Dynamic Metastable Characteristics of Carbon Cages Embedded with Er2C2.

Novel endohedral metallofullerenes (EMFs), namely, Er2C2@C2v(5)-C80, Er2C2@Cs(6)-C82, Er2C2@Cs(15)-C84, Er2C2@C2v(9)-C86, Er2C2@Cs(15)-C86, and Er2C2@Cs(32)-C88, had been experimentally synthesized, and the unique structures and many fascinating properties had also been widely explored. Nevertheless, the position of the Er atoms inside the cage shows a severe disorder within the stable EMF monomer, which is difficult to understand and explain from the experimental point of view. In this work, based on the density functional theoretical calculations, the Er2C2@Cs(6)-C82 has 73 directional isomers and 2 Er atoms that are far beyond from Er-Er single bonding and tend to be close to the cage side (marked as "shell"), and the core (Er2C2 units) takes on a butterfly shape as generally revealed. The energy difference between any two of the isomers is in the range of 0.05 to 25.6 kcal/mol, indicating a relatively easy thermodynamic transition between the isomers. The other five Er carbide cluster EMFs (Er2C2@C2v(5)-C80, Er2C2@Cs(15)-C84, Er2C2@C2v(9)-C86, Er2C2@Cs(15)-C86, and Er2C2@Cs(32)-C88) are also studied in the same way, and 30, 37, 39, and 43 most stable Er-oriented sites inside the cage, respectively, are obtained. In addition, the shape of the Er2C2 gradually changed from butterfly to linear. Moreover, the electronic structure and molecular orbital analyses show that it is easy for Er2C2@C80-88 to form a charge transfer state of [Er2C2]4+@[C80-88]4- via the dynamic core-shell coordination equilibrium. Er2C2 with a steep drop in chemical stability is restricted to forming varying degrees of metastable states in the shell, determined by the shell size, to ensure the overall stability. The lowest unoccupied molecular orbital energy level of these EMFs is increased by 0.5-1.1 eV compared with fullerenes C80-88, potentially providing favorable conditions for suitable energy level matching with EMF as an electron acceptor used in organic solar cell devices.

Identification of Robust Antibiotic Subgroups by Integrating Multi-Species Drug-Drug Interactions.

Previous studies have shown that antibiotics can be divided into groups, and drug-drug interactions (DDI) depend on their groups. However, these studies focused on a specific bacteria strain (i.e., Escherichia coli BW25113). Existing datasets often contain noise. Noisy labeled data may have a bad effect on the clustering results. To address this problem, we developed a multi-source information fusion method for integrating DDI information from multiple bacterial strains. Specifically, we calculated drug similarities based on the DDI network of each bacterial strain and then fused these drug similarity matrices to obtain a new fused similarity matrix. The fused similarity matrix was combined with the T-distributed stochastic neighbor embedding algorithm, and hierarchical clustering algorithm can effectively identify antibiotic subgroups. These antibiotic subgroups are strongly correlated with known antibiotic classifications, and group-group interactions are almost monochromatic. In summary, our method provides a promising framework for understanding the mechanism of action of antibiotics and exploring multi-species group-group interactions.

AADB: A Manually Collected Database for Combinations of Antibiotics With Adjuvants.

Antimicrobial resistance is a global public health concern. The lack of innovations in antibiotic development has led to renewed interest in antibiotic adjuvants. However, there is no database to collect antibiotic adjuvants. Herein, we build a comprehensive database named Antibiotic Adjuvant DataBase (AADB) by manually collecting relevant literature. Specifically, AADB includes 3,035 combinations of antibiotics with adjuvants, covering 83 antibiotics, 226 adjuvants, and 325 bacterial strains. AADB provides user-friendly interfaces for searching and downloading. Users can easily obtain these datasets for further analysis. In addition, we also collected related datasets (e.g., chemogenomic and metabolomic data) and proposed a computational strategy to dissect these datasets. As a test case, we identified 10 candidates for minocycline, and 6 of 10 candidates are the known adjuvants that synergize with minocycline to inhibit the growth of E. coli BW25113. We hope that AADB can help users to identify effective antibiotic adjuvants. AADB is freely available at http://www.acdb.plus/AADB.

