@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}
}
