Electro-assisted Molecular Assembly Giving Atomic-Scale Catalytic Active-Site Detection

The artificially accurate design of nonmetal electrocatalysts’ active site has been a huge challenge because no pure active species with the specific structure could be strictly controlled by traditional synthetic methods. Species with a multiconfiguration in the catalyst hinder identification of the active site and the subsequent comprehension of the reaction mechanism. We have developed a novel electro-assisted molecular assembly strategy to obtain a pure pentagon ring on perfect graphene avoiding other reconstructed structures. More importantly, the active atom was confirmed by the subtle passivation process as the topmost carbon atom. Recognition of the carbon-defect electrocatalysis reaction mechanism was first downsized to the single-atom scale from the experimental perspective. It is expected that this innovative electro-assisted molecular assembly strategy could be extensively applied in the active structure-controlled synthesis of nonmetal electrocatalysts and verification of the exact active atom.     

桉树杂交种与其亲本的近红外光谱判别

研究桉树控制授粉后目标性状的基因作用方式是探索其基因重组规律的重要内容。常规的数量统计分析精度往往不高,而DNA分析的专业要求高,且费时费力。该研究利用近红外光谱(NIRs)研究不同基因型桉树杂交种、亲本及杂交种与亲本间近红外光谱信息的关系,探索NIRs用于桉树杂交种与其亲本判别的可行性和准确性。以控制授粉的桉树亲本及其杂交F1代材料为对象,每种基因型从各自田间试验分别选取10个单株,采集树冠中上部新鲜健康叶片。用手持式近红外仪Phazir Rx(1624)采集桉树杂交种与其亲本叶片的NIRs信息。每单株选10片完全生理成熟的健康叶片,避开叶脉扫描其正面光谱5次,以50条NIRs信息的均值代表单个叶片的NIRs信息,最终每个基因型获得10条NIRs信息。对原始NIRs采用二阶多项式S.G一阶导数预处理。预处理后的NIRs用于多元统计分析,首先对桉树杂交亲本和子代样本进行主成分分析(PCA),直观展示不同基因型的分类情况。然后运用簇类独立软模式(SIMCA)和偏最小二乘判别分析(PLS-DA)两种有监督的判别模式验证NIRs用于桉树杂交种与其亲本树种的分类判别效果。PCA结果显示,不同的亲本间、杂交种间及杂交种与亲本间样本的主因子得分可以清晰地将各基因型分开。SIMCA模式判别分析中,桉树杂交种样本到亲本PCA模型的样本距离显示,待判别样本能够形成单独的聚类,且能直观反映两者的遗传相似。PLS-DA判别结果显示,桉树杂交亲本的PLS模型能通过预测其杂交子代的响应变量将其与亲本准确分开。结果表明,桉树叶片的NIRs信息可以准确地反映桉树杂交子代遗传信息的传递规律,NIRs判别模型可以准确地将各种基因型予以区分。因此,NIRs信息不仅可用于桉树杂交种和纯种的定性判别,还可以分析桉树基因重组过程中加性遗传效应的大小,从而为桉树遗传基础分析及其育种改良研究提供理论支撑。     

Quinazoline Derivatives Designed as Efflux Pump Inhibitors: Molecular Modeling and Spectroscopic Studies

Multidrug resistance of bacteria is a worrying concern in the therapeutic field and an alternative method to combat it is designing new efflux pump inhibitors (EPIs). This article presents a molecular study of two quinazoline derivatives, labelled BG1189 and BG1190, proposed as EPIs. In silico approach investigates the pharmacodynamic and pharmacokinetic profile of BG1189 and BG1190 quinazolines. Molecular docking and predicted ADMET features suggest that BG1189 and BG1190 may represent attractive candidates as antimicrobial drugs. UV-Vis absorption spectroscopy was employed to study the time stability of quinazoline solutions in water or in dimethyl sulfoxide (DMSO), in constant environmental conditions, and to determine the influence of usual storage temperature, normal room lighting and laser radiation (photostability) on samples stability. The effects of irradiation on BG1189 and BG1190 molecules were also assessed through Fourier-transform infrared (FTIR) spectroscopy. FTIR spectra showed that laser radiation breaks some chemical bonds affecting the substituents and the quinazoline radical of the compounds.     

