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Heteroatom cobalt-based metal-organic framework and reduced graphene oxide nanocomposite for dispersive solid phase extraction of caffeine from exhaled breath condensate samples of premature infants prior to HPLC-PDA 异构体钴基金属有机框架和还原氧化石墨烯纳米复合材料用于在 HPLC-PDA 前从早产儿呼出气体冷凝物样品中分散固相萃取咖啡因
IF 2.8 3区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-01 DOI: 10.1016/j.jchromb.2024.124339
A cobalt-based metal–organic framework and graphene oxide were combined to prepare a new nanocomposite for extracting of caffeine from exhaled breath condensate (EBC) samples. Dispersive micro solid phase extraction of caffeine was conducted using the nanocomposite as a sorbent by adding 10 mg of it to the sample solution and vortexing for 3 min. After extracting of the analyte, it was eluted using the mobile phase. The analyte was then analyzed using high performance liquid chromatography-photodiode array detector. Under optimal conditions, the limit of detection, limit of quantification, and linear range of the calibration curve were found to be 1.7, 5.9, and 10–500 µg/L, respectively. To assess the precision of the method, five replicates of standard solutions containing caffeine at two different concentration levels (50 and 100 µg/L) were tested. The relative standard deviations for intra- and inter-day precisions ranged from 4.3 to 6.8 %. The applicability of the method was demonstrated by analyzing the samples obtained from premature infants undergoing caffeine treatment and caffeine concentrations were 4.9 ± 0.6, 2.7 ± 0.2 µg/L in the EBC samples of who were under treatment by a 5-mg dose. Also, caffeine concentrations were 5.9 ± 0.3 and 18 ± 0.6 µg/L in the the infants who obtained the 10-mg and 25-mg doses, respectively. The results indicated a satisfactory, extraction recovery of 86 % showcasing the method’s reliability and effectiveness in analyzing real samples.
研究人员将钴基金属有机框架和氧化石墨烯结合起来,制备了一种新型纳米复合材料,用于从呼气冷凝液(EBC)样品中提取咖啡因。在样品溶液中加入 10 毫克纳米复合材料并涡旋 3 分钟,以纳米复合材料为吸附剂进行咖啡因的分散微固相萃取。提取分析物后,使用流动相进行洗脱。然后使用高效液相色谱-光电二极管阵列检测器对分析物进行分析。在最佳条件下,校准曲线的检出限、定量限和线性范围分别为 1.7、5.9 和 10-500 µg/L。为了评估该方法的精密度,对含有咖啡因的两种不同浓度水平(50 微克/升和 100 微克/升)的标准溶液进行了五次重复检测。日内和日间精密度的相对标准偏差为 4.3% 至 6.8%。通过分析接受咖啡因治疗的早产儿样本,证明了该方法的适用性,在接受 5 毫克剂量治疗的早产儿 EBC 样本中,咖啡因浓度分别为 4.9 ± 0.6 µg/L、2.7 ± 0.2 µg/L。此外,服用 10 毫克和 25 毫克剂量的婴儿体内咖啡因浓度分别为 5.9 ± 0.3 微克/升和 18 ± 0.6 微克/升。结果表明,该方法的提取回收率为 86%,令人满意,显示了该方法在分析实际样品时的可靠性和有效性。
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引用次数: 0
Enhancing Photogenerated Radical Pair Properties in Donor-Chromophore-Acceptor Systems for Quantum Information Applications. 增强供体-色团-受体系统中的光生自由基对特性,促进量子信息应用。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-10-31 Epub Date: 2024-10-16 DOI: 10.1021/acs.jpca.4c05015
Paige J Brown, Yunfan Qiu, Elisabeth I Latawiec, Brian T Phelan, Nikolai A Tcyrulnikov, Jonathan R Palmer, Matthew D Krzyaniak, Sebastian M Kopp, Yuheng Huang, Ryan M Young, Michael R Wasielewski

