Error analysis of idealized nanopore sequencing

This numerical study provides an error analysis of an idealized nanopore sequencing method in which ionic current measurements are used to sequence intact single‐stranded DNA in the pore, while an enzyme controls DNA motion. Examples of systematic channel errors when more than one nucleotide affects the current amplitude are detailed, which if present will persist regardless of coverage. Absent such errors, random errors associated with tracking through homopolymer regions are shown to necessitate reading known sequences (Escherichia coli K‐12) at least 140 times to achieve 99.99% accuracy (Q40). By exploiting the ability to reread each strand at each pore in an array, arbitrary positioning on an error rate versus throughput tradeoff curve is possible if systematic errors are absent, with throughput governed by the number of pores in the array and the enzyme turnover rate.     

The B2–B7 phase transition in symmetrical bent‐shaped mesogens with methoxy substitution

New mesogens composed of achiral bent molecules with thermally stable ester linkages, and laterally substituted by a methoxy group symmetrically near the central benzene ring, were synthesized. Texture, calorimetric, electro‐optical, X‐ray and dielectric measurements were performed. In most of studied compounds the antiferroelectric B₂ phase was found on cooling from the isotropic phase, followed by the B₇ phase at lower temperatures. Undulation of layers in the B₇ phase was confirmed by precise synchrotron studies.     

Butterfly‐Shaped Pentanuclear Dysprosium Single‐Molecule Magnets

Two new “butterfly‐shaped” pentanuclear dysprosium(III) clusters, [Dy₅(μ₃‐OH)₃(opch)₆(H₂O)₃] ? 3 MeOH ? 9 H₂O ( 1 ) and [Dy₅(μ₃‐OH)₃(Hopch)₂(opch)₄(MeOH)(H₂O)₂] ? (ClO₄)₂ ? 6 MeOH ? 4 H₂O ( 2 ), which were based on the heterodonor‐chelating ligand o‐vanillin pyrazine acylhydrazone (H₂opch), have been successfully synthesized by applying different reaction conditions. Single‐crystal X‐ray diffraction analysis revealed that the butterfly‐shaped cores in both compounds were comparable. However, their magnetic properties were drastically different. Indeed, compound 1 showed dual slow‐relaxation processes with a transition between them that corresponded to energy gaps (Δ) of 8.1 and 37.9 K and pre‐exponential factors (τ₀) of 1.7×10^?5 and 9.7×10^?8 s for the low‐ and high‐temperature domains, respectively, whilst only a single relaxation process was noted for compound 2 (Δ=197 K, τ₀=3.2×10^?9 s). These significant disparities are most likely due to the versatile coordination of the H₂opch ligands with particular keto–enol tautomerism, which alters the strength of the local crystal field and, hence, the nature or direction of the easy axes of anisotropic dysprosium ions.     

Heterodinuclear Lanthanoid‐Containing Polyoxometalates: Stepwise Synthesis and Single‐Molecule Magnet Behavior

Polyoxometalates (POMs) with heterodinuclear lanthanoid cores, TBA₈H₄[{Ln(μ₂‐OH)₂Ln′}(γ‐SiW₁₀O₃₆)₂] ( LnLn′ ; Ln=Gd, Dy; Ln′=Eu, Yb, Lu; TBA=tetra‐n‐butylammonium), were successfully synthesized through the stepwise incorporation of two types of lanthanoid cations into the vacant sites of lacunary [γ‐SiW₁₀O₃₆]^8? units without the use of templating cations. The incorporation of a Ln³⁺ ion into the vacant site between two [γ‐SiW₁₀O₃₆]^8? units afforded mononuclear Ln³⁺‐containing sandwich‐type POMs with vacant sites ( Ln1 ; TBA₈H₅[{Ln(H₂O)₄}(γ‐SiW₁₀O₃₆)₂]; Ln=Dy, Gd, La). The vacant sites in Ln1 were surrounded by coordinating W? O and Ln? O oxygen atoms. On the addition of one equivalent of [Ln′(acac)₃] to solutions of Dy1 or Gd1 in 1,2‐dichloroethane (DCE), heterodinuclear lanthanoid cores with bis(μ₂‐OH) bridging ligands, [Dy(μ₂‐OH)₂Ln′]⁴⁺, were selectively synthesized ( LnLn′ ; Ln=Dy, Gd; Ln′=Eu, Yb, Lu). On the other hand, La1 , which contained the largest lanthanoid cation, could not accommodate a second Ln′³⁺ ion. DyLn′ showed single‐molecule magnet behavior and their energy barriers for magnetization reversal (ΔE/k_B) could be manipulated by adjusting the coordination geometry and anisotropy of the Dy³⁺ ion by tuning the adjacent Ln′³⁺ ion in the heterodinuclear [Dy(μ₂‐OH)₂Ln′]⁴⁺ cores. The energy barriers increased in the order: DyLu (ΔE/k_B=48 K)< DyYb (53 K)< DyDy (66 K)< DyEu (73 K), with an increase in the ionic radii of Ln′³⁺; DyEu showed the highest energy barrier.     

