Development and Molecular Understanding of a Pd-Catalyzed Cyanation of Aryl Boronic Acids Enabled by High-Throughput Experimentation and Data Analysis

A synthetic method for the palladium-catalyzed cyanation of aryl boronic acids using bench stable and non-toxic N-cyanosuccinimide has been developed. High-throughput experimentation facilitated the screen of 90 different ligands and the resultant statistical data analysis identified that ligand σ-donation, π-acidity and sterics are key drivers that govern yield. Categorization into three ligand groups – monophosphines, bisphosphines and miscellaneous – was performed before the analysis. For the monophosphines, the yield of the reaction increases for strong σ-donating, weak π-accepting ligands, with flexible pendant substituents. For the bisphosphines, the yield predominantly correlates with ligand lability. The applicability of the designed reaction to a wider substrate scope was investigated, showing good functional group tolerance in particular with boronic acids bearing electron-withdrawing substituents. This work outlines the development of a novel reaction, coupled with a fast and efficient workflow to gain understanding of the optimal ligand properties for the design of improved palladium cross-coupling catalysts.     

Computer Simulation Study on Adsorption and Conformation of Polymer Chains Driven by External Force

In this work, Monte Carlo simulations are used to study the critical adsorption behaviors of flexible polymer chains under the action of an external driving force F parallel to an attractive flat surface. The critical adsorption temperature T_c decreases linearly with increasing F,indicating that the driving force suppresses the adsorption of polymer. The conformation of polymer is also affected by the driving force.However, the effect of F is dependent on the competition between the driving force and temperature. Under strong force or at low temperature,the polymer is stretched along the direction of the force, while under weak force or at high temperature, the polymer is not stretched. When the force is comparable to the temperature, the polymer may be stretched perpendicular to the driving force, and below T_c, we observe conformational transitions from parallel to perpendicular and again to parallel by decreasing the temperature. We found that the perpendicular stretched conformation leads the polymer chain to synchronously move along the direction of the driving force. Moreover, the conformational transitions are attributed to the competition and cooperation between the driving force and the temperature.     

In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria

The impact of lifestyle on shaping the genome content of an organism is a well-known phenomenon and cytochrome P450 enzymes (CYPs/P450s), heme-thiolate proteins that are ubiquitously present in organisms, are no exception. Recent studies focusing on a few bacterial species such as Streptomyces, Mycobacterium, Cyanobacteria and Firmicutes revealed that the impact of lifestyle affected the P450 repertoire in these species. However, this phenomenon needs to be understood in other bacterial species. We therefore performed genome data mining, annotation, phylogenetic analysis of P450s and their role in secondary metabolism in the bacterial class Gammaproteobacteria. Genome-wide data mining for P450s in 1261 Gammaproteobacterial species belonging to 161 genera revealed that only 169 species belonging to 41 genera have P450s. A total of 277 P450s found in 169 species grouped into 84 P450 families and 105 P450 subfamilies, where 38 new P450 families were found. Only 18% of P450s were found to be involved in secondary metabolism in Gammaproteobacterial species, as observed in Firmicutes as well. The pathogenic or commensal lifestyle of Gammaproteobacterial species influences them to such an extent that they have the lowest number of P450s compared to other bacterial species, indicating the impact of lifestyle on shaping the P450 repertoire. This study is the first report on comprehensive analysis of P450s in Gammaproteobacteria.     

Optimization of Vacuum-Microwave-Assisted Extraction of Natural Polyphenols and Flavonoids from Raw Solid Waste of the Orange Juice Producing Industry at Industrial Scale

Orange pomace (OP) is a solid waste produced in bulk as a byproduct of the orange juice industry and accounts for approximately 50% of the quantity of the fruits processed into juice. In numerous literature references there is information about diverse uses of orange pomace for the production of high-added-value products including production of natural antioxidant and antimicrobial extracts rich in polyphenols and flavonoids which can substitute the hazardous chemical antioxidants/antimicrobials used in agro-food and cosmetics sectors. In this work and for the first time, according to our knowledge, the eco-friendly aqueous vacuum microwave assisted extraction of orange pomace was investigated and optimized at real industrial scale in order to produce aqueous antioxidant/antimicrobial extracts. A Response Surface Optimization methodology with a multipoint historical data experimental design was employed to obtain the optimal values of the process parameters in order to achieve the maximum rates of extraction of OP total polyphenols and/or total flavonoids for economically optimum production at industrial scale. The three factors used for the optimization were: (a) microwave power (b) water to raw pomace ratio and (c) extraction time. Moreover, the effectiveness and statistical soundness of the derived cubic polynomial predictive models were verified by ANOVA.     

