Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling

Small molecule receptor-binding is dominated by weak, non-covalent interactions such as van-der-Waals hydrogen bonding or electrostatics. Calculating these non-covalent ligand-receptor interactions is a challenge to computational means in terms of accuracy and efficacy since the ligand may bind in a number of thermally accessible conformations. The conformational rotamer ensemble sampling tool (CREST) uses an iterative scheme to efficiently sample the conformational space and calculates energies using the semi-empirical ‘Geometry, Frequency, Noncovalent, eXtended Tight Binding’ (GFN2-xTB) method. This combined approach is applied to blind predictions of the modes and free energies of binding for a set of 10 drug molecule ligands to the cucurbit[n]urils CB[8] receptor from the recent ‘Statistical Assessment of the Modeling of Proteins and Ligands’ (SAMPL) challenge including morphine, hydromorphine, cocaine, fentanyl, and ketamine. For each system, the conformational space was sufficiently sampled for the free ligand and the ligand-receptor complexes using the quantum chemical Hamiltonian. A multitude of structures makes up the final conformer-rotamer ensemble, for which then free energies of binding are calculated. For those large and complex molecules, the results are in good agreement with experimental values with a mean error of 3 kcal/mol. The GFN2-xTB energies of binding are validated by advanced density functional theory calculations and found to be in good agreement. The efficacy of the automated QM sampling workflow allows the extension towards other complex molecular interaction scenarios.     

The advantages of using impact resonance test in dynamic modulus master curve construction through the abbreviated test protocol

Asphalt concrete behavior is heavily dependent on temperature and loading rate. Hence, the material is typically tested at a range of temperatures and loading frequencies to capture its properties. Results are then used to develop a master curve exhibiting material behavior at the full spectrum of loading frequencies. An abbreviated testing protocol, under AASHTO PP 61-13, proposes a practical approach for development of this master curve. In this practice, the low temperature asymptote of the master curve is dominated by the limiting maximum modulus estimated through the Hirsch model. In this study, the dynamic modulus (DM) testing coupled with impact resonance (IR) test was used to evaluate the effect of this limiting maximum modulus on construction of the asphalt concrete master curve. Three different asphalt mixtures prepared with the same gradation and binder content, but different grades of stiffness were tested. The DM testing was performed at multiple temperatures and loading frequencies. The IR tests were conducted on the same specimens at the same temperatures. Two sigmoid functions (MEPDG and Richards models), and three shift factors (Arrhenius, Williams–Landel–Ferry, and polynomial) were utilized in the analysis. Richards sigmoid function coupled with polynomial shift factor provided the best fitting accuracy to the measured data. It was observed that the limiting maximum modulus obtained from experimental data was underpredicted by that obtained from the Hirsch model. The results indicated potential benefits of the IR test as a complementary testing tool to the abbreviated DM testing protocol to reliably characterize asphalt concrete.     

Synthesis and Characterization of Ferromagnetic Nickel Nanoparticles

Nickel nanoparticles on mass production scale have been prepared using a modified polyol process with Ni(CH₃COO)₂?4H₂O, NaOH, 1,2 propandiol and hydrazinium hydroxide (N₂H₄?H₂O). A?mixture of face centered cubic (fcc) metallic nickel nanoparticles with 12 nm diameter were obtained. We have experimentally studied the structure of nanoparticle by X-ray and Scanning Electron Microscopy (SEM, EDS). The magnetic properties of the prepared Ni film have been studied by Ferromagnetic Resonance (FMR) technique, Vibrating Sample Magnetometer (VSM) and Vector Network Analyzer (VNA). The effective g-factor and magnetic anisotropy constant were determined as g _eff=2.25 and K _eff=85?Oe, respectively.     

