Minimum energy paths in the excited and ground states of short protonated Schiff bases and of the analogous polyenes

Fluorescent Rhodopsins: A Challenging Test for Cost-Effective QM/MM Approaches

In this study, we evaluate the performance of two cost-effective models, namely, TD-DFT and ΔSCF methods, combined with different molecular mechanics models, to predict the photophysical and photochemical properties of a set of fluorescent mutants of the microbial rhodopsin Archaerhodopsin-3. We investigate absorption energies and excited-state isomerization barriers of the embedded retinal protonated Schiff-base chromophore by comparing different DFT functionals as well as different approximations of the embedding model. For absorption energies, CAM-B3LYP demonstrates the most consistent alignment with experiments among the functionals tested, whereas the embedding potentials exhibit similar accuracy. However, incorporating linear response corrections within the polarizable TD-DFT/MM framework enhances accuracy. The photoisomerization barriers, instead, exhibit a pronounced sensitivity to the choice of embedding model, underscoring the complex role that environmental factors play in modulating predictions of excited-state processes. For the two properties here investigated, ΔSCF/MM presents qualitatively similar behavior with respect to TD-DFT for all the tested embedding models.

Locality of conical intersections in semiconductor nanomaterials

A predictive theory connecting atomic structure to the rate of recombination would enable the rational design of semiconductor nanomaterials for optoelectronic applications. Recently our group has demonstrated that the theoretical study of conical intersections can serve this purpose. Here we review recent work in this area, focusing on the thesis that low-energy conical intersections in nanomaterials share a common feature: locality. We define a conical intersection as local if (a) the intersecting states differ by the excitation of an electron between spatially local orbitals, and (b) the intersection is accessed when the energies of these orbitals are tuned by local distortions of the geometry. After illustrating the locality of the conical intersection responsible for recombination at dangling bond defects in silicon, we demonstrate the locality of low-energy conical intersections in cases where locality may be a surprise. First, we demonstrate the locality of low-energy self-trapped conical intersections in a pristine silicon nanocrystal, which has no defects that one would expect to serve as the center of a local intersection. Second, we demonstrate that the lowest energy intersection in a silicon system with two neighboring dangling bond defects localizes to a single defect site. We discuss the profound implications of locality for predicting the rate of recombination and suggest that the locality of intersections could be exploited in the experimental study of recombination, where spectroscopic studies of molecular models of defects could provide new insights.

Control Mechanisms of Photoisomerization in Protonated Schiff Bases

We performed ab initio excited-state molecular dynamics simulations of a gas-phase photoexcited protonated Schiff base (C1-N2═C3-C4═C5-C6) to search for control mechanisms of its photoisomerization. The excited molecule twists by ∼90° around either the N2C3 bond or the C4C5 bond and relaxes to the ground electronic state through a conical intersection with either a trans or cis outcome. We show that a large initial distortion of several dihedral angles and a specific normal vibrational mode combining pyramidalization and double-bond twisting can lead to a preferential rotation of atoms around the C4C5 bond. We also show that selective pretwisting of several dihedral angles in the initial ground state thermal ensemble (by analogy to a protein pocket) can significantly increase the fraction of photoreactive (cis → trans) trajectories. We demonstrate that new ensembles with higher degrees of control over the photoisomerization reaction can be obtained by a computational directed evolution approach on the ensembles of molecules with the pretwisted geometries.

Acceleration of the Z to E photoisomerization of penta-2,4-dieniminium by hydrogen out-of-plane motion: theoretical study on a model system of retinal protonated Schiff base

We report the result of comparison between two reaction coordinates [on the potential energy surface of the first excited state (S(1))] produced by CASSCF and these energies recalculated by MRMP2 in the Z to E photoisomerization of penta-2,4-dieniminium (PDI) as the minimal model of the retinal protonated Schiff base (RPSB). One coordinate is the S(1) state minimum-energy-path (MEP) in mass-weighted coordinates from the S(1) vertically excited point, where a strong hydrogen-out-of plane (HOOP) motion is not exhibited. The energy profile of the S(1) MEP at the MRMP2//CASSCF level shows a barrier for the rotation around the reactive C-C and hits the S(1)/S(0) degeneracy space where the central C-C-C-C dihedral angle is distorted by 65 degrees . The other coordinate is an S(1) coordinate obtained by the relaxed scan strategy. The relaxed coordinate along the central C-C-C-C dihedral angle, which we call the HOOP coordinate, shows strong HOOP motion. According to the MRMP2//CASSCF calculation, there is no barrier on the HOOP coordinate. Furthermore, the S(1) to S(0) transition may be possible without the large skeletal deformation by HOOP motion because the HOOP coordinate encounters the S(1)/S(0) degeneracy space where the central C-C-C-C dihedral angle is distorted by only 40 degrees . Consequently, if PDI is a suitable model molecule for the RPSB as often assumed, the 11-cis to all-trans photoisomerization is predicted to be accelerated by the HOOP motion.