We report on new donor-chromophore-acceptor triads BDX-ANI-NDI and BDX-ANI-xy-NDI where the BDX donor is 2,2,6,6-tetramethylbenzo[1,2-d;4,5-d]bis[1,3]dioxole, the ANI chromophore is 4-(N-piperidinyl)naphthalene-1,8-dicarboximide, the NDI acceptor is naphthalene-1,8:4,5-bis(dicarboximide), and xy is a 2,5-xylyl spacer. The results on these compounds are compared to the analogous derivatives having a p-methoxyaniline (MeOAn) as the donor. BDX+ has no nitrogen atoms and only a single hydrogen atom coupled to its unpaired electron spin, and therefore has significantly decreased hyperfine interactions compared to MeOAn•+. We use femtosecond transient absorption (fsTA) and nanosecond TA (nsTA) spectroscopies, the latter with an applied static magnetic field, to study the charge transfer dynamics and determine the spin-spin exchange interaction (J) for BDX•+-ANI-NDI•- and BDX•+-ANI-xy-NDI•- at both ambient and cryogenic temperatures. Time-resolved electron paramagnetic resonance (EPR) and pulse-EPR measurements on these spin-correlated radical pairs (SCRPs) were used to probe their spin dynamics. We demonstrate that BDX•+-ANI-xy-NDI•- has an unusually long lifetime of ∼550 μs in glassy butyronitrile (PrCN) at 85 K, which makes it useful for pulse-EPR studies that target quantum information science (QIS) applications. We also show that rotation of the BDX group about the single bond linking it to the neighboring phenyl group has a significant impact on the spin dynamics, and in particular the magnitude of J. By comparing the results on these compounds to the analogous MeOAn series, insights into design principles for creating improved spin-correlated radical pair systems for QIS studies are obtained.

我们报告了新的供体-发色团-受体三元组 BDX-ANI-NDI 和 BDX-ANI-xy-NDI,其中 BDX 供体是 2,2,6,6-四甲基苯并[1,2-d;4,5-d]双[1,3]二恶茂,ANI 发色团是 4-(N-哌啶基)萘-1,8-二甲酰亚胺,NDI 受体是萘-1,8:4,5-双(二甲酰亚胺),xy 是 2,5-xylyl 间隔物。这些化合物的研究结果与以对甲氧基苯胺(MeOAn)为供体的类似衍生物进行了比较。与 MeOAn-+ 相比,BDX-+ 没有氮原子,只有一个氢原子与其非配对电子自旋耦合,因此超频相互作用显著减少。我们使用飞秒瞬态吸收(fsTA)和纳秒 TA(nsTA)光谱(后者在施加静态磁场的情况下)研究电荷转移动力学,并确定 BDX-+-ANI-NDI-- 和 BDX-+-ANI-xy-NDI-- 在环境温度和低温下的自旋-自旋交换相互作用 (J)。对这些自旋相关自由基对(SCRPs)的时间分辨电子顺磁共振(EPR)和脉冲电子顺磁共振测量被用来探测它们的自旋动力学。我们证明,BDX-+-ANI-xy-NDI--在 85 K 的玻璃丁腈(PrCN)中具有 ∼550 μs 的超长寿命,这使得它可以用于针对量子信息科学(QIS)应用的脉冲-EPR 研究。我们还表明,BDX 基团围绕连接它与邻近苯基的单键的旋转对自旋动力学,特别是 J 的大小有重大影响。通过将这些化合物的研究结果与类似的 MeOAn 系列进行比较,我们深入了解了为量子信息科学研究创建更好的自旋相关自由基对系统的设计原则。
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引用次数: 0
Taylor-Aris Dispersion in Nanotubes: Analytical Solution, Effects of Slip and Surface Potential Landscape, and Measurement of the Slip Length. 纳米管中的 Taylor-Aris 分散:解析解、滑移和表面电位景观的影响以及滑移长度的测量。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-10-31 Epub Date: 2024-10-18 DOI: 10.1021/acs.jpcb.4c04221
Fatemeh Ebrahimi, Mehdi Neek-Amal, Muhammad Sahimi

Taylor-Aris (T-A) dispersion of a solute in a flowing solvent is a fundamental phenomenon in most mass-transfer processes. Despite its significance and numerous applications in microreactors, colloidal transport in confined media, chromatographic separation, and transport in biological tissues, the effect of the slip length and the topology of surface potential landscapes on T-A dispersion in nanostructured channels has not been studied in detail. We propose a novel methodology for molecular dynamics (MD) simulation of T-A dispersion in such systems, derive an analytical expression for the dispersion coefficient in them, and report on the results of extensive MD simulations of the phenomenon in carbon nanotubes and hexagonal carbon nanochannels. By broadening the topology of the surface energy landscape, we vary the slip lengths, making it possible to distinguish between the effects of confinement, the topology of the energy landscape, and the slip length on the T-A dispersion coefficient. It is demonstrated that measuring the T-A dispersion coefficient in laminar flow is a straightforward and reliable approach for estimating the slip length in nanotubes and other nanostructured materials.

