对化学反应数据分类获取反应知识的新方法

尽管已有大量化学反应数据可供使用,但化学家仍常常感到很难便捷地从中得到所需的信息.这主要是由于反应数据库基于结构的检索方法与化学家解决问题的方法相去甚远.为解决这一问题而发展了一种通过对反应进行二级分类得到精细描述反应知识的层次模型的方法.第一次分类时不同的同类反应都在由一组普适性好的称作反应结构一级描述符构成的空间中进行.在第一次分类结果的基础上,得到每一类反应的公共结构特征作为第二次分类的结构描述符,利用它们进行更精细的分类,即可从原始反应数据中得到所需的基核反应.由特定反应、基核反应和基型反应就可将反应知识更合理地组织在同类反应知识库中,使它们得到更好的利用.     

Electrochemical nanomachining

Free of tool wear, residual stress, and surface damage, electrochemical nanomachining (ECNM) plays an irreplaceable role in advanced manufacturing, via the production of ultra-large scale integrated circuits, microelectromechanical systems, and various nanodevices. The principles of ECNM are classified as electroforming, electrolysis, electrochemical corrosion, and etching. The working modes of ECNM include direct writing and template forming. ECNM applies to not only the fabrication of three-dimensional nanostructures but also the production of super-smooth surfaces with roughness no higher than 1 nm. Both of these are crucial in modern advanced manufacturing. The key point of ECNM is the spatial confinement of electrochemical reactions. This review will focus on this point and briefly introduce the principles, methodologies, applications, and prospects of ECNM.     

Micro fabrication of microlens arrays by micro dispensing

In this study, master of the microlens arrays is fabricated using micro dispensing technology, and then electroforming technology is employed to replicate the Ni mold insert of the microlens arrays. Finally, micro hot embossing is performed to replicate the molded microlens arrays from the Ni mold insert. The resin material is used as the dispensing material, which is dropped on a glass substrate. The resin is exposed to a 380 W halogen light. It becomes convex under surface tension on the glass substrate. A master for the microlens arrays is then obtained. A 150‐nm‐thick copper layer is sputtered on the master as an electrically conducting layer. The electroforming method replicates the Ni mold insert from the master of the microlens arrays. Finally, micro hot embossing is adopted to replicate the molded microlens arrays. The micro hot embossing experiment employs optical films of polymethylmethacrylate (PMMA) and polycarbonate (PC). The processing parameters of micro hot embossing are processing temperature, embossing pressure, embossing time, and de‐molding temperature. Taguchi's method is applied to optimize the processing parameters of micro hot embossing for molded microlens arrays. An optical microscope and a surface profiler are utilized to measure the surface profile of the master, the Ni mold insert and the molded microlens arrays. AFM is employed to measure the surface roughness of the master, the Ni mold insert and the molded microlens arrays. The sag height and focal length are determined to elucidate the optical characteristics of the molded microlens arrays. Copyright © 2009 John & Sons, Ltd.     

Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate‐controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition‐state structure and bonding optimally requires the use of theoretical models. In this work, we apply density‐functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2′‐O‐transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well‐studied series of phosphate and phosphorothioate mono‐, di‐ and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non‐enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate–KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.     

Structures for controlling synthesis design and reaction modelling via knowledge acquisition

The performance of programs for computer-assisted organic synthesis (CAOS) is directly related to the knowledge base and to the procedures for deciding how the knowledge base should be used. The architecture of a knowledge base (text base, data base, rule base, model base and commonsense base) is discussed. The problem of knowledge acquisition is described with regard to pruning the productivity of CAOS systems. The commercial program 1stCLASS (for symbolic processing) is used with the SAAO (devised here for numeric processing) to form a commonsense base. For this purpose, knowledge was acquired by induction from the solutions provided by human experts to given problems. The general procedure is applied to the recognition of reaction sites which are crucial in the simulation of organic reactions.     

Rapid Chemical Reaction Monitoring by Digital Microfluidics‐NMR: Proof of Principle Towards an Automated Synthetic Discovery Platform

Microcoil nuclear magnetic resonance (NMR) has been interfaced with digital microfluidics (DMF) and is applied to monitor organic reactions in organic solvents as a proof of concept. DMF permits droplets to be moved and mixed inside the NMR spectrometer to initiate reactions while using sub‐microliter volumes of reagent, opening up the potential to follow the reactions of scarce or expensive reagents. By setting up the spectrometer shims on a reagent droplet, data acquisition can be started immediately upon droplet mixing and is only limited by the rate at which NMR data can be collected, allowing the monitoring of fast reactions. Here we report a cyclohexene carbonate hydrolysis in dimethylformamide and a Knoevenagel condensation in methanol/water. This is to our knowledge the first time rapid organic reactions in organic solvents have been monitored by high field DMF‐NMR. The study represents a key first step towards larger DMF‐NMR arrays that could in future serve as discovery platforms, where computer controlled DMF automates mixing/titration of chemical libraries and NMR is used to study the structures formed and kinetics in real time.     