水分子对α相CL-20热分解机理影响的分子动力学研究

研究六硝基六氮杂异伍兹烷(CL-20)晶体不同晶型在不同温度下的反应机理, 对于深入认识含能材料在极端条件下的冲击起爆、冲击点火和爆轰过程等具有重要意义. 基于反应力场, 研究水分子在纯α相CL-20及其水合物的晶体结构中数量随时间的变换, 分析水分子对两种体系的初始分解和第二阶段的分解路径的影响. 计算结果表明: CL-20 分子的初始分解路径与水分子无关, 第二阶段的分解反应与水分子有关. 在低温(T<1500 K)下, 水分子对两种体系没有影响, 二者的初始分解路径均为N-NO₂键生成NO₂自由基; 在1500 K≤T≤2500 K时, 水分子作为反应物或与NO₂、、OH自由基等组成催化体系, 生成O₂、H₂O₂等产物, 加速水合物体系在高温下的第二阶段反应, 使得高温下水合物体系的化学反应速率和反应生成的NO₂自由基的数量比纯CL-20体系的化学反应速率和反应生成的NO₂自由基的数量大; 在T>2500 K时, 水分子的催化反应抑制CL-20初始分解反应, 使得在3000 K时纯CL-20体系的反应速率大于水合物体系中CL-20的反应速率.     

水在HfO2(111)和(110)表面的吸附与解离

运用广义梯度近似密度泛函理论方法(GGA-PW91)结合周期平板模型, 研究水分子在二氧化铪(111)和(110)表面不同吸附位置在不同覆盖度下的吸附行为. 通过比较不同吸附位的吸附能和几何构型参数发现:(111)和(110)表面铪原子(top 位)是活性吸附位. 水分子与表面的吸附能值随覆盖度的变化影响较小. 在(111)和(110)表面, 水分子都倾向以氧端与表面铪原子相互作用. 同时也计算了羟基、氧和氢在表面的吸附, Mulliken 电荷布居, 态密度及部分频率. 结果表明, 在两种表面羟基以氧端与表面铪相互作用, 氧原子与表面铪和氧原子同时成键, 而氢原子直接与表面氧原子相互作用形成羟基. 通过过渡态搜索, 水分子在(111)和(110)表面发生解离, 反应能垒分别为9.7和17.3 kJ·mol^-1, 且放热为59.9和47.6 kJ·mol^-1.     

甲硫醇在Cu(111)表面的解离吸附: 密度泛函理论研究

采用基于密度泛函理论的第一性原理方法和平板模型研究了CH₃SH分子在Cu(111)表面的吸附反应.系统地计算了S原子在不同位置以不同方式吸附的一系列构型, 第一次得到未解离的CH₃SH分子在Cu(111)表面顶位上的稳定吸附构型,该构型吸附属于弱的化学吸附, 吸附能为0.39 eV. 计算同时发现在热力学上解离结构比未解离结构更加稳定. 解离的CH₃S吸附在桥位和中空位之间, 吸附能为0.75-0.77 eV. 计算分析了未解离吸附到解离吸附的两条反应路径, 最小能量路径的能垒为0.57 eV. 计算结果还表明S―H键断裂后的H原子并不是以H₂分子的形式从表面解吸附而是以与表面成键的形式存在. 通过比较S原子在独立的CH₃SH分子和吸附状态下的局域态密度, 发现S―H键断裂后S原子和表面的键合强于未断裂时S原子和表面的键合.     

An updated version of the computational package SIMPRE that uses the standard conventions for Stevens crystal field parameters

The crystal field approach used by SIMPRE is analyzed, verifying the exactness of the results concerning energy levels and magnetic properties calculated by the package. To coincide with the prevailing conventions, we reformulate the presentation of the crystal field parameters, so that the results are now, also from a formal point of view, strictly correct. New calculations are presented to test the influence of neglecting the excited J states, a common but critical approximation employed by SIMPRE. For that, we examine the case of Er(trensal) complex (H₃trensal = 2,2′,2″‐tris(salicylideneimino)triethylamine) where the influence of this approximation is found to be minimal. A patched version of the code, SIMPRE 1.1, and an updated version of the user manual are now available. Finally, we comment on “Software package SIMPRE – revisited,” which apparently revisits a software package without inspecting or using the code. © 2014 Wiley Periodicals, Inc.     

Effect of HAP on Stability and Plugging Property of LPFR Dispersion

To improve the stability and plugging property of low-solubility phenol formaldehyde resin (LPFR) in the injection water from Daqing Oilfield, hydrophobically associating polymers (HAP) as a stabilizing agent were used. The size and zeta potential of LPFR, LPFR/HAP molecule aggregates, and turbidity and plugging properties of LPFR dispersions were measured in deionized water, simulation water, and injection water, respectively. The results show that the hydrophobic grouping on the HAP molecule has a similar molecular structure as LPFR, and HAP and LPFR can form complex molecule aggregates in the injection water. The zeta potential of LPFR/HAP molecule aggregates is larger than that of LPFR molecule aggregates. Therefore, the repulsive force operating between LPFR/HAP complex molecule aggregates is increased. HAP enhances the stability of LPFR in the injection water and plugging property of LPFR dispersion in porous medium.     

(5RS)‐5‐(4‐Methoxyphenyl)‐2‐(methylsulfanyl)benzo[g]pyrimido[4,5‐b]quinoline‐4,6,11(3H,5H,12H)‐trione,with Z′ = 3, forms a three‐dimensional hydrogen‐bonded framework containing five types of hydrogen bond

The title compound, C₂₃H₁₇N₃O₄S, crystallizes with Z′ = 3 in the space group P. Two of the three independent molecules are broadly similar in terms of both their molecular conformations and their participation in hydrogen bonds, but the third molecule differs from the other two in both of these respects. The molecules are linked by a combination of N—H...O, N—H...N, C—H...O, C—H...N and C—H...π(arene) hydrogen bonds to form a continuous three‐dimensional framework structure within which a centrosymmetric six‐molecule aggregate can be identified as a key structural element.