Controlled-advancement rigid-body optimization of nanosystems

In this study, we propose a novel optimization algorithm, with application to the refinement of molecular complexes. Particularly, we consider optimization problem as the calculation of quasi-static trajectories of rigid bodies influenced by the inverse-inertia-weighted energy gradient and introduce the concept of advancement region that guarantees displacement of a molecule strictly within a relevant region of conformational space. The advancement region helps to avoid typical energy minimization pitfalls, thus, the algorithm is suitable to work with arbitrary energy functions and arbitrary types of molecular complexes without necessary tuning of its hyper-parameters. Our method, called controlled-advancement rigid-body optimization of nanosystems (Carbon), is particularly useful for the large-scale molecular refinement, as for example, the putative binding candidates obtained with protein–protein docking pipelines. Implementation of Carbon with user-friendly interface is available in the SAMSON platform for molecular modeling at https://www.samson-connect.net . © 2019 Wiley Periodicals, Inc.     

High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge

Recent advances in the development of low-cost quantum chemical methods have made the prediction of conformational preferences and physicochemical properties of medium-sized drug-like molecules routinely feasible, with significant potential to advance drug discovery. In the context of the SAMPL6 challenge, macroscopic pKa values were blindly predicted for a set of 24 of such molecules. In this paper we present two similar quantum chemical based approaches based on the high accuracy calculation of standard reaction free energies and the subsequent determination of those pKa values via a linear free energy relationship. Both approaches use extensive conformational sampling and apply hybrid and double-hybrid density functional theory with continuum solvation to calculate free energies. The blindly calculated macroscopic pKa values were in excellent agreement with the experiment.     

Stereo- and Regiochemical Effect of N,N-Dialkylamide Extractants on the Speciation of Pu Complexes

The relationship between extractant stereochemistry and their extraction performance has only poorly been established. In order to address a part of this concern, we investigated the Pu(IV) liquid-liquid extraction (LLE) by using the N,N-di-(2-ethylhexyl)butyramide (DEHBA), as well as those of its position isomers. DEHBA (ββ-isomer) and N-(2-ethylhexyl)-N-(oct-3-yl)butyramide (EHOBA or αβ-isomer) were synthesized as a mixture of stereoisomer or stereoenriched (R,S)- and (S,S)-diastereoisomers, and were all assessed for Pu^IV LLE. The results showed that both the position and the stereoisomerism of the aliphatic substituents affect Pu^IV complexation and extraction. We found that Pu extraction is lowered by factor 2 to 4 when the ethyl branching group is closer to the complexing site. UV-vis spectroscopy showed that this extraction decrease was affected by steric hindrance inducing a deprivation of Pu inner sphere complex. Effect of stereoisomerism is highlighted for branching closer to the complexing site (α-position). Enantiopure DEHBA stereoisomers provided similar Pu extraction, whereas a slight decrease could be noticed for the more cluttered stereoenriched (αβ)-isomers, which was also concomitant with a smaller population of inner sphere complex. In contrast, the stereoisomers mixture led to a strong decrease of Pu extraction because of an antagonistic association in the mixed complexes.     

Determination of added sulfites in dried garlic with a modified version of the optimized Monier-Williams method

The optimized Monier-Williams method is slightly modified so that it could be applied for determining sulfite content in dried garlic. Dried garlic sample is directly acidified in a reactor at a pH below 3. At this pH level, the alliinase enzyme activity is irreversibly blocked, and the sulfur-containing amino acids such as alliin (the most abundant) present in dried garlic cannot be transformed into corresponding thiosulfinates such as allicin, which is absent in dried garlic. This prevents allicin from reacting with added sulfites and being probably converted to S-allyl thiosulfate, which is not volatile and has no taste. It is found that at a pH below 2.4 and at boiling water temperature, allicin produces sulfur dioxide in adequate quantity to explain the false-positive results when utilizing the optimized Monier-Williams method with allicin suppression for unsulfited dried garlic samples. Finally, when garlic samples are stabilized in a phosphoric acid buffer at a final pH around 2.4, no sulfite is produced during the Monier-Williams distillation, which is further proof there are no naturally occurring sulfites in unsulfited dried garlic under these mild conditions.     

同轴结构中压力波法测量空间电荷分布的物理模型研究

从压力波法测量平板样本中空间电荷分布的理论分析出发,提出了对于同轴结构的固体电介质中空间电荷分布的压力波法测量的物理模型,并得出了测量电流的解析的数学表达式.依据泊松方程,考虑样品内的电场强度、介电常数和空间电荷密度随外界声波扰动而发生变化,将圆柱试样受到的压力波的影响分解成样品形变和质点位移两部分,进而得到了以同轴结构中空间电荷分布的压力波法测量的电压与电流表达式.测量电流的数学表达式表明,对于同轴结构,压力波法的测量电流信号不像平板结构中那样基本正比于空间电荷分布,而是应该做进一步的修正处理.     

Improvement of the mechanical and barrier properties of methylcellulose-based films by treatment with HEMA and silane monomers under gamma radiation

Methylcellulose (MC)-based films were prepared by casting from its 1% aqueous solution containing 0.5% vegetable oil, 0.25% glycerol and 0.025% Tween^®-80. Puncture strength (PS), puncture deformation (PD) and water vapor permeability (WVP) of the films were found to be 147 N/mm, 3.46 mm, and 6.34 g mm/m² day kPa, respectively. The monomer, 2-hydroxyethyl methacrylate (HEMA) (0.1–1%, w/w) was incorporated into the MC-based solution and films were prepared by casting. Films were then exposed to gamma radiation (5–25 kGy) and it revealed that 1% HEMA containing films showed the highest PS values (282 N/mm at 10 kGy). Silane monomer (3-aminopropyl tri-ethoxy silane) (0.1–1%, w/w) was also added into the MC-based films and were found to improve the strength of the films significantly. In comparison between HEMA and silane treatment onto MC-based films, it was observed that silane performed better strength and barrier properties. Surface morphology of the monomer treated films was examined by scanning electron microscopy and suggested better appearance than MC-based film.