tongue and without deprotonation of propC. The Meta-F state of these variants displays low photochemical activity, but electronic excitation causes ultrafast alterations of the hydrogen bond network surrounding the chromophore. In all variants studied here, thermal back conversion from the photoproducts to Pfr is decelerated but substitution of His278 or Phe192 is not critical for the Pfr-to-Pr photoconversion. These variants do not impair deprotonation of propC or the α-helix/β-sheet transformation of the tongue during the Meta-F-to-Pr decay. Thus, we conclude that propC deprotonation is essential for restructuring of the tongue.},
	isbn = {0006-2960},
	url = {https://doi.org/10.1021/acs.biochem.0c00053},
	author = {Kraskov, Anastasia and Nguyen, Anh Duc and Goerling, Jan and Buhrke, David and Velazquez Escobar, Francisco and Fernandez Lopez, Maria and Michael, Norbert and Sauthof, Luisa and Schmidt, Andrea and Piwowarski, Patrick and Yang, Yang and Stensitzki, Till and Adam, Suliman and Bartl, Franz and Schapiro, Igor and Heyne, Karsten and Siebert, Friedrich and Scheerer, Patrick and Mroginski, Maria Andrea and Hildebrandt, Peter}
}
@article {24350,
	title = {Structural elements regulating the photochromicity in a cyanobacteriochrome},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {117},
	number = {5},
	year = {2020},
	month = {2020/01/20},
	pages = {2432-2440},
	abstract = {Phytochromes and related photoreceptors distinguish themselves for their long-wavelength absorption and large spectral shift between parental state and photoproduct. Both features are not well understood, partly due to lack of high-resolution structural data and insufficient support from quantum-chemical calculations. The red{\textendash}green switching cyanobacteriochrome Slr1393g3 shows an absorption shift larger than 110 nm. Both parental state and photoproduct could be crystallized with high resolution, together with a {\textquotedblleft}hybrid{\textquotedblright} form carrying the chromophore in parental state geometry, whereas the protein remained in the photoproduct conformation. The crystal structures reveal how chromophore and protein mutually regulate their conformational changes, yielding the observed spectral shift. Quantum-chemical calculations, based on these structures, provide a deeper understanding of the spectral tuning mechanisms.The three-dimensional (3D) crystal structures of the GAF3 domain of cyanobacteriochrome Slr1393 (Synechocystis PCC6803) carrying a phycocyanobilin chromophore could be solved in both 15-Z dark-adapted state, Pr, λmax = 649 nm, and 15-E photoproduct, Pg, λmax = 536 nm (resolution, 1.6 and 1.86 {\r A}, respectively). The structural data allowed identifying the large spectral shift of the Pr-to-Pg conversion as resulting from an out-of-plane rotation of the chromophore{\textquoteright}s peripheral rings and an outward movement of a short helix formed from a formerly unstructured loop. In addition, a third structure (2.1-{\r A} resolution) starting from the photoproduct crystals allowed identification of elements that regulate the absorption maxima. In this peculiar form, generated during X-ray exposition, protein and chromophore conformation still resemble the photoproduct state, except for the D-ring already in 15-Z configuration and tilted out of plane akin the dark state. Due to its formation from the photoproduct, it might be considered an early conformational change initiating the parental state-recovering photocycle. The high quality and the distinct features of the three forms allowed for applying quantum-chemical calculations in the framework of multiscale modeling to rationalize the absorption maxima changes. A systematic analysis of the PCB chromophore in the presence and absence of the protein environment showed that the direct electrostatic effect is negligible on the spectral tuning. However, the protein forces the outer pyrrole rings of the chromophore to deviate from coplanarity, which is identified as the dominating factor for the color regulation.},
	url = {http://www.pnas.org/content/early/2020/01/17/1910208117.abstract},
	author = {Xu, Xiuling and Port, Astrid and Wiebeler, Christian and Zhao, Kai-Hong and Schapiro, Igor and Wolfgang G{\"a}rtner}
}
@article {24116,
	title = {Nuclear spin-hyperpolarization generated in a flavoprotein under illumination: experimental field-dependence and theoretical level crossing analysis},
	journal = {Scientific Reports},
	volume = {9},
	number = {1},
	year = {2019},
	pages = {18436},
	abstract = {The solid-state photo-chemically induced dynamic nuclear polarization (photo-CIDNP) effect generates non-equilibrium nuclear spin polarization in frozen electron-transfer proteins upon illumination and radical-pair formation. The effect can be observed in various natural photosynthetic reaction center proteins using magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, and in a flavin-binding light-oxygen-voltage (LOV) domain of the blue-light receptor phototropin. In the latter system, a functionally instrumental cysteine has been mutated to interrupt the natural cysteine-involving photochemistry allowing for an electron transfer from a more distant tryptophan to the excited flavin mononucleotide chromophore. We explored the solid-state photo-CIDNP effect and its mechanisms in phototropin-LOV1-C57S from the green alga Chlamydomonas reinhardtii by using field-cycling solution NMR. We observed the\&nbsp;13C and, to our knowledge, for the first time,\&nbsp;15N photo-CIDNP signals from phototropin-LOV1-C57S. Additionally, the\&nbsp;1H photo-CIDNP signals of residual water in the deuterated buffer of the protein were detected. The relative strengths of the photo-CIDNP effect from the three types of nuclei,\&nbsp;1H,\&nbsp;13C and\&nbsp;15N were measured in dependence of the magnetic field, showing their maximum polarizations at different magnetic fields. Theoretical level crossing analysis demonstrates that anisotropic mechanisms play the dominant role at high magnetic fields.},
	author = {Ding, Yonghong and Kiryutin, Alexey S. and Yurkovskaya, Alexandra V. and Sosnovsky, Denis V. and Sagdeev, Renad Z. and Bannister, Saskia and Kottke, Tilman and Kar, Rajiv Kumar and Schapiro, Igor and Ivanov, Konstantin L. and Matysik, J{\"o}rg}
}
@article {C9PP00223E,
	title = {Synthesis, spectroscopy and QM/MM simulations of a biomimetic ultrafast light-driven molecular motor},
	journal = {Photochem. Photobiol. Sci.},
	volume = {18},
	year = {2019},
	pages = {2259-2269},
	publisher = {The Royal Society of Chemistry},
	abstract = {A molecular motor potentially performing a continuous unidirectional rotation is studied by a multidisciplinary approach including organic synthesis, transient spectroscopy and excited state trajectory calculations. A stereogenic center was introduced in the N-alkylated indanylidene{\textendash}pyrroline Schiff base framework of a previously investigated light-driven molecular switch in order to achieve the unidirectional CC rotary motion typical of Feringa{\textquoteright}s motor. Here we report that the specific substitution pattern of the designed chiral molecule must critically determine the unidirectional efficiency of the light-induced rotary motion. More specifically, we find that a stereogenic center containing a methyl group and a hydrogen atom as substituents does not create a differential steric effect large enough to fully direct the motion in either the clockwise or counterclockwise direction especially along the E {\textrightarrow} Z coordinate. However, due to the documented ultrafast character and electronic circular dichroism activity of the investigated system, we find that it provides the basis for development of a novel generation of rotary motors with a biomimetic framework and operating on a picosecond time scale.},
	doi = {10.1039/C9PP00223E},
	url = {http://dx.doi.org/10.1039/C9PP00223E},
	author = {Schapiro, Igor and Gueye, Moussa and Paolino, Marco and Fusi, Stefania and Marchand, Gabriel and Haacke, Stefan and Martin, M. Elena and Mark Huntress and Vysotskiy, Victor P. and Veryazov, Valera and L{\'e}onard, J{\'e}r{\'e}mie and Olivucci, Massimo}
}
@article {molecules24091720,
	title = {QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra},
	journal = {Molecules},
	volume = {24},
	number = {9},
	year = {2019},
