Egebergroth9542

Quantum chemical calculations of the C6H5O2 potential energy surface (PES) were carried out to study the mechanism of the phenoxy + O(3P) and phenyl + O2 reactions. CASPT2(15e,13o)/CBS//CASSCF(15e,13o)/DZP multireference calculations were utilized to map out the minimum energy path for the entrance channels of the phenoxy + O(3P) reaction. Stationary points on the C6H5O2 PES were explored at the CCSD(T)-F12/cc-pVTZ-f12//B3LYP/6-311++G** level for the species with a single-reference character of the wave function and at the CASPT2(15e,13o)/CBS//B3LYP/6-311++G** level of theory for the species with a multireference character of the wave function. Conventional, variational, and variable reaction coordinate transition-state theories were employed in Rice-Ramsperger-Kassel-Marcus master equation calculations to assess temperature- and pressure-dependent phenomenological rate constants and product branching ratios. The main bimolecular product channels of the phenoxy + O(3P) reaction are concluded to be para/ortho-benzoquinone + H, 2,4-cyclopentadienone + HCO and, at high temperatures, also phenyl + O2. The main bimolecular product channels of the phenyl + O2 reaction include 2,4-cyclopentadienone + HCO at lower temperatures and phenoxy + O(3P) at higher temperatures. For both the phenoxy + O(3P) and phenyl + O2 reactions, the collisional stabilization of peroxybenzene at low temperatures and high pressures competes with the bimolecular product channels.In recent years, constant applied potential molecular dynamics has allowed researchers to study the structure and dynamics of the electrochemical double-layer of a large variety of nanoscale capacitors. Nevertheless, it has remained impossible to simulate polarized electrodes at fixed total charge. Here, we show that combining a constant potential electrode with a finite electric displacement fills this gap by allowing us to simulate open-circuit conditions. The method can be extended by applying an electric displacement ramp to perform computational amperometry experiments at different current intensities. As in experiments, the full capacitance of the system is obtained at low intensity, but this quantity decreases when the applied ramp becomes too fast with respect to the microscopic dynamics of the liquid.To understand and control key electrochemical processes-metal plating, corrosion, intercalation, etc.-requires molecular-scale details of the active species at electrochemical interfaces and their mechanisms for desolvation from the electrolyte. Using free energy sampling techniques we reveal the interfacial speciation of divalent cations in ether-based electrolytes and mechanisms for their delivery to an inert graphene electrode interface. Surprisingly, we find that anion solvophobicity drives a high population of anion-containing species to the interface that facilitate the delivery of divalent cations, even to negatively charged electrodes. Our simulations indicate that cation desolvation is greatly facilitated by cation-anion coupling. We propose anion solvophobicity as a molecular-level descriptor for rational design of electrolytes with increased efficiency for electrochemical processes limited by multivalent cation desolvation.Non-radiative relaxation of the photoexcited thymine in the gas phase shows an unusually long excited-state lifetime, and, over the years, a number of models, i.e., S1-trapping, S2-trapping, and S1&S2-trapping, have been put forward to explain its mechanism. Here, we investigate this mechanism using non-adiabatic molecular dynamics (NAMD) simulations in connection with the recently developed mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. Foxy-5 research buy We show that the previously predicted S2-trapping model was due to an artifact caused by an insufficient account of the dynamic electron correlation. The current work supports the S1-trapping mechanism with two lifetimes, τ1 = 30 ± 1 fs and τ2 = 6.1 ± 0.035 ps, quantitatively consistent with the recent time-resolved experiments. Upon excitation to the S2 (ππ*) state, thymine undergoes an ultrafast (ca. 30 fs) S2→S1 internal conversion and resides around the minimum on the S1 (nOπ*) surface, slowly decaying to the ground state (ca. 6.1 ps). While the S2→S1 internal conversion is mediated by fast bond length alternation distortion, the subsequent S1→S0 occurs through several conical intersections, involving a slow puckering motion.The regioselectivity in the 1,3-dipolar cycloaddition (1,3-DC) between five-membered cyclic nitrone and methylenecyclopropane (MCP) has been studied through density functional theory (DFT) calculations. The computational study of 1,3-DC with different 1-alkyl- (or 1,1-dialkyl)-substituted alkenes and the comparison with MCP have evidenced that the electrostatic interaction has a central role in the regioselectivity of the reactions. It has been observed that the electronic effect of the substituent (donor or attractor groups) determines the polarization of the alkene double bond and the reaction mechanism, consequently determining the interaction with nitrones and favoring an orientation between this moiety and the dipolarophile.Active matter contains self-propelled units able to convert stored or ambient free energy into motion. Such systems demonstrate amazing features related to the phenomenon of self-organization and phase transitions and can be used for the development of artificial materials and machines that operate away from equilibrium. Significant advances in the fabrication of active matter were achieved when studying low-density gas and small crystallites. However, the technique of preparation of active matter, where one can observe the formation of stable crystals, is extremely challenging. Here, we describe the novel method to obtain a stable 2D crystal in the active octane-in-water emulsion during the process of heterogeneous crystallization. Active motion is driven by the Marangoni flow emerging at the interface of the droplet. It is established that the crystal volume increases linearly in time