Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge

A major challenge in computer-aided drug design is the accurate estimation of ligand binding affinity. Here, a new approach that combines the adaptive steered molecular dynamics (ASMD) and partial atomic charges calculated by semi-empirical quantum mechanics (SQMPC), namely ASMD-SQMPC, is suggested to predict the ligand binding affinities, with 24 HIV-1 protease inhibitors as testing examples. In the ASMD-SQMPC, the relative binding free energy (ΔG) is reflected by the average maximum potential of mean force (<PMF>_max) between bound and unbound states. The correlation coefficient (R²) between the <PMF>_max and experimentally determined ΔG is 0.86, showing a significant improvement compared with the conventional ASMD (R² = 0.52). Therefore, this study provides an efficient approach to predict the relative ΔG and reveals the significance of precise partial atomic charges in the theoretical simulations.     

On the strength of hydrogen bonding within water clusters on the coordination limit

Hydrogen bonds (HB) are arguably the most important noncovalent interactions in chemistry. We study herein how differences in connectivity alter the strength of HBs within water clusters of different sizes. We used for this purpose the interacting quantum atoms energy partition, which allows for the quantification of HB formation energies within a molecular cluster. We could expand our previously reported hierarchy of HB strength in these systems (Phys. Chem. Chem. Phys., 2016, 18 , 19557) to include tetracoordinated monomers. Surprisingly, the HBs between tetracoordinated water molecules are not the strongest HBs despite the widespread occurrence of these motifs (e.g., in ice I_h). The strongest HBs within H₂O clusters involve tricoordinated monomers. Nonetheless, HB tetracoordination is preferred in large water clusters because (a) it reduces HB anticooperativity associated with double HB donors and acceptors and (b) it results in a larger number of favorable interactions in the system. Finally, we also discuss (a) the importance of exchange-correlation to discriminate among the different examined types of HBs within H₂O clusters, (b) the use of the above-mentioned scale to quickly assess the relative stability of different isomers of a given water cluster, and (c) how the findings of this research can be exploited to indagate about the formation of polymorphs in crystallography. Overall, we expect that this investigation will provide valuable insights into the subtle interplay of tri- and tetracoordination in HB donors and acceptors as well as the ensuing interaction energies within H₂O clusters.     

Fluorescence studies of the interaction between chloramphenicol and nitrogen-doped graphene quantum dots and determination of chloramphenicol in chicken feed

Chloramphenicol (CAP) is a veterinary antibiotic that has been banned due to its severe side effects in humans. Through the application of manure, veterinary antibiotics can enter the soil, where they can be taken up by crops and vegetables and pose a potential health hazard to humans. Thus, it is highly desirable to develop a rapid and sensitive tool for on-site detection of CAP to ensure food safety and to control the abuse of antibiotics. To this end, nitrogen-doped graphene quantum dots (N-GQDs) were successfully prepared via microwave-assisted synthesis using citric acid and urea as carbon and nitrogen sources, respectively. Analytical results suggested that the interaction between N-GQDs and CAP could occurs via π-π stacking, which quenched N-GQD fluorescence. CAP spiked into chicken feed could be rapidly extracted with ethanol and quantified based on N-GQD fluorescence quenching without further separation. This method showed good recovery (97–102.6%), a low detection limit (1.8 ppm), and was not affected by interference from florfenicol, and thiamphenicol, legal substitute antibiotics. This method has excellent potential for determination of CAP in livestock feed and soil.     

Identification of decomposition reactions for HMDSO organosilicon using quantum chemical calculations

Hexamethyldisiloxane [HMDSO, (CH₃)₃-SiOSi-(CH₃)₃] is an important precursor for SiO₂ formation during flame-based silica material synthesis. As a result, HMDSO reactions in flame have been widely investigated experimentally, and many results have indicated that HMDSO decomposition reactions occur very early in this process. In this paper, quantum chemical calculations are performed to identify the initial decomposition of HMDSO and its subsequent reactions using the density functional theory at the level of B3LYP/6-311+G (d, p). Four reaction pathways—(a) Si O bond dissociation of HMDSO, (b) Si C bond dissociation of HMDSO, (c) dissociation and recombination of Si O and Si C bonds, and (d) elimination of a methane molecule from HMDSO—have been examined and identified. From the results, it is found that the barrier of 84.38 kcal/mol and Si O bond dissociation energy of 21.55 kcal/mol are required for the initial decomposition reaction of HMDSO in the first pathway, but the highest free energy barrier (100.69 kcal/mol) is found in the third reaction pathway. By comparing the free energy barriers and reaction rate constants, it is concluded that the most possible initial decomposition reaction of HMDSO is to eliminate the CH₃ radical by Si C bond dissociation.     