溶质在流动溶剂中的泰勒-阿里斯(T-A)分散是大多数传质过程中的基本现象。尽管它在微反应器、密闭介质中的胶体传输、色谱分离和生物组织传输中具有重要意义和大量应用,但人们尚未详细研究滑移长度和表面电位拓扑图对纳米结构通道中 T-A 分散的影响。我们提出了一种新的分子动力学(MD)模拟 T-A 在此类系统中分散的方法,推导出了其中分散系数的解析表达式,并报告了对碳纳米管和六角碳纳米通道中的这一现象进行大量 MD 模拟的结果。通过拓宽表面能谱的拓扑结构,我们改变了滑移长度,从而有可能区分约束、能谱拓扑结构和滑移长度对 T-A 弥散系数的影响。实验证明,测量层流中的 T-A 分散系数是估算纳米管和其他纳米结构材料中滑移长度的一种直接而可靠的方法。
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引用次数: 0
Synthesis of Polyether Block Copolymers from 1,2-Epoxybutane and AEOn and Comparative Study of Physicochemical and Application Properties before and after the Synthesis. 由 1,2-环氧丁烷和 AEOn 合成聚醚嵌段共聚物以及合成前后的物理化学和应用特性对比研究。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-10-31 Epub Date: 2024-10-17 DOI: 10.1021/acs.jpcb.4c05555
Fengqin Li, Jingjie Zhou, Huibin Liang, Jinyuan Sun, Ke Zhang, Yuqi Liu, Chunyu Wang, Tao Geng

In this study, the AEOnBO2 series of block polyoxybutenol ethers was synthesized by combining the AEO series of polyoxyethylene and preparing 1,2-epoxybutane (BO) block polyether using a semicontinuous method. The synthesis was performed by HPLC, MALDI-TOF-MS, FT-IR, and 1H NMR for structural analysis. The interaction parameters and surface tension of the systems before and after synthesis were studied using surface tension meter. The diffusion process of the systems before and after synthesis was studied using a KRÜSS bubble pressure tensiometer. The surfactant properties of AEOn and AEOnBO2 were evaluated by static and dynamic surface tension measurements. Each system formed a saturated adsorption layer in a water solution. The critical micelle concentration decreased dramatically after the introduction of BO groups, and the diffusion-adsorption process was consistent with the kinetic mechanism of hybrid diffusion. The microscopic self-assembled aggregate micellar behavior of all the systems was investigated using DLS, TEM, and SEM. The micellization process in all systems was spontaneous and enthalpy-driven, forming spherical aggregates, with the BO block reducing the aggregate diameter of the feedstock from 220.06 nm to about one-third of 80.02 nm. In addition, the dynamic contact angle, application, and physicochemical properties such as foaming and foam stabilization of each system were investigated. The contact angle was reduced from 70 to 50° at 120 s of stabilization, with a foam volume of 80 mL in all systems at 200 s. However, the AEOnBO2 showed accelerated foam decay at 500 s, with an increase in the contact angle from 70 to 50° at 200 s, but the AEOnBO2 showed accelerated foam decay at 500 s, with a decrease in the contact angle from 70 to 50° at 120 s stabilization. At 200 s, the foam volume of all systems was 80 mL, but AEOnBO2 showed an accelerated foam decay process, which shows that the BO group can accelerate the foam decay, and the comparative results show that the BO group can also optimize other application properties and physicochemical properties.

