Rapid parameterization of small molecules using the force field toolkit

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide‐scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error‐prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM‐compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure‐solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). © 2013 Wiley Periodicals, Inc.     

ADSORPTION OF METAL IONS ON STEARIC ACID-NONADECANE PARTICLES IN AQUEOUS SOLUTION

The adsorption of metal ions at the stearic acid/electrolyte and nnonadccane-stearic acid mixture/electrolyte interface was investigated by means of the potentiometric titration, zeta potential and adsorption measurements. It was found that the studied colloidal suspensions exhibited an adsorption affinity towards multivalent metal ions. The adsorption of Ca²⁺, Cd²⁺ and Al³⁺ ions caused a strong decrease of surface charge density and zeta potential values in this systems. The adsorption reactions occur by way of cation exchange with protons from two surface carboxyl groups. Al high metal concentrations, in adsorption reactions there are involved also carboxyl groups from the subsurface layer. On the basis of the adsorption data, the cation surface complexation constants were calculated by Shindler's method.     

Encapsulation of Quantum Dots Inside Liposomal Hybrid Cerasome Using a One-Pot Procedure

A one-pot strategy for the fabrication of the quantum dots loaded cerasome has been successfully developed based on the condensation of dihexadecylamine and 3-isocyanatopropyltriethoxysilane, followed by spontaneous encapsulation and solubilization of hydrophobic quantum dots into the hybrid liposomal cerasomes in combination of self-assembly and sol-gel process. Fourier transform infrared spectroscopy and mass spectra prove the formation of the intermediate organoalkoxysilane with a lipid-like structure, which forms cerasome vesicles. After encapsulation into cerasome, quantum dots become well dispersed in aqueous solution. Such water-soluble QD cerasomes exhibit a better photostability and retain the luminescence property of the original hydrophobic quantum dots.     

Chitosan‐Based Glucose Oxidase Electrodes Enhanced by Silver Nanoparticles

Silver nanoparticles enhanced glucose oxidase electrodes were prepared on the basis of chitosan matrix. The enzyme electrodes exhibited high sensitivity and excellent response performance to glucose with a linear range from 1×10^?6 to 8×10^?3 mol · L^?1. And the time reaching the steady‐state amperometric response was less than 5 seconds. The inhibition percentage of this enzyme electrode against copper ions concentration was linear ranging from 1.2×10^?6 to 5×10^?5 mol · L^?1. These properties of enzyme electrodes are probably due to the excellent electron transfer of silver nanoparticles and the orientation of glucose oxidase molecule.     

Formula Optimization of Emulsifiers for Preparation of Multiple Emulsions Based on Artificial Neural Networks

Formulation optimization of emulsifiers for preparing multiple emulsions was performed in respect of stability by using artificial neural network (ANN) technique. Stability of multiple emulsions was expressed by the percentage of reserved emulsion volume of freshly prepared sample after centrifugation. Individual properties of multiple emulsions such as droplet size, δ, viscosity of the primary and the multiple emulsions were also considered. A back‐propagation (BP) network was well trained with experimental data pairs and then used as an interpolating function to estimate the stability of emulsions of different formulations. It is found that using mixtures of Span 80 and Tween 80 with different mass ratio as both lipophilic and hydrophilic emulsifiers, multiple W/O/W emulsions can be prepared and the stability is sensitive to the mixed HLB numbers and concentration of the emulsifiers. By feeding ANN with 39 pairs of experimental data, the ANN is well trained and can predict the influences of several formulation variables to the immediate emulsions stability. The validation examination indicated that the immediate stability of the emulsions predicted by the ANN is in good agreement with measured values. ANN therefore could be a powerful tool for rapid screening emulsifier formulation. However, the long‐term stability of the emulsions is not good, possibly due to the variation of the HLB number of the mixed monolayers by diffusion of emulsifier molecules, but can be greatly improved by using a polymer surfactant Arlacel P135 to replace the lipophilic emulsifier.     

Fast concentration of dissolved forms of cesium radioisotopes from large seawater samples

The method developed for cesium concentration from large freshwater samples was tested and adapted for analysis of cesium radionuclides in seawater. Concentration of dissolved forms of cesium in large seawater samples (about 100 L) was performed using composite absorbers AMP-PAN and KNiFC-PAN with ammonium molybdophosphate and potassium–nickel hexacyanoferrate(II) as active components, respectively, and polyacrylonitrile as a binding polymer. A specially designed chromatography column with bed volume (BV) 25 mL allowed fast flow rates of seawater (up to 1,200 BV h^?1). The recovery yields were determined by ICP-MS analysis of stable cesium added to seawater sample. Both absorbers proved usability for cesium concentration from large seawater samples. KNiFC-PAN material was slightly more effective in cesium concentration from acidified seawater (recovery yield around 93 % for 700 BV h^?1). This material showed similar efficiency in cesium concentration also from natural seawater. The activity concentrations of ¹³⁷Cs determined in seawater from the central Pacific Ocean were 1.5 ± 0.1 and 1.4 ± 0.1 Bq m^?3 for an offshore (January 2012) and a coastal (February 2012) locality, respectively, ¹³⁴Cs activities were below detection limit (<0.2 Bq m^?3).     