	abstract = {Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that are promising candidates for biotechnological applications. Computational studies can contribute to an understanding at a molecular level of their wide spectral tuning and diversity. In this contribution, we benchmark methods to model a 110 nm shift in the UV/Vis absorption spectrum from a red- to a green-absorbing form of the cyanobacteriochrome Slr1393g3. Based on an assessment of semiempirical methods to describe the chromophore geometries of both forms in vacuo, we find that DFTB2+D leads to structures that are the closest to the reference method. The benchmark of the excited state calculations is based on snapshots from quantum mechanics/molecular mechanics molecular dynamics simulations. In our case, the methods RI-ADC(2) and sTD-DFT based on CAM-B3LYP ground state calculations perform the best, whereas no functional can be recommended to simulate the absorption spectra of both forms with time-dependent density functional theory. Furthermore, the difference in absorption for the lowest energy absorption maxima of both forms can already be modelled with optimized structures, but sampling is required to improve the shape of the absorption bands of both forms, in particular for the second band. This benchmark study can guide further computational studies, as it assesses essential components of a protocol to model the spectral tuning of both cyanobacteriochromes and the related phytochromes.},
	issn = {1420-3049},
	doi = {10.3390/molecules24091720},
	url = {https://www.mdpi.com/1420-3049/24/9/1720},
	author = {Wiebeler, Christian and Schapiro, Igor}
}
@article {doi:10.1002/anie.201810266,
	title = {The Effective Conjugation Length Is Responsible for the Red/Green Spectral Tuning in the Cyanobacteriochrome Slr1393g3},
	journal = {Angewandte Chemie International Edition},
	volume = {58},
	number = {7},
	year = {2019},
	pages = {1934-1938},
	abstract = {Abstract The origin of the spectral shift from a red- to a green-absorbing form in a cyanobacteriochrome, Slr1393g3, was identified by combined quantum mechanics/molecular mechanics simulations. This protein, related to classical phytochromes, carries the open-chain tetrapyrrole chromophore phycocyanobilin. Our calculations reveal that the effective conjugation length in the chromophore becomes shorter upon conversion from the red to the green form. This is related to the planarity of the entire chromophore. A large distortion was found for the terminal pyrrole rings A and D; however, the D ring contributes more strongly to the photoproduct tuning, despite a larger change in the twist of the A ring. Our findings implicate that the D ring twist can be exploited to regulate the absorption of the photoproduct. Hence, mutations that affect the D ring twist can lead to rational tuning of the photoproduct absorption, allowing the tailoring of cyanobacteriochromes for biotechnological applications such as optogenetics and bioimaging.},
	keywords = {chromophores, cyanobacteriochromes, hybrid QM/MM, spectral tuning, tetrapyrroles},
	doi = {10.1002/anie.201810266},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201810266},
	author = {Wiebeler, Christian and Aditya G. Rao and Wolfgang G{\"a}rtner and Schapiro, Igor}
}
@article {24112,
	title = {OpenMolcas: From Source Code to Insight},
	journal = {Journal of Chemical Theory and ComputationJournal of Chemical Theory and Computation},
	volume = {15},
	number = {11},
	year = {2019},
	note = {doi: 10.1021/acs.jctc.9b00532},
	month = {2019},
	pages = {5925 - 5964},
	publisher = {American Chemical Society},
	abstract = {In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.},
	isbn = {1549-9618},
	url = {https://doi.org/10.1021/acs.jctc.9b00532},
	author = {Fdez. Galv{\'a}n, Ignacio and Vacher, Morgane and Alavi, Ali and Angeli, Celestino and Aquilante, Francesco and Autschbach, Jochen and Bao, Jie J. and Bokarev, Sergey I. and Bogdanov, Nikolay A. and Carlson, Rebecca K. and Chibotaru, Liviu F. and Creutzberg, Joel and Dattani, Nike and Delcey, Micka{\"e}l G. and Dong, Sijia S. and Andreas Dreuw and Freitag, Leon and Frutos, Luis Manuel and Gagliardi, Laura and Gendron, Fr{\'e}d{\'e}ric and Giussani, Angelo and Gonz{\'a}lez, Leticia and Grell, Gilbert and Guo, Meiyuan and Hoyer, Chad E. and Johansson, Marcus and Keller, Sebastian and Knecht, Stefan and Kova{\v c}evi{\'c}, Goran and K{\"a}llman, Erik and Li Manni, Giovanni and Lundberg, Marcus and Ma, Yingjin and Mai, Sebastian and Malhado, Jo{\~a}o Pedro and Malmqvist, Per {\r A}ke and Marquetand, Philipp and Mewes, Stefanie A. and Norell, Jesper and Olivucci, Massimo and Oppel, Markus and Phung, Quan Manh and Pierloot, Kristine and Plasser, Felix and Reiher, Markus and Sand, Andrew M. and Schapiro, Igor and Sharma, Prachi and Stein, Christopher J. and S{\o}rensen, Lasse Kragh and Donald G. Truhlar and Ugandi, Mihkel and Ungur, Liviu and Valentini, Alessio and Vancoillie, Steven and Veryazov, Valera and Weser, Oskar and Weso{\l}owski, Tomasz A. and Widmark, Per-Olof and Wouters, Sebastian and Zech, Alexander and Zobel, J. Patrick and Lindh, Roland}
}
@article {app9224905,
	title = {Atomistic Insight into the Role of Threonine 127 in the Functional Mechanism of Channelrhodopsin-2},
	journal = {Applied Sciences},
	volume = {9},
	number = {22},
	year = {2019},
	abstract = {Channelrhodopsins (ChRs) belong to the unique class of light-gated ion channels. The structure of channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) has been resolved, but the mechanistic link between light-induced isomerization of the chromophore retinal and channel gating remains elusive. Replacements of residues C128 and D156 (DC gate) resulted in drastic effects in channel closure. T127 is localized close to the retinal Schiff base and links the DC gate to the Schiff base. The homologous residue in bacteriorhodopsin (T89) has been shown to be crucial for the visible absorption maximum and dark\&ndash;light adaptation, suggesting an interaction with the retinylidene chromophore, but the replacement had little effect on photocycle kinetics and proton pumping activity. Here, we show that the T127A and T127S variants of CrChR2 leave the visible absorption maximum unaffected. We inferred from hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and resonance Raman spectroscopy that the hydroxylic side chain of T127 is hydrogen-bonded to E123 and the latter is hydrogen-bonded to the retinal Schiff base. The C=N\&ndash;H vibration of the Schiff base in the T127A variant was 1674 cm\&minus;1, the highest among all rhodopsins reported to date. We also found heterogeneity in the Schiff base ground state vibrational properties due to different rotamer conformations of E123. The photoreaction of T127A is characterized by a long-lived P2380 state during which the Schiff base is deprotonated. The conservative replacement of T127S hardly affected the photocycle kinetics. Thus, we inferred that the hydroxyl group at position 127 is part of the proton transfer pathway from D156 to the Schiff base during rise of the P3530 intermediate. This finding provides molecular reasons for the evolutionary conservation of the chemically homologous residues threonine, serine, and cysteine at this position in all channelrhodopsins known so far.},
	issn = {2076-3417},
	doi = {10.3390/app9224905},
	url = {https://www.mdpi.com/2076-3417/9/22/4905},
	author = {Ehrenberg, David and Krause, Nils and Saita, Mattia and Bamann, Christian and Kar, Rajiv K. and Hoffmann, Kirsten and Heinrich, Dorothea and Schapiro, Igor and Heberle, Joachim and Schlesinger, Ramona}
}
@article {22577,
	title = {Spectroscopic Properties of Lumiflavin: A Quantum Chemical Study},
	journal = {Photochemistry and Photobiology},
	volume = {95},
	number = {2},
	year = {2019},
	note = {doi: 10.1111/php.13023},
	month = {2018},
	pages = {662-674},
	publisher = {John Wiley \& Sons, Ltd},