Phase Transfer Catalysis with Quaternary Ammonium Type Gemini Surfactants: <Emphasis Type="Italic">O</Emphasis>-Alkylation of Isovanillin

In this paper, O-alkylation of isovanillin with unusual phase transfer catalysts alkandiyl-α,ω-bis(dimethylalkylammonium bromide) dimeric surfactants (also known as gemini surfactants) is described. Some dimeric surfactants with simple hydrophobic alkyl chains and others with hydrophobic alkyl chains containing ester functionalities with different lengths were synthesized and characterized in our laboratory. The alkylation of isovanillin with alkyl halide was successively carried out in the presence of potassium carbonate and a phase transfer catalyst in tetrahydrofuran. The same reactions were also performed with both the traditional phase transfer catalyst tetrabutylammonium bromide and without any catalyst. The results were compared with those of dimeric surfactants. Consequently, it was expressed that alkandiyl-α,ω-bis(dimethylalkylammonium bromide) dimeric surfactants successively exhibit the character of phase transfer catalysts through environmentally friendly procedures under mild conditions. The most significant feature of this work is that dimeric surfactants have been determined to act as phase transfer agents.     

Global optimization method for controlling a plant

A control system that contains a generic plant has been built. Its controller parameters have been designed by using a global search algorithm for a given plant, and its performance has been evaluated for the heat control of a thermal system, and the speed control of a DC motor. This paper explains this control system with a DC motor as its plant, the speed of which is controlled by the controller.     

Evaluation of two-dimensional approach for computational modelling of heat and momentum transfer in liquid containing horizontal cans and experimental validation

Axi-symmetric approach in vertical cans lead to 2-dimensional (2D) model with shorter computational times. For horizontal cans containing liquids, this approach is not possible due to internally evolved natural convection. If an assumption is made to neglect gravitational effect in horizontal direction, it may be possible to use a 2D model. Therefore, the objective of this study was to evaluate this approach numerically and experimentally. In simulations, continuity, energy and momentum equations were solved in 2D and 3D using Ansys CFX 12.1 for horizontal cans containing water and another viscous liquid. In experiments, water filled cans were prepared, and temperature data were compared with simulation results. The results demonstrated the possible use of 2D approach in modelling for liquid containing horizontal cans with significant reduction in computational times. Optimization algorithms of simulation programs are also expected to be used in combination with simulation studies since computation times are reduced significantly.     

An economic synthesis of 1,2,3,4-tetra-O-acetyl-5-thio-D-xylopyranose and its transformation into 4-substituted-phenyl 1,5-dithio-D- xylopyranosides possessing antithrombotic activity

D-Xylose was converted via 1,2-O-isopropylidene-alpha-D-xylofuranose (4) into 3-O-benzoyl-5-S-benzoyl-1,2-O-isopropylidene-alpha-D-xylofuranose which, after methanolysis, acetylation and subsequent acetolysis afforded 1,2,3,4-tetra-O-acetyl-5-thio-alpha-D-xylopyranose (14) in an overall yield of 36%. Reaction of 4 with thionyl chloride gave a mixture of the diastereomeric cyclic sulfites, the structures of which were established by X-ray crystallography. Their oxidation with sodium periodate afforded the corresponding cyclic sulfate 23. Treatment of 23 with potassium thioacetate gave the potassium salt of 5-S-acetyl-1,2-O-isopropylidene-alpha-D-xylofuranose 3-O-sulfonic acid (26) which, after methanolysis, acetylation and subsequent acetolysis afforded 14 in an overall yield of 56%. Treatment of 4 with sulfuryl chloride gave a mixture containing 5-chloro-3-O-chlorosulfonyl-5-deoxy-1,2-O-isopropylidene-alpha-D- xylofuranose, 3,7,9,11-tetraoxa-4-thia-10-dimethyl-tricyclo[6,3,0, 0(2,6)]undecane S-dioxide and 23 in a 2:3:7 ratio. Tetraacetate 14 was converted into the alpha-1-bromide 18 as well as into the alpha-1-O-trichloroacetimidate 17. These three compounds were used as donors for the glycosylation with 4-cyanothiophenol, affording the 4-cyanophenyl 2,3,4-tri-O-acetyl-1,5-dithio-alpha- (29) and beta-D-xylopyranoside (30) in different ratios, depending on the reaction conditions. When donor 18 was used in the presence of potassium carbonate, besides 29 and 30 two aryl C-glycosylated-thioglycosides, i.e. 4-cyano-2-(2,3,4-tri-O-acetyl-5-thio-beta-D-xylopyranosyl)phenyl 2,3,4-tri-O-acetyl-1,5-dithio-alpha- and beta-D-xylopyranoside (32 and 33) as well as 4-cyano-2-(2,3,4-tri-O-acetyl-5-thio-beta-D-xylopyranosyl)phenyl disulfide 34 could be isolated as byproducts. Deacetylation of 30 with sodium methoxide in methanol afforded, besides 4-cyano-phenyl 1,5-dithio-beta-D-xylopyranoside (1), the corresponding 4-[(methoxy)(imino)methyl]phenyl glycoside 2. The 4-cyano group of 1 was converted into the 4-aminothiocarbonyl, the 4-(methyl-thio)(imino)methyl, the 4-amidino and the 4-(imino)(hydrazino)methyl group. All of these glycosides showed a significant antithrombotic activity on rats.     

