2,3,3'-三氯联苯与人血清白蛋白之间相互作用的计算模拟及光谱研究

利用分子对接、分子动力学模拟、荧光光谱、紫外光谱及同步荧光光谱法研究了2,3,3'-三氯联苯(PCB-20)与人血清白蛋白(HSA)的相互作用。分子对接结果表明,PCB-20与HSA通过疏水作用力稳定结合于HSA的疏水空腔内。光谱法实验结果表明,PCB-20通过与HSA形成HSA-PCB20复合物从而对HSA具有荧光猝灭作用,猝灭原因是静态猝灭和非辐射能量转移,热力学参数也表明两者结合的主要驱动力为疏水作用力,计算模拟与实验结果吻合度较高。分子动力学模拟结果表明,PCB-20能够与HSA稳定结合,且与同步荧光光谱实验共同证明其对HSA的构象变化产生了一定影响。     

2,3,3′-三氯联苯与人血清白蛋白之间相互作用的计算模拟及光谱研究

利用分子对接、分子动力学模拟、荧光光谱、紫外光谱及同步荧光光谱法研究了2,3,3′-三氯联苯(PCB-20)与人血清白蛋白(HSA)的相互作用。分子对接结果表明,PCB-20与HSA通过疏水作用力稳定结合于HSA的疏水空腔内。光谱法实验结果表明,PCB-20通过与HSA形成HSA-PCB20复合物从而对HSA具有荧光猝灭作用,猝灭原因是静态猝灭和非辐射能量转移,热力学参数也表明两者结合的主要驱动力为疏水作用力,计算模拟与实验结果吻合度较高。分子动力学模拟结果表明,PCB-20能够与HSA稳定结合,且与同步荧光光谱实验共同证明其对HSA的构象变化产生了一定影响。     

分子荧光光谱法结合分子动力学模拟研究2′-OH-BDE-68与HSA的相互作用

结合分子荧光光谱法、分子对接和分子动力学模拟等方法研究了在生理条件(pH 7.40)下2′-羟基-2,3′,4,5-四溴二苯醚(2′-OH-BDE-68)与人血清白蛋白(HSA)的相互作用及其对HSA构象的影响。结果表明:1 2′-OH-BDE-68对HSA内源性荧光的猝灭属静态猝灭和非辐射能量转移过程;2两者之间的反应是以疏水作用力为主辅以微弱的静电作用的自发反应过程;3 2′-OH-BDE-68与HSA的结合在10ns内趋于平衡,结合位点在SiteⅠ;4复合物的形成使HSA分子中的色氨酸的疏水性增加,从而HSA的二级结构发生改变。     

光谱法及分子对接研究邻苯二甲酸单乙基己基酯与人血清白蛋白的相互作用

通过荧光光谱法、紫外分光光度法以及分子对接技术探究邻苯二甲酸单乙基己基酯(MEHP)与人血清白蛋白(HSA)之间的相互作用及其作用机制。光谱学数据显示,MEHP诱导HSA内源荧光猝灭是因为两者间发生非辐射能量转移并形成稳定的复合物;不同温度下的热力学常数表明范德华力或氢键为MEHP与HSA结合的主要驱动力;三维荧光光谱结果证实MEHP改变了HSA的构象;同步荧光光谱和位点实验表明,MEHP在位点Ⅰ与HSA结合。根据光谱学的研究结果,采用分子对接技术模拟MEHP与HSA在分子水平上的相互作用机制,结果与光谱学研究结果一致。     

基于分子模拟和光谱法分析漆酶与甲酚的相互作用

该文运用计算模拟与光谱法研究了甲酚与漆酶的相互作用。首先,计算模拟表明漆酶与3种甲酚同分异构体都能发生相互作用,分子对接研究结果表明漆酶与甲酚同分异构体能以氢键和疏水作用力相结合,且结合位点相似。通过分子动力学模拟比较漆酶结合甲酚前后残基的柔性差异,验证了分子对接结合位点的可靠性。其次,选取计算模拟中结果较好的间甲酚,利用光谱法探究间甲酚与漆酶的荧光猝灭机制及结合前后漆酶二级结构的变化。荧光猝灭实验证实漆酶与间甲酚间是形成非荧光复合物的静态猝灭,与分子对接结果一致。红外光谱研究结果表明,漆酶与间甲酚结合后二级结构发生变化,其内部的β-转角和β-反向平行结构向β-折叠、无规则卷曲和α-螺旋结构转化,这与分子动力学模拟结果相呼应。该研究为利用漆酶转化环境中甲酚污染物提供了理论基础与数据支持。     