	abstract = {Abstract In this work, the electronic structure and spectroscopic properties of lumiflavin are calculated using various quantum chemical methods. The excitation energies for ten singlet and triplet states as well as the analysis of the electron density difference are assessed using various wave function-based methods and density functionals. The relative order of singlet and triplet excited states is established on the basis of the coupled cluster method CC2. We find that at least seven singlet excited states are required to assign all peaks in the UV/Vis spectrum. In addition, we have studied the solvatochromic effect on the excitation energies and found differential effects except for the first bright excited state. Vibrational frequencies as well as IR, Raman and resonance Raman intensities are simulated and compared to their experimental counterparts. We have assigned peaks, assessed the effect of anharmonicity, and confirmed the previous assignments in case of the most intense transitions. Finally, we have studied the NMR shieldings and established the effect of the solvent polarity. The present study provides data for lumiflavin in the gas phase and in implicit solvent model that can be used as a reference for the protein-embedded flavin simulations and assignment of experimental spectra.},
	isbn = {0031-8655},
	url = {https://doi.org/10.1111/php.13023},
	author = {Kar, Rajiv Kumar and Borin, Veniamin A. and Ding, Yonghong and Matysik, J{\"o}rg and Schapiro, Igor}
}
@article {22576,
	title = {Counterion-controlled spectral tuning of the protonated Schiff-base retinal},
	journal = {Physical Review A},
	volume = {98},
	number = {4},
	year = {2018},
	month = {2018/10/23/},
	pages = {043428},
	publisher = {American Physical Society},
	abstract = {Color vision is based on the ability of different opsin proteins to tune the absorption band of their chromophore, the retinal protonated Schiff base (RPSB). Two main mechanisms proposed for this tunability are geometric and electrostatic. Here we probe the latter effect experimentally and by a quantum chemical calculation of the absorption by an isolated complex containing the retinal chromophore and molecules with a strong dipole moment. Betaine complexation causes an anomalously large blue shift. The shift provides direct evidence that the strong charge-transfer character of the electronic transition is the cause of the opsin shift, and shows that the electric field of the counterion is responsible for the color tuning, which allows absorption of light in the blue region of the visible spectrum by opsin proteins.},
	url = {https://link.aps.org/doi/10.1103/PhysRevA.98.043428},
	author = {Toker, Yoni and Langeland, Jeppe and Gruber, Elisabeth and Kj{\ae}r, Christina and Nielsen, Steen Br{\o}ndsted and Andersen, Lars H. and Borin, Veniamin A. and Schapiro, Igor}
}
@article {22575,
	title = {Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2},
	journal = {Physical Chemistry Chemical Physics},
	volume = {20},
	number = {43},
	year = {2018},
	month = {2018},
	pages = {27501 - 27509},
	publisher = {The Royal Society of Chemistry},
	abstract = {The first event of the channelrhodopsin-2 (ChR2) photocycle, i.e. trans-to-cis photoisomerization, is studied by means of quantum mechanics/molecular mechanics, taking into account the flexible retinal environment in the ground state. By treating the chromophore at the ab initio multiconfigurational level of theory, we can rationalize the experimental findings based on pump{\textendash}probe spectroscopy, explaining the different and more complex scenario found for ChR2 in comparison to other rhodopsins. In particular, we find that depending on the hydrogen bonding pattern, different excited states are involved, hence making it possible to suggest one pattern as the most productive. Moreover, after photoisomerization the structure of the first photocycle intermediate, P5001, is characterized by simulating the infrared spectrum and compared to available experimental data. This was obtained by extensive molecular dynamics, where the chromophore is described by a semi-empirical method based on density functional theory. The results clearly identify which counterion is responsible for accepting the proton from the retinal Schiff base: the side chain of the glutamic acid E123.},
	isbn = {1463-9076},
	url = {http://dx.doi.org/10.1039/C8CP05210G},
	author = {Guo, Yanan and Wolff, Franziska E. and Schapiro, Igor and Elstner, Marcus and Marazzi, Marco}
}
@article {22173,
	title = {A comprehensive benchmark of the XMS-CASPT2 method for the photochemistry of a retinal chromophore model},
	journal = {Molecular Physics},
	volume = {116},
	number = {19 - 20},
	year = {2018},
	note = {doi: 10.1080/00268976.2018.1501112},
	month = {2018},
	pages = {2571 - 2582},
	publisher = {Taylor \& Francis},
	abstract = {ABSTRACT The performance of the extended multi-state (XMS)-complete active space second-order perturbation theory (CASPT2) method has been assessed for the benchmark of a truncated retinal model, the penta-2,4-dieniminium cation (PSB3). This benchmark presents a challenge for multireference electronic structure methods because the wave function character is changing considerably. The assessment comprises ground and excited state pathways of the isomerisation, including transition states and conical intersection (CI) points. It also includes circular paths centred around different CIs, and 2D potential energy scans located in the branching planes. In this work, we compare the performance of the previous formulations of CASPT2, the single-state and the multi-state, with the recently developed XMS-CASPT2. Besides, we have also tested two variants of internal contraction in XMS-CASPT2, namely, the single-state single reference (SS-SR) and multi-state multireference (MS-MR) schemes. In our study, we find that XMS-CASPT2 corrects the artefacts and discontinuities present in other CASPT2 variants. The investigation of a circular loop and 2D potential energy surfaces around the surface crossing point shows that XMS-CASPT2 exhibits a smooth topology at the CI with the correct degeneracy. It also agrees better with the reference method MRCISD+Q in regions of the potential energy surfaces further away from CIs. Another observation is the close agreement between the results from the SS-SR contraction scheme and the more demanding MS-MR scheme.},
	isbn = {0026-8976},
	url = {https://doi.org/10.1080/00268976.2018.1501112},
	author = {Sen, Saumik and Schapiro, Igor}
}
@article {21973,
	title = {Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser},
	journal = {Science},
	year = {2018},
	month = {2018/06/14},
	abstract = {Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion-transport across bacterial membranes. We studied the sub-picosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin using an x-ray laser. A series of structural snapshots with near-atomic spatial and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket prior to passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key ingredient for this stereo-selective and efficient photochemical reaction.},
	url = {http://science.sciencemag.org/content/early/2018/06/13/science.aat0094.abstract},
	author = {Nogly, Przemyslaw and Weinert, Tobias and James, Daniel and Carbajo, Sergio and Ozerov, Dmitry and Furrer, Antonia and Gashi, Dardan and Borin, Veniamin and Skopintsev, Petr and Jaeger, Kathrin and Nass, Karol and B{\r a}th, Petra and Bosman, Robert and Koglin, Jason and Seaberg, Matthew and Lane, Thomas and Kekilli, Demet and Br{\"u}nle, Steffen and Tanaka, Tomoyuki and Wu, Wenting and Milne, Christopher and White, Thomas and Barty, Anton and Weierstall, Uwe and Panneels, Valerie and Nango, Eriko and Iwata, So and Hunter, Mark and Schapiro, Igor and Schertler, Gebhard and Neutze, Richard and Standfuss, J{\"o}rg}
}
@article {21526,
	title = {15N photo-CIDNP MAS NMR analysis of reaction centers of Chloracidobacterium thermophilum},
	journal = {Photosynthesis Research},
	volume = {137},
	number = {2},
	year = {2018},
	pages = {295-305},
	abstract = {Photochemically induced dynamic nuclear polarization (photo-CIDNP) has been observed in the homodimeric, type-1 photochemical reaction centers (RCs) of the acidobacterium, Chloracidobacterium (Cab.) thermophilum, by 15N magic-angle spinning (MAS) solid-state NMR under continuous white-light illumination. Three light-induced emissive (negative) signals are detected. In the RCs of Cab. thermophilum, three types of (bacterio)chlorophylls have previously been identified: bacteriochlorophyll a (BChl a), chlorophyll a (Chl a), and Zn-bacteriochlorophyll a' (Zn-BChl a') (Tsukatani et al. in J Biol Chem 287:5720{\textendash}5732, 2012). Based upon experimental and quantum chemical 15N NMR data, we assign the observed signals to a Chl a cofactor. We exclude Zn-BChl because of its measured spectroscopic properties. We conclude that Chl a is the primary electron acceptor, which implies that the primary donor is most likely Zn-BChl a'. Chl a and 81-OH Chl a have been shown to be the primary electron acceptors in green sulfur bacteria and heliobacteria, respectively, and thus a Chl a molecule serves this role in all known homodimeric type-1 RCs.},