Integrating multi-source drug information to cluster drug-drug interaction network.

Characterizing drug-drug interactions is important to improve efficacy and/or slow down the evolution of antimicrobial resistance. Experimental methods are both time-consuming and laborious for characterizing drug-drug interactions. In recent years, many computational methods have been proposed to explore drug-drug interactions. However, these methods failed to effectively integrate multi-source drug information. In this study, we propose a similarity matrix fusion (SMF) method to integrate four drug information (i.e., structural similarity, pharmaceutical similarity, phenotypic similarity and therapeutic similarity). SMF combined with t-distributed stochastic neighbor embedding (t-SNE) and hierarchical clustering algorithm can effectively identify drug groups and group-group interactions are almost monochromatic (purely synergetic or purely antagonistic). To evaluate clustering quality (i.e., monochromaticity), two measures (edge purity and edge normalized mutual information) are proposed, and SMF showed the best performance. In addition, clustered drug-drug interaction network can also be used to predict new drug-drug interactions (accuracy = 0.741). Overall, SMF provides a comprehensive view to understand drug groups and group-group interactions.

Improving CO2 photoconversion with ionic liquid and Co single atoms.

Photocatalytic CO2 conversion promises an ideal route to store solar energy into chemical bonds. However, sluggish electron kinetics and unfavorable product selectivity remain unresolved challenges. Here, an ionic liquid, 1-ethyl-3-methylimidazolium tetrafluoroborate, and borate-anchored Co single atoms were separately loaded on ultrathin g-C3N4 nanosheets. The optimized nanocomposite photocatalyst produces CO and CH4 from CO2 and water under UV-vis light irradiation, exhibiting a 42-fold photoactivity enhancement compared with g-C3N4 and nearly 100% selectivity towards CO2 reduction. Experimental and theoretical results reveal that the ionic liquid extracts electrons and facilitates CO2 reduction, whereas Co single atoms trap holes and catalyze water oxidation. More importantly, the maximum electron transfer efficiency for CO2 photoreduction, as measured with in-situ µs-transient absorption spectroscopy, is found to be 35.3%, owing to the combined effect of the ionic liquid and Co single atoms. This work offers a feasible strategy for efficiently converting CO2 to valuable chemicals.

Interface Reversible Electric Field Regulated by Amphoteric Charged Protein-Based Coating Toward High-Rate and Robust Zn Anode.

Metallic interface engineering is a promising strategy to stabilize Zn anode via promoting Zn2+ uniform deposition. However, strong interactions between the coating and Zn2+ and sluggish transport of Zn2+ lead to high anodic polarization. Here, we present a bio-inspired silk fibroin (SF) coating with amphoteric charges to construct an interface reversible electric field, which manipulates the transfer kinetics of Zn2+ and reduces anodic polarization. The alternating positively and negatively charged surface as a build-in driving force can expedite and homogenize Zn2+ flux via the interplay between the charged coating and adsorbed ions, endowing the Zn-SF anode with low polarization voltage and stable plating/stripping. Experimental analyses with theoretical calculations suggest that SF can facilitate the desolvation of [Zn(H2O)6]2+ and provide nucleation sites for uniform deposition. Consequently, the Zn-SF anode delivers a high-rate performance with low voltage polarization (83 mV at 20 mA cm-2) and excellent stability (1500 h at 1 mA cm-2; 500 h at 10 mA cm-2), realizing exceptional cumulative capacity of 2.5 Ah cm-2. The full cell coupled with ZnxV2O5·nH2O (ZnVO) cathode achieves specific energy of ~ 270.5/150.6 Wh kg-1 (at 0.5/10 A g-1) with ~ 99.8% Coulombic efficiency and retains ~ 80.3% (at 5.0 A g-1) after 3000 cycles.

Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields.

The water-octanol partition coefficient is an important physicochemical property for small molecule drug design. Here, we report our participation in the SAMPL6 logP prediction challenge with free energy perturbation (FEP) calculations in the water phase and in the 1-octanol phase using Drude polarizable force fields. Root mean square error (RMSE) and mean absolute error (MAE) of our prediction are equal to 1.85 and 1.25 logP units. The errors are not evenly distributed. Out of eleven SAMPL6 solutes, FEP/Drude performed very badly on three molecules (deviations all larger than 2 logP units) but good on the remaining eight (deviations all less than 1 logP unit). We find while FEP converges well within one nanosecond in water, simulations in 1-octanol need much longer simulation time and possibly more independent runs for sampling. We also find out that 1-octanol, albeit being a non-polar solvent, still polarizes solute molecules and forms stable hydrogen bonds with them. At the end, we attempt to reweight FEP trajectories with QM/Drude calculations and discuss possible caveats in our simulation setup.

Structural basis of fullerene derivatives as novel potent inhibitors of protein acetylcholinesterase without catalytic active site interaction: insight into the inhibitory mechanism through molecular modeling studies.

Acetylcholinesterase (AChE) is an important kind of esterase that plays a key biological role in the central and peripheral nervous systems. Recent research has demonstrated that some fullerene derivatives serve as a new nanoscale class of potent inhibitors of AChE, but the specific inhibition mechanism remains unclear. In the present article, several molecular modeling methods, such as molecular docking, molecular dynamics simulations and molecular mechanics/generalized Born surface area calculations, were used for the investigation of the binding mode and inhibition mechanism of fullerene inhibitions for AChE. Results revealed that fullerene inhibitors block the entrance of substrates by binding with the peripheral anionic site (PAS) region. Thus, fullerene derivatives might mainly serve as competitive inhibitors. The interactions of a fullerene backbone with AChE are at the same level in different single side chain systems and seem to be related to the length or aromaticity of the side chain. The inhibitor with multihydroxyl side chains shows an obviously large electrostatic interaction as it forms additional hydrogen bonds with AChE. Moreover, fullerene derivatives might exhibit noncompetitive inhibition partly by affecting some secondary structures around them. Thus, the destructions of these secondary structures can lead to conformational changes in some important regions, such as the catalytic triad and acyl pocket. The investigation is of great importance to the discovery of good fullerene inhibitors.Communicated by Ramaswamy H. Sarma.

Insight into the process of product expulsion in cellobiohydrolase Cel6A from Trichoderma reesei by computational modeling.

Glycoside hydrolase cellulase family 6 from Trichoderma reesei (TrCel6A) is an important cellobiohydrolase to hydrolyze cellooligosaccharide into cellobiose. The knowledge of enzymatic mechanisms is critical for improving the conversion efficiency of cellulose into ethanol or other chemicals. However, the process of product expulsion, a key component of enzymatic depolymerization, from TrCel6A has not yet been described in detail. Here, conventional molecular dynamics and steered molecular dynamics (SMD) were applied to study product expulsion from TrCel6A. Tyr103 may be a crucial residue in product expulsion given that it exhibits two different posthydrolytic conformations. In one conformation, Tyr103 rotates to open the -3 subsite. However, Tyr103 does not rotate in the other conformation. Three different routes for product expulsion were proposed on the basis of the two different conformations. The total energy barriers of the three routes were calculated through SMD simulations. The total energy barrier of product expulsion through Route 1, in which Tyr103 does not rotate, was 22.2 kcal·mol-1. The total energy barriers of product expulsion through Routes 2 and 3, in which Tyr103 rotates to open the -3 subsite, were 10.3 and 14.4 kcal·mol-1, respectively. Therefore, Routes 2 and 3 have lower energy barriers than Route 1, and Route 2 is the thermodynamically optimal route for product expulsion. Consequently, the rotation of Tyr103 may be crucial for product release from TrCel6A. Results of this work have potential applications in cellulase engineering.