Determination of 129I in biomonitors collected in the vicinity of a nuclear power plant by neutron activation analysis

Neutron activation analysis (NAA) was used to determine ¹²⁹I and the ¹²⁹I/¹²⁷I ratio in bovine thyroid, moss, and river sediment samples collected in the vicinity of the Temelín nuclear power plant (NPP) in south Bohemia. The NAA procedures comprised pre-irradiation separation of ¹²⁹I by combustion of the samples in the stream of oxygen at 1,000 °C and trapping the liberated iodine in a LiOH/(NH₄)₂SO₃ solution. Post-irradiation separation of ¹³⁰I produced by the reaction ¹²⁹I(n,γ)¹³⁰I was carried out by extraction of elementary iodine with chloroform followed by precipitation of PdI₂. Nondestructive, epithermal NAA was used to determine ¹²⁷I employing the ¹²⁷I(n,γ)¹²⁸I reaction. The results showed that mean values of ¹²⁹I and the ¹²⁹I/¹²⁷I ratio in the bovine thyroids varied from 22 to 61 mBq kg^?1 (dry mass) and 2.8 × 10^?9 to 5.4 × 10^?9, respectively. These values are close to the lower end of results reported from various regions non-polluted with ¹²⁹I. No significant differences were found between ¹²⁹I concentrations and the ¹²⁹I/¹²⁷I ratios in the bovine thyroids collected prior to the start and after several years of operation of the NPP. The mean value and standard deviation of ¹²⁹I in mBq kg^?1, dry mass and the ¹²⁹I/¹²⁷I ratio in moss Pleurozium schreberi were 23 ± 16 and 2.3 × 10^?9, respectively, whereas values of ¹²⁹I in the river sediments were below 8–10 mBq kg^?1 (dry mass) after several years of the NPP operation.     

Synthesis, radiochemistry and stability of the conjugates of technetium-99m complexes with Substance P

Two types of technetium-99m complexes: (i) with the Hynic ligand linked to Substance P(1–11) and (ii) of the type ‘4 + 1’ consisting of tetradentate tripodal chelator tris(2-mercaptoethyl)-amine and monodentate isocyanide ligand previously coupled with Substance P(1–11), have been prepared on the n.c.a. scale. The obtained conjugates exhibit different lipophilicity and high stability in neutral aqueous solutions, even in the presence of excess concentration of histidine/cysteine competitive standard ligands. The conjugate (^99mTc(NS₃)(CN))₂–SP containing two technetium-99m species in the molecule may be expected to be an extremely good diagnostic radiopharmaceutical.     

微米及纳米丝光沸石分子筛上二甲醚羰基化反应的积碳分析

对比研究了在传统微米尺寸和新结构纳米丝光沸石催化剂上二甲醚羰基化合成乙酸甲酯的反应行为.结果表明,通过减小分子筛的尺寸到纳米水平,可以有效提高反应物和产物到达或者脱离反应活性位的效率,从而提高了二甲醚的转化率;更重要的是,抑制了硬积碳的生成,使催化剂保持了更高的稳定性.     

仿生制备有机-无机复合微囊固定化葡萄糖氧化酶

将层层自组装技术与仿生矿化技术相结合,由聚苯乙烯磺酸钠、聚二甲基二烯丙基氯化铵和二氧化硅成功制备(聚苯乙烯磺酸钠-聚二甲基二烯丙基氯化铵)₂-二氧化硅复合微囊.采用扫描电子显微镜、红外光谱和热重对微囊的形貌和化学结构进行了表征.以该复合微囊作为理想载体固定化葡萄糖氧化酶.结果表明,固定于复合微囊中的葡萄糖氧化酶的热稳定性、pH稳定性、操作稳定性得到了提高;在最适条件下,复合微囊固定化葡萄糖氧化酶的酶活回收率为72.85%,米氏常数是游离葡萄糖氧化酶的2.21倍.复合微囊在化学/生物催化、药物/基因传递系统和生物传感器应用方面具有一定的潜能.