	url = {https://link.springer.com/article/10.1007\%2Fs11120-018-0504-1},
	author = {Jeremias C. Zill and Zhihui He and Marcus Tank and Bryan H. Ferlez and Daniel P. Canniffe and Yigal Lahav and Peter Bellstedt and A. Alia and Schapiro, Igor and John H. Golbeck and Donald A. Bryant and Matysik, J{\"o}rg}
}
@article {21715,
	title = {Evidence for a vibrational phase-dependent isotope effect on the photochemistry of vision},
	journal = {Nature Chemistry},
	volume = {10},
	number = {4},
	year = {2018},
	month = {2018},
	pages = {449 - 455},
	abstract = {Vibronic coupling is key to efficient energy flow in molecular systems and a critical component of most mechanisms invoking quantum effects in biological processes. Despite increasing evidence for coherent coupling of electronic states being mediated by vibrational motion, it is not clear how and to what degree properties associated with vibrational coherence such as phase and coupling of atomic motion can impact the efficiency of light-induced processes under natural, incoherent illumination. Here, we show that deuteration of the H11{\textendash}C11=C12{\textendash}H12 double-bond of the 11-cis retinal chromophore in the visual pigment rhodopsin significantly and unexpectedly alters the photoisomerization yield while inducing smaller changes in the ultrafast isomerization dynamics assignable to known isotope effects. Combination of these results with non-adiabatic molecular dynamics simulations reveals a vibrational phase-dependent isotope effect that we suggest is an intrinsic attribute of vibronically coherent photochemical processes.},
	isbn = {1755-4349},
	url = {https://doi.org/10.1038/s41557-018-0014-y},
	author = {Schnedermann, C. and Yang, X. and Liebel, M. and Spillane, K. M. and Lugtenburg, J. and Fern{\'a}ndez, I. and Valentini, A. and Schapiro, I. and Olivucci, M. and Kukura, P. and Mathies, R. A.}
}
@article {22579,
	title = {Guiding a divergent reaction by photochemical control: bichromatic selective access to levulinates and butenolides},
	journal = {Chemical Science},
	volume = {9},
	number = {5},
	year = {2018},
	pages = {2041 - 6520},
	abstract = {Allylic and acrylic substrates may be efficiently transformed by a sequential bichromatic photochemical process into derivatives of levulinates or butenolides with high selectivity when phenanthrene is used as a regulator. Thus, UV-A photoinduced cross-metathesis (CM) couples the acrylic and allylic counterparts and subsequent UV-C irradiation initiates E{\textendash}Z isomerization of the carbon{\textendash}carbon double bond, followed by one of two competing processes; namely, cyclization by transesterification or a 1,5-H shift and tautomerization. Quantum chemical calculations demonstrate that intermediates are strongly blue-shifted for the cyclization while red-shifted for the 1,5-H shift reaction. Hence, delaying the double bond migration by employing UV-C absorbing phenanthrene, results in a selective novel divergent all-photochemical pathway for the synthesis of fundamental structural motifs of ubiquitous natural products.},
	url = {http://dx.doi.org/10.1039/C7SC05094A},
	author = {Sutar, Revannath~L. and Sen, Saumik and Eivgi, Or and Segalovich, Gal and Schapiro, Igor and Reany, Ofer and Lemcoff, N. Gabriel}
}
@article {19291,
	title = {A QM/MM study of the initial excited state dynamics of green-absorbing Proteorhodopsin},
	journal = {Faraday Discussions},
	volume = {207},
	year = {2018},
	note = {\&nbsp;Faraday Discussion: Light induced charge and energy transport in nucleic acids and proteins: general discussion\&nbsp;},
	month = {2017},
	pages = {137 - 152},
	publisher = {The Royal Society of Chemistry},
	abstract = {The primary photochemical reaction of the green-absorbing Proteorhodopsin is studied by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The simulations are based on a homology model derived from the blue-absorbing Proteorhodopsin crystal structure. The geometry of retinal and the surrounding sidechains in the protein binding pocket were optimized using the QM/MM method. Starting from this geometry the isomerization was studied with a relaxed scan along the C13=C14 dihedral. It revealed an "aborted bicycle pedal" mechanism of isomerization that was originally proposed by Warshel for bovine rhodopsin and bacteriorhodopsin. However, the isomerization involved the concerted rotation about C13=C14 and C15=N, with the latter being highly tiwsted but not isomerized. Further, the simulation showed an increased steric interaction between the hydrogen at the C14 of the isomerizing bond and the hydroxyl group at the neighbouring tyrosine 200. In addition, we have simulated a nonadiabatic trajectory which showed the timing of the isomerization. In the first 20 fs upon excitation the order of the conjugated double and single bonds is inverted, consecutively the C13=C14 rotation is activated for 200 fs until the S1-S0 transition is detected. However, the isomerization is reverted due to the specific interaction with the tyrosine as observed along the relaxed scan calculation. Our simulations indicate that the retinal - tyrosine 200 interaction plays an important role in the outcome of the photoisomerization.},
	isbn = {1359-6640},
	url = {http://dx.doi.org/10.1039/C7FD00198C},
	author = {Borin, Veniamin and Wiebeler, Christian and Schapiro, Igor}
}
@article {19294,
	title = {Introduction \&ndash; Festschrift in Honor of Prof. Volker Buβ},
	journal = {Photochemistry and Photobiology},
	volume = {93},
	number = {6},
	year = {2017},
	pages = {1335 - 1335},
	abstract = {We are very pleased to present this Festschrift in honor of our colleague, mentor and friend Prof. Volker Bu{\ss}, which was initiated to celebrate his 75th birthday. The aim of this special issue is to recollect his substantial contributions and achievements of his career in the field of Theoretical/Computational Photochemistry. This article is protected by copyright. All rights reserved.},
	isbn = {1751-1097},
	url = {http://dx.doi.org/10.1111/php.12850},
	author = {Schapiro, Igor and Weingart, Oliver}
}
@article {19293,
	title = {Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores},
	journal = {Chemical Reviews},
	volume = {117},
	number = {22},
	year = {2017},
	note = {doi: 10.1021/acs.chemrev.7b00177},
	month = {2017},
	pages = {13502 {\textendash} 13565},
	publisher = {American Chemical Society},
	abstract = {Ultrafast processes in light-absorbing proteins have been implicated in the primary step in the light-to-energy conversion and the initialization of photoresponsive biological functions. Theory and computations have played an instrumental role in understanding the molecular mechanism of such processes, as they provide a molecular-level insight of structural and electronic changes at ultrafast time scales that often are very difficult or impossible to obtain from experiments alone. Among theoretical strategies, the application of hybrid quantum mechanics and molecular mechanics (QM/MM) models is an important approach that has reached an evident degree of maturity, resulting in several important contributions to the field. This review presents an overview of state-of-the-art computational studies on subnanosecond events in rhodopsins, photoactive yellow proteins, phytochromes, and some other photoresponsive proteins where photoinduced double-bond isomerization occurs. The review also discusses current limitations that need to be solved in future developments.Ultrafast processes in light-absorbing proteins have been implicated in the primary step in the light-to-energy conversion and the initialization of photoresponsive biological functions. Theory and computations have played an instrumental role in understanding the molecular mechanism of such processes, as they provide a molecular-level insight of structural and electronic changes at ultrafast time scales that often are very difficult or impossible to obtain from experiments alone. Among theoretical strategies, the application of hybrid quantum mechanics and molecular mechanics (QM/MM) models is an important approach that has reached an evident degree of maturity, resulting in several important contributions to the field. This review presents an overview of state-of-the-art computational studies on subnanosecond events in rhodopsins, photoactive yellow proteins, phytochromes, and some other photoresponsive proteins where photoinduced double-bond isomerization occurs. The review also discusses current limitations that need to be solved in future developments.},
