DNA molecular configurations in flows near adsorbing and nonadsorbing surfaces

We investigate experimentally -phage and T2-coliphage DNA molecules near both non-adsorbing glass and adsorbing 3-aminopropyltriethoxysilane (APTES)-coated glass surfaces in a simple steady shearing flow generated by a torsional flow cell. The DNA molecular deformations near the surface are found to be considerably weaker than in bulk flow at the same shear rate. This affects the DNA molecules deposition and stretching on the adsorbing surface. Surprisingly, for a simple shearing flow in the torsional shearing device, the observed stretch, for molecules both near (<10 µm) the surface and adsorbed to it, is much less than predicted by simulations.     

Molecular characterization,modeling and docking of CYP107CB2 from Bacillus lehensis G1, an alkaliphile

Cytochrome P450s are a superfamily of heme monooxygenases which catalyze a wide range of biochemical reactions. The reactions involve the introduction of an oxygen atom into an inactivated carbon of a compound which is essential to produce an intermediate of a hydroxylated product. The diversity of chemical reactions catalyzed by cytochrome P450s has led to their increased demand in numerous industrial and biotechnology applications. A recent study showed that a gene sequence encoding a CYP was found in the genome of Bacillus lehensis G1, and this gene shared structural similarity with the bacterial vitamin D hydroxylase (Vdh) from Pseudonocardia autotrophica. The objectives of present study was to mine, for a novel CYP from a new isolate B. lehensis G1 alkaliphile and determine the biological properties and functionalities of CYP in this bacterium. Our study employed the usage of computational methods to search for the novel CYP from CYP structural databases to identify the conserved pattern, functional domain and sequence properties of the uncharacterized CYP from B. lehensis G1. A computational homology model of the protein’s structure was generated and a docking analysis was performed to provide useful structural knowledge on the enzyme’s possible substrate and their interaction. Sequence analysis indicated that the newly identified CYP, termed CYP107CB2, contained the fingerprint heme binding sequence motif FxxGxxxCxG at position 336-345 as well as other highly conserved motifs characteristic of cytochrome P450 proteins. Using docking studies, we identified Ser-79, Leu-81, Val-231, Val-279, Val-383, Ala-232, Thr-236 and Thr-283 as important active site residues capable of stabilizing interactions with several potential substrates, including vitamin D₃, 25-hydroxyvitamin D₃ and 1α-hydroxyvitamin D₃, in which all substrates docked proximally to the enzyme’s heme center. Biochemical analysis indicated that CYP107CB2 is a biologically active protein to produce 1α,25-dihydroxyvitamin D₃ from 1α-hydroxyvitamin D₃. Based on these results, we conclude that the novel CYP107CB2 identified from B. lehensis G1 is a putative vitamin D hydroxylase which is possibly capable of catalyzing the bioconversion of parental vitamin D₃ to calcitriol, or related metabolic products.     

Molecularly imprinted polymers with synthetic dummy templates for the preparation of capsaicin and dihydrocapsaicin from chili peppers

In this work, dummy molecularly imprinted polymers with high selectivity and affinity to capsaicin and dihydrocapsaicin are designed using N‐vanillylnonanamide as a dummy template. The performance of dummy molecularly imprinted polymers and nonimprinted polymers was evaluated using adsorption isotherms, adsorption kinetics, and selective recognition capacity. Dummy molecularly imprinted polymers were found to exhibit good site accessibility, taking just 20 min to achieve adsorption equilibrium; they were also highly selective toward capsaicin and dihydrocapsaicin. We successfully used dummy molecularly imprinted polymers as a specific sorbent for selectively enriching capsaicin and dihydrocapsaicin from chili pepper samples. In a scaled‐up experiment, the selective recovery of capsaicinoids was calculated to be 77.8% using solid‐phase extraction. To the best of our knowledge, this is the first example of the use of N‐vanillylnonanamide as a dummy template in molecularly imprinted polymers to simultaneously enrich capsaicin and dihydrocapsaicin.     

