Mikhail N. Ryazantsev

The ultrafast photoisomerizations of rhodopsin and bathorhodopsin are modulated by bond length alternation and HOOP driven electronic effects.

Rhodopsin (Rh) and bathorhodopsin (bathoRh) quantum-mechanics/molecular-mechanics models based on ab initio multiconfigurational wave functions are employed to look at the light induced π-bond breaking and reconstitution occurring during the Rh → bathoRh and bathoRh → Rh isomerizations. More specifically, semiclassical trajectory computations are used to compare the excited (S(1)) and ground (S(0)) state dynamics characterizing the opposite steps of the Rh/bathoRh photochromic cycle during the first 200 fs following photoexcitation. We show that the information contained in these data provide an unprecedented insight into the sub-picosecond π-bond reconstitution process which is at the basis of the reactivity of the protein embedded 11-cis and all-trans retinal chromophores. More specifically, the data point to the phase and amplitude of the skeletal bond length alternation stretching mode as the key factor switching the chromophore to a bonding state. It is also confirmed/found that the phase and amplitude of the hydrogen-out-of-plane mode controls the stereochemical outcome of the forward and reverse photoisomerizations.

An artificial molecular switch that mimics the visual pigment and completes its photocycle in picoseconds

Single molecules that act as light-energy transducers (e.g., converting the energy of a photon into atomic-level mechanical motion) are examples of minimal molecular devices. Here, we focus on a molecular switch designed by merging a conformationally locked diarylidene skeleton with a retinal-like Schiff base and capable of mimicking, in solution, different aspects of the transduction of the visual pigment Rhodopsin. Complementary ab initio multiconfigurational quantum chemistry-based computations and time-resolved spectroscopy are used to follow the light-induced isomerization of the switch in methanol. The results show that, similar to rhodopsin, the isomerization occurs on a 0.3-ps time scale and is followed by <10-ps cooling and solvation. The entire (2-photon-powered) switch cycle was traced by following the evolution of its infrared spectrum. These measurements indicate that a full cycle can be completed within 20 ps.

Modeling, Preparation, and Characterization of a Dipole Moment Switch Driven by Z/E Photoisomerization

We report the results of a multidisciplinary research effort where the methods of computational photochemistry and retrosynthetic analysis/synthesis have contributed to the preparation of a novel N-alkylated indanylidene-pyrroline Schiff base featuring an exocyclic double bond and a permanent zwitterionic head. We show that, due to its large dipole moment and efficient photoisomerization, such a system may constitute the prototype of a novel generation of electrostatic switches achieving a reversible light-induced dipole moment change on the order of 30 D. The modeling of a peptide fragment incorporating the zwitterionic head into a conformationally rigid side chain shows that the switch can effectively modulate the fluorescence of a tryptophan probe.

Computational Photobiology and Beyond

In this paper we review the results of a group of computational studies of the spectroscopy and photochemistry of light-responsive proteins. We focus on the use of quantum mechanics/molecular mechanics protocols based on a multiconfigurational quantum chemical treatment. More specifically, we discuss the use, limitations, and application of the ab initio CASPT2//CASSCF protocol that, presently, constitutes the method of choice for the investigation of excited state organic molecules, most notably, biological chromophores and fluorophores. At the end of this Review we will also see how the computational investigation of the visual photoreceptor rhodopsin is providing the basis for the design of light-driven artificial molecular devices.

An experimental and theoretical study on the formation of 2-methylnaphthalene (C11H10/C11H3D7) in the reactions of the para-tolyl (C7H7) and para-tolyl-d7 (C7D7) with vinylacetylene (C4H4).