	isbn = {0009-2665},
	url = {http://dx.doi.org/10.1021/acs.chemrev.7b00177},
	author = {Samer Gozem and Luk, Hoi Ling and Schapiro, Igor and Olivucci, Massimo}
}
@article {19292,
	title = {Ir(III)-PC(sp3)P Bifunctional Catalysts for Production of H2 by Dehydrogenation of Formic Acid: Experimental and Theoretical Study},
	journal = {ACS Catalysis},
	year = {2017},
	note = {doi: 10.1021/acscatal.7b02482},
	month = {2017},
	pages = {8139 - 8146},
	publisher = {American Chemical Society},
	abstract = {Reversible storage of hydrogen in the form of stable and relatively harmless chemical substances such as formic acid (FA) is one of the cornerstones of a fossil-fuel-free economy. Recently, Ru(III)-PC(sp3)P (where PC(sp3)P = modular dibenzobarrelene-based pincer ligand possessing a pendant functional group) complex 1 has been reported as a mild and E-selective catalyst in semihydrogenation of alkynes with stoichiometric neat formic acid. Discovery of the additive-free protocol for dehydrogenation of FA launched further studies aiming at the rational design of highly efficient catalysts for this reaction operating under neutral conditions. We now report the results of our investigation on a series of bifunctionl PC(sp3)P complexes equipped with different outer-sphere auxiliaries, that allowed us to identify an amine-functionalized Ir(III)-PC(sp3)P complex 3, as a clean and efficient catalyst for the FA dehydrogenation. The catalyst is suitable for fuel-cell applications demonstrating a TON up to 5 {\texttimes} 105 and TOF up to 2 {\texttimes} 104 h{\textendash}1 (3.8 {\texttimes} 105 and 1.2 {\texttimes} 104 h{\textendash}1 with no additives). In addition to the practical value of the catalyst, experimental and computational mechanistic studies provide rationale for the design of improved next-generation catalysts.Reversible storage of hydrogen in the form of stable and relatively harmless chemical substances such as formic acid (FA) is one of the cornerstones of a fossil-fuel-free economy. Recently, Ru(III)-PC(sp3)P (where PC(sp3)P = modular dibenzobarrelene-based pincer ligand possessing a pendant functional group) complex 1 has been reported as a mild and E-selective catalyst in semihydrogenation of alkynes with stoichiometric neat formic acid. Discovery of the additive-free protocol for dehydrogenation of FA launched further studies aiming at the rational design of highly efficient catalysts for this reaction operating under neutral conditions. We now report the results of our investigation on a series of bifunctionl PC(sp3)P complexes equipped with different outer-sphere auxiliaries, that allowed us to identify an amine-functionalized Ir(III)-PC(sp3)P complex 3, as a clean and efficient catalyst for the FA dehydrogenation. The catalyst is suitable for fuel-cell applications demonstrating a TON up to 5 {\texttimes} 105 and TOF up to 2 {\texttimes} 104 h{\textendash}1 (3.8 {\texttimes} 105 and 1.2 {\texttimes} 104 h{\textendash}1 with no additives). In addition to the practical value of the catalyst, experimental and computational mechanistic studies provide rationale for the design of improved next-generation catalysts.},
	url = {http://dx.doi.org/10.1021/acscatal.7b02482},
	author = {Shirel Cohen and Borin, Veniamin and Schapiro, Igor and Musa, Sanaa and De-Botton, Sophie and Natalia V. Belkova and Gelman, Dmitri}
}
@article {15777,
	title = {Introduction, Festschrift in honor of Wolfgang G{\"a}rtner},
	journal = {Photochem Photobiol},
	volume = {93},
	number = {3},
	year = {2017},
	month = {2017},
	pages = {640 - 641},
	isbn = {1751-1097},
	url = {http://dx.doi.org/10.1111/php.12782},
	author = {Braslavsky, Silvia E. and Matysik, J{\"o}rg and Schapiro, Igor}
}
@article {15776,
	title = {Excitation Energies of Canonical Nucleobases Computed by Multiconfigurational Perturbation Theories},
	journal = {Photochem Photobiol},
	volume = {93},
	number = {3},
	year = {2017},
	month = {2017},
	pages = {888 - 902},
	abstract = {In this computational work, we assessed the performance of ab~initio multireference (MR) methods for the calculation of vertical excitation energies of five nucleobases: adenine, guanine, cytosine, thymine and uracil. In total, we have studied 38 singlet and 30 triplet excited states. Where possible we used the multireference configuration interaction (MRCI) method as a reference for various flavors of multireference perturbation theory to second order. In particular, we have benchmarked CASPT2, NEVPT2 and XMCQDPT2. For CASPT2, we have analyzed the single-state, multistate (MS) and extended MS variants. In addition, we have assessed the effect of the ionization potential electron affinity (IPEA) shift. For NEVPT2, we have used the partially and the strongly contracted variants. Further, we have tested the commonly used RI-CC2, RI-ADC2 and EOM-CCSD methods. Generally, we observe the following trends for singlet excited states: NEVPT2 is the closest MR method to MRCISD+Q, closely followed by CASPT2 with the default IPEA shift. The same trend is observed for triplet states, although NEVPT2 and CASPT2-IPEA are getting closer. Interestingly, the n, π* singlet excited states were described more accurately than π, π* excited states, while for triplet states the trend is inverted except for NEVPT2. This work is an important benchmark for future photochemical investigations.},
	isbn = {1751-1097},
	url = {http://dx.doi.org/10.1111/php.12765},
	author = {Wiebeler, Christian and Borin, Veniamin and Sanchez de Ara{\'u}jo, Adalberto Vasconcelos and Schapiro, Igor and Borin, Antonio Carlos}
}
@article {C6CP05231B,
	title = {Mechanism of excited state deactivation of indan-1-ylidene and fluoren-9-ylidene malononitriles},
	journal = {Phys. Chem. Chem. Phys.},
	volume = {18},
	year = {2016},
	pages = {32786-32795},
	publisher = {The Royal Society of Chemistry},
	abstract = {Herein, we report complementary computational and experimental evidence supporting the existence, for indan-1-ylidene malononitrile and fluoren-9-ylidene malononitrile, of a non-radiative decay channel involving double bond isomerisation motion. The results of UV-Vis transient absorption spectroscopy highlight that the decay takes place within hundreds of picoseconds. In order to understand the related molecular mechanism, photochemical reaction paths were computed by employing multiconfigurational quantum chemistry. The results indicate that the excited state deactivation occurs via concerted double bond twisting of the dicyanovinyl (DCV) unit coupled with a pyramidalisation of its substituted carbon. It is also shown that the observed differences in the excited state lifetimes when passing from indan-1-ylidene malononitrile to fluoren-9-ylidene are associated with the change in the topography of the conical intersection driving the decay from intermediate to sloped, respectively.},
	doi = {10.1039/C6CP05231B},
	url = {http://dx.doi.org/10.1039/C6CP05231B},
	author = {Estrada, Leandro A. and Frances-Monerris, Antonio and Schapiro, Igor and Olivucci, Massimo and Roca-Sanjuan, Daniel}
}
@article {9985,
	title = {Space and Time Evolution of the Electrostatic Potential during the Activation of a Visual Pigment},
	journal = {Journal of Physical Chemistry Letters},
	volume = {7},
	number = {13},
	year = {2016},
	note = {Export Date: 14 September 2016},
	month = {2016},
	pages = {2563 - 2567},
