Syntheses and crystal structures of triorganotin(IV) complexes based on mixed ligands of 2,4,5-trifluoro-3-methoxybenzoic acid and 4,4′-bipy

Four new complexes have been synthesized based on the 2,4,5-trifluoro-3-methoxybenzoic acid and 4,4′-bipy of the type [R₃Sn(OOCC₆HF₃OCH₃)]₂·(4,4′-bpy). All complexes were characterized by elemental, IR, ¹H, ¹³C and ¹¹⁹Sn NMR spectra analyses. Complexes 1 and 4 were also characterized by X-ray crystallography. Crystal structures of 1 and 4 show that the coordination number of tin atom is five and the 2D network is connected by intermolecular C–H···O interactions.     

FDM 3D printing of combustible structures: First results

For the first time, complex geometry combustible structures of an ammonium perchlorate–polylactic acid composite have been successfully printed using fused deposition modeling (FDM). The structural and energetic capabilities of the printed structures are demonstrated. Combined with the ability to be produced by FDM printing, these combustible elements could afford many practical applications.     

2D representation of protein secondary structure sequences and its applications

In terms of the classification of the protein secondary structures, we propose a 2D representation of protein secondary structure sequences. The representation are used to display, analyze, and compare the secondary structure sequences. Based on this representation, we assign the structural class to the protein, and verify the advantage or disadvantage of the methods of predicted protein second structure.     

Search of ligands for the amyloidogenic protein beta2-microglobulin by capillary electrophoresis and other techniques

Beta2-microglobulin (beta2-m) is a small amyloidogenic protein normally present on the surface of most nucleated cells and responsible for dialysis-related amyloidosis, which represents a severe complication of long-term hemodialysis. A therapeutic approach for this amyloidosis could be based on the stabilization of beta2-m through the binding to a small molecule, and consequent inhibition of protein misfolding and amyloid fibril formation. A few compounds have been described to weakly bind beta2-m, including the drug suramin. The lack of a binding site for nonpolypeptidic ligands on the beta2-m structure makes it difficult for both the identification of functional groups responsible for the binding and the search of hits to be optimized. The characterization of the binding properties of suramin for beta2-m by using three different techniques (surface plasmon resonance, affinity CE (ACE), ultrafiltration) is here described and the results obtained are compared. The common features of the chemical structures of the compounds known to bind the protein led us to select 200 sulfonated/suramin-like molecules from a wider chemical library on the basis of similarity rules, so as to possibly single out some interesting hits and to gain more information on the functional groups involved in the binding. The development of screening methods to test the compounds by using ultrafiltration and ACE is described.     

Distilling the essential features of a protein surface for improving protein-ligand docking,scoring, and virtual screening

For the successful identification and docking of new ligands to a protein target by virtual screening, the essential features of the protein and ligand surfaces must be captured and distilled in an efficient representation. Since the running time for docking increases exponentially with the number of points representing the protein and each ligand candidate, it is important to place these points where the best interactions can be made between the protein and the ligand. This definition of favorable points of interaction can also guide protein structure-based ligand design, which typically focuses on which chemical groups provide the most energetically favorable contacts. In this paper, we present an alternative method of protein template and ligand interaction point design that identifies the most favorable points for making hydrophobic and hydrogen–bond interactions by using a knowledge base. The knowledge-based protein and ligand representations have been incorporated in version 2.0 of SLIDE and resulted in dockings closer to the crystal structure orientations when screening a set of 57 known thrombin and glutathione S–transferase (GST) ligands against the apo structures of these proteins. There was also improved scoring enrichment of the dockings, meaning better differentiation between the chemically diverse known ligands and a 15,000-molecule dataset of randomly-chosen small organic molecules. This approach for identifying the most important points of interaction between proteins and their ligands can equally well be used in other docking and design techniques. While much recent effort has focused on improving scoring functions for protein-ligand docking, our results indicate that improving the representation of the chemistry of proteins and their ligands is another avenue that can lead to significant improvements in the identification, docking, and scoring of ligands.(These authors contributed equally to this work)     

Program Fullerene: A software package for constructing and analyzing structures of regular fullerenes

Fullerene (Version 4.4) is a general purpose open‐source program that can generate any fullerene isomer, perform topological and graph theoretical analysis, as well as calculate a number of physical and chemical properties. The program creates symmetric planar drawings of the fullerene graph and generates accurate molecular 3D geometries by way of force‐field optimization, serving as a good starting point for further quantum theoretical treatments. It includes a number of fullerene‐to‐fullerene transformations, such as Goldberg–Coxeter transforms, Stone–Wales transforms, Endo–Kroto, Yoshida–Fowler, and Brinkmann–Fowler vertex insertions. The program is written in standard Fortran and C++ and can easily be installed in a Linux or UNIX environment. © 2013 Wiley Periodicals, Inc.     