Accurate thermochemistry of hydrocarbon radicals via an extended generalized bond separation reaction scheme

Detailed knowledge of hydrocarbon radical thermochemistry is critical for understanding diverse chemical phenomena, ranging from combustion processes to organic reaction mechanisms. Unfortunately, experimental thermochemical data for many radical species tend to have large errors or are lacking entirely. Here we develop procedures for deriving high-quality thermochemical data for hydrocarbon radicals by extending Wheeler et al.'s "generalized bond separation reaction" (GBSR) scheme (J. Am. Chem. Soc., 2009, 131, 2547). Moreover, we show that the existing definition of hyperhomodesmotic reactions is flawed. This is because transformation reactions, in which one molecule each from the predefined sets of products and reactants can be converted to a different product and reactant molecule, are currently allowed. This problem is corrected via a refined definition of hyperhomodesmotic reactions in which there are equal numbers of carbon-carbon bond types inclusive of carbon hybridization and number of hydrogens attached. Ab initio and density functional theory (DFT) computations using the expanded GBSRs are applied to a newly derived test set of 27 hydrocarbon radicals (HCR27). Greatly reduced errors in computed reaction enthalpies are seen for hyperhomodesmotic and other highly balanced reactions classes, which benefit from increased matching of hybridization and bonding requirements. The best performing DFT methods for hyperhomodesmotic reactions, M06-2X and B97-dDsC, give average deviations from benchmark computations of only 0.31 and 0.44 (±0.90 and ±1.56 at the 95% confidence level) kcal/mol, respectively, over the test set. By exploiting the high degree of error cancellation provided by hyperhomodesmotic reactions, accurate thermochemical data for hydrocarbon radicals (e.g., enthalpies of formation) can be computed using relatively inexpensive computational methods.     

Magnetic field-assisted electroforming of complex geometries

A new magnetic field-enhanced electroforming process for complex 3D structures was presented. The procedure was optimized for the electroforming of thick-walled nickel tools used in automotive or aerospace manufacturing. It was shown that the variation of the current density and also the use of leveling agents are not suitable for the filling of notches or for the homogeneous growth of undercuts. The problem was solved by the superposition of the electrochemical deposition process with a magnetic field. The authors developed a procedure with permanent magnets positioned in the backing of the cathode. It could be shown that the local magnetic field enhances the local metal deposition rate. This work demonstrates the homogeneous notch filling in dependence of the magnetic field strength, the position of the magnetic field sources, and the material of cathode backing. Beside the influence on the deposition rate, a superposed magnetic field also enhances the material properties of deposited metals. Investigations on grain size and hardness were performed in relation to applied magnetic field.     

Automated derivation of reaction rules for the EROS 6.0 system for reaction prediction

The purpose of the EROS 6.0 system is to predict the products of chemical reactions and to model reaction mechanisms. This is accomplished by elementary reaction steps that are selected through the rules that constitute the knowledge base of the EROS 6.0 system. These rules are derived by methods of machine learning. The learning process is based on reaction in data bases. An overview of the EROS 6.0 system is given and the structure of the knowledge as well as the generation of reaction rules are described.     

Radiochemical determination of nuclear data for theory and applications

A vast knowledge of nuclear data is available and is grouped under three headings, namely, nuclear structure, nuclear decay and nuclear reaction data. Still newer aspects are under continuous investigation. Data measurements are done using a large number of techniques, including the radiochemical method, which has been extensively worked out at Jülich. This method entails preparation of high-quality sample for irradiation, isolation of the desired radioactive product from the strong matrix activity, and preparation of thin source suitable for accurate measurement of the radioactivity. It is especially useful for fundamental studies on light complex particle emission reactions and formation of low-lying isomeric states, both of which are rather difficult to describe by nuclear model calculations. The neutron induced reaction cross section data are of practical application in fusion reactor technology, particularly for calculations on tritium breeding, gas production in structural materials and activation of reactor components. The charged particle induced reaction cross section data, on the other hand, are of significance in medicine, especially for developing new production routes of novel positron emitters and therapeutic radionuclides at a cyclotron. Both neutron and charged particle data also find application in radiation therapy. A brief overview of advances made in all those areas is given, with major emphasis on nuclear reaction cross section data.     

Study of the overall behavior of thin films of the 7,7,8,8-tetracyanoquinodimethane neutral/anion couple on glassy carbon electrodes in the presence of cesium ion

The overall electrochemistry of 7,7,8,8-tetracyanoquinodimethane thin films on glassy carbon electrodes in media containing Cs+ ions is explained in light of a layer-by-layer nucleation and growth model, and kinetic data for the processes involved are reported. Using in situ UV-vis spectroelectrochemistry allowed available mechanistic knowledge on such processes to be expanded and the presence of various intermediates in the redox reactions confirmed.     