	abstract = {Animal and microbial retinal proteins employ the Schiff base of retinal as their chromophore. Here, the possible consequences of the charge translocation associated with the light-induced dynamics of the chromophore of a visual opsin are investigated along a representative semiclassical trajectory. We show that the evolution of the electrostatic potential projected by the chromophore onto the surrounding protein displays intense but topographically localized sudden variations in proximity of the decay region. pKa calculations carried out on selected snapshots used as probes, indicate that the only residue which may be sensitive to the electrostatic potential shift is Glu181. Accordingly, our results suggest that the frail Tyr191/268-Glu181-Wat2-Ser186 hydrogen bond network may be perturbed by the transient variations of the electrostatic potential. {\textcopyright} 2016 American Chemical Society.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84978953855\&partnerID=40\&md5=96815305f38750d3f5880b3bbe3dd8a7},
	author = {Melaccio, F. and Calimet, N. and Schapiro, I. and Valentini, A. and Cecchini, M. and Olivucci, M.}
}
@article {9986,
	title = {The Origin of Bond Selectivity and Excited-State Reactivity in Retinal Analogues},
	journal = {Journal of Physical Chemistry A},
	volume = {120},
	number = {19},
	year = {2016},
	note = {Export Date: 14 September 2016},
	month = {2016},
	pages = {3353 - 3365},
	abstract = {The effect of different conformations and substitutions on the photoisomerization of a retinal protonated Schiff base model is investigated by nonadiabatic molecular dynamics simulations. Three groups of retinal analogues are studied: (i) conformational isomers, (ii) methyl-substituted retinals, and (iii) C11-C12 bond locked retinals. In total 259 trajectories are calculated in the gas phase starting from different initial conditions. The effect on bond selectivity, the directionality of the isomerization, excited-state lifetime, and product distribution is derived from the ensemble of trajectories. Among the group of four isomers (9-, 11-, 13-cis, and all-trans) the 11-cis analogue is the most selective in terms of isomerizing double bond, while the other three produce a mixture of isomers. However, there is no preference for isomerization directionality and the product formation for the 11-cis isomer. In the group of analogues with different methylation patterns, it is found that a methyl group at position C10 can introduce unidirectionality. This methyl group also speeds the photoisomerization. In case of the analogue that is demethylated at the positions C10 and C13, all trajectories isomerize successfully from cis to trans conformation. The three C11-C12 bond locked retinals are found to have very different properties, which depend on the number of methylene units bridging this bond. The five-membered ring imposes a too-large restriction; hence, all trajectories remain on the excited state in the simulation time of 300 fs. The seven-membered ring is more flexible with preference for isomerization of the C9-C10 bond. Interestingly, the eight-membered ring leads to the fastest isomerization time and full directionality of C11-C12 bond isomerization. The trends observed in these simulations can help to understand whether the effects are intrinsic to the chromophore or are induced by the protein environment, by comparing to the trends from experiment. Furthermore, the derived understanding can support design of molecular motors to achieve high product yield and unidirectionality. {\textcopyright} 2016 American Chemical Society.},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84971324278\&partnerID=40\&md5=bb7c1e1c142d9feb1ab7be20a2ff8d4d},
	author = {Schapiro, I.}
}
@article {6208,
	title = {Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table},
	journal = {Journal of Computational Chemistry},
	volume = {37},
	number = {5},
	year = {2016},
	month = {2016/02/15},
	pages = {506 - 541},
	abstract = {In this report, we summarize and describe the recent unique updates and additions to the Molcas\&nbsp;quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas{\textendash}Kroll{\textendash}Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus\&nbsp;package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.},
	keywords = {electron correlation, gradients, molecular dynamics, parallelization, relativistic},
	isbn = {1096-987X},
	url = {http://dx.doi.org/10.1002/jcc.24221},
	author = {Aquilante, Francesco and Autschbach, Jochen and Carlson, Rebecca K. and Chibotaru, Liviu F. and Delcey, Micka{\"e}l G. and De Vico, Luca and Fdez. Galv{\'a}n, Ignacio and Ferr{\'e}, Nicolas and Frutos, Luis Manuel and Gagliardi, Laura and Garavelli, Marco and Giussani, Angelo and Hoyer, Chad E. and Li Manni, Giovanni and Lischka, Hans and Ma, Dongxia and Malmqvist, Per {\r A}ke and M{\"u}ller, Thomas and Nenov, Artur and Olivucci, Massimo and Pedersen, Thomas Bondo and Peng, Daoling and Plasser, Felix and Pritchard, Ben and Reiher, Markus and Rivalta, Ivan and Schapiro, Igor and Segarra-Mart{\'\i}, Javier and Stenrup, Michael and Truhlar, Donald G. and Ungur, Liviu and Valentini, Alessio and Vancoillie, Steven and Veryazov, Valera and Vysotskiy, Victor P. and Weingart, Oliver and Zapata, Felipe and Lindh, Roland}
}
@article {6209,
	title = {Rhodopsins carrying modified chromophores - the {\textquoteright}making of{\textquoteright}, structural modelling and their light-induced reactivity},
	journal = {Photochemical \& Photobiological Sciences},
	volume = {15},
	number = {2},
	year = {2016},
	month = {2016},
	pages = {297 - 308},
	publisher = {The Royal Society of Chemistry},
	abstract = {A series of vitamin-A aldehydes (retinals) with modified alkyl group substituents (9-demethyl-, 9-ethyl-, 9-isopropyl-, 10-methyl, 10-methyl-13-demethyl-, and 13-demethyl retinal) was synthesized and their 11-cis isomers were used as chromophores to reconstitute the visual pigment rhodopsin. Structural changes were selectively introduced around the photoisomerizing C11C12 bond. The effect of these structural changes on rhodopsin formation and bleaching was determined. Global fit of assembly kinetics yielded lifetimes and spectral features of the assembly intermediates. Rhodopsin formation proceeds stepwise with prolonged lifetimes especially for 9-demethyl retinal (longest lifetime τ3 = 7500 s, cf., 3500 s for retinal), and for 10-methyl retinal (τ3 = 7850 s). These slowed-down processes are interpreted as either a loss of fixation (9dm) or an increased steric hindrance (10me) during the conformational adjustment within the protein. Combined quantum mechanics and molecular mechanics (QM/MM) simulations provided structural insight into the retinal analogues-assembled, full-length rhodopsins. Extinction coefficients, quantum yields and kinetics of the bleaching process (μs-to-ms time range) were determined. Global fit analysis yielded lifetimes and spectral features of bleaching intermediates, revealing remarkably altered kinetics: whereas the slowest process of wild-type rhodopsin and of bleached and 11-cis retinal assembled rhodopsin takes place with lifetimes of 7 and 3.8 s, respectively, this process for 10-methyl-13-demethyl retinal was nearly 10 h (34670 s), coming to completion only after ca. 50 h. The structural changes in retinal derivatives clearly identify the precise interactions between chromophore and protein during the light-induced changes that yield the outstanding efficiency of rhodopsin.},
	isbn = {1474-905X},
	url = {http://dx.doi.org/10.1039/C5PP00322A},
	author = {Ockenfels, Andreas and Schapiro, Igor and Gartner, Wolfgang}
}
@article {5768,
	title = {Directionality of double-bond photoisomerization dynamics induced by a single stereogenic center},
	journal = {Journal of Physical Chemistry Letters},
	volume = {6},
	number = {4},
	year = {2015},
	note = {Cited By :3Export Date: 25 January 2016},
	month = {2015},
	pages = {599 - 604},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84923358361\&partnerID=40\&md5=4a363f7a65dfcd55c11ccd3088d13ab6},
	author = {Marchand, G. and Eng, J. and Schapiro, I. and Valentini, A. and Frutos, L.M. and Pieri, E. and Olivucci, M. and L{\'e}onard, J. and Gindensperger, E.}
}
@article {5767,
	title = {A surface hopping algorithm for nonadiabatic minimum energy path calculations},
	journal = {Journal of Computational Chemistry},
	volume = {36},
	number = {5},
	year = {2015},
	note = {Export Date: 25 January 2016},
	month = {2015},
	pages = {312 - 320},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84921503767\&partnerID=40\&md5=84aef23989ed2cc1d09b75db8c2aee12},