A review on two-dimensional (2D) and 2D-3D multidimensional perovskite solar cells: Perovskites structures,stability, and photovoltaic performances

Perovskite solar cells (PSCs) fabricated with two-dimensional (2D) halide and 2D-3D mixed-halide materials are remarkable for their optoelectronic properties. The 2D perovskite structures are extremely stable but show limited charge transport and large bandgap for solar cell applications. To overcome these challenges, multidimensional 2D-3D perovskite materials are used to maintain simultaneously, a long-term stability, and high performance. In this review, we discuss the recent progress and the advantages of 2D and 2D-3D perovskite materials as absorber for solar cell applications. First, we discuss the structure and the unique properties of 2D and multidimensional 2D-3D perovskites materials. Second, the stability of 2D and 2D-3D mixed perovskites and the perspects of PSCs are hashed out.     

The identification of new ATAD2 bromodomain inhibitors: the application of combined ligand and structure-based virtual screening

Ligand-based virtual screening (LBVS) and structure-based virtual screening (SBVS) approaches were used to identify new inhibitors for ATAD2 bromodomain. The LBVS approach was used to search 23,129,083 clean compounds to identify compounds similar to an active compound with reported pIC₅₀ equal to 7.2. Based on LBVS results, 19 compounds were selected. To perform SBVS, by applying nine filters on 23,129,083 clean compounds, 1,057,060 compounds were selected. After performing SBVS on these selected compounds with idock software, 16 compounds with the lowest binding energies were selected. More accurate molecular docking analysis was performed on these 35 selected compounds by using iGEMDOCK software and six of them with the lowest binding energies were selected as hit compounds. These compounds were zinc36647229, zinc77969074, zinc13637358, zinc77971540, zinc12991296 and zinc19374204.     

Theoretical studies on the structures and isomerization of the LiSiF_3 system

Various possible isomers of LiSiF_3 system and isomerization between them have been studied at G2(MP2) level using ab initio calculations. The relative energies of four minimum points on the potential energy surface are -128.6, -194.3, -12.7 and -122.8 kJ/mol (taking the sum of the energies of LiF and SiF_2 as zero) . The structural energy of the four-membered ring that contains three F-Si-F-Li four-membered rings with C_(3v) symmetry is the lowest. The highest potential barrier for the isomerization of the remaining three-or four-membered structure is 12.5 kJ/mol.     

Inhibitors of an AdoMet-dependent 3-amino-3-carboxypropyl transferase and their use as ligands for protein affinity chromatography

The screening of potential affinity ligands and the development of a two-stage affinity purification of an S-adenosylmethionine-dependent 3-amino-3-carboxypropyl transferase involved in the biosynthesis of the β-lactam antibiotic nocardicin A is described from a cell-free extract of Nocardia uniformis subsp. tsuyamanesis. This protein is particularly sensitive to ion exchange and salt effects necessitating a pair of neutral ligands to be used in the final purification.     

Discovery novel VEGFA inhibitors through structure-based virtual screening and verify the ability to inhibit the proliferation,invasion and migration of gastric cancer

This paper aims to screen small molecule inhibitors 1,2,3,4,6-penta-O-galloyl-beta-D-glucose (PGG) targeting vascular endothelial growth factor A (VEGFA) through structure based virtual screening and molecular dynamics simulation, and verify the effect of anti gastric cancer.First, Based on Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, the candidate small-molecule compounds targeting VEGFA were screened by a molecular docking method using Computer-Aided Drug Design. Second, CCK8 was used to determine the effect of three commercially available candidate drugs on the proliferation activity of HGC27 and AGS. PGG was selected for further cell cloning, invasion, migration and apoptosis experiments. Finally, the complex system of three compounds and VEGFA was analyzed by molecular dynamics simulation.According to the ranking of the scoring function, the selected small molecular compounds are PGG, 2,3,4,6-tetra-O-galactosyl-D-glucopyranoside, rutin, quercetin-5,3-d-galactoside and 1F-Fructofuranosylnystose (1FF). CCK8 showed that PGG had the best inhibitory effect on the proliferation of AGS and HGC27 cells, and it was concentration and time dependent. Treatment of AGS and HGC27 with IC₅₀ PGG can significantly inhibit the cloning of HGC27 and AGS, block their invasion and migration, and induce their apoptosis. Molecular dynamics simulation experiments showed that the binding of PGG to VEGFA target protein was better than that of other two small molecular compounds, which was consistent with the results of molecular docking and biological activity experiments.     