2'-羟基-2,4-二溴二苯醚与人血清白蛋白作用机制的光谱研究与计算模拟

采用分子对接、分子动力学模拟和光谱法研究了2'-羟基-2,4-二溴二苯醚(2'-OH-BDE-7)与人血清白蛋白(HSA)的相互作用.同步荧光光谱研究表明,2'-OH-BDE-7诱导HSA的构象产生变化,并与分子动力学模拟的结果相吻合.荧光光谱表明,2'-OH-BDE-7能引起HSA荧光猝灭,且其作用机制为静态猝灭和非辐射能量转移.热力学分析得出ΔG0,ΔH0和ΔS0,表明氢键和范德华力在HSA-2'-OH-BDE-7的体系中起着重要作用.竞争实验和分子对接结果表明2'-OH-BDE-7主要结合在HSA的位点Ⅰ.将计算模拟和光谱实验研究相结合,为研究小分子和蛋白质相互作用机制提供更多的信息.     

2-(4-甲基苯基)-3-(N-乙酰基)-5-(2-羟基苯基)-1,3,4-噁唑啉的合成及与人血清白蛋白的相互作用

合成了2-(4-甲基苯基)-3-(N-乙酰基)-5-(2-羟基苯基)-1,3,4-噁唑啉(MPAHO),并用核磁共振波谱法和红外光谱法对其进行了表征。采用荧光光谱技术研究了MPAHO与人血清白蛋白(HSA)的相互作用。结果表明:MPAHO对HSA有较强的荧光猝灭作用,根据Stern-Volmer方程得到的荧光猝灭常数,可判断由于与MPAHO反应而导致HSA的荧光猝灭均属于静态猝灭。采用位点结合模型公式和Frster非辐射能量转移理论计算了结合常数、结合位点数、结合距离。从计算得到的热力学参数焓变ΔH和熵变ΔS,推断MPAHO与HSA之间的作用力为静电引力。并应用同步荧光光谱和三维荧光技术研究了MPAHO对HSA构象的影响。     

吡虫啉与人血清白蛋白相互作用热力学行为

在模拟人体生理条件下,综合利用荧光光谱、紫外吸收光谱、圆二色谱和分子模拟等方法,研究了吡虫啉(IMI)和人血清白蛋白(HSA)相互作用的热力学行为。荧光光谱和紫外吸收光谱的分析表明：吡虫啉能有效猝灭HSA的内源荧光,猝灭机制为静态猝灭;通过所获取的相互作用热力学参数,可知两者之间的相互作用是一个吉布斯自由能降低的自发过程,且二者之间的主要作用力为氢键和范德华力。位点竞争实验和分子模拟的结果表明：吡虫啉在HSA的主要结合位置为位点?。圆二色谱、同步荧光光谱和三维荧光的分析发现：吡虫啉引起HSA的构象发生改变,其α-螺旋含量降低,无规卷曲含量升高,肽链结构在吡虫啉的作用下有所伸展。     

噻螨酮与人血清白蛋白的作用机制

用分子对接方法及紫外-可见吸收光谱、同步荧光光谱、三维荧光光谱等实验手段研究了噻螨酮(HEX)与人血清白蛋白(HSA)的相互作用及对HSA构象的影响.预测结果表明,HEX能与HSA发生相互作用,且作用位点site II比site I的打分小约4.5.实验结果表明,HEX猝灭HSA的内源荧光且作用机制为静态猝灭;HEX使HSA周围的微环境发生变化,导致蛋白质的肽链结构改变;298和291 K时HEX与HSA相互作用的结合常数(KA)和结合位点数分别为7.35×103 mol/L、0.82和1.02×104 mol/L、0.86,证实HEX仅在site II存在作用位点;HEX与Trp214的结合距离为3.01 nm,作用力主要为氢键、范德华力和疏水作用力.这些研究所获得的多种信息有助于在分子水平上理解农药对人体造成的毒性及可能的生物累积性.     