本研究采用半连续法将 AEO 系列聚氧乙烯与制备 1,2-环氧丁烷 (BO) 嵌段聚醚相结合,合成了 AEOnBO2 系列嵌段聚氧丁烯醚。合成过程采用 HPLC、MALDI-TOF-MS、FT-IR 和 1H NMR 进行结构分析。使用表面张力仪研究了合成前后体系的相互作用参数和表面张力。使用 KRÜSS 气泡压力张力计研究了合成前后体系的扩散过程。通过静态和动态表面张力测量评估了 AEOn 和 AEOnBO2 的表面活性剂特性。每个体系都在水溶液中形成了饱和吸附层。引入 BO 基团后,临界胶束浓度急剧下降,扩散-吸附过程符合混合扩散的动力学机制。利用 DLS、TEM 和 SEM 对所有体系的微观自组装聚集胶束行为进行了研究。所有体系的胶束化过程都是自发的,由焓驱动,形成球形聚集体,BO 块使原料的聚集体直径从 220.06 nm 减小到约 80.02 nm 的三分之一。此外,还研究了每种体系的动态接触角、应用以及发泡和泡沫稳定等理化特性。在稳定 120 秒时,接触角从 70°减小到 50°,在 200 秒时,所有体系的泡沫体积均为 80 mL。然而,AEOnBO2 在 500 秒时显示出泡沫加速衰减,在 200 秒时接触角从 70°增大到 50°,但 AEOnBO2 在 500 秒时显示出泡沫加速衰减,在稳定 120 秒时接触角从 70°减小到 50°。在 200 秒时,所有体系的泡沫体积均为 80 毫升,但 AEOnBO2 的泡沫衰减过程加快,这表明 BO 组能加速泡沫衰减,比较结果表明 BO 组还能优化其他应用特性和理化特性。
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引用次数: 0
Probing the Molecular Interactions of A22 with Prokaryotic Actin MreB and Eukaryotic Actin: A Computational and Experimental Study. 探索 A22 与原核肌动蛋白 MreB 和真核肌动蛋白的分子相互作用:计算与实验研究。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-10-31 Epub Date: 2024-10-16 DOI: 10.1021/acs.jpcb.4c02963
Anuj Kumar, Samiksha Kukal, Anusha Marepalli, Saran Kumar, Sutharsan Govindarajan, Debabrata Pramanik

Actin is a major cytoskeletal system that mediates the intricate organization of macromolecules within cells. The bacterial cytoskeletal protein MreB is a prokaryotic actin-like protein governing the cell shape and intracellular organization in many rod-shaped bacteria, including pathogens. MreB stands as a target for antibiotic development, and compounds like A22 and its analogue, MP265, are identified as potent inhibitors of MreB. The bacterial actin MreB shares structural homology with eukaryotic actin despite lacking sequence similarity. It is currently not clear whether small molecules that inhibit MreB can act on eukaryotic actin due to their structural similarity. In this study, we investigate the molecular interactions between A22 and its analogue MP265 with MreB and eukaryotic actin through a molecular dynamics approach. Employing MD simulations and free energy calculations with an all-atom model, we unveil the robust interaction of A22 and MP265 with MreB, and substantial binding affinity is observed for A22 and MP265 with eukaryotic actin. Experimental assays reveal A22's toxicity to eukaryotic cells, including yeast and human glioblastoma cells. Microscopy analysis demonstrates the profound effects of A22 on actin organization in human glioblastoma cells. This integrative computational and experimental study provides new insights into A22's mode of action, highlighting its potential as a versatile tool for probing the dynamics of both prokaryotic and eukaryotic actins.

肌动蛋白是一种主要的细胞骨架系统,介导着细胞内大分子的复杂组织。细菌细胞骨架蛋白 MreB 是一种原核类肌动蛋白,在包括病原体在内的许多杆状细菌中负责细胞形状和细胞内组织。MreB 是抗生素开发的目标,A22 及其类似物 MP265 等化合物已被确定为 MreB 的强效抑制剂。细菌肌动蛋白 MreB 与真核生物肌动蛋白尽管缺乏序列相似性,但在结构上具有同源性。目前还不清楚抑制 MreB 的小分子是否能对真核生物肌动蛋白产生作用,因为它们的结构相似。在本研究中,我们通过分子动力学方法研究了 A22 及其类似物 MP265 与 MreB 和真核肌动蛋白之间的分子相互作用。通过使用全原子模型进行 MD 模拟和自由能计算,我们揭示了 A22 和 MP265 与 MreB 的强相互作用,并观察到 A22 和 MP265 与真核肌动蛋白有很强的结合亲和力。实验测定揭示了 A22 对真核细胞(包括酵母和人类胶质母细胞瘤细胞)的毒性。显微镜分析表明了 A22 对人类胶质母细胞瘤细胞肌动蛋白组织的深刻影响。这项计算与实验相结合的研究为 A22 的作用模式提供了新的见解,凸显了它作为探究原核和真核肌动蛋白动态的多功能工具的潜力。
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引用次数: 0
Reactions of Diphenylamine with OH Radicals in the Environment: Theoretical Insights into the Mechanism, Kinetics, Temperature, and pH Effects. 环境中二苯基胺与羟基自由基的反应:关于机理、动力学、温度和 pH 值影响的理论见解。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-10-31 DOI: 10.1021/acs.jpcb.4c05366
Quan V Vo

