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The FF parameters with these LJ cutoff methods are extensively validated by reproducing structural, interfacial, and mechanical properties. We find that the computed density and surface energies are in good agreement with reported experimental results, although the simulation results increase in the following order 10-12 fsw less then 12 cutoff less then LJPME. Nanomaterials in which LJ interactions are a major component show relatively higher deviations (up to 4% in density and 8% in surface energy differences) compared with the experiment. Nanomaterial Modeler's capability is also demonstrated by generating complex systems of nanomaterial-biomolecule and nanomaterial-polymer interfaces with a combination of existing CHARMM-GUI modules. We hope that Nanomaterial Modeler can be used to carry out innovative nanomaterial modeling and simulations to acquire insight into the structure, dynamics, and underlying mechanisms of complex nanomaterial-containing systems.Herein, we present a fragment-based approach for calculating the charged and neutral excited states in molecular systems, based on the many-body Green's function method within the GW approximation and the Bethe-Salpeter equation (BSE). The implementation relies on the many-body expansion of the total irreducible polarizability on the basis of fragment molecular orbitals. The GW quasi-particle energies in complex molecular environments are obtained by the GW calculation for the target fragment plus induced polarization contributions of the surrounding fragments at the static Coulomb-hole plus screened exchange level. In addition, we develop a large-scale GW/BSE method for calculating the delocalized excited states of molecular aggregates, based on the fragment molecular orbital method and the exciton model. The accuracy of fragment-based GW and GW/BSE methods was evaluated on molecular clusters and molecular crystals. We found that the accuracy of the total irreducible polarizability can be improved systematically by including two-body correction terms, and the fragment-based calculations can reasonably reproduce the results of the corresponding unfragmented calculations with a relative error of less than 100 meV. The proposed approach enables efficient excited-state calculations for large molecular systems with reasonable accuracy.Native mass spectrometry and collision-induced unfolding (CIU) workflows continue to grow in utilization due to their ability to rapidly characterize protein conformation and stability. To perform these experiments, the instrument must be capable of collisionally activating ions prior to ion mobility spectrometry (IMS) analyses. Trapped ion mobility spectrometry (TIMS) is an ion mobility implementation that has been increasingly adopted due to its inherently high resolution and reduced instrumental footprint. In currently deployed commercial instruments, however, typical modes of collisional activation do not precede IMS analysis, and thus, the instruments are incapable of performing CIU. In this work, we expand on a recently developed method of activating protein ions within the TIMS device and explore its analytical utility toward the unfolding of native-like protein ions. We demonstrate the unfolding of native-like ions of ubiquitin, cytochrome C, β-lactoglobulin, and carbonic anhydrase. These ions undergo extensive unfolding upon collisional activation. Additionally, the improved resolution provided by the TIMS separation uncovers previously obscured unfolding complexity.Macrocyclization is a popular method for preparing hosts, but it can have unintended effects, like limiting molecular free rotation to yield mixtures of inseparable isomers. We report a [3 + 3] Schiff-base macrocycle (1) with anthracene bridges. Restricted rotation about the phenyl-anthracene bonds leads 1 to exist as a mixture of conformations (1Cs and 1C3v). Macrocycle 1 was photooxidized to tris(endoperoxide) adduct 4, alleviating restricted rotation. These results were supported by spectroscopic, structural, and computational analyses.Uncontrolled zinc electrodeposition is an obstacle to long-cycling zinc batteries. Much has been researched on regulating zinc electrodeposition, but rarely are the studies performed in the presence of a separator, as in practical cells. Selleck BIRB 796 Here, we show that the microstructure of separators determines the electrodeposition behavior of zinc. Porous separators direct zinc to deposit into their pores and leave "dead zinc" upon stripping. In contrast, a nonporous separator prevents zinc penetration. Such a difference between the two types of separators is distinguished only if caution is taken to preserve the attachment of the separator to the zinc-deposited substrate during the entire electrodeposition-morphological observation process. Failure to adopt such a practice could lead to misinformed conclusions. Our work reveals the mere use of porous separators as a universal yet overlooked challenge for metal anode-based rechargeable batteries. Countermeasures to prevent direct exposure of the metal growth front to a porous structure are suggested.The current IUPAC-recommended definition of the term "monoisotopic mass" of a chemical species is based on the most abundant isotopes of the constituent elements. It has even been proposed to constrain the definition to be based only on the atomic masses of the most abundant stable isotopes. Such an approach is flawed because in this way several elements and their compounds, in addition to isotopically enriched species, would not merit to be assigned a monoisotopic mass. Furthermore, for large molecules, such as proteins, the monoisotopic mass as currently defined loses its significance. Therefore, we propose