荧光与紫外光谱法研究柚皮素与人血清白蛋白的结合模式

在模拟生理条件下,利用荧光光谱法和紫外吸收光谱法研究了柚皮素(NG)与人血清白蛋白(HSA)的相互作用。实验结果表明,NG对HSA的内源性荧光具有猝灭作用,属于静态猝灭过程。计算了NG-HSA体系的结合常数、结合位点数及反应的热力学参数ΔG,ΔH和ΔS,由此推出二者主要通过氢键和范德华力自发形成了摩尔比为1∶1的非共价复合物。依据Frster非辐射能量转移理论求得二者之间的结合距离为3.41 nm。三维荧光、同步荧光光谱和结合位点取代实验指出,NG主要与HSA的III A亚结构域中site II位点的酪氨酸结合。     

Potentiometric study of Cd(II) and Pb(II) complexation with two high molecular weight poly(acrylic acids); comparison with Cu(II) and Ni(II)

The cadmium (II) or lead (II) complex formation with two poly(acrylic acids) of high molecular weight (Mw=2.5×10⁵ and 3×10⁶) was investigated in dilute aqueous solution (NaNO₃ 0.1 mol l⁻¹; 25°C). Potentiometric titrations were carried out to determine the stability constants of the MA and MA₂ complex species formed. Bjerrum’s method, modified by Gregor et al. (J. Phys. Chem. 59 (1955) 34–39), for the study of polymeric acids was used. The results were compared to those previously obtained in the same conditions with copper (II) and nickel (II) . It appeared that the two polymers under study present similar binding properties and that the stability constants of the complex species formed increased in the following order, depending on the metal ion: Ni(II)β₁₀₂ was found to be close to 7.0) and allowed the formation of the predominant PbA₂ species in a quite large pH domain. Finally, the greater stability of PAA complexes compared to those of their monomeric analogs, glutaric and acetic acids, was confirmed.     

Molecular Modifications and Control of Processes to Facilitate the Synergistic Degradation of Polybrominated Diphenyl Ethers in Soil by Plants and Microorganisms Based on Queuing Scoring Method

In this paper, a combination of modification of the source and regulation of the process was used to control the degradation of PBDEs by plants and microorganisms. First, the key proteins that can degrade PBDEs in plants and microorganisms were searched in the PDB (Protein Data Bank), and a molecular docking method was used to characterize the binding ability of PBDEs to two key proteins. Next, the synergistic binding ability of PBDEs to the two key proteins was evaluated based on the queuing integral method. Based on this, three groups of three-dimensional quantitative structure-activity relationship (3D-QSAR) models of plant-microbial synergistic degradation were constructed. A total of 30 PBDE derivatives were designed using BDE-3 as the template molecule. Among them, the effect on the synergistic degradation of six PBDE derivatives, including BDE-3-4, was significantly improved (increased by more than 20%) and the environment-friendly and functional evaluation parameters were improved. Subsequently, studies on the synergistic degradation of PBDEs and their derivatives by plants and microorganisms, based on the molecular docking method, found that the addition of lipophilic groups by modification is beneficial to enhance the efficiency of synergistic degradation of PBDEs by plants and microorganisms. Further, while docking PBDEs, the number of amino acids was increased and the binding bond length was decreased compared to the template molecules, i.e., PBDE derivatives could be naturally degraded more efficiently. Finally, molecular dynamics simulation by the Taguchi orthogonal experiment and a full factorial experimental design were used to simulate the effects of various regulatory schemes on the synergistic degradation of PBDEs by plants and microorganisms. It was found that optimal regulation occurred when the appropriate amount of carbon dioxide was supplied to the plant and microbial systems. This paper aims to provide theoretical support for enhancing the synergistic degradation of PBDEs by plants and microorganisms in e-waste dismantling sites and their surrounding polluted areas, as well as, realize the research and development of green alternatives to PBDE flame retardants.     