Spectral phase effects on nonlinear resonant photochemistry of 1,3-cyclohexadiene in solution

We have investigated the ring opening of 1,3-cyclohexadiene to form 1,3,5-cis-hexatriene (Z-HT) using optical pulse shaping to enhance multiphoton excitation. A closed-loop learning algorithm was used to search for an optimal spectral phase function, with the effectiveness or fitness of each optical pulse assessed using the UV absorption spectrum. The learning algorithm was able to identify pulses that increased the formation of Z-HT by as much as a factor of 2 and to identify pulse shapes that decreased solvent fragmentation while leaving the formation of Z-HT essentially unaffected. The highest yields of Z-HT did not occur for the highest peak intensity laser pulses. Rather, negative quadratic phase was identified as an important control parameter in the formation of Z-HT.

Femtosecond stimulated Raman study of excited-state evolution in bacteriorhodopsin

Femtosecond time-resolved stimulated Raman spectroscopy (FSRS) is used to examine the photoisomerization dynamics in the excited state of bacteriorhodopsin. Near-IR stimulated emission is observed in the FSRS probe window that decays with a 400-600-fs time constant. Additionally, dispersive vibrational lines appear at the locations of the ground-state vibrational frequencies and decay with a 260-fs time constant. The dispersive line shapes are caused by a nonlinear effect we term Raman initiated by nonlinear emission (RINE) that generates vibrational coherence on the ground-state surface. Theoretical expressions for the RINE line shapes are developed and used to fit the spectral and temporal evolution of the spectra. The rapid 260-fs decay of the RINE peak intensity, compared to the slower evolution of the stimulated emission, indicates that the excited-state population moves in approximately 260 fs to a region on the potential energy surface where the RINE signal is attenuated. This loss of RINE signal is best explained by structural evolution of the excited-state population along multiple low-frequency modes that carry the molecule out of the harmonic photochemically inactive Franck-Condon region and into the photochemically active geometry.

Counterion Controlled Photoisomerization of Retinal Chromophore Models: a Computational Investigation

CASPT2//CASSCF photoisomerization path computations have been used to unveil the effects of an acetate counterion on the photochemistry of two retinal protonated Schiff base (PSB) models: the 2-cis-penta-2,4-dieniminium and the all-trans-epta-2,4,6-trieniminium cations. Different positions/orientations of the counterion have been investigated and related to (i) the spectral tuning and relative stability of the S0, S1, and S2 singlet states; (ii) the selection of the photochemically relevant excited state; (iii) the control of the radiationless decay and photoisomerization rates; and, finally, (iv) the control of the photoisomerization stereospecificity. A rationale for the results is given on the basis of a simple (electrostatic) qualitative model. We show that the model readily explains the computational results providing a qualitative explanation for different aspects of the experimentally observed "environment" dependent PSB photochemistry. Electrostatic effects likely involved in controlling retinal photoisomerization stereoselectivity in the protein are also discussed under the light of these results, and clues for a stereocontrolled electrostatically driven photochemical process are presented. These computations provide a rational basis for the formulation of a mechanistic model for photoisomerization electrostatic catalysis.

Isomerization around a CN double bond and a CC double bond with a nitrogen atom attached: thermal and photochemical routes

The Longuet-Higgins phase change theorem is used to show that, in certain photochemical reactions, a single product is formed via a conical intersection. The cis-trans isomerization around the double bond in the formaldiminium cation and vinylamine are shown to be possible examples. This situation is expected to hold when the reactant can be converted to the product via two distinct elementary ground-state reactions that differ in their phase characteristics. In one, the total electronic wavefunction preserves its phase in the reaction; in the other, the phase is inverted. Under these conditions, a conical intersection necessarily connects the first electronic excited state to the ground state, leading to rapid photochemical isomerization following optical excitation. Detailed quantum chemical calculations support the proposed model. The possibility that a similar mechanism is operative in other systems, among them the rapid photo-induced cis-trans isomerization of longer protonated Schiff bases (the parent chromophores of rhodopsins), is discussed.