Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure–Activity Resource Benchmark

In this study, we use the recently released 2012 Community Structure–Activity Resource (CSAR) data set to evaluate two knowledge-based scoring functions, ITScore and STScore, and a simple force-field-based potential (VDWScore). The CSAR data set contains 757 compounds, most with known affinities, and 57 crystal structures. With the help of the script files for docking preparation, we use the full CSAR data set to evaluate the performances of the scoring functions on binding affinity prediction and active/inactive compound discrimination. The CSAR subset that includes crystal structures is used as well, to evaluate the performances of the scoring functions on binding mode and affinity predictions. Within this structure subset, we investigate the importance of accurate ligand and protein conformational sampling and find that the binding affinity predictions are less sensitive to non-native ligand and protein conformations than the binding mode predictions. We also find the full CSAR data set to be more challenging in making binding mode predictions than the subset with structures. The script files used for preparing the CSAR data set for docking, including scripts for canonicalization of the ligand atoms, are offered freely to the academic community

Computation and Simulation of the Structural Characteristics of the Kidney Urea Transporter and Behaviors of Urea Transport

Urea transporters are a family of membrane proteins that transport urea molecules across cell membranes and play important roles in a variety of physiological processes. Although the crystal structure of bacterial urea channel <i>dv</i>UT has been solved, there lacks an understanding of the dynamics of urea transport in <i>dv</i>UT. In this study, by using molecular dynamics simulations, Monte Carlo methods, and the adaptive biasing force approach, we built the equilibrium structure of <i>dv</i>UT, calculated the variation in the free energy of urea, determined the urea-binding sites of <i>dv</i>UT, gained insight into the microscopic process of urea transport, and studied the water permeability in <i>dv</i>UT including the analysis of a water chain in the pore. The strategy used in this work can be applied to studying transport behaviors of other membrane proteins

Self-Supported Fibrous Porous Aromatic Membranes for Efficient CO₂/N₂ Separations

In this paper, we describe a new synthesis protocol for the preparation of self-supported hollow fiber membranes composed of porous aromatic framework PAF-56P and PSF. PAF-56P was facilely prepared by the cross-coupling reaction of triangle-shaped cyanuric chloride and linear <i>p</i>-terophenyl monomers. The prepared PAF-56P material possesses an extended conjugated network, the structure of which is confirmed by nuclear magnetic resonance and infrared characterizations, as well as a permanent porosity with a BET surface area of 553.4 m² g^–1 and a pore size of 1.2 nm. PAF-56P was subsequently integrated with PSF matrix into PAF-56P/PSF asymmetric hollow fiber membranes via the dry jet-wet quench method employing PAF-56P/PSF suspensions. Scanning electron microscopy studies show that PAF-56P particles are embedded in the PSF matrix to form continuous membranes. Fabricated PAF-56P/PSF membranes were further exploited for CO₂ capture, which was exemplified by gas separations of CO₂/N₂ mixtures. The PAF-56P/PSF membranes show a high selectivity of CO₂ over N₂ with a separation factor of 38.9 due to the abundant nitrogen groups in the PAF-56P framework. A preferred permeance for CO₂ in the binary CO₂/N₂ gas mixture is obtained in the range of 93–141 GPU due to the large CO₂ adsorption capacity and a large pore size of PAF-56P. Additionally, PAF-56P/PSF membranes exhibit excellent thermal and mechanical stabilities, which were examined by thermal analysis and gas separation tests with the dependencies of temperatures and pressures. The merits of high selectivity for CO₂, good stability, and easy scale up make PAF-56P/PSF hollow fiber membranes of great interest for the industrial separations of CO₂ from the gas exhausts

Detection of Harmful Gases by Copper-Containing Metal–Organic Framework Films

The stabilization of copper clusters in nanosized metal–organic framework crystals, Cu-Y­(BTC), was achieved by a solvent-exchange approach, followed by hydrogen reduction. The formation of copper clusters in the Y­(BTC) nanocrystals generated during the hydrogen reduction process was followed by UV–vis spectroscopy. The Cu-Y­(BTC) nanocrystals were further assembled in thin films with a thickness of 250 nm. The distribution and size of the copper clusters in the films were studied by CO chemisorption, followed by FT-IR spectroscopy combined with transmission electron microscopy. It was shown that the copper clusters with a mean diameter of 6 nm were homogeneously distributed and stabilized in the Cu-Y­(BTC) films. Further, the Cu-Y­(BTC) films were utilized for detection of single harmful gases, such as CO, chloroform, and 2-ethylthiophene, or mixtures of two compounds. The high sensitivity, selectivity, and reversibility of the Cu-Y­(BTC) films toward single CO, chloroform, and 2-ethylthiophene were demonstrated. Noteworthy, the Cu-Y­(BTC) films exhibited a fast response toward CO, even in the presence of chloroform and 2-ethylthiophene, which was due to the high activity and accessibility of copper clusters. The response of Cu-Y­(BTC) toward 2-ethylthiophene was slower in comparison with chloroform, which was attributed to the bigger size and higher viscosity of 2-ethylthiophene

Porous Aromatic Frameworks for Size-Selective Halogenation of Aryl Compounds

Organic halides are vitally important chemical precursors or intermediates in the fields of agrochemical synthesis, molecular recognition, and material science. However, it is difficult to selectively synthesize these compounds due to the multiple reactive sites in aryl fragments. In this work, we prepared the first fully fluorinated porous aromatic framework (PAF). Its −C–F bond and hierarchical porosity have great benefits for PAF functionalization. After being decorated with different cyclodextrins (CDs), CD-PAF materials can incorporate diverse aryl compounds to protect their ortho sites from being attacked to produce para-substituted molecules. This selectivity obviously increased with a decrease in the substrate size (from 0.97 to 0.41 nm). In addition, the CD-PAFs can undergo long-term use in both chlorination and bromination