5 research outputs found
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 CO<sub>2</sub>/N<sub>2</sub> 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 m<sup>2</sup> g<sup>–1</sup> 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 CO<sub>2</sub> capture, which was exemplified by gas separations of CO<sub>2</sub>/N<sub>2</sub> mixtures. The PAF-56P/PSF membranes show a
high selectivity of CO<sub>2</sub> over N<sub>2</sub> with a separation
factor of 38.9 due to the abundant nitrogen groups in the PAF-56P
framework. A preferred permeance for CO<sub>2</sub> in the binary
CO<sub>2</sub>/N<sub>2</sub> gas mixture is obtained in the range
of 93–141 GPU due to the large CO<sub>2</sub> 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
CO<sub>2</sub>, good stability, and easy scale up make PAF-56P/PSF
hollow fiber membranes of great interest for the industrial separations
of CO<sub>2</sub> 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