High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor
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In this work, we present a new stochastic extended Lagrangian molecular dynamics solution to charge equilibration that eliminates self-consistent field (SCF) calculations, thus eliminating the computational bottleneck in solving the charge distribution with standard SCF solvers. By formulating both charges and chemical potential as latent variables and introducing a holonomic constraint that satisfies charge conservation, the SC-XLMD method accurately reproduces thermodynamic, dynamic, and structural properties within the framework of ReaxFF for a bulk water system and highly reactive RDX molecules simulated at high temperature. The SC-XLMD method shows excellent computational performance and is available in the publicly available LAMMPS package.
Reactive force fields provide an affordable model for simulating chemical reactions at a fraction of the cost of quantum mechanical approaches. However, classically accounting for chemical reactivity often comes at the expense of accuracy and transferability, while computational cost is still large relative to nonreactive force fields. Here, we summarize recent efforts for improving the performance of reactive force fields in these three areas with a focus on the ReaxFF theoretical model. To improve accuracy, we describe recent reformulations of charge equilibration schemes to overcome unphysical long-range charge transfer, new ReaxFF models that account for explicit electrons, and corrections for energy conservation issues of the ReaxFF model. To enhance transferability we also highlight new advances to include explicit treatment of electrons in the ReaxFF and hybrid nonreactive/reactive simulations that make it possible to model charge transfer, redox chemistry, and large systems such as reverse micelles within the framework of a reactive force field. To address the computational cost, we review recent work in extended Lagrangian schemes and matrix preconditioners for accelerating the charge equilibration method component of ReaxFF and improvements in its software performance in LAMMPS.
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Enediynes are among the most potent antitumor and antibacterial natural products. Studies on their biosynthetic pathways have identified a shared, linear polyene precursor generated from an iterative type I polyketide synthase (PKSE) as the source of the enediyne warhead. A key step is the release of this polyene from the PKSE by a discrete thioesterase (TE). Here, in this study, we used X-ray crystallography, site-directed mutagenesis, and heterologous coexpression of PKSEs and TEs to elucidate how enediyne TEs mediate the production of the polyene. We solved the structure of wild-type EspE7 from esperamicin producer Actinomodura verrucosospora. The substrate binding pocket was also defined upon serendipitous cocrystallization of an EspE7 mutant with a fatty acyl-CoA ligand. Structural data and in vitro activity assays with EspE7 mutants provide strong evidence that Glu68 in EspE7 and the analogous Glu residue in other enediyne TEs functions as a key catalytic residue, thus supporting a hydrolysis mechanism for enediyne TEs that aligns with that of Pseudomonas sp. 4-HB-CoA TE. Furthermore, combinations of 9- and 10-membered enediyne PKSEs and TEs produced 1,3,5,7,9,11,13-pentadecaheptaene (1) as the major product. Thus, the data further support previous conclusions that 1 serves as the sole precursor for the biosynthesis of all enediyne cores.
We investigate ultrafast dynamics of the lowest singlet excited electronic state in liquid nitrobenzene using ultrafast transient polarization spectroscopy, extending the well-known technique of optical Kerr effect spectroscopy to excited electronic states. The third-order nonlinear response of the excited molecular ensemble is measured using a pair of femtosecond pulses following a third femtosecond pulse that populates the S 1 excited state. By measuring this response, which is highly sensitive to details of the excited state character and structure, as a function of time delays between the three pulses involved, we extract the dephasing time of the wave packet on the excited state. The dephasing time, measured as a function of time delay after pump excitation, shows oscillations indicating oscillatory wave packet dynamics on the excited state. Finally, from the experimental measurements and supporting theoretical calculations, we deduce that the wave packet completely leaves the S 1 state potential energy surface after three traversals of the intersystem crossing between the singlet S 1 and triplet T 2 states.