利用分子路径指数矢量对烷烃摩尔响应值的估计与预测

 利用分子路径指数矢量表示烷烃分子结构方法 ,结合多元线性回归算法及反传神经网络算法 ,对烷烃摩尔响应值进行处理 ,获得了比文献更佳的预测效果 ,交互校验的相关系数达 0 96 8以上。     

Fluorescent Molecular Logic Gates Driven by Temperature and by Protons in Solution and on Solid

Temperature-driven fluorescent NOT logic is demonstrated by exploiting predissociation in a 1,3,5-trisubstituted Δ²-pyrazoline on its own and when grafted onto silica microparticles. Related Δ²-pyrazolines become proton-driven YES and NOT logic gates on the basis of fluorescent photoinduced electron transfer (PET) switches. Additional PASS 1 and YES+PASS 1 logic gates on silica are also demonstrated within the same family. Beside these small-molecule systems, a polymeric molecular thermometer based on a benzofurazan-derivatized N-isopropylacrylamide copolymer is attached to silica to produce temperature-driven fluorescent YES logic.     

Hydration Structure and Dynamic Properties of the Square Planar Pt(II) Aquaion Compared to the Pd(II) Case

This work examines, by means of classical Molecular Dynamics simulations, the hydration of a square planar hydrate, [Pt(H₂O)₄]²⁺, focussing the attention on the structure and dynamics adopted by water molecules in the regions above and underneath the molecular plane. Results obtained are compared with those previously derived for the case of the [Pd(H₂O)₄]²⁺ where the concept of meso-shell was introduced to define this axial region [Martínez et al. (J Phys Chem B 108:15851, 2004)]. Specific ab initio intermolecular potentials describing the interaction between the ion and the solvent have been developed following the statistical implementation of the hydrated ion concept for the case of a planar aquaion. A meso-shell is characterized by a peak in the Pt–O RDF centered at 2.95 Å which integrates to two water molecules; the mean residence time for these molecules is in the range 1–7 ps. The vibrational frequency associated to the dynamic variable defined from the distance meso-shell water molecule-cation is used to quantify the linkage degree of the water molecule in this shell. The meso-shell in Pt(II) is more labile than in the Pd(II) case, whereas the first and second hydration shells of both cations are highly similar. The observed differences in meso-shell are discussed in relation with the mechanistic interpretation of the solvent exchange at the first hydration shell.     

DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules

DAMQT‐2.1.0 is a new version of DAMQT package which includes topographical analysis of molecular electron density (MED) and molecular electrostatic potential (MESP), such as mapping of critical points (CPs), creating molecular graphs, and atomic basins. Mapping of CPs is assisted with algorithmic determination of Euler characteristic in order to provide a necessary condition for locating all possible CPs. Apart from the mapping of CPs and determination of molecular graphs, the construction of MESP‐based atomic basin is a new and exclusive feature introduced in DAMQT‐2.1.0. The GUI in DAMQT provides a user‐friendly interface to run the code and visualize the final outputs. MPI libraries have been implemented for all the tasks to develop the parallel version of the software. Almost linear scaling of computational time is achieved with the increasing number of processors while performing various aspects of topography. A brief discussion of molecular graph and atomic basin is provided in the current article highlighting their chemical importance. Appropriate example sets have been presented for demonstrating the functions and efficiency of the code. © 2015 Wiley Periodicals, Inc.     

Alcohols,ethers, carbohydrates,and related compounds. I. The MM4 force field for simple compounds

Simple alcohols and ethers have been studied with the MM4 force field. The structures of 13 molecules have been well fit using the MM4 force field. Moments of inertia have been fit with rms percentage errors as indicated: 18 moments for ethers, 0.28%; 21 moments for alcohols, 0.22%. Rotational barriers and conformational equilibria have also been examined, and the experimental and ab initio results are reproduced substantially better with MM4 than they were with MM3. Much of the improvement comes from the use of additional interaction terms in the force constant matrix, of which the torsion-bend and torsion-torsion are particularly important. Induced dipoles are included in the calculation, and dipole moments are reasonably well fit. It has been possible for the first time to fit conformational energetic data for both open chain and cyclic alcohols (e.g., propanol and cyclohexanol) with the same parameter set. For vibrational spectra, over a total of 82 frequencies, the rms error is 27 cm(-1), as opposed to 38 cm(-1) with MM3. Both the alpha and beta bond shortening resulting from the presence of the electronegative oxygen atom in the molecule are well reproduced. The electronegativity of the oxygen is sufficient that one must also include not only the alpha and beta electronegativity effects on bond lengths, but also on angle distortions, if structures are to be well reproduced. The heats of formation of 32 alcohols and ethers were fit overall to within experimental error (weighted standard deviation error 0.26 kcal/mol).