Diphenylamine (DPL) has been widely utilized in industrial chemicals, but its degradation by HO radicals in the environment has not been fully studied yet. The present study uses quantum chemical calculations to evaluate the reaction of DPL with HO radicals in atmospheric and aqueous environments. The results showed that, in the atmosphere, the diphenylamine reacted with the HO radical rapidly, with an overall rate constant of 9.24 × 1011 to 1.34 × 1011 M-1 s-1 and a lifetime of 0.17 to 1.55 h at 253-323 K. The calculated overall rate constant in water (koverall = 1.95 × 1010 M-1 s-1, pH = 3-14) is in excellent agreement with the experimental value (koverall = 1.00 × 1010-1.36 × 1010 M-1 s-1). The HO + DPL reaction in water could occur following the hydrogen transfer (15.4%), single electron transfer (41.6%), and radical adduct formation (41.7%) mechanisms, clarifying that addition products were not exclusive products. Nevertheless, variations in temperature and pH within aqueous environments had an impact on the mechanisms, kinetics, and degradation products of the reaction of DPL with HO radicals.

二苯胺(DPL)已被广泛应用于工业化学品中,但其在环境中被 HO- 自由基降解的情况尚未得到充分研究。本研究利用量子化学计算评估了二苯胺在大气和水环境中与 HO- 自由基的反应。结果表明,在大气中,二苯胺与 HO- 自由基的反应速度很快,在 253-323 K 的条件下,总速率常数为 9.24 × 1011 至 1.34 × 1011 M-1 s-1,寿命为 0.17 至 1.55 h。HO- + DPL 在水中的反应可能发生在氢转移(15.4%)、单电子转移(41.6%)和自由基加合物形成(41.7%)机制之后,这说明加成产物并不是唯一的产物。然而,水环境中温度和 pH 值的变化会对 DPL 与 HO- 自由基反应的机理、动力学和降解产物产生影响。
{"title":"Reactions of Diphenylamine with OH Radicals in the Environment: Theoretical Insights into the Mechanism, Kinetics, Temperature, and pH Effects.","authors":"Quan V Vo","doi":"10.1021/acs.jpcb.4c05366","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c05366","url":null,"abstract":"<p><p>Diphenylamine (<b>DPL</b>) has been widely utilized in industrial chemicals, but its degradation by HO<sup>•</sup> radicals in the environment has not been fully studied yet. The present study uses quantum chemical calculations to evaluate the reaction of <b>DPL</b> with HO<sup>•</sup> radicals in atmospheric and aqueous environments. The results showed that, in the atmosphere, the diphenylamine reacted with the HO<sup>•</sup> radical rapidly, with an overall rate constant of 9.24 × 10<sup>11</sup> to 1.34 × 10<sup>11</sup> M<sup>-1</sup> s<sup>-1</sup> and a lifetime of 0.17 to 1.55 h at 253-323 K. The calculated overall rate constant in water (<i>k</i><sub>overall</sub> = 1.95 × 10<sup>10</sup> M<sup>-1</sup> s<sup>-1</sup>, pH = 3-14) is in excellent agreement with the experimental value (<i>k</i><sub>overall</sub> = 1.00 × 10<sup>10</sup>-1.36 × 10<sup>10</sup> M<sup>-1</sup> s<sup>-1</sup>). The HO<sup>•</sup> + <b>DPL</b> reaction in water could occur following the hydrogen transfer (15.4%), single electron transfer (41.6%), and radical adduct formation (41.7%) mechanisms, clarifying that addition products were not exclusive products. Nevertheless, variations in temperature and pH within aqueous environments had an impact on the mechanisms, kinetics, and degradation products of the reaction of <b>DPL</b> with HO<sup>•</sup> radicals.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Describing the Disulfide Bond: From the Density Functional Theory and Back through the "Lego Brick" Approach. 描述二硫键:从密度泛函理论到 "乐高积木 "方法。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-10-31 Epub Date: 2024-10-18 DOI: 10.1021/acs.jpca.4c05198
Silvia Alessandrini, Hexu Ye, Malgorzata Biczysko, Cristina Puzzarini

