Critical assessment of solvent effects on absorption and fluorescence of 3HF in acetonitrile in the QM/PCM framework: A synergic computational and experimental study

Evaluation of molecular photophysical and photochemical properties using linear response time-dependent density functional theory with classical embedding: Successes and challenges

Time-dependent density functional theory (TDDFT) based approaches have been developed in recent years to model the excited-state properties and transition processes of the molecules in the gas-phase and in a condensed medium, such as in a solution and protein microenvironment or near semiconductor and metal surfaces. In the latter case, usually, classical embedding models have been adopted to account for the molecular environmental effects, leading to the multi-scale approaches of TDDFT/polarizable continuum model (PCM) and TDDFT/molecular mechanics (MM), where a molecular system of interest is designated as the quantum mechanical region and treated with TDDFT, while the environment is usually described using either a PCM or (non-polarizable or polarizable) MM force fields. In this Perspective, we briefly review these TDDFT-related multi-scale models with a specific emphasis on the implementation of analytical energy derivatives, such as the energy gradient and Hessian, the nonadiabatic coupling, the spin–orbit coupling, and the transition dipole moment as well as their nuclear derivatives for various radiative and radiativeless transition processes among electronic states. Three variations of the TDDFT method, the Tamm–Dancoff approximation to TDDFT, spin–flip DFT, and spin-adiabatic TDDFT, are discussed. Moreover, using a model system (pyridine–Ag20 complex), we emphasize that caution is needed to properly account for system–environment interactions within the TDDFT/MM models. Specifically, one should appropriately damp the electrostatic embedding potential from MM atoms and carefully tune the van der Waals interaction potential between the system and the environment. We also highlight the lack of proper treatment of charge transfer between the quantum mechanics and MM regions as well as the need for accelerated TDDFT modelings and interpretability, which calls for new method developments.

Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery

Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.

Molecular Dynamics Simulation of the Excited-State Proton Transfer Mechanism in 3-Hydroxyflavone Using Explicit Hydration Models

3-Hydroxyflavon (3-HF) represents an interesting paradigmatic compound to study excited-state intramolecular proton transfer (ESIPT) and intermolecular (ESInterPT) processes to explain the experimentally observed dual fluorescence in solvents containing protic contamination (water) as opposed to single fluorescence in highly purified nonpolar solvents. In this work, adiabatic on-the-fly molecular dynamics simulations have been performed for isolated 3-HF in an aqueous solution using a polarizable continuum model and including explicit water molecules to represent adequately hydrogen bonding. For the calculation of the excited state, time-dependent density functional theory and the Becke-3-Lee-Yang-Parr (B3LYP) functional have been used. For the isolated 3-HF, ultrafast ESIPT from the enol group to the neighboring keto group has been observed. The calculated PT time of 48 fs agrees well with the experimental value of 39 fs. Addition of one water molecule quenches this ESIPT process but shows an intermolecular concerted or stepwise tautomerization process via the bridging water molecule. Adding a second or more water molecules inhibits this ESInterPT process to a large degree. Most of the trajectories do not show any PT, preserving the initial excited-state enol structure, which is the origin of the violet-blue fluorescence appearing in the solvents contaminated with protic components.