Reactions of fullerene C60 with methyl methacrylate radicals: A density functional theory study

We have investigated the stepwise addition of four growing methyl methacrylate (MMA) radicals to C₆₀ fullerene, taking into account all possible types of the formed adducts. This reaction set is a reliable approximation for understanding the MMA polymerization process in the presence of C₆₀ fullerene. We have analyzed the structures of the fullerene-MMA adducts and energy parameters of their formation (heat effects and activation enthalpies). We found that up to three MMA growing radicals are favorably attached to C₆₀ as the fullerene-MMA trisadduct is a stable radical of the allyl type. It is inactive for further radical addition, and the elimination of the hydrogen atom from the growing MMA radical becomes preferable. The effects of steric factors and structures of the products of multiple growing MMA radical additions to C₆₀ on the radical polymerization of MMA in the presence of C₆₀ fullerene are considered.     

Moving boundary truncated grid method: Multidimensional quantum dynamics

The moving boundary truncated grid (TG) method is used to study wave packet dynamics of multidimensional quantum systems. As time evolves, appropriate Eulerian grid points required for propagating a wave packet are activated and deactivated with no advance information about the dynamics. This method is applied to the Henon-Heiles potential and wave packet barrier scattering in two, three, and four dimensions. Computational results demonstrate that the TG method not only leads to a great reduction in the number of grid points needed to perform accurate calculations but also is computationally more efficient than the full grid calculations.     

炭-/石墨烯量子点在超级电容器中的应用

炭-/石墨烯量子点作为新兴的炭纳米材料,因具有独特的小尺寸效应和丰富的边缘活性位点而在高性能超级电容器电极材料的研发方面展现出巨大潜力。针对目前炭-/石墨烯量子点在超级电容器电极材料方面的应用优势和存在的关键问题,本文以炭-/石墨烯量子点、量子点/导电炭复合材料、量子点/金属氧化物复合材料、量子点/导电聚合物复合材料以及量子点衍生炭这些电极材料为脉络,梳理了近年来该领域的发展状况,尝试阐释炭-/石墨烯量子点在电极材料、复合材料和衍生炭电极材料中所起到的关键作用,最后对炭-/石墨烯量子点电极材料的发展进行了展望。本综述以期为炭-/石墨烯量子点基电极材料的研究提供一定参考和依据。     

氮掺杂碳点的制备及其对阿莫西林高灵敏检测

以天然物质石斛为原料,一步水热法合成高荧光量子产率的氮掺杂碳点(NCDs),通过透射电子显微镜(TEM)、X射线光电子能谱(XPS)、傅里叶变换红外光谱(FT-IR)、紫外-可见光吸收图谱(UV-Vis)及荧光光谱(PL)对合成的NCDs进行表征。 实验结果显示合成的NCDs发强烈的蓝色荧光,呈现为球形或准球形,均匀分散,尺寸范围在1~5 nm;其表面含有丰富的COOH、OH和NH₂等水溶性基团,最佳激发和发射波长分别为350和435 nm,且具有良好的发光稳定性。 通过测定,合成的NCDs的荧光量子产率高达29.19%。在pH=7.4的缓冲溶液中测定不同物质对NCDs的荧光影响,相同条件下发现只有阿莫西林能够对NCDs荧光进行明显猝灭,表明合成的NCDs可选择性的识别阿莫西林,通过NCDs的荧光强度变化构建一种可灵敏检测阿莫西林的传感器,检测线性范围为2.6~30 μmol/L,检出限为0.15 μmol/L。     

Ag3PO4量子点/石墨相氮化碳纳米片复合光催化剂的制备及其对苯甲醇选择性氧化活性

以热氧化剥离法得到的超薄石墨相氮化碳(g-C₃N₄)纳米片为载体,首次在室温条件下,制备了系列Ag₃PO₄量子点/g-C₃N₄纳米片复合光催化剂;通过透射电子显微镜(TEM)、高分辨透射电子显微镜(HRTEM)、X射线衍射(XRD)、傅里叶变换红外光谱(FT-IR)、紫外-可见漫反射光谱(UV-Vis DRS)、荧光光谱(PL),对复合光催化剂的形貌、结构和光学性质进行了表征,考察了系列光催化剂对苯甲醇的光催化选择性氧化性能。 结果表明,粒径为3~5 nm Ag₃PO₄颗粒均匀分散g-C₃N₄纳米片上,结晶度良好。 以乙腈为溶剂时,当m(Ag₃PO₄)/m(g-C₃N₄)=0.6时,苯甲醇具有32.1%的最大转化率,对产物苯甲醛具有90%的最高选择性;活性物种捕捉实验结果表明,该催化氧化反应的主要活性物是光生空穴的氧化作用,能带计算结果表明,该复合催化剂结构具有合适的苯甲醇的氧化电位而选择性生成苯甲醛。