U(NO_3)_4-HNO_3-H_2O/30%TBP-煤油萃取体系平衡分配数据及其数学描述

为了较准确地估计U(NO_3)_4在Purex分离柱(槽)中的分配行为,本文提供了74组平衡分配数据(平衡水相中HNO_3为0.2—4 N,U(NO_3)_4为1—30 mg/ml,25±0.5℃)。用拟平衡常数作为平衡水相硝酸根浓度和离子强度的函数这一形式,描述了这批数据。用这组模型得到的计算值与实验值符合得较好。相对误差绝对值平均:U(IV)为7.1%,HNO_3为6.3%。     

Synthesis and proton conductivity studies of 5‐aminotetrazole‐doped sulfonated polymer electrolyte membranes

This work reports the preparation and characterization of a new anhydrous proton conducting membrane based on poly(vinyl alcohol) (PVA), sulfosuccinic acid (SSA), and 5‐aminotetrazole (ATet) at various stoichiometric ratios. The proton conductivities of membranes were investigated as a function of ATet composition, SSA composition, and temperature. New anhydrous proton conducting membranes were characterized by infrared spectra, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), dynamic mechanical analysis (DMA), methanol permeability, and impedance measurements for proton conductivity. TGA showed that the samples were thermally stable up to 150°C. DSC results illustrated the homogeneity of the materials. Mechanical analysis showed that the storage modulus of the PVA–SSA–ATet blend polymer membranes decreased with increasing ATet content. The membranes with higher tetrazole content, or higher acid doping level presented the higher proton conductivity. PVA–SSA–ATet4 can exhibit an anhydrous proton conductivity of 1.7 × 10⁻³ S/cm at 130°C and the proton conductivity increased with increasing temperature and acid doping level. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers     

Catalytic hydrodechlorination of 2,4-dichlorophenol on Pd/Rh/C catalysts

Catalytic hydrodechlorination of 2,4-dichlorophenol was studied over 0.97% Pd/C, 0.98% Rh/C and 0.8% Pd-0.19% Rh/C catalysts. The catalysts were prepared by incipient wetness impregnation of support and characterized by BET surface area, temperature programmed reduction (TPR) and X-ray diffraction (XRD). The 0.97% Pd/C catalyst, which had the largest crystallite size, was the most active and selective towards the formation of 2- and 4-chlorophenols among three catalysts in liquid phase. Hydrodechlorination activity of carbon-supported catalysts were in the order of Pd/C>Pd/Rh/C>Rh/C. The kinetic equation explained experimental data well and kinetic parameters of three catalysts were provided and discussed.