Normanpetersson9658

Nonradiative relaxation of excited molecules is central to many crucial issues in photochemistry. Condensed phases are typical contexts in which such problems are considered, and the nonradiative relaxation dynamics are expected to be significantly affected by interactions with the environment, for example, a solvent. We developed a nonadiabatic molecular dynamics simulation technique that can treat the nonradiative relaxation and explicitly include the environment in the calculations without a heavy computational burden. Specifically, we combined trajectory surface hopping with Tully's fewest-switches algorithm, a tight-binding approximated version of spin-flip time-dependent density-functional theory, and divide-and-conquer (DC) spatial fragmentation scheme. Numerical results showed that this method can treat systems with thousands of atoms within reasonable computational resources, and the error arising from DC fragmentation is negligibly small. Using this method, we obtained molecular insights into the solvent dependence of the photoexcited-state dynamics of trans-azobenzene, which demonstrate the importance of the environment for condensed-phase nonradiative relaxation.Viruses avoid exposure of the viral genome to harmful agents with the help of a protective protein shell known as the capsid. A secondary effect of this protective barrier is that macromolecules that may be in high concentration on the outside cannot freely diffuse across it. Therefore, inside the cell and possibly even outside, the intact virus is generally under a state of osmotic stress. Viruses deal with this type of stress in various ways. In some cases, they might harness it for infection. However, the magnitude and influence of osmotic stress on virus physical properties remains virtually unexplored for single-stranded RNA viruses-the most abundant class of viruses. Here, we report on how a model system for the positive-sense RNA icosahedral viruses, brome mosaic virus (BMV), responds to osmotic pressure. ML265 PKM activator Specifically, we study the mechanical properties and structural stability of BMV under controlled molecular crowding conditions. We show that BMV is mechanically reinforced under a small external osmotic pressure but starts to yield after a threshold pressure is reached. We explain this mechanochemical behavior as an effect of the molecular crowding on the entropy of the "breathing" fluctuation modes of the virus shell. The experimental results are consistent with the viral RNA imposing a small negative internal osmotic pressure that prestresses the capsid. Our findings add a new line of inquiry to be considered when addressing the mechanisms of viral disassembly inside the crowded environment of the cell.Accurate and rapid calculation of protein-small molecule interaction free energies is critical for computational drug discovery. Because of the large chemical space spanned by drug-like molecules, classical force fields contain thousands of parameters describing atom-pair distance and torsional preferences; each parameter is typically optimized independently on simple representative molecules. Here, we describe a new approach in which small molecule force field parameters are jointly optimized guided by the rich source of information contained within thousands of available small molecule crystal structures. We optimize parameters by requiring that the experimentally determined molecular lattice arrangements have lower energy than all alternative lattice arrangements. Thousands of independent crystal lattice-prediction simulations were run on each of 1386 small molecule crystal structures, and energy function parameters of an implicit solvent energy model were optimized, so native crystal lattice arrangements had the lowest energy. The resulting energy model was implemented in Rosetta, together with a rapid genetic algorithm docking method employing grid-based scoring and receptor flexibility. The success rate of bound structure recapitulation in cross-docking on 1112 complexes was improved by more than 10% over previously published methods, with solutions within less then 1 Å in over half of the cases. Our results demonstrate that small molecule crystal structures are a rich source of information for guiding molecular force field development, and the improved Rosetta energy function should increase accuracy in a wide range of small molecule structure prediction and design studies.The dynamic role of the conical intersection "seam" coordinate has been first revealed in the H fragmentation reaction of ortho(o)-cresol conformers. One of the (3N - 8) dimensional seam coordinates of the S1(ππ*)/S2(πσ*) conical intersection has been identified as the CH3 torsional potential function. The tunneling dynamics of the reactive flux is dictated by its nuclear layout with respect to the CH3 torsional angle, as the multidimensional tunneling barrier is dynamically shaped along the conical intersection seam. The effective tunneling-barrier weight-averaged over the quantum-mechanical probability along the CH3 torsional angle perfectly explains the experimental finding the sharp variation of the tunneling rate ((700-400) ps-1) with the CH3 torsional mode excitations within the narrow (0-100 cm-1) energetic window. The much longer S1 lifetime of cis compared to trans is ascribed to the higher-lying S1/S2 conical intersection of the former. With the use of distinct lifetimes, vibronic bands of each conformer could be completely separated.As an effective method to improve the optical properties and stability of perovskite matrix, doped halide perovskites have attracted extensive attention in the field of optoelectronic applications. Herein, a series of all inorganic lead-free Te4+-doped Cs2ZrCl6 vacancy-ordered perovskites were successfully synthesized with different Te-doping concentrations by a solvothermal method, and deliberate Te4+-doping results in green-yellow triplet self-trapped exciton (STE) emission with a high photoluminescence quantum yield (PLQY) of 49.0%. The efficient energy transfer was observed from singlet to triplet emission. Further, the effects of A-site Rb alloying on the optical properties and stability were investigated. We found that A-site Rb alloying and C-site cohalogenation did not change the luminescence properties of Te4+, but the addition of a small amount of Rb+ can improve the PL intensity and moisture stability. Our results provide physical insights into the nS2 Te4+-ion-doping-induced emissive mechanism and shed light on improving the environmental stability for further applications.