Spatially resolved Raman spectroelectrochemistry of solid-state polythiophene/viologen memory devices

A three terminal molecular memory device was monitored with in situ Raman spectroscopy during bias-induced switching between two metastable states having different conductivity. The device structure is similar to that of a polythiophene field effect transistor, but ethylviologen perchlorate was added to provide a redox counter-reaction to accompany polythiophene redox reactions. The conductivity of the polythiophene layer was reversibly switched between high and low conductance states with a "write/erase" (W/E) bias, while a separate readout circuit monitored the polymer conductance. Raman spectroscopy revealed reversible polythiophene oxidation to its polaron form accompanied by a one-electron viologen reduction. "Write", "read", and "erase" operations were repeatable, with only minor degradation of response after 200 W/E cycles. The devices exhibited switching immediately after fabrication and did not require an "electroforming" step required in many types of memory devices. Spatially resolved Raman spectroscopy revealed polaron formation throughout the polymer layer, even away from the electrodes in the channel and drain regions, indicating that thiophene oxidation "propagates" by growth of the conducting polaron form away from the source electrode. The results definitively demonstrate concurrent redox reactions of both polythiophene and viologen in solid-state devices and correlate such reactions with device conductivity. The mechanism deduced from spectroscopic and electronic monitoring should guide significant improvements in memory performance.     

镁电沉积研究评述

Mg离子二次电池是有望用于电动汽车的“绿色”蓄电池，它比Li离子二次电池低价、较高的安全性和环境友好及可大电流、大容量放电。本文对迄今为止关于镁的电沉积及镁离子二次电池的电解质溶液的研究进行综述；并对今后的研究提出了设想。     

The Chemistry of Protein Oxidation in Food

Oxidation is one of the deterioration reactions of proteins in food, the importance of which is comparable to others such as Maillard, lipation, or protein‐phenol reactions. While research on protein oxidation has led to a precise understanding of the processes and consequences in physiological systems, knowledge about the specific effects of protein oxidation in food or the role of “oxidized” dietary protein for the human body is comparatively scarce. Food protein oxidation can occur during the whole processing axis, from primary production to intestinal digestion. The present review summarizes the current knowledge and mechanisms of food protein oxidation from a chemical, technological, and nutritional–physiological viewpoint and gives a comprehensive classification of the individual reactions. Different analytical approaches are compared, and the relationship between oxidation of food proteins and oxidative stress in vivo is critically evaluated.     

LJUNGSKILE: a program for assessing uncertainties in speciation calculations

Speciation calculations are often the base upon which further and more important conclusions are drawn, e.g., solubilities and sorption estimates used for retention of hazardous materials. Since speciation calculations are based on experimentally determined stability constants of the relevant chemical reactions, the measurement and experimental uncertainty in these constants will affect the reliability of the simulation output. The present knowledge of the thermodynamic data relevant for predicting the behaviour of a complex chemical system is quite heterogeneous. In order to predict the impact of these uncertainties on the reliability of a simulation output requires sophisticated modelling codes. In this paper, we will present a computer program, LJUNGSKILE, which utilises the thermodynamic equilibrium code PHREEQC to statistically calculate uncertainties in speciation based on uncertainties in stability constants. A short example is included.     

Single-Molecule Study of a Plasmon-Induced Reaction for a Strongly Chemisorbed Molecule

Chemical reactions induced by plasmons achieve effective solar-to-chemical energy conversion. However, the mechanism of these reactions, which generate a strong electric field, hot carriers, and heat through the excitation and decay processes, is still controversial. In addition, it is not fully understood which factor governs the mechanism. To obtain mechanistic knowledge, we investigated the plasmon-induced dissociation of a single-molecule strongly chemisorbed on a metal surface, two O₂ species chemisorbed on Ag(110) with different orientations and electronic structures, using a scanning tunneling microscope (STM) combined with light irradiation at 5 K. A combination of quantitative analysis by the STM and density functional theory calculations revealed that the hot carriers are transferred to the antibonding (π*) orbitals of O₂ strongly hybridized with the metal states and that the dominant pathway and reaction yield are determined by the electronic structures formed by the molecule–metal chemical interaction.     

Cyanocomplexes with one-dimensional structures: preparations,crystal structures and magnetic properties

The review surveys the preparation methods, crystallochemistry and magnetic properties of one-dimensional cyanocomplexes. Their preparation methods are mainly based on reactions in solutions containing suitable building blocks as precursors of the polymeric structure. The analysis of published data on crystal structures is given, as the knowledge of the crystal structure is essential for the study of magneto-structural correlation. Published data on magnetic properties are discussed along with the methods used for the study of magnetic properties.     

Solvent effects upon reactions between ions: hexacyanoferrate(II)-peroxodisulphate and sulphite-hexacyanoferate(III)

Summary Different approaches to the interpretation of solvent effects on reactions between ionic reactants are analysed, taking as a basis the kinetic data corresponding to the sulphite-hexacyanoferrate(III) and peroxodisulphate-hexacyanoferrate(III) oxidations. It is concluded that the approach based on the use of solvent parameters is the more promising, although knowledge of the transfer chemical potentials of the reactants may also be useful in the interpretation of kinetic behaviour.