Multivariate analysis of extremely large ToFSIMS imaging datasets by a rapid PCA method

Principal component analysis (PCA) and other multivariate analysis methods have been used increasingly to analyse and understand depth profiles in X‐ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES) and secondary ion mass spectrometry (SIMS). These methods have proved equally useful in fundamental studies as in applied work where speed of interpretation is very valuable. Until now these methods have been difficult to apply to very large datasets such as spectra associated with 2D images or 3D depth‐profiles. Existing algorithms for computing PCA matrices have been either too slow or demanded more memory than is available on desktop PCs. This often forces analysts to ‘bin’ spectra on much more coarse a grid than they would like, perhaps even to unity mass bins even though much higher resolution is available, or select only part of an image for PCA analysis, even though PCA of the full data would be preferred. We apply the new ‘random vectors’ method of singular value decomposition proposed by Halko and co‐authors to time‐of‐flight (ToF)SIMS data for the first time. This increases the speed of calculation by a factor of several hundred, making PCA of these datasets practical on desktop PCs for the first time. For large images or 3D depth profiles we have implemented a version of this algorithm which minimises memory needs, so that even datasets too large to store in memory can be processed into PCA results on an ordinary PC with a few gigabytes of memory in a few hours. We present results from ToFSIMS imaging of a citrate crystal and a basalt rock sample, the largest of which is 134GB in file size corresponding to 67 111 mass values at each of 512 × 512 pixels. This was processed into 100 PCA components in six hours on a conventional Windows desktop PC. © 2015 The Authors. Surface and Interface Analysis published by John Wiley & Sons Ltd.     

Nucleic acid reactivity: Challenges for next‐generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next‐generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self‐consistent density‐functional tight‐binding semiempirical models are evaluated against high‐level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density‐functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d‐PhoT model is the most robust at predicting proton affinities. AM1/d‐PhoT and DFTB3‐3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear‐scaling “modified divide‐and‐conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next‐generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.     

Correlation between conformation change of polyelectrolyte brushes and lubrication

We directly monitor the absolute separation profiles that function as film thickness between a single glass disk and the charged polyelectrolyte brushes decorated steel slider in water using a home-made slider-on-disk apparatus, which reflects the structural conformation variations and interactions of polymer brushes under externally applied pressure, in addition to probing the relative variation of friction forces under different applied loads and sliding velocities. We find that the polyelectrolyte brushes modified surfaces can sustain high pressure and have extremely low friction coefficients(around 0.006 at pressures of 0.13 MPa; 0.5-0.6 without brushes). The water-lubrication characteristics are correlated to the structural conformation changes of the polyelectrolyte brushes that are mainly governed by electrostatic interactions and the osmotic pressure of counterions inside the polymer chains, which can be used to support and distribute the normal pressure. The apparent thickness of the brush decreases with the increase of loading forces, an increase in the ionic strength causes the polymer chains collapse, and the friction forces increase. This fundamental research is of great importance to understand the mechanical and structural properties of polyelectrolyte brushes and their influences on the tribological behaviors, and helps to design friction/lubrication-controlled surface/interface by taking advantage of polyelectrolyte brushes.     

新烟碱类杀虫剂生物活性的理论研究和结构修饰*

在B3LYP/6-311G基组水平下,运用密度泛函理论(DFT)的量子化学方法,对20种重氮乙烷新烟碱类杀虫剂分子的电子结构特征进行了研究,获得了它们的前线轨道能(EHOMO、ENHOMO、ELUMO、ENLUMO等)、原子电荷(Qi)、摩尔熵(Sm)、偶极矩(μ)等量化参数与物理性质。经最佳变量子集回归研究发现,重氮乙烷新烟碱类杀虫剂分子对果蝇n AChRs、哺乳动物α4β2亚型的亲和力常数(p KD、p KA)分别与ELUMO、QW、QF、QN等参数具有良好的线性关系。逐一或逐四剔除交互验证以及VIF、tα/2检验,所建2个QSAR模型具有良好的稳健性及预测能力。根据2个QSAR模型推断了重氮乙烷新烟碱类分子可能的杀虫机理。进一步研究发现,在重氮乙烷新烟碱类分子的吡啶环上的合适部位,选用不含复键的吸电子能力较强的取代基团对其进行结构修饰,有利于提高修饰后分子的生物活性。基于分子17,设计出4种经结构修饰后对果蝇n AChRs亲和力显著提高的重氮乙烷新烟碱类分子(分别是分子27,28,30和31),希望能得到实验的证实。     

表面增强拉曼散射光谱研究聚苯胺纳米棒的构象转变

采用电化学沉积法制备了聚苯胺(Polyaniline,PANI)纳米棒、树枝状银和纳米颗粒银基体。并利用表面增强拉曼散射光谱技术(Surface-enhanced Raman Scattering,SERS)研究了PANI纳米棒的分子链在Ag金属表面的构象变化。实验结果表明由于Ag金属表面的等离子共振效应,PANI分子中N原子的孤对电子与Ag的自由电子产生共轭效应,使得PANI分子链上的电荷重新分布,结果 C—H面内弯曲振动频率和C—C键的伸缩频率向低波数方向移动(蓝移);拉曼散射频率增强的基团在金属表面倾向垂直于分子链的主轴,拉曼散射频率减弱的基团在金属表面倾向平行于分子链主轴。     

Ill-posed problems in rheology

Experimental data are always noisy and often incomplete. This leads to ambiguities if one wants to infer from the data some functions, which are related to the measured quantity through an integral equation of the first kind. In rheology many of such so-called ill-posed problems appear. Two techniques to treat such problems, the regularization method and the maximum entropy method, are applied to the determination of the relaxation spectrum from data of small oscillatory shear flow. With simulated data from a reference spectrum it is discussed how the inferred spectrum depends on the region, in which data are available. It turns out that information about the asymptotic behavior of the measured quantity can be of great help in determining the full spectrum also from incomplete data.Dedicated to Prof. Dr. J. Meissner on the occasion of his 60th birthday.