Selected molecular species containing the disulfide bond, RSSR, have been considered, these ranging from hydrogen disulfide, H2S2 (R = H), to diphenyl disulfide with R = C6H5. The aim of this work is two-fold: (i) to investigate different computational approaches in order to derive accurate equilibrium structures at an affordable cost, (ii) to employ the results from the first goal in order to benchmark cheaper methodologies rooted in the density functional theory. Among the strategies used for the accurate geometrical determinations, the semiexperimental approach has been exploited in combination with a reduced-dimensionality VPT2 model, without however obtaining satisfactory results. Instead, the so-called "Lego brick" approach turned out to be very effective despite the flexibility of the systems investigated. Concerning the second target of this work, the focus was mainly on the S-S bond and the structural parameters related to it. Among those tested, PBE0(-D3BJ), M06-2X(-D3) and DSD-PBEP86-D3BJ have been found to be the best-performing functionals.

我们考虑了含有二硫键 RSSR 的部分分子物种,包括二硫化氢 H2S2(R = H)和 R = C6H5 的二苯基二硫化物。这项工作有两个目的:(i) 研究不同的计算方法,以便以可承受的成本推导出精确的平衡结构;(ii) 利用第一个目标的结果,为以密度泛函理论为基础的成本更低的方法提供基准。在用于精确确定几何结构的策略中,半实验方法与降维 VPT2 模型相结合,但并未取得令人满意的结果。相反,所谓的 "乐高砖块 "方法却非常有效,尽管所研究的系统具有灵活性。关于这项工作的第二个目标,重点主要放在 S-S 键及其相关的结构参数上。在所测试的函数中,PBE0(-D3BJ)、M06-2X(-D3) 和 DSD-PBEP86-D3BJ 被认为是性能最好的函数。
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引用次数: 0
Insights into the Role of Side-Chain Team Work in nDsbDOx/Red Proteins: Mechanism of Substrate Binding. 对 nDsbDOx/Red 蛋白中侧链协同作用的见解:底物结合机制。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-10-31 Epub Date: 2024-09-04 DOI: 10.1021/acs.jpcb.4c02155
Aparna G Nair, Padmesh Anjukandi

N-terminal disulfide bond oxidoreductase (nDsbDOx/Red) proteins display divergent substrate binding mechanisms depending on the conformational changes to the Phe70 cap, which is also dependent on the disulfide redox state. In nDsbDOx, the cap dynamics is complex (shows both open/closed Phe70 cap conformations), resulting in an active site that is highly flexible. So the system's active site is conformationally selective (the active site adapts before substrate binding) toward its substrate. In nDsbDRed, the cap is generally closed, resulting in induced fit-type binding (adapts after substrate approach). Recent studies predict Tyr40 and Tyr42 residues to act as internal nucleophiles (Tyr40/42O-) for disulfide association/dissociation in nDsbDOx/Red, supplementing the electron transfer channel. From this perspective, we investigate the cap dynamics and the subsequent substrate binding modes in these proteins. Our molecular dynamics simulations show that the cap opening eliminates Tyr42O- electrostatic interactions irrespective of the disulfide redox state. The active site becomes highly flexible, and the conformational selection mechanism governs. However, Tyr40O- formation does not alter the chemical environment; the cap remains mostly closed and plausibly follows the induced fit mechanism. Thus, it is apparent that mostly Tyr42O- facilitates the internal nucleophile-mediated self-preparation of nDsbDOx/Red proteins for binding.