in the process of crystallization. Moreover, the dependence of the crystal growth rate on the average velocity of droplets motion in the emulsion has a maximum. The kinetics of crystal growth is defined by a competition between the processes of attachment and detachment of droplets from the crystal surface. Crystallization proceeds via condensation of droplets from the gas phase through the formation of liquid as an intermediate phase, which covers the crystal surface with a thin layer. Inside the liquid layer the bond-orientational order of droplets decreases from the crystal surface toward the gas phase. We anticipate our study to be a starting point for the development of new materials and technologies on the basis of nonequilibrium droplet systems.We develop an approach by which reliable estimates of the transfer entropy can be obtained from the variance-covariance matrix of atomic fluctuations, which converges quickly and retains sensitivity to the full chemical profile of the biomolecular system. We validate our method on ERK2, a well-studied kinase involved in the MAPK signaling cascade for which considerable computational, experimental, and mutation data are available. We present the results of transfer entropy analysis on data obtained from molecular dynamics simulations of wild-type active and inactive ERK2, along with mutants Q103A, I84A, L73P, and G83A. We show that our method is systematically consistent within the context of other approaches for calculating transfer entropy, and we provide a method for interpreting networks of interconnected residues in the protein from a perspective of allosteric coupling. We introduce new insights about possible allosteric activity of the extreme N-terminal region of the kinase, and we describe evidence that suggests that activation may occur by different paths or routes in different mutants. Our results highlight systematic advantages and disadvantages of each method for calculating transfer entropy and show the important role of transfer entropy analysis for understanding allosteric behavior in biomolecular systems.Cetyltrimethyl ammonium bromide (CTAB) is used to decorate the SiC particle surface. The mechanism of the decoration process has been studied by simulation and experimental approaches. Molecular dynamics (MD) simulation finds a bilayer adsorbed structure of CTAB on the SiC particles, which is then verified by Fourier-transform infrared and thermal gravimetric analysis measurements. The MD simulation also finds that the decorative effects of CTAB on the SiC particle surface are related to the surface charge condition of the SiC particles and the concentration of CTAB. The measured zeta potential of the SiC particles shows dependence on the pH condition and the concentration of CTAB. The decorated SiC particles are used to produce composition by the co-deposition technology. With the help of CTAB, SiC particles are successfully incorporated in the deposited layer, where the content of SiC particles is dependent on the concentration of CTAB and the pH of the bath.Structural and biochemical studies of the severe acute respiratory syndrome (SARS)-CoV-2 spike glycoproteins and complexes with highly potent antibodies have revealed multiple conformation-dependent epitopes highlighting conformational plasticity of spike proteins and capacity for eliciting specific binding and broad neutralization responses. In this study, we used coevolutionary analysis, molecular simulations, and perturbation-based hierarchical network modeling of the SARS-CoV-2 spike protein complexes with a panel of antibodies targeting distinct epitopes to explore molecular mechanisms underlying binding-induced modulation of dynamics and allosteric signaling in the spike proteins. Through coevolutionary analysis of the SARS-CoV-2 spike proteins, we identified highly coevolving hotspots and functional clusters that enable a functional cross-talk between distant allosteric regions in the SARS-CoV-2 spike complexes with antibodies. Coarse-grained and all-atom molecular dynamics simulations combined with mutational sensitivity mapping and perturbation-based profiling of the SARS-CoV-2 receptor-binding domain (RBD) complexes with CR3022 and CB6 antibodies enabled a detailed validation of the proposed approach and an extensive quantitative comparison with the experimental structural and deep mutagenesis scanning data. By combining in silico mutational scanning, perturbation-based modeling, and network analysis of the SARS-CoV-2 spike trimer complexes with H014, S309, S2M11, and S2E12 antibodies, we demonstrated that antibodies can incur specific and functionally relevant changes by modulating allosteric propensities and collective dynamics of the SARS-CoV-2 spike proteins. The results provide a novel insight into regulatory mechanisms of SARS-CoV-2 S proteins showing that antibody-escaping mutations can preferentially target structurally adaptable energy hotspots and allosteric effector centers that control functional movements and allosteric communication in the complexes.Herein, we describe the discovery and optimization of a novel series that inhibits bacterial DNA gyrase and topoisomerase IV via binding to, and stabilization of, DNA cleavage complexes. Optimization of this series led to the identification of compound 25, which has potent activity against Gram-positive bacteria, a favorable in vitro safety profile, and excellent in vivo pharmacokinetic properties. Compound 25 was found to be efficacious against fluoroquinolone-sensitive Staphylococcus aureus infection in a mouse thigh model at lower doses than moxifloxacin. An X-ray crystal structure of the ternary complex formed by topoisomerase IV from Klebsiella pneumoniae, compound 25, and cleaved DNA indicates that this compound does not engage in a water-metal ion bridge interaction and forms no direct contacts with residues in the quinolone resistance determining region (QRDR). This suggests a structural basis for the reduced impact of QRDR mutations on antibacterial activity of 25 compared to fluoroquinolones.