	author = {Schapiro, I. and Roca-Sanju{\'a}n, D. and Lindh, R. and Olivucci, M.}
}
@article {5766,
	title = {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},
	journal = {Journal of Chemical Theory and Computation},
	volume = {11},
	number = {12},
	year = {2015},
	note = {Export Date: 25 January 2016},
	month = {2015},
	pages = {5758 - 5781},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84949671523\&partnerID=40\&md5=38d806751d8d606d85ee86faa6f666f3},
	author = {Tuna, D. and Lefrancois, D. and Wola{\'n}ski, L. and Gozem, S. and Schapiro, I. and Andruni{\'o}w, T. and Dreuw, A. and Olivucci, M.}
}
@article {21645,
	title = {Quantum coherence in photosynthesis for efficient solar-energy conversion},
	volume = {10},
	year = {2014},
	month = {2014},
	url = {https://doi.org/10.1038/nphys3017},
	author = {Romero, E.}
}
@article {5770,
	title = {A conical intersection controls the deactivation of the bacterial luciferase fluorophore},
	journal = {Angewandte Chemie - International Edition},
	volume = {53},
	number = {37},
	year = {2014},
	note = {Cited By :3Export Date: 25 January 2016},
	month = {2014},
	pages = {9870 - 9875},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84906950877\&partnerID=40\&md5=b2663920a0b15f28e97f5cde7b991843},
	author = {Gozem, S. and Mirzakulova, E. and Schapiro, I. and Melaccio, F. and Glusac, K.D. and Olivucci, M.}
}
@article {5769,
	title = {Initial excited-state dynamics of an N -alkylated indanylidene-pyrroline (NAIP) rhodopsin analog},
	journal = {Journal of Physical Chemistry B},
	volume = {118},
	number = {42},
	year = {2014},
	note = {Export Date: 25 January 2016},
	month = {2014},
	pages = {12243 - 12250},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84908134210\&partnerID=40\&md5=3c46971148ca54acbe67bc58a6474134},
	author = {Schapiro, I. and Fusi, S. and Olivucci, M. and Andruni{\'o}w, T. and Sasidharanpillai, S. and Loppnow, G.R.}
}
@article {5771,
	title = {SORCI for photochemical and thermal reaction paths: A benchmark study},
	journal = {Computational and Theoretical Chemistry},
	volume = {1040-1041},
	year = {2014},
	note = {Cited By :5Export Date: 25 January 2016},
	month = {2014},
	pages = {84 - 98},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84903815693\&partnerID=40\&md5=cf31f8865feaa5d98f9da69aecede555},
	author = {Schapiro, I. and Neese, F.}
}
@article {5772,
	title = {Ultrafast photochemistry of Anabaena Sensory Rhodopsin: Experiment and theory},
	journal = {Biochimica et Biophysica Acta - Bioenergetics},
	volume = {1837},
	number = {5},
	year = {2014},
	note = {Cited By :4Export Date: 25 January 2016},
	month = {2014},
	pages = {589 - 597},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84897115935\&partnerID=40\&md5=0760d32f0dc6369eefb91896f4fd49f9},
	author = {Schapiro, I. and Ruhman, S.}
}
@article {5776,
	title = {Assessment of density functional theory for describing the correlation effects on the ground and excited state potential energy surfaces of a retinal chromophore model},
	journal = {Journal of Chemical Theory and Computation},
	volume = {9},
	number = {9},
	year = {2013},
	note = {Cited By :22Export Date: 25 January 2016},
	month = {2013},
	pages = {3917 - 3932},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84884190066\&partnerID=40\&md5=84f294576d12ce54163bad11cdaab6a5},
	author = {Huix-Rotllant, M. and Filatov, M. and Gozem, S. and Schapiro, I. and Olivucci, M. and Ferr{\'e}, N.}
}
@article {5778,
	title = {Assessment of n-electron valence state perturbation theory for vertical excitation energies},
	journal = {Journal of Chemical Theory and Computation},
	volume = {9},
	number = {8},
	year = {2013},
	note = {Cited By :15Export Date: 25 January 2016},
	month = {2013},
	pages = {3567 - 3580},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84882423819\&partnerID=40\&md5=44882097a98e464172307bee840aaa5f},
	author = {Schapiro, I. and Sivalingam, K. and Neese, F.}
}
@article {5779,
	title = {Electronic structures of octahedral Ni(II) complexes with "click" derived triazole ligands: A combined structural, magnetometric, spectroscopic, and theoretical study},
	journal = {Inorganic Chemistry},
	volume = {52},
	number = {12},
	year = {2013},
	note = {Cited By :32Export Date: 25 January 2016},
	month = {2013},
	pages = {6880 - 6892},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84879245074\&partnerID=40\&md5=adfa2afefbc27600cb0a2f5e1ea143f1},
	author = {Schweinfurth, D. and Krzystek, J. and Schapiro, I. and Demeshko, S. and Klein, J. and Telser, J. and Ozarowski, A. and Su, C.-Y. and Meyer, F. and Atanasov, M. and Neese, F. and Sarkar, B.}
}
@article {5777,
	title = {Toward an understanding of the retinal chromophore in rhodopsin mimics},
	journal = {Journal of Physical Chemistry B},
	volume = {117},
	number = {35},
	year = {2013},
	note = {Cited By :5Export Date: 25 January 2016},
	month = {2013},
	pages = {10053 - 10070},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84883694932\&partnerID=40\&md5=57331adfd0199c99536539c56bcb682d},
	author = {Huntress, M.M. and Gozem, S. and Malley, K.R. and Jailaubekov, A.E. and Vasileiou, C. and Vengris, M. and Geiger, J.H. and Borhan, B. and Schapiro, I. and Larsen, D.S. and Olivucci, M.}
}
@article {5775,
	title = {Probing vibrationally mediated ultrafast excited-state reaction dynamics with multireference (CASPT2) trajectories},
	journal = {Journal of Physical Chemistry A},
	volume = {117},
	number = {44},
	year = {2013},
	note = {Export Date: 25 January 2016},
	month = {2013},
	pages = {11271 - 11275},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84887778137\&partnerID=40\&md5=6061219c28d5b0dd741f8e749b110e4e},
	author = {El-Khoury, P.Z. and Joseph, S. and Schapiro, I. and Gozem, S. and Olivucci, M. and Tarnovsky, A.N.}
}
@inbook {6279,
	title = {Ab Initio Investigation of Photochemical Reaction Mechanisms: From Isolated Molecules to Complex Environments},
	booktitle = {Handbook of Computational Chemistry},
	year = {2012},
	pages = {1359-1404},
	publisher = {Springer Netherlands},
	organization = {Springer Netherlands},
	address = {Amsterdam},
	abstract = {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.},
	url = {http://link.springer.com/referenceworkentry/10.1007/978-94-007-0711-5_39},
	author = {Schapiro, Igor and Patrick El-Khoury and Olivucci, Massimo}
}
@inbook {6280,
	title = {Computational Photochemistry and Photobiology},
	booktitle = {CRC Handbook of Organic Photochemistry and Photobiology},
	volume = {1},
	year = {2012},
	pages = {1029-1056},
	publisher = {CRC Press},
	organization = {CRC Press},
	edition = {3rd},
	address = {Boca Raton},
	url = {http://www.crcnetbase.com/doi/abs/10.1201/b12252-42},
	author = {Patrick Zakhia El-Khoury and Igor Schaprio and Mark Huntress and Federico Melaccio and Samer Gozem and Frutos, Luis Manuel and Olivucci, Massimo}
}
@article {5782,
	title = {Dynamic electron correlation effects on the ground state potential energy surface of a retinal chromophore model},
	journal = {Journal of Chemical Theory and Computation},
	volume = {8},
	number = {11},
	year = {2012},
	note = {Cited By :48Export Date: 25 January 2016},
	month = {2012},
	pages = {4069 - 4080},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84869024856\&partnerID=40\&md5=fa92048e5d00b8bc8096366e9f87e385},
	author = {Gozem, S. and Huntress, M. and Schapiro, I. and Lindh, R. and Granovsky, A.A. and C. Angeli and Olivucci, M.}
}
@article {5783,
	title = {The molecular mechanism of thermal noise in rod photoreceptors},
	journal = {Science},
	volume = {337},
	number = {6099},
	year = {2012},
	note = {Cited By :28Export Date: 25 January 2016},
	month = {2012},
	pages = {1225 - 1228},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84865826150\&partnerID=40\&md5=0248715067dccace5db88470283c0c57},
	author = {Gozem, S. and Schapiro, I. and Ferr{\'e}, N. and Olivucci, M.}
}
@article {5781,
	title = {Mechanistic origin of the vibrational coherence accompanying the photoreaction of biomimetic molecular switches},
	journal = {Chemistry - A European Journal},
	volume = {18},
	number = {48},
	year = {2012},
	note = {(selected as VIP: Very Important Paper and Journal Cover)},
	month = {2012},
	pages = {15296 - 15304},
	abstract = {
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{\textendash}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.