N-末端二硫键氧化还原酶(nDsbDOx/Red)蛋白显示出不同的底物结合机制,这取决于Phe70帽的构象变化,而Phe70帽的构象变化也取决于二硫键氧化还原状态。在 nDsbDOx 中,帽子的动态是复杂的(显示出开放/封闭的 Phe70 帽子构象),导致活性位点高度灵活。因此,该系统的活性位点对其底物具有构象选择性(活性位点在与底物结合之前就已适应)。而在 nDsbDRed 中,活性位点帽通常是封闭的,从而导致诱导拟合型结合(在接近底物后适应)。最近的研究预测 Tyr40 和 Tyr42 残基在 nDsbDOx/Red 中作为内部亲核物(Tyr40/42O-)进行二硫键结合/解离,补充了电子传递通道。从这个角度出发,我们研究了这些蛋白质中的帽子动力学和随后的底物结合模式。我们的分子动力学模拟结果表明,无论二硫氧化还原状态如何,盖帽打开都会消除 Tyr42O 与静电相互作用。活性位点变得高度灵活,并受构象选择机制的支配。然而,Tyr40O- 的形成并没有改变化学环境;盖帽大部分仍然是封闭的,并且可能遵循诱导拟合机制。因此,很明显,大部分 Tyr42O- 会促进 nDsbDOx/Red 蛋白由内部亲核剂介导的自我准备,以利于结合。
{"title":"Insights into the Role of Side-Chain Team Work in nDsbD<sub>Ox/Red</sub> Proteins: Mechanism of Substrate Binding.","authors":"Aparna G Nair, Padmesh Anjukandi","doi":"10.1021/acs.jpcb.4c02155","DOIUrl":"10.1021/acs.jpcb.4c02155","url":null,"abstract":"<p><p>N-terminal disulfide bond oxidoreductase (nDsbD<sub>Ox/Red</sub>) proteins display divergent substrate binding mechanisms depending on the conformational changes to the Phe<sub>70</sub> cap, which is also dependent on the disulfide redox state. In nDsbD<sub>Ox</sub>, the cap dynamics is complex (shows both open/closed Phe<sub>70</sub> cap conformations), resulting in an active site that is highly flexible. So the system's active site is conformationally selective (the active site adapts before substrate binding) toward its substrate. In nDsbD<sub>Red</sub>, the cap is generally closed, resulting in induced fit-type binding (adapts after substrate approach). Recent studies predict Tyr<sub>40</sub> and Tyr<sub>42</sub> residues to act as internal nucleophiles (Tyr<sub>40/42</sub>O<sup>-</sup>) for disulfide association/dissociation in nDsbD<sub>Ox/Red</sub>, supplementing the electron transfer channel. From this perspective, we investigate the cap dynamics and the subsequent substrate binding modes in these proteins. Our molecular dynamics simulations show that the cap opening eliminates Tyr<sub>42</sub>O<sup>-</sup> electrostatic interactions irrespective of the disulfide redox state. The active site becomes highly flexible, and the conformational selection mechanism governs. However, Tyr<sub>40</sub>O<sup>-</sup> formation does not alter the chemical environment; the cap remains mostly closed and plausibly follows the induced fit mechanism. Thus, it is apparent that mostly Tyr<sub>42</sub>O<sup>-</sup> facilitates the internal nucleophile-mediated self-preparation of nDsbD<sub>Ox/Red</sub> proteins for binding.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
New Insight into Quantity-Dependent Self-Assembly Pattern of Light Levitating Droplet Clusters. 光悬浮液滴团数量依赖性自组装模式的新见解。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-10-31 Epub Date: 2024-10-16 DOI: 10.1021/acs.jpca.4c06443
Pengcheng Jiang, Yijing Yang, Xun Zhu, Dingding Ye, Yang Yang, Hong Wang, Liang An, Alexander A Fedorets, Qiang Liao, Rong Chen, Michael Nosonovsky

It has been reported that the self-assembly pattern of light levitating droplet clusters above the hot gas-liquid interface is dependent on the quantity of droplets. However, the already-reported theoretical explanation of the quantity-dependent self-assembly pattern cannot work well when the quantity of the light levitating droplet exceeds 15. Herein, we propose a new theoretical perspective to understand the self-assembly of a light levitating droplet cluster by referring to the classical densest packing problem of identical rigid circles in a larger circle with the introduction of the minimum total potential energy principle. Amazingly, the theoretical results obtained by this new approach agree well with experimental results, even though the quantity of the light levitating droplet is up to 142. This study deepens our understanding of the quantity-dependent self-assembly pattern of the light levitating droplet clusters and provides significant inspiration for other analogous self-assembly phenomena.