Cobalt(II) coordination polymers built on isomeric dipyridyl triazole ligands with pyromellitic acid: Synthesis, characterization and their effects on the thermal decomposition of ammonium perchlorate

Three new cobalt(Ⅱ) coordination compounds,[Co(3,3’-Hbpt)2(H2pm)(H2O)2]·2H2O(1),[Co(4,4’-Hbpt)(pm)0.5(H2O)]·3H2O (2) and [Co(3,4’-Hbpt)(pm) 0.5 (H2O)3]·2H2O(3)(3,3’-Hbpt=3,5-bis(3-pyridyl)-1H-1,2,4-triazole;4,4’-bpt=3,5-bis(4-pyridyl)1H-1,2,4-triazole,3,4’-Hbpt=3-(3-pyridyl)-5-(4’-pyridyl)-1H-1,2,4-triazole and H4pm=pyromellitic acid) have been synthesized by hydrothermal reactions.Single-crystal X-ray diffraction reveals that compound 1 has a one-dimensional (1D) chain network,2 exhibits a four-connected three-dimensional (3D) structure with 1D open channels encapsulated by water molecules,while 3 displays a regular two-dimensional (2D) architecture connected through 1D metal helical chains.In addition,the efficacy of compounds 1-3 as additives to promote the thermal decomposition of ammonium perchlorate (AP) is explored by differential scanning calorimetry (DSC).     

Identification of novel nt-MGAM inhibitors for potential treatment of type 2 diabetes: Virtual screening,atom based 3D-QSAR model,docking analysis and ADME study

In this study, a virtual screening procedure was applied to identify new potential nt-MGAM inhibitors as a possible medication for type 2 diabetes. To this aim, a series of salacinol analogues were first investigated by docking analysis for their binding to the X-ray structure of the biological target nt-MGAM. Key interactions for ligand binding into the receptor active site were identified which shared common features to those found for other known inhibitors, which strengthen the results of this study. 3D QSAR model was then built and showed to be statistically significant and with a good predictive power for the training (R² = 0.99, SD = 0.17, F = 555.3 and N = 27) and test set (Q² = 0.81, Pearson(r) = 0.92, RMSE = 0.52, N = 08). The model was then used to virtually screen the ZINC database with the aim of identifying novel chemical scaffolds as potential nt-MGAM inhibitors. Further, in silico predicted ADME properties were investigated for the most promising molecules. The outcome of this investigation sheds light on the molecular characteristics of the binding of salacinol analogues to nt-MGAM enzyme and identifies new possible inhibitors which have the potential to be developed into drugs, thus significantly contributing to the design and optimization of therapeutic strategies against type 2 diabetes.     

Theoretical studies on the structures and isomerization of the LiSiF3 system

Various possible isomers of LiSiF₃ system and isomerization between them have been studied at G2(MP2) level usingab initio calculations. The relative energies of four minimum points on the potential energy surface are-128.6,-194.3,-12.7 and-122.8 kJ/mol (taking the sum of the energies of LiF and SiF₂ as zero). The structural energy of the four-membered ring that contains three F-Si-F-Li four-membered rings with C_3v symmetry is the lowest. The highest potential barrier for the isomerization of the remaining three- or four-membered structure is 12.5 kJ/ mol. Project supported by the National Natural Science Foundation of China (Grant No. 29673026).     

Si2CN分子结构的理论研究

在B3LYP／6－311G（d）水平上对Si2CN的各种可能异构体进行了研究，得到了其几何构型，结果表明：Si2CN有11个稳定的异构体，能量最低的是直线型异构体SiCNSi1,其次是四元环构型具有SiC桥键，电子态为^2A″的cSiSiCN6，第三稳定的是具有CSiSi三元环和环外NC键的N－cCSiSi10^2A1，第四稳定的是四元环具有SiN桥键^2A″电子态异构体cSiSiCN7。     

CarbBuilder: Software for building molecular models of complex oligo‐ and polysaccharide structures

CarbBuilder is a portable software tool for producing three‐dimensional molecular models of carbohydrates from the simple text specification of a primary structure. CarbBuilder can generate a wide variety of carbohydrate structures, ranging from monosaccharides to large, branched polysaccharides. Version 2.0 of the software, described in this article, supports monosaccharides of both mammalian and bacterial origin and a range of substituents for derivatization of individual sugar residues. This improved version has a sophisticated building algorithm to explore the range of possible conformations for a specified carbohydrate molecule. Illustrative examples of models of complex polysaccharides produced by CarbBuilder demonstrate the capabilities of the software. CarbBuilder is freely available under the Artistic License 2.0 from https://people.cs.uct.ac.za/~mkuttel/Downloads.html . © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Purification of a crystallin domain of Yersinia crystallin from inclusion bodies and its comparison to native protein from the soluble fraction

It has been established that many heterologously produced proteins in E. coli accumulate as insoluble inclusion bodies. Methods for protein recovery from inclusion bodies involve solubilization using chemical denaturants such as urea and guanidine hydrochloride, followed by removal of denaturant from the solution to allow the protein to refold. In this work, we applied on-column refolding and purification to the second crystallin domain D2 of Yersinia crystallin isolated from inclusion bodies. We also purified the protein from the soluble fraction (without using any denaturant) to compare the biophysical properties and conformation, although the yield was poor. On-column refolding method allows rapid removal of denaturant and refolding at high protein concentration, which is a limitation in traditionally used methods of dialysis or dilution. We were also able to develop methods to remove the co-eluting nucleic acids during chromatography from the protein preparation. Using this protocol, we were able to rapidly refold and purify the crystallin domain using a two-step process with high yield. We used biophysical techniques to compare the conformation and calcium-binding properties of the protein isolated from the soluble fraction and inclusion bodies.     