Theoretical Design of Biodegradable Phthalic Acid Ester Derivatives in Marine and Freshwater Environments

The biodegradability of phtalic acid esters in marine and freshwater environments was characterized by their binding free energy with corresponding degrading enzymes. According to comprehensive biodegradation effects weights, the binding free energy values were converted into dimensionless efficacy coefficient using ratio normalization method. Then, considering comprehensive dual biodegradation effects value and the structural parameters of PAEs in both marine and freshwater environments, a 3D-QSAR pharmacophore model was constructed, five PAE derivatives (DBP−COOH, DBP−CHO, DBP−OH, DINP−NH₂, and DINP−NO₂) were screened out based on their environmental friendliness, functionality and stability. The prediction of biodegradation effects on five PAE derivatives by biodegradation models in marine and freshwater environment increased by 15.90 %, 15.84 %, 27.21 %, 12.33 %, and 8.32 %, and 21.57 %, 15.21 %, 20.99 %, 15.10 %, and 9.74 %, respectively. By simulating the photodegradation path of the PAE derivative molecular, it was found that DBP−OH can generate ^.OH and provides free radicals for the photodegradation of microplastics in the environment.     

Chemical Profiles and Pharmacological Properties with in Silico Studies on Elatostema papillosum Wedd

The current study attempted, for the first time, to qualitatively and quantitatively determine the phytochemical components of Elatostema papillosum methanol extract and their biological activities. The present study represents an effort to correlate our previously reported biological activities with a computational study, including molecular docking, and ADME/T (absorption, distribution, metabolism, and excretion/toxicity) analyses, to identify the phytochemicals that are potentially responsible for the antioxidant, antidepressant, anxiolytic, analgesic, and anti-inflammatory activities of this plant. In the gas chromatography-mass spectroscopy analysis, a total of 24 compounds were identified, seven of which were documented as being bioactive based on their binding affinities. These seven were subjected to molecular docking studies that were correlated with the pharmacological outcomes. Additionally, the ADME/T properties of these compounds were evaluated to determine their drug-like properties and toxicity levels. The seven selected, isolated compounds displayed favorable binding affinities to potassium channels, human serotonin receptor, cyclooxygenase-1 (COX-1), COX-2, nuclear factor (NF)-κB, and human peroxiredoxin 5 receptor proteins. Phytol acetate, and terpene compounds identified in E. papillosum displayed strong predictive binding affinities towards the human serotonin receptor. Furthermore, 3-trifluoroacetoxypentadecane showed a significant binding affinity for the KcsA potassium channel. Eicosanal showed the highest predicted binding affinity towards the human peroxiredoxin 5 receptor. All of these findings support the observed in vivo antidepressant and anxiolytic effects and the in vitro antioxidant effects observed for this extract. The identified compounds from E. papillosum showed the lowest binding affinities towards COX-1, COX-2, and NF-κB receptors, which indicated the inconsequential impacts of this extract against the activities of these three proteins. Overall, E. papillosum appears to be bioactive and could represent a potential source for the development of alternative medicines; however, further analytical experiments remain necessary.     

A molecular fluorophore in citric acid/ethylenediamine carbon dots identified and quantified by multinuclear solid-state nuclear magnetic resonance