Molybdenum-catalyzed reduction of molecular dinitrogen into ammonia under ambient reaction conditions

Synthesis of transition metal–dinitrogen complexes and stoichiometric transformations of their coordinated dinitrogen into ammonia and hydrazine have so far been well investigated in order to achieve a novel nitrogen fixation under ambient conditions. As an extension of our study, the dimolybdenum–dinitrogen complex bearing PNP pincer ligands has been found to work as an effective catalyst for the formation of ammonia from dinitrogen, where 52 equiv of ammonia are produced based on the catalyst (26 equiv of ammonia are produced based on the molybdenum atom of the catalyst). This is the most effective catalytic reaction system for the formation of ammonia from molecular dinitrogen catalyzed by transition metal–dinitrogen complexes as catalysts under ambient reaction conditions. Herein, we describe recent results concerning the catalytic reaction, including the proposed reaction pathway.     

Gas-phase thermochemical properties of some tri-substituted phenols: A density functional theory study

The study of the energetics of phenolic compounds has a considerable practical interest since this family of compounds includes numerous synthetic and naturally occurring antioxidants. In this work, density functional theory (DFT) has been used to investigate gas-phase thermochemical properties of the following tri-substituted phenols: 2,4,6-trimethylphenol, 2,6-dimethyl-4-tert-butylphenol, 2,6-dimethyl-4-methoxyphenol, 2,4,6-tri-tert-butylphenol, 2,6-di-tert-butyl-4-methylphenol, 2,6-di-tert-butyl-4-methoxyphenol, 2,4,6-trimethoxyphenol, 2,6-dimethoxy-4-methylphenol and 2,6-dimethoxy-4-tert-butylphenol. Molecular structures were computed with the B3LYP and the ωB97X-D functionals and the 6-31G(d) basis set. More accurate energies were obtained from single-point energy calculations with both functionals and the 6-311++G(2df,2pd) basis set. Standard enthalpies of formation of the phenolic molecules and phenoxyl radicals were derived using an appropriate homodesmotic reaction. The OH homolytic bond dissociation enthalpies, gas-phase acidities and adiabatic ionization enthalpies were also calculated. The general good agreement found between the calculated and the few existent experimental gas-phase thermochemical parameters gives confidence to the estimates concerning the phenolic compounds which were not yet experimentally studied.     

Solubility of tridecanedioic acid in pure solvent systems: An experimental and computational study

Solubility has been extensively investigated by the phase equilibria approach at the mesoscale level, but its origin on the molecular and electronic levels is poorly understood. This study explored the solubility behaviour of crystalline solid in selected pure solvents with various functional groups by using both phase equilibria and molecular modelling methods. The model compound tridecanedioic acid (TDDA) solubility in methanol, ethanol, acetic acid, acetone, and ethyl acetate was determined from T = (283.15 to 323.15) K by a static method. It was found that almost all solutions studied exhibit non-ideal behaviour and deviate positively from Raoult’s law indicating the important role of homo-molecules interactions. Thermodynamic analyses of solution suggest that both enthalpy and entropy of solution govern the dissolution process. Computational studies on solubility behaviour were performed by using both density functional theory (DFT) calculations and molecular dynamic (MD) simulations. The results conclude that the (solute + solvent) interaction is not the only factor determining solubility, and (solvent + solvent) interaction also plays an important role. The simulated results are found to be qualitatively consistent with experimental values. Finally, solubility values were correlated by the empirically modified Apelblat equation and two local composition models of Wilson and NRTL.     

树形大分子基药物传输系统结合强度及构型的分子动力学研究

采用全原子分子动力学方法系统研究了聚酰胺(PAMAM)型树形大分子非共价搭载4种抗癌药物分子(CE6,DOX,MTX及SN38)的药物传输复合体系.考察了药物分子种类、数量及树形大分子的代数和聚乙二醇化表面修饰对复合体系的结合强度、尺寸及溶剂中扩散行为的影响.研究发现,PAMAM自身变形能对药物-PAMAM间的结合有重要影响.搭载较多的药物分子可以使PAMAM自身增大,但同样搭载条件下经过聚乙二醇化修饰过的PAMAM变化并不明显.PAMAM分子表面的聚乙二醇化可以更高的强度结合更多的药物分子,并减缓其扩散速度,因而提高药物分子的搭载效率和体内滞留时间.为新型树形大分子基药物传输体系的设计提供理论依据.     

