Modeling linear absorption spectra of solvated chromophores is highly challenging as contributions are present both from coupling of the electronic states to nuclear vibrations and from solute–solvent interactions. In systems where excited states intersect in the Condon region, significant non-adiabatic contributions to absorption line shapes can also be observed. Here, we introduce a robust approach to model linear absorption spectra accounting for both environmental and non-adiabatic effects from first principles. This model parameterizes a linear vibronic coupling (LVC) Hamiltonian directly from energy gap fluctuations calculated along molecular dynamics (MD) trajectories of the chromophore in solution, accounting for both anharmonicity in the potential and direct solute–solvent interactions. The resulting system dynamics described by the LVC Hamiltonian are solved exactly using the thermalized time-evolving density operator with orthogonal polynomials algorithm (T-TEDOPA). The approach is applied to the linear absorption spectrum of methylene blue in water. We show that the strong shoulder in the experimental spectrum is caused by vibrationally driven population transfer between the bright S1 and the dark S2 states. The treatment of the solvent environment is one of many factors that strongly influence the population transfer and line shape; accurate modeling can only be achieved through the use of explicit quantum mechanical solvation. The efficiency of T-TEDOPA, combined with LVC Hamiltonian parameterizations from MD, leads to an attractive method for describing a large variety of systems in complex environments from first principles.

Environmentally sensitive (ES) dyes have been used for many decades to study the lipid order of cell membranes, as different lipid phases play a crucial role in a wide variety of cell processes. Yet, the understanding of how ES dyes behave, interact, and affect membranes at the atomistic scale is lacking, partially due to the lack of molecular dynamics (MD) models of these dyes. Here, we present ground-and excited-state MD models of commonly used ES dyes, Laurdan and di-4-ANEPPDHQ, and use MD simulations to study the behavior of these dyes in a disordered and an ordered membrane. We also investigate the effect that these two dyes have on the hydration and lipid order of the membranes, where we see a significant effect on the hydration of lipids proximal to the dyes. These findings are combined with experimental fluorescence experiments of ordered and disordered vesicles and live HeLa cells stained by the aforementioned dyes, where the generalized polarization (GP) values were measured at different concentrations of the dyes. We observe a small but significant decrease of GP at higher Laurdan concentrations in vesicles, while the same effect is not observed in cell membranes. The opposite effect is observed with di-4-ANEPPDHQ where no significant change in GP is seen for vesicles but a very substantial and significant decrease is seen in cell membranes. Together, our results show the profound effect that ES dyes have on membranes, and the presented MD models will be important for further understanding of these effects.

In this paper we tackle the challenge of gaining control of the photophysical properties of PAHs through a site-specific N-doping within the structural aromatic framework.

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The simulation of optical spectra is essential to molecular characterization and, in many cases, critical for interpreting experimental spectra. The most common method for simulating vibronic absorption spectra relies on the geometry optimization and computation of normal modes for ground and excited electronic states. In this report, we show that the utilization of such a procedure within an adiabatic linear response (LR) theory framework may lead to state mixings and a breakdown of the Born−Oppenheimer approximation, resulting in a poor description of absorption spectra. In contrast, computing excited states via a self-consistent field method in conjunction with a maximum overlap model produces states that are not subject to such mixings. We show that this latter method produces vibronic spectra much more aligned with vertical gradient and molecular dynamics (MD) trajectory-based approaches. For the methylene blue chromophore, we compare vibronic absorption spectra computed with the following: an adiabatic Hessian approach with LR theory-optimized structures and normal modes, a vertical gradient procedure, the Hessian and normal modes of maximum overlap method-optimized structures, and excitation energy time-correlation functions generated from an MD trajectory. Because of mixing between the bright S 1 and dark S 2 surfaces near the S 1 minimum, computing the adiabatic Hessian with LR theory and timedependent density functional theory with the B3LYP density functional predicts a large vibronic shoulder for the absorption spectrum that is not present for any of the other methods. Spectral densities are analyzed and we compare the behavior of the key normal mode that in LR theory strongly couples to the optical excitation while showing S 1 /S 2 state mixings. Overall, our study provides a note of caution in computing vibronic spectra using the excited-state adiabatic Hessian of LR theory-optimized structures and also showcases three alternatives that are less sensitive to adiabatic state mixing effects.

Simulation of optical spectra is essential to molecular characterization and, in many cases, critical for interpreting experimental spectra. The most common method for simulating vibronic absorption spectra relies on the geometry optimization and computation of normal modes for ground and excited states. In this report, we show that utilization of such a procedure within an adiabatic linear response theory framework may lead to state mixings and a breakdown of the Born-Oppenheimer approximation, resulting in a poor description of absorption spectra. In contrast, computing excited states via a self-consistent eld method in conjunction with a maximum overlap model produces states that are not subject to such mixings. We show that this latter method produces vibronic spectra much more aligned with vertical excitation procedures, such as those computed from a vertical gradient or molecular dynamics trajectory-based approach. For the methylene blue chromophore, we compare vibronic absorption spectra computed with: an adiabatic Hessian approach with linear response theory optimized structures and normal modes, a vertical gradient procedure, the Hessian and normal modes of maximum overlap method optimized structures, and excitation energy time correlation functions generated from a molecular dynamics trajectory. Due to mixing between the bright S1 and dark S2 surfaces near the S1 minimum, computing the adiabatic Hessian with linear response theory time-dependent density functional theory with the B3LYP density functional predicts a large vibronic shoulder for the absorption spectrum that is not present for any of the other methods. Spectral densities are analyzed and we compare the behavior of the key normal mode that in linear response theory strongly couples to the optical excitation while showing S1/ S2 state mixings. Overall, our study provides a note of caution in computing vibronic spectra using the excited state adiabatic Hessian of linear response theory optimized structures and also showcases three alternatives that are not as subject to adiabatic state mixing effects.