The composition of fluorescent polymer nanoparticles, commonly referred to as carbon dots, synthesized by microwave-assisted reaction of citric acid and ethylenediamine was investigated by ¹³C, ¹³C{¹H}, ¹H─¹³C, ¹³C{¹⁴N}, and ¹⁵N solid-state nuclear magnetic resonance (NMR) experiments. ¹³C NMR with spectral editing provided no evidence for significant condensed aromatic or diamondoid carbon phases. ¹⁵N NMR showed that the nanoparticle matrix has been polymerized by amide and some imide formation. Five small, resolved ¹³C NMR peaks, including an unusual ═CH signal at 84 ppm (¹H chemical shift of 5.8 ppm) and ═CN₂ at 155 ppm, and two distinctive ¹⁵N NMR resonances near 80 and 160 ppm proved the presence of 5-oxo-1,2,3,5-tetrahydroimidazo[1,2-a]pyridine-7-carboxylic acid (IPCA) or its derivatives. This molecular fluorophore with conjugated double bonds, formed by a double cyclization reaction of citric acid and ethylenediamine as first shown by Y. Song, B. Yang, and coworkers in 2015, accounts for the fluorescence of the carbon dots. Cross-peaks in a ¹H─¹³C HETCOR spectrum with brief ¹H spin diffusion proved that IPCA is finely dispersed in the polyamide matrix. From quantitative ¹³C and ¹⁵N NMR spectra, a high concentration (18 ± 2 wt%) of IPCA in the carbon dots was determined. A pronounced gradient in ¹³C chemical-shift perturbations and peak widths, with the broadest lines near the COO group of IPCA, indicated at least partial transformation of the carboxylic acid of IPCA by amide or ester formation.     

Identifying aspirin polymorphs from combined DFT-based crystal structure prediction and solid-state NMR

A combined experimental and computational approach was used to distinguish between different polymorphs of the pharmaceutical drug aspirin. This method involves the use of ab initio random structure searching (AIRSS), a density functional theory (DFT)-based crystal structure prediction method for the high-accuracy prediction of polymorphic structures, with DFT calculations of nuclear magnetic resonance (NMR) parameters and solid-state NMR experiments at natural abundance. AIRSS was used to predict the crystal structures of form-I and form-II of aspirin. The root-mean-square deviation between experimental and calculated ¹H chemical shifts was used to identify form-I as the polymorph present in the experimental sample, the selection being successful despite the large similarities between the molecular environments in the crystals of the two polymorphs.     

What is the form of muscimol from fly agaric mushroom (Amanita muscaria) in water? An insight from NMR experiment supported by molecular modeling

The biologically active alkaloid muscimol is present in fly agaric mushroom (Amanita muscaria), and its structure and action is related to human neurotransmitter _γ-aminobutyric acid (GABA). The current study reports on determination of muscimol form present in water solution using multinuclear ¹H and ¹³C nuclear magnetic resonance (NMR) experiments supported by density functional theory molecular modeling. The structures of three forms of free muscimol molecule both in the gas phase and in the presence of water solvent, modeled by polarized continuous model, and nuclear magnetic isotropic shieldings, the corresponding chemical shifts, and indirect spin–spin coupling constants were calculated. Several J-couplings observed in proton and carbon NMR spectra, not available before, are reported. The obtained experimental spectra, supported by theoretical calculations, favor the zwitterion form of muscimol in water. This structure differs from NH isomer, previously determined in dimethyl sulfoxide (DMSO) solution. In addition, positions of signals C3 and C5 are reversed in both solvents.     

A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions

DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson–Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15–25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35–90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.     

Effect of additive length and chemistry on the morphology of blends of conjugated thiophenes and fullerene derivative acceptor molecules

Small molecule additives have been shown to increase the device efficiency of conjugated polymer (donor) and fullerene derivative (acceptor) based organic solar cells by modifying the morphology of the device active layer. In this paper we conduct a systematic study of how additives affect the donor‐acceptor morphology using molecular dynamics simulations of blends of thiophene‐based oligomers, mimicking poly(3‐dodecylthiophene) (P3DDT) or poly(2,2′:5′,2”‐3,3”‐didocyl‐terthiophene) (PTTT), and fullerene derivatives with additives of varying length and chemical functionalization, mimicking experimentally used additives like methyl ester additives, diiodooctane, and alkanedithiols. We find that functionalization of additives with end groups that are attracted to acceptor molecules are necessary to induce increased donor‐acceptor macrophase separation. In blends where acceptors intercalate between oligomer alkyl side chains, functionalized additives decrease acceptor intercalation. Functionalized additives with shorter alkyl segments increase acceptor macrophase separation more than additives with same chemical functionalization but longer alkyl segments. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1046–1057