},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84869476439\&partnerID=40\&md5=cc38a9ec62ec7359515fac3b2ee5654e},
	author = {L{\'e}onard, J. and Schapiro, I. and Briand, J. and Fusi, S. and Paccani, R.R. and Olivucci, M. and Haacke, S.}
}
@article {5786,
	title = {The ultrafast photoisomerizations of rhodopsin and bathorhodopsin are modulated by bond length alternation and HOOP driven electronic effects},
	journal = {Journal of the American Chemical Society},
	volume = {133},
	number = {10},
	year = {2011},
	note = {Cited By :61Export Date: 25 January 2016},
	month = {2011},
	pages = {3354 - 3364},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79952601991\&partnerID=40\&md5=59910b8f619978086e4ad1577bba4842},
	author = {Schapiro, I. and Ryazantsev, M.N. and Frutos, L.M. and Ferr{\'e}, N. and Lindh, R. and Olivucci, M.}
}
@article {5784,
	title = {Fast excited-state deactivation in N(5)-ethyl-4a-hydroxyflavin pseudobase},
	journal = {Journal of Physical Chemistry B},
	volume = {115},
	number = {21},
	year = {2011},
	note = {Cited By :8Export Date: 25 January 2016},
	month = {2011},
	pages = {7136 - 7143},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79957602111\&partnerID=40\&md5=4e323aed46548b20f019cb7ca590d015},
	author = {Zhou, D. and Mirzakulova, E. and Khatmullin, R. and Schapiro, I. and Olivucci, M. and Glusac, K.D.}
}
@article {5785,
	title = {Using the computer to understand the chemistry of conical intersections},
	journal = {Photochemical and Photobiological Sciences},
	volume = {10},
	number = {6},
	year = {2011},
	note = {Cited By :22Export Date: 25 January 2016},
	month = {2011},
	pages = {867 - 886},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79958064739\&partnerID=40\&md5=6182e2f3ca0273a9a214f23d806dca95},
	author = {Schapiro, I. and Melaccio, F. and Laricheva, E.N. and Olivucci, M.}
}
@article {21649,
	title = {Experimental probing of conical intersection dynamics in the photodissociation of thioanisole},
	volume = {2},
	year = {2010},
	month = {2010},
	url = {https://doi.org/10.1038/nchem.702},
	author = {Lim, J. S. and Kim, S. K.}
}
@article {5788,
	title = {Computational photobiology and beyond},
	journal = {Australian Journal of Chemistry},
	volume = {63},
	number = {3},
	year = {2010},
	note = {Cited By :18Export Date: 25 January 2016},
	month = {2010},
	pages = {413 - 429},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-77950225543\&partnerID=40\&md5=ded94336b727fd6f7602842dab7cd6ae},
	author = {Schapiro, I. and Ryazantsev, M.N. and Ding, W.J. and Huntress, M.M. and Melaccio, F. and Andruniow, T. and Olivucci, M.}
}
@article {5787,
	title = {Matrix isolation and computational studies of the CF2I radical},
	journal = {Chemical Physics Letters},
	volume = {496},
	number = {1-3},
	year = {2010},
	note = {Cited By :5Export Date: 25 January 2016},
	month = {2010},
	pages = {68 - 73},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-77955557248\&partnerID=40\&md5=bd4b7c22f2ec5c88e836a141904321df},
	author = {El-Khoury, P.Z. and George, L. and Kalume, A. and Schapiro, I. and Olivucci, M. and Tarnovsky, A.N. and Reid, S.A.}
}
@article {5790,
	title = {Bicycle-pedal isomerization in a rhodopsin chromophore model},
	journal = {Journal of the American Chemical Society},
	volume = {131},
	number = {1},
	year = {2009},
	note = {Cited By :27Export Date: 25 January 2016},
	month = {2009},
	pages = {16 - 17},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-62649169301\&partnerID=40\&md5=a2146fcde465e5eed15639c82d0912f2},
	author = {Schapiro, I. and Weingart, O. and Buss, V.}
}
@article {5789,
	title = {Structure of the photochemical reaction path populated via promotion of CF2i2 into its first excited state},
	journal = {Journal of Physical Chemistry A},
	volume = {113},
	number = {40},
	year = {2009},
	note = {Cited By :6Export Date: 25 January 2016},
	month = {2009},
	pages = {10767 - 10771},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-70349693943\&partnerID=40\&md5=a9af4c3945a94ab7624a6dc26bae9a0e},
	author = {El-Khoury, P.Z. and Tarnovsky, A.N. and Schapiro, I. and Ryazantsev, M.N. and Olivucci, M.}
}
@article {5791,
	title = {Photochemistry of visual pigment chromophore models by ab initio molecular dynamics},
	journal = {Journal of Physical Chemistry B},
	volume = {111},
	number = {14},
	year = {2007},
	note = {Cited By :35Export Date: 25 January 2016},
	month = {2007},
	pages = {3782 - 3788},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-34248214178\&partnerID=40\&md5=b1ae39f8a1b37326144bbe38cf26f24d},
	author = {Weingart, O. and Schapiro, I. and Buss, V.}
}
@article {5792,
	title = {Bond torsion affects the product distribution in the photoreaction of retinal model chromophores},
	journal = {Journal of Molecular Modeling},
	volume = {12},
	number = {5},
	year = {2006},
	note = {Cited By :17Export Date: 25 January 2016},
	month = {2006},
	pages = {713 - 721},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-33746421450\&partnerID=40\&md5=6cf80e774a014ed9b7bc1b078d404439},
	author = {Weingart, O. and Schapiro, I. and Buss, V.}
}
