Combining the biased and unbiased sampling strategy into one convenient free energy calculation method

Constructing a free energy landscape for a large molecule is difficult. One has to use either a high temperature or a strong driving force to enhance the sampling on the free energy barriers. In this work, we propose a mixed method that combines these two kinds of acceleration strategies into one simulation. First, it applies an adaptive biasing potential to some replicas of the molecule. These replicas are particularly accelerated in a collective variable space. Second, it places some unbiased and exchangeable replicas at various temperature levels. These replicas generate unbiased sampling data in the canonical ensemble. To improve the sampling efficiency, biased replicas transfer their state variables to the unbiased replicas after equilibrium by Monte Carlo trial moves. In comparison to previous integrated methods, it is more convenient for users. It does not need an initial reference biasing potential to guide the sampling of the molecule. And it is also unnecessary to insert many replicas for the requirement of passing the free energy barriers. The free energy calculation is accomplished in a single stage. It samples the data as fast as a biased simulation and it processes the data as simple as an unbiased simulation. The method provides a minimalist approach to the construction of the free energy landscape. © 2019 Wiley Periodicals, Inc.     

Tail behavior of supremum of a random walk when Cramér’s condition fails

We investigate tail behavior of the supremum of a random walk in the case that Cramer＇s condition fails, namely, the intermediate case and the heavy-tailed ease. When the integrated distribution of the increment of the random walk belongs to the intersection of exponential distribution class and O-subexponential distribution class, under some other suitable conditions, we obtain some asymptotic estimates for the tail probability of the supremum and prove that the distribution of the supremum also belongs to the same distribution class. The obtained results generalize some corresponding results of N. Veraverbeke. Finally, these results are applied to renewal risk model, and asymptotic estimates for the ruin probability are presented.     

常压低温等离子体有效去除催化CO氧化的金原子团簇的保护剂（英文）

采用介质阻挡放电等离子体技术可以在低温、常压下实现对纳米金催化剂中保护基团的有效去除.本文通过对不同保护基团(聚乙烯吡咯烷酮和半胱氨酸)保护的金催化剂进行等离子体预处理,发现采用该技术能有效去除载体中的层间阴离子,还可能将金原子与保护基团之间的化学键打断.通过X射线粉末衍射对等离子体处理后的样品和未经处理的样品进行表征,发现经等离子体处理后的样品,载体从水滑石结构变为复合氧化物结构,这说明等离子体处理可将载体中的羟基和羰基除去,从而引起载体结构变化.热重分析结果显示,经等离子体处理后的样品失重量(19%-23%)与未处理样品的失重量(31%)相比差10%左右,这说明采用该方法可以在一定程度上去除纳米金表面保护基团和载体的层间阴离子.用紫外-可见光谱和高角环形暗场像-扫描透射电子显微镜对催化剂中金颗粒的尺寸分布和平均粒径进行分析,发现金颗粒在等离子体处理过后其粒径没有发生严重聚集,平均粒径由未处理时的1.4-1.7 nm轻微长大至2.4-3.7 nm.以含硫醇化合物(半胱氨酸)保护的金原子团簇催化剂为例考察了等离子体不同处理时间的影响,发现随着处理时间从25 min延长至150 min,样品的颜色从浅紫色变为暗紫色.结合XRD和TGA等结果可知,随着处理时间的延长,催化剂中保护基团的去除度逐渐提高.CO氧化反应活性评价结果显示,与未经处理的样品相比,经等离子体处理后的样品催化CO氧化反应活性有明显提高,且随预处理时间延长,活性有提高的趋势.动力学测试结果表明,经等离子体处理后的样品催化CO氧化的表观活化能低至1.2-2.9 k J/mol,接近于文献中报道的Au/TiO_2催化剂.这说明作为一种催化剂处理方法,介质阻挡放电等离子体技术可以有效去除催化剂中的保护剂,且因其处理条件相对温和,可在一定程度上保持金颗粒尺寸的稳定,这对于控制合成负载型小尺寸的金催化剂具有重要意义.     

Ion-pair recognition based on halogen bonding: a case of the crown-ether receptor with iodo-trizole moiety

The development of halogen-bond-based ditopic receptors capable of binding simultaneously both a cation and an anion has attracted recent research interest. In this work, the crown-ether receptor 1, which consists of an iodo-trizole moiety for anion recognition through halogen bonding and a Lewis-basic center for cation binding, was investigated using density functional theory calculations. The structural and energetic features for the complexes of 1 with single cations, single halide anions, and ion pairs were explored. Intermolecular interactions in these complexes were systematically analyzed by the atoms in molecules and noncovalent interaction index methods. The presence of the coordinated cation significantly increases the anion-binding affinity, while the binding of halide anions has a slight influence on the cation-binding affinity. Anti-cooperative effects were found in the ion-pair recognition of 1, due to the strong attraction between the two counterions in the complexes. The solvent weakens the interaction strength considerably, and anti-cooperativity becomes very small in solvent. The results reported in this work are of fundamental importance in the design of ion-pair receptors based on halogen bonding.     