Active-site models for the nickel-iron hydrogenases: effects of ligands on reactivity and catalytic properties

Described are new derivatives of the type [HNiFe(SR)(2)(diphosphine)(CO)(3)](+), which feature a Ni(diphosphine) group linked to a Fe(CO)(3) group by two bridging thiolate ligands. Previous work had described [HNiFe(pdt)(dppe)(CO)(3)](+) ([1H](+)) and its activity as a catalyst for the reduction of protons (J. Am. Chem. Soc. 2010, 132, 14877). Work described in this paper focuses on the effects on properties of NiFe model complexes of the diphosphine attached to nickel as well as the dithiolate bridge, 1,3-propanedithiolate (pdt) vs 1,2-ethanedithiolate (edt). A new synthetic route to these Ni-Fe dithiolates is described, involving reaction of Ni(SR)(2)(diphosphine) with FeI(2)(CO)(4) followed by in situ reduction with cobaltocene. Evidence is presented that this route proceeds via a metastable μ-iodo derivative. Attempted isolation of such species led to the crystallization of NiFe(Me(2)pdt)(dppe)I(2), which features tetrahedral Fe(II) and square planar Ni(II) centers (H(2)Me(2)pdt = 2,2-dimethylpropanedithiol). The new tricarbonyls prepared in this work are NiFe(pdt)(dcpe)(CO)(3) (2, dcpe = 1,2-bis(dicyclohexylphosphino)ethane), NiFe(edt)(dppe)(CO)(3) (3), and NiFe(edt)(dcpe)(CO)(3) (4). Attempted preparation of a phenylthiolate-bridged complex via the FeI(2)(CO)(4) + Ni(SPh)(2)(dppe) route gave the tetrametallic species [(CO)(2)Fe(SPh)(2)Ni(CO)](2)(μ-dppe)(2). Crystallographic analysis of the edt-dcpe compund [2H]BF(4) and the edt-dppe compound [3H]BF(4) verified their close resemblance. Each features pseudo-octahedral Fe and square pyramidal Ni centers. Starting from [3H]BF(4) we prepared the PPh(3) derivative [HNiFe(edt)(dppe)(PPh(3))(CO)(2)]BF(4) ([5H]BF(4)), which was obtained as a ～2:1 mixture of unsymmetrical and symmetrical isomers. Acid-base measurements indicate that changing from Ni(dppe) (dppe = Ph(2)PCH(2)CH(2)PPh(2)) to Ni(dcpe) decreases the acidity of the cationic hydride complexes by 2.5 pK(a)(PhCN) units, from ～11 to ～13.5 (previous work showed that substitution at Fe leads to more dramatic effects). The redox potentials are more strongly affected by the change from dppe to dcpe, for example the [2](0/+) couple occurs at E(1/2) = -820 for [2](0/+) vs -574 mV (vs Fc(+/0)) for [1](0/+). Changes in the dithiolate do not affect the acidity or the reduction potentials of the hydrides. The acid-independent rate of reduction of CH(2)ClCO(2)H by [2H](+) is about 50 s(-1) (25 °C), twice that of [1H](+). The edt-dppe complex [2H](+) proved to be the most active catalyst, with an acid-independent rate of 300 s(-1).     

eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity

With the development of computer technology, computer-aided drug design (CADD) has become an important means for drug research and development, and its representative method is virtual screening. Various virtual screening platforms have emerged in an endless stream and play great roles in the field of drug discovery. With the increasing number of compound molecules, virtual screening platforms face two challenges: low fluency and low visibility of software operations. In this article, we present an integrated and graphical drug design software eSHAFTS based on three-dimensional (3D) molecular similarity to overcome these shortcomings. Compared with other software, eSHAFTS has four main advantages, which are integrated molecular editing and drawing, interactive loading and analysis of proteins, multithread and multimode 3D molecular similarity calculation, and multidimensional information visualization. Experiments have verified its convenience, usability, and reliability. By using eSHAFTS, various tasks can be submitted and visualized in one desktop software without locally installing any dependent plug-ins or software. The software installation package can be downloaded for free at http://lilab.ecust.edu.cn/home/resource.html . © 2019 Wiley Periodicals, Inc.