to eliminate using the current definition altogether. Instead, the term isotopologue mass should be applied uniformly to every species denoted by a specific chemical formula.Molecular structures of hole transport materials (HTMs) have significant impact on the optoelectronic properties of perovskite/HTM heterojunction. But the structure-property relationship in the heterojunction remains poorly understood. By using poly(3-alkylthiophene) (P3AT) as the HTM model, here we apply sum frequency generation vibrational spectroscopy to establish correlations among conformations of P3ATs, the hole extraction ability of P3ATs from the perovskite layer, and the charge mobility of P3ATs. It is revealed that with similar energy-level alignment, the conformational order of alkyl side chains in regioregular P3ATs can effectively regulate the hole extraction ability of P3ATs from perovskite layer by tuning reorganization energy. By contrast, the charge mobility of P3ATs strongly depends on the P3AT backbone's coplanarity. Our findings decouple the roles of the long-hidden conformational order of alkyl side chain and the polythiophene backbone's coplanarity on the performance of perovskite/HTM heterojunction, offering useful guidelines for boosting the performance of optoelectronic devices.The presence of adsorbed water on hydrophilic solid surfaces should be taken into account, especially in humid environments. It significantly reduces the adhesive strength between the epoxy resin and the adherend surface. Here, the adhesion structure of interfacial water sandwiched between bisphenol A epoxy resin and a hydroxylated silica (001) surface is investigated with microsecond molecular dynamics simulations. Specifically, interfacial water layers with initial thicknesses of 7.5, 10, and 20 Å are modeled. The density curves of water and the diglycidyl ether of bisphenol A show that at room temperature, the surface of the silica with hydroxyl groups is completely covered with a thick layer of water. For water layers thinner than 10 Å, the density of epoxy resin on the silica surface increases when the system is heated and does not return to the original density when the system is cooled. Furthermore, calculation of the interaction energy revealed that the exclusion of water from the hydroxylated surface by epoxy resin during heating can contribute to the increase in the adhesive interaction between the epoxy resin and the silica surface with hydroxyl groups.(-)-Epigallocatechin-3-gallate (EGCG) undergoes auto-oxidation at physiological pH and therefore may be poorly absorbed in the intestine. Fructooligosaccharides (FOS), comprising a group of 1-kestose, nystose, and 1F-β fructofuranosyl-nystose, are fermentable by gut bacteria and converted mainly into lactate. This study was conducted to determine whether dietary FOS may help to increase the plasma concentration of EGCG in rats by preventing it from auto-oxidation. Rats consumed an assigned diet, either a 0.3% (w/w) EGCG diet or an EGCG diet with additional 1, 3, or 5% (w/w) FOS, for 2 weeks. The results showed that the plasma concentration of EGCG was 0.21 ± 0.05 μM for the EGCG alone group, and it was significantly higher at 0.65 ± 0.12 μM for the EGCG plus 5% FOS group. Treatments with FOS resulted in a dose-dependent increase in the cecal level of lactate and brought the cecal pH down, with an accompanying alteration in the abundance of Lactobacillus and Collinsella. Because EGCG concentrations in the cecal digesta of rats fed the FOS-containing diet maintained comparatively high levels, FOS likely contributed to the protection of EGCG from auto-oxidation. In conclusion, FOS reduced the pH of the lumen of the intestine, kept EGCG intact to a certain degree, and consequently allowed EGCG to be taken into the blood circulation from the intestine.Most enveloped viruses rely on the host cell endoplasmic reticulum (ER) quality control (QC) machinery for proper folding of glycoproteins. The key ER α-glucosidases (α-Glu) I and II of the ERQC machinery are attractive targets for developing broad-spectrum antivirals. Iminosugars based on deoxynojirimycin have been extensively studied as ER α-glucosidase inhibitors; however, other glycomimetic compounds are less established. Accordingly, we synthesized a series of N-substituted derivatives of valiolamine, the iminosugar scaffold of type 2 diabetes drug voglibose. To understand the basis for up to 100,000-fold improved inhibitory potency, we determined high-resolution crystal structures of mouse ER α-GluII in complex with valiolamine and 10 derivatives. The structures revealed extensive interactions with all four α-GluII subsites. We further showed that N-substituted valiolamines were active against dengue virus and SARS-CoV-2 in vitro. This study introduces valiolamine-based inhibitors of the ERQC machinery as candidates for developing potential broad-spectrum therapeutics against the existing and emerging viruses.The electroreductive coupling of phthalimides with α,β-unsaturated carbonyl compounds in the presence of TMSCl and successive treatment of the electrochemically coupled products with TFA gave two types of rearranged products, 3- and 2-substituted 4-aminonaphthalen-1-ols. The substituent (R) on the nitrogen atom of phthalimides determined which type of 4-aminonaphthalen-1-ol was preferentially formed. Bulky and less bulky N substituents selectively afforded 3- and 2-substituted 4-aminonaphthalen-1-ols, respectively. It was presumed by the density functional theory calculations for the acid-catalyzed rearrangement of silyl ketene acetals produced by the electroreductive coupling that the rearranged product selectivity depends on whether O or N protonation of the amide group of the silyl ketene acetals occurs more rapidly.