Comprehensive characterization of natural organic matter by MALDI- and ESI-Fourier transform ion cyclotron resonance mass spectrometry

Natural organic matter (NOM) is a complex and non-uniform mixture of organic compounds which plays an important role in environmental processes. Due to the complexity, it is challenging to obtain fully detailed structural information about NOM. Although Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) has been demonstrated to be a powerful tool for providing molecular information about NOM, multiple ionization methods are needed for comprehensive characterization of NOM at the molecular level considering the ionizing selectivity of different ionization methods. This paper reports the first use of matrix assisted laser desorption/ionization (MALDI) method coupled with FT-ICR-MS for molecular characterization of NOM within a mass range of 200–800 Da. The mass spectral data obtained by MALDI were systematically compared with data generated by electrospray ionization (ESI). It showed that complementary molecular information about NOM which could not be detected by ESI, were provided by MALDI. More unsaturated and aromatic constituents of NOM with lower O/C ratio (O/C ratio < 0.5) were preferentially ionized in MALDI negative mode, whereas more polar constituents of NOM with higher O/C ratio were preferentially ionized in ESI negative mode. Molecular anions of NOM appearing at even m/z in MALDI negative ion mode were detected. The results show that NOM molecules with aromatic structures, moderate O/C ratio (0.7 > O/C ratio > 0.25) and lower H/C ratio were liable to form molecular anions at even m/z, whereas those with higher H/C ratio are more likely to form deprotonated ions at odd m/z. It is speculated that almost half of the NOM molecules identified by MALDI may be aromatic or condensed aromatic compounds with special groups which are liable to absorb electron from other molecules to generate free radical anions during MALDI ionization.     

Polyglycerol based coatings to reduce non-specific protein adsorption in sample vials and on SPR sensors

Coatings based on dendritic polyglycerol (dPG) were investigated for their use to control nonspecific protein adsorption in an assay targeted to analyze concentrations of a specific protein. We demonstrate that coating of the sample vial with dPG can significantly increase the recovery of an antibody after incubation. First, we determine the concentration dependent loss of an antibody due to nonspecific adsorption to glass via quartz crystal microbalance (QCM). Complementary to the QCM measurements, we applied the same antibody as analyte in an surface plasmon resonance (SPR) assay to determine the loss of analyte due to nonspecific adsorption to the sample vial. For this purpose, we used two different coatings based on dPG. For the first coating, which served as a matrix for the SPR sensor, carboxyl groups were incorporated into dPG as well as a dithiolane moiety enabling covalent immobilization to the gold sensor surface. This SPR-matrix exhibited excellent protein resistant properties and allowed the immobilization of amyloid peptides via amide bond formation. The second coating which was intended to prevent nonspecific adsorption to glass vials comprised a silyl moiety that allowed covalent grafting to glass. For demonstrating the impact of the vial coating on the accuracy of an SPR assay, we immobilized amyloid beta (Aβ) 1-40 and used an anti-Aβ 1-40 antibody as analyte. Alternate injection of analyte into the flow cell of the SPR device from uncoated and coated vials, respectively gave us the relative signal loss (1 − RU_uncoated/RU_coated) caused by the nonspecific adsorption. We found that the relative signal loss increases with decreasing analyte concentration. The SPR data correlate well with concentration dependent non-specific adsorption experiments of the analyte to glass surfaces performed with QCM. Our measurements show that rendering both the sample vial and the sensor surface is crucial for accurate results in protein assays.     

Water revealed as molecular mirror when measuring low concentrations of sugar with near infrared light

Near infrared spectroscopy is an overtone spectroscopy regarded as a quick and non-destructive method that provides analytical solutions for components that represent approximately 1% or more of the total mass of the investigated composite samples. Aquaphotomics offers the possibility for disentanglement of information remaining hidden in the spectra when conventional data evaluation methods are used, since this concept utilizes changes of the water structure induced by the measured solute as specific molecular vibrations at water bands. Here, near infrared technique and aquaphotomics are applied for non-destructive identification and quantification of mono- and di-saccharide solutes at 100–0.02 mM concentration that is accepted as unachievable with near infrared spectroscopy. The results presented in this study support the aquaphotomics' water molecular mirror concept that explores spectral changes related to water molecular rearrangements caused by minute changes of the solutes in the aqueous systems. The method provides quick and accurate alternative for classical analytical measurements of saccharides even at millimolar concentration levels.