We present for the very first time single collision experimental evidence that a methyl-substituted polycyclic aromatic hydrocarbon (PAH)-2-methylnaphthalene-can be formed without an entrance barrier via indirect scattering dynamics through a bimolecular collision of two non-PAH reactants: the para-tolyl radical and vinylacetylene. Theory shows that this reaction is initiated by the addition of the para-tolyl radical to either the terminal acetylene carbon (C(4)) or a vinyl carbon (C(1)) leading eventually to two distinct radical intermediates. Importantly, addition at C(1) was found to be barrierless via a van der Waals complex implying this mechanism can play a key role in forming methyl substituted PAHs in low temperature extreme environments such as the interstellar medium and hydrocarbon-rich atmospheres of planets and their moons in the outer Solar System. Both reaction pathways involve a sequence of isomerizations via hydrogen transfer, ring closure, ring-opening and final hydrogen dissociation through tight exit transition states to form 2-methylnaphthalene in an overall exoergic process. Less favorable pathways leading to monocyclic products are also found. Our studies predict that reactions of substituted aromatic radicals can mechanistically deliver odd-numbered PAHs which are formed in significant quantities in the combustion of fossil fuels.

Color Tuning in Rhodopsins: The Origin of the Spectral Shift between the Chloride-Bound and Anion-Free Forms of Halorhodopsin

Detailed knowledge of the molecular mechanisms that control the spectral properties in the rhodopsin protein family is important for understanding the functions of these photoreceptors and for the rational design of artificial photosensitive proteins. Here we used a high-level ab initio QM/MM method to investigate the mechanism of spectral tuning in the chloride-bound and anion-free forms of halorhodopsin from Natronobacterium pharaonis (phR) and the interprotein spectral shift between them. We demonstrate that the chloride ion tunes the spectral properties of phR via two distinct mechanisms: (i) electrostatic interaction with the chromophore, which results in a 95 nm difference between the absorption maxima of the two forms, and (ii) induction of a structural reorganization in the protein, which changes the positions of charged and polar residues and reduces this difference to 29 nm. The present study expands our knowledge concerning the role of the reorganization of the internal H-bond network for color tuning in general and provides a detailed investigation of the tuning mechanism in phR in particular.

Formation of 6-methyl-1,4-dihydronaphthalene in the reaction of the p-tolyl radical with 1,3-butadiene under single-collision conditions.

Crossed molecular beam reactions of p-tolyl (C7H7) plus 1,3-butadiene (C4H6), p-tolyl (C7H7) plus 1,3-butadiene-d6 (C4D6), and p-tolyl-d7 (C7D7) plus 1,3-butadiene (C4H6) were carried out under single-collision conditions at collision energies of about 55 kJ mol(-1). 6-Methyl-1,4-dihydronaphthalene was identified as the major reaction product formed at fractions of about 94% with the monocyclic isomer (trans-1-p-tolyl-1,3-butadiene) contributing only about 6%. The reaction is initiated by barrierless addition of the p-tolyl radical to the terminal carbon atom of the 1,3-butadiene via a van der Waals complex. The collision complex isomerizes via cyclization to a bicyclic intermediate, which then ejects a hydrogen atom from the bridging carbon to form 6-methyl-1,4-dihydronaphthalene through a tight exit transition state located about 27 kJ mol(-1) above the separated products. This is the dominant channel under the present experimental conditions. Alternatively, the collision complex can also undergo hydrogen ejection to form trans-1-p-tolyl-1,3-butadiene; this is a minor contributor to the present experiment. The de facto barrierless formation of a methyl-substituted aromatic hydrocarbons by dehydrogenation via a single event represents an important step in the formation of polycyclic aromatic hydrocarbons (PAHs) and their partially hydrogenated analogues in combustion flames and the interstellar medium.

Structure Of The Photochemical Reaction Path Populated Via Promotion Of Cf2i2 Into Its First Excited State

The photochemical reaction path following the promotion of CF(2)I(2) into its lowest-lying excited electronic singlet state has been modeled using ab initio multiconfigurational quantum chemical calculations. It is found that a conical intersection drives the electronically excited CF(2)I(2)* species either to the CF(2)I + I radical pair or back to the starting CF(2)I(2) structure. The structures of the computed relaxation pathways explain the photoproduct selectivity previously observed in the gas phase. Furthermore, the results provide the basis for explaining the condensed-phase photochemistry of CF(2)I(2).