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Here, a new experimental method, i.e., isochoric cooling/heating cycle measurement using differential scanning calorimeter (DSC), is applied to investigate the hysteretic phenomenon of pure components and mixtures confined in two different types of cylindrical nanopores (SBA-15 and KIT-6). The capillary condensation/evaporation hysteresis end point (T he ) for a specific system is determined by performing a series of measurements with different densities by increasing initial temperature and pressure. We confirm that for a pure component, T he is lower when confined in smaller nanopores, whereas T he for CH 4 /CO 2 and CH 4 /C 2 H 6 mixtures at the specific composition investigated are higher than that of pure CO 2 and C 2 H 6 , respectively, when confined in the same nanopores. To the best of our knowledge, this is the first time that T he of fluid mixture is experimentally studied, which further demonstrates that binary mixtures behave similarly to pure fluids when confined in nanoporous media. At low temperatures where hysteresis is observed, the shape as well as the duration of the exothermic peak (due to capillary condensation) and endothermic peak (due to capillary evaporation) indicate that capillary condensation, rather than capillary evaporation, takes place at/near a thermodynamic equilibrium. Within the accuracy of the measurements, we find that the total heat of capillary condensation is identical to that of capillary evaporation for all systems examined, regardless of the presence of hysteresis. By comparing the heat per unit volume among different systems, we also find that the heat per unit volume of the phase transition of confined pure fluid is lower than that of bulk, which further demonstrates that the molar density of confined pure liquid is less than that of bulk pure liquid at saturation.
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The past decade has witnessed the unprecedented boost of power conversion efficiency (PCE) of photovoltaics based on halide perovskite materials since its early discovery. Despite its remarkably good performance, long-term stability is yet one of the last barriers before commercializing halide perovskite photovoltaics is possible. In this perspective, we discuss the challenges and concurrently the strategies regarding the stability of the perovskite materials, photoactive crystal phases, and the performance as well as stability limiting interfaces. Future perspectives of stable halide perovskite and perovskite solar cells are also proposed to shine light on letting perovskite technology satisfy long-term operation warranty.
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The performance of proton-exchange membrane fuel cells is strongly dependent on the efficiency of the electrochemical oxygen reduction reaction (ORR). Here, we report both two-dimensional (4 monolayer, ML) and three-dimensional Bi (16 ML) (11̅0) facets deliver a strong correlation between nontrivial topological surface states and low electrochemical overpotential toward ORR. Both topological Bi (11̅0) film and slab have two slightly gapped (9–45 meV) Dirac cones with the invariant Z 2 =1, derived from the parity products for the occupied states at four time-reversal invariant momentum points. By contrast, the Bi (110) film is stabilized as an ordinary insulator due to atomic buckling. The much lower thermodynamic ORR overpotential (η = 0.58 V) and higher H 2 O selectivity by four steps of H + /e – transfer are obtained on the topological Bi (11̅0) surface compared with the nontopological (110) facet (η = 0.84 V). This promotional effect can be attributed to the accumulation of topological surface bands (Bi 6p orbitals) near the Fermi energy, which provide stronger electronic transport channels along the surface Bi–Bi and Bi–O bonds. Finally, a 16 ML Bi (11̅0) slab is also constructed to simulate the topological (11̅0) surface of three-dimensional bulk Bi as a topological crystalline insulator (TCI). Furthermore, the consistent topological properties and slightly lower thermodynamic ORR overpotential (η = 0.53 V) are also observed on the thicker slab.
The stability of halide perovskites has been a long-standing issue for their real-world application. Approaches to improve stability include nanostructuring, dimensionality reduction, and strain engineering, where surfaces play an important role in the formation of a stable structure. To understand the mechanism we compute the lattice dynamics of the surface of CsPbI 3 using density functional theory. We demonstrate, for the first time, that CsPbI 3 crystals exhibit surface phonons that are localized on the outermost layers of the slabs, and we perform a complete symmetry characterization including an identification of the Raman/IR active modes. These surface phonons are present in the optically active cubic phase but are absent in the optically inactive "yellow" phase. Furthermore, we show that the surface suppresses bulk instabilities by hardening soft modes of the bulk cubic phase, resulting in phase stabilization and quenching of dynamical disorder. Finally, this study is fundamental for understanding the structural behavior of halide perovskite materials with high surface area-to-volume ratios, and for guiding stabilization strategies.
Here, we present an experimental and theoretical study of the interplay between ultrafast electron dynamics and librational dynamics in liquid nitrobenzene. A femtosecond ultraviolet pulse and two femtosecond near-infrared pulses interact with nitrobenzene molecules, generating a four-wave mixing nonlinear signal measured in the Optical Kerr Effect geometry. The signal is measured to be nonzero only at negative time delays, corresponding to the near-infrared pulses arriving before the ultraviolet pulse. We perform time-dependent Quantum Master Equation calculations with classical libration to simulate the experiment. The simulations support the conclusion that the near-infrared pulses launch librational motion while creating electronic coherences resulting in a libration-modulated electronic nonlinear response. The analysis of the phase-matched four-wave mixing signals suggests a nonparametric process leaving the molecules in an excited electronic state, providing new insight into ultrafast nonlinear optical interactions in liquids and advancing toward probing ultrafast electronic coherences in complex molecular liquids.