Ab‐initio molecular dynamics and hybrid explicit‐implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Abstract

Solute–solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non‐bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical–physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute–solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.

Accounting for Vibronic Features through a Mixed Quantum-Classical Scheme: Structure, Dynamics, and Absorption Spectra of a Perylene Diimide Dye in Solution

“…In this way, the effect of the extension of the QM partition on the description of solvent shifts, 111 solvent broadening, 75 or other photochemical properties, 112 has been investigated. From the methodological point of view, beside the possibility of combining explicit and continuum models, 113 recent progresses have been made in the use of ab initio dynamics with non periodic boundary conditions, 114 polarizable force fields, 115,116 or clustering methods combined to the perturbation matrix method to recover the effect of local fluctuations of the environment. 51,52 Interestingly, most of the proposed compu-tational protocols are often indicated as MQC, with implicit reference to the description of the electrons, or more precisely, to whether solute/solvent interactions are computed according to quantum mechanics or with force fields.…”

“…In this way, the effect of the extension of the QM partition on the description of solvent shifts, solvent broadening, or other photochemical properties, has been investigated. From the methodological point of view, besides the possibility of combining explicit and continuum models, recent progress has been made in ab initio dynamics with nonperiodic boundary conditions, polarizable force fields, , or clustering methods combined to the perturbation matrix method to recover the effect of local fluctuations of the environment. , Interestingly, most of the proposed computational protocols are often indicated as MQC, with implicit reference to the description of the electrons, or more precisely, to whether solute/solvent interactions are computed according to quantum mechanics or with force fields. , Here, on the contrary, as done also in refs and , we mainly focused on a different aspect of the problem, i.e., the need for an MQC description of the nuclear motion. These two research topics are clearly related and it is easy to foresee that in the next years, the different developments in the two fields will be combined in innovative ways.…”

Water-Mediated Excited State Proton Transfer of Pyranine–Acetate in Aqueous Solution: Vibrational Fingerprints from Ab Initio Molecular Dynamics

“…The implicit and structureless solvent surrounding the explicit sphere was accounted for in the energy potential and completed the hybrid explicit/implicit solvation model. More specifically, nonperiodic boundary conditions accounted for the interactions of both electrostatic and dispersion–repulsion nature between the explicit molecular system and the implicit bulk solvent. − The solvent molecules were explicitly represented by the TIP3P water model, while the implicit bulk solvent was represented by the polarizable continuum model in its conductor-like version. , The explicit system itself is treated at different levels of theory according to the hybrid QM/MM ONIOM extrapolative method employing an electronic embedding scheme. − In particular, the pyranine–water–acetate system is described by DFT and TD-DFT in the ground and excited electronic state, respectively, by adopting the global hybrid B3LYP functional and the 6-31g­(d,p) basis set. The obtained energy potential ruled the AIMD simulations in both the ground and the first singlet excited state.…”

Photochemistry of 1-Phenyl-4-Allyl-Tetrazol-5-One: A Theoretical Study Contribution towards Mechanism Elucidation

“…For the S n and P(T 1 ) states faith, the intersystem crossing, spin-orbit coupling, and conical intersection model will test the rate of conversion towards the T 1 state and competing processes, like fast decay to S 1 , fluorescence, and phosphorescence. The use of an explicit solvation method [52] may also be relevant in the description of the interaction between the solvent and detail interactions with the solvent cage. Drift effects due to the solvent molecules may also change the steric behaviour of the rotations present in the mechanism.…”