发酵过程与双