据报道,热气-液界面上方的轻悬浮液滴团的自组装模式取决于液滴的数量。然而,当光悬浮液滴的数量超过 15 个时,已报道的关于数量依赖性自组装模式的理论解释就不能很好地发挥作用。在此,我们提出了一个新的理论视角,即通过引入最小总势能原理,参照经典的大圆中相同刚性圆的最密堆积问题,来理解轻悬液滴团的自组装。令人惊奇的是,尽管轻悬液滴的数量多达 142 个,但这种新方法得到的理论结果与实验结果非常吻合。这项研究加深了我们对光悬浮液滴团数量依赖性自组装模式的理解,并为其他类似的自组装现象提供了重要启示。
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引用次数: 0
OH Radical Oxidation of Organosulfates in the Atmospheric Aqueous Phase. 大气水相中有机硫酸盐的羟基自由基氧化作用。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-10-31 Epub Date: 2024-10-21 DOI: 10.1021/acs.jpca.4c02877
Daniel T Gweme, Sarah A Styler

Organosulfates (OS, ROSO3-), ubiquitous constituents of atmospheric particulate matter (PM), influence both the physicochemical and climatic properties of PM. Although the formation pathways of OS have been extensively researched, only a few studies have investigated the atmospheric fate of this class of compounds. Here, to better understand the reactivity and transformation of OS under cloudwater- and aerosol-relevant conditions, we investigate the hydroxyl radical (OH) oxidation bimolecular rate constants (kOS+OHII) and products of five atmospherically relevant OS as a function of pH and ionic strength: methyl sulfate (MeS), ethyl sulfate (EtS), propyl sulfate (PrS), hydroxyacetone sulfate (HaS) and phenyl sulfate (PhS). Our results show that OS are oxidized by OH with kOS+OHII between 108 - 109 M-1 s-1, which corresponds to atmospheric lifetimes of minutes in aqueous aerosol to days in cloudwater. We find that kOS+OHII increases with carbon chain length (MeS < EtS < PrS) and aromaticity (PrS < PhS), but does not depend on solution pH (2, 9). In addition, we find that whereas the OH reactivity of the aliphatic OS studied here decreases by ∼2× with increasing ionic strength (0-15 M), the reactivity of PhS decreases by ∼10×. The oxidation of EtS and PrS produced organic peroxides (ROOH) as first-generation oxidation products, which subsequently photolyzed; the oxidation of PhS resulted in hydroxylated aromatic products. These results highlight the need for inclusion of OS loss pathways in atmospheric models, and suggest caution in using ambient OS concentration measurements alone to estimate their production rates.

有机硫酸盐(OS,ROSO3-)是大气颗粒物(PM)中无处不在的成分,对 PM 的物理化学和气候特性都有影响。虽然人们对有机硫酸盐的形成途径进行了广泛研究,但只有少数研究调查了这一类化合物在大气中的归宿。在此,为了更好地了解操作系统在云水和气溶胶相关条件下的反应性和转化,我们研究了羟基自由基(OH)氧化双分子速率常数(kOS+OHII)以及五种与大气相关的操作系统(硫酸甲酯(MeS)、硫酸乙酯(EtS)、硫酸丙酯(PrS)、硫酸羟基丙酮(HaS)和硫酸苯基(PhS))的产物与 pH 值和离子强度的函数关系。我们的研究结果表明,OS 被羟基氧化的 kOS+OHII 介于 108 - 109 M-1 s-1 之间,这相当于水气溶胶中几分钟到云水中几天的大气寿命。我们发现,kOS+OHII 随碳链长度(MeS < EtS < PrS)和芳香度(PrS < PhS)的增加而增加,但与溶液 pH 值无关(2, 9)。此外,我们还发现,本文所研究的脂肪族 OS 的羟基反应性随离子强度(0-15 M)的增加而降低 ∼ 2 倍,而 PhS 的反应性则降低 ∼ 10 倍。EtS 和 PrS 氧化产生的第一代氧化产物是有机过氧化物(ROOH),随后发生光解;PhS 氧化则产生羟基芳香产物。这些结果突出表明,有必要将操作系统的损失途径纳入大气模型,并建议谨慎使用环境操作系统浓度测量值来估算其生成率。
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