Phosphoric Acid Catalyzed Asymmetric [2+2] Cyclization/Penicillin–Penillonic Acid Rearrangement

Enantioselective synthesis of imidazolidin‐5‐ones through a phosphoric acid catalyzed reaction between azlactones and N‐substituted β‐carbolines is reported. The reaction takes place via an initial formal [2+2] cycloaddition to generate an α‐amino‐β‐lactam, which subsequently undergoes an acid‐catalyzed asymmetric penicillin–penillonic acid (PPA) rearrangement with high diastereo‐ and enantioselectivity. To the best of our knowledge, this represents the first [2+2] cyclization of azlactones with imines and the first asymmetric PPA rearrangement, which are linked together by the phosphoric acid catalyst.     

A novel detector using a fluorescent sensor array and discrimination of pesticides

A novel, simple, and rapid detector using a fluorescent sensor array for discrimination and quantification of different concentrations (ppb level) of pesticides was proposed in this paper. Employing porphyrin, porphyrin derivatives, and chemically responsive dyes as the sensing elements, the developed sensor array based on a cross-responsive mechanism showed a unique pattern of fluorescence changes upon the reaction that lasted just 10 min. The eigenvalues from raw fluorescence spectra were analyzed via a pattern recognition algorithm, including hierarchical cluster analysis (HCA), principal component analysis (PCA), and back-propagation neural network (BPNN). The results showed that HCA, which were used to assess the feasibility and effectiveness of discrimination of the fluorescent sensor array, revealed a distinct separation between different pesticides. PCA and BPNN were used for automatically predicting the concentration of pesticides, and the recovery was 91.29–109.81 % while the lowest relative standard deviation was up to 3.12 %. It indicates a detector based on the fluorescent sensor array is a rapid and feasible sensing platform for the discrimination and quantitative analysis of pesticides, and also shows the possibilities in the related fields of pesticides identification and detection.     

Identification and analysis of alpha1,6-fucosylated proteins in human normal liver tissues by a target glycoproteomic approach

alpha1,6-Fucose residues within the N-glycan core structures were commonly observed in many glycoproteins. Our previous studies showed that aberrantly alpha1,6-fucosylated glycoproteins might be associated with metastasis of hepatocellular carcinoma (HCC). Little is known about human normal liver tissues (HNLTs) in the literatures. In this study, a target glycoproteomic approach which consists of lectin-affinity chromatography, 2-DE, protein immunoprecipitation and lectin blot, and MALDI-MS/MS, was utilized to screen physiologically alpha1,6-fucosylated glycoproteins. Lens culinaris agglutinin (LCA)-affinity glycoprotein profiles of HNLT were established and analyzed, which allowed identification of 53 proteins by MS analysis, including haptoglobin precursor, alpha-enolase, etc. Gene ontology (GO) annotation proved that these proteins distribute predominately in organelle and play crucial roles in binding and catalytic reactions. The present methodology enabled the identification of all the specific subsets of glycoprotein, and the corresponding data could contribute to the finding of more aberrantly alpha1,6-fucosylated glycoproteins related to liver diseases.     

Analogy in the adsorption of random copolymers and homopolymers at solid-liquid interface: a Monte Carlo simulation study

The adsorption of random copolymers at solid-liquid interface from a nonselective solvent has been studied by Monte Carlo simulation in a cubic lattice. The polymeric molecules are modeled as self-avoiding linear chains composed of two types of segments A and B. The effects of copolymer composition (A/B ratio), segment-surface interaction, and bulk concentration are examined on the thermodynamic and structural adsorption properties including surface coverage, adsorption amount, adsorption layer thickness, and microscopic density distribution. At a given newly introduced effective adsorption energy, random copolymers are found to behave quantitatively as homopolymers regardless of the copolymer composition and surface affinity. This remarkable analogy provides an efficient way in predicting the adsorption of random copolymers from homopolymers.     

Recognition of multiblock copolymers on nanopatterned surfaces: insight from molecular simulations

The recognition of multiblock copolymers on nanopatterned surfaces has been investigated by molecular simulations. All the copolymers (AnB12-n)5 are composed of 60 square-well segments, but with various architectures by changing n. Segment density profiles, radii of gyration, pattern transfer parameters, and three adsorption conformations (tail, loop, and train) are examined quantitatively. It is found that the copolymer can recognize the adsorbing stripes on surface and the surface vicinity. The recognition affinity becomes stronger with increasing the stripe width, the adsorption strength, and the number of adsorbing segments in copolymer chain. From surface to bulk phase, the shape of copolymer changes from elongated to elliptical, and finally to globular. Among the three adsorption conformations, tail has the greatest average size while train has the smallest. With the increased number of nonadsorbing segments, the average size shows an increase in tail but a decrease in train.