Ejlersenjespersen2077

DIBOA-glc and DIMBOA-glc were absorbed by the roots of the cocultivated hairy vetch plants and translocated to the shoots. These findings will strongly improve our understanding of the exudation of BXs from the rye plant and their role in interaction with other plant species.We demonstrate how to quantify the amount of dispersion interaction recovered by supermolecular calculations with the multiconfigurational self-consistent field (MCSCF) wave functions. For this purpose, we present a rigorous derivation which connects the portion of dispersion interaction captured by the assumed wave function model-the residual dispersion interaction-with the size of the active space. Based on the obtained expression for the residual dispersion contribution, we propose a dispersion correction for the MCSCF that avoids correlation double counting. Numerical demonstration for model four-electron dimers in both ground and excited states described with the complete active space self-consistent field (CASSCF) reference serves as a proof-of-concept for the method. Accurate results, largely independent of the size of the active space, are obtained. For many-electron systems, routine CASSCF interaction energy calculations recover a tiny fraction of the full second-order dispersion energy. We found that the residual dispersion is non-negligible only for purely dispersion-bound complexes.We report a new method for X-ray density ligand fitting and refinement that is suitable for a wide variety of small-molecule ligands, including macrocycles. The approach (called "xGen") augments a force field energy calculation with an electron density fitting restraint that yields an energy reward during the restrained conformational search. The resulting conformer pools balance goodness-of-fit with ligand strain. Sulfobutylether-β-Cyclodextrin Real-space refinement from pre-existing ligand coordinates of 150 macrocycles resulted in occupancy-weighted conformational ensembles that exhibited low strain energy. The xGen ensembles improved upon electron density fit compared with the PDB reference coordinates without making use of atom-specific B-factors. Similarly, on nonmacrocycles, de novo fitting produced occupancy-weighted ensembles of many conformers that were generally better-quality density fits than the deposited primary/alternate conformational pairs. The results suggest ubiquitous low-energy ligand conformational ensembles in X-ray diffraction data and provide an alternative to using B-factors as model parameters.In this paper, we compare the ability of different quasiclassical mapping Hamiltonian methods to accurately simulate the absorption spectra of multiexcitonic molecular systems. Two distinctly different approaches for simulating the absorption spectra are considered (1) a perturbative approach, which relies on the first-order perturbation theory with respect to the field-matter interaction; (2) a nonperturbative approach, which mimics the experimental measurement of the absorption spectra from the free-induction decay that follows a short laser pulse. The methods compared are several variations of the linearized semiclassical (LSC) method, the symmetrical quasiclassical (SQC) method, and the mean-field (Ehrenfest) method. The comparison is performed in the context of a biexcitonic model and a seven-excitonic model of the Fenna-Matthews-Olson (FMO) complex. The accuracy of the various methods is tested by comparing their predictions to the quantum-mechanically exact results obtained via the hierarchy of the equations of motion (HEOM) method, as well as to the results based on the Redfield quantum master equation. The results show that the LSC-based quasiclassical mapping Hamiltonian methods can yield the accurate and robust absorption spectra in the high-temperature and/or slow-bath limit, where the nuclear degrees of freedom can be treated as classical.Quantum mechanics/molecular mechanics (QM/MM) is a standard computational tool for describing chemical reactivity in systems with many degrees of freedom, including polymers, enzymes, and reacting molecules in complex solvents. However, QM/MM is less suitable for systems with complex MM dynamics due to associated long relaxation times, the high computational cost of QM energy evaluations, and expensive long-range electrostatics. Recently, a systematic coarse graining of the MM part was proposed to overcome these QM/MM limitations in the form of the quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM) approach. Herein, we recast QM/CG-MM in the density functional theory formalism and, by employing the force-matching variational principle, assess the method performance for the two model systems QM CCl4 in the MM CCl4 liquid and the reaction of tert-butyl hypochlorite with the benzyl radical in the MM CCl4 solvent. We find that density functional theory (DFT)-QM/CG-MM accurately reproduces DFT-QM/MM radial distribution functions and three-body correlations between the QM and CG-MM subsystems. The free-energy profile of the reaction is also described well, with an error less then 1-2 kcal/mol. DFT-QM/CG-MM is a general, systematic, and computationally efficient approach to include chemical reactivity in coarse-grained molecular models.Carbohydrate side chain conformation confers a significant influence on reactivity during glycosylation and anomeric bond hydrolysis due to stabilization of the oxocarbenium-like transition state. By analysis of 513 pyranoside-bound glycoside hydrolase (GH) crystal structures, we determine that most glucosidases and β-mannosidases preferentially bind their substrates in the most reactive gauche,gauche (gg) conformation, thereby maximizing stabilization of the corresponding oxocarbenium ion-like transition state during hydrolysis. α-Galactoside hydrolases mostly show a preference for the second most activating gauche,trans (gt) conformation to avoid the energy penalty that would arise from imposing the gg conformation on galacto-configured ligands. These preferences stand in stark contrast to the side chain populations observed for these sugars both in free solution and bound to nonhydrolytic proteins, where for the most part a much greater diversity of side chain conformations is observed. Analysis of sequences of GH-ligand complexes reveals that side chain restriction begins with the enzyme-substrate complex and persists through the transition state until release of the hydrolysis product, despite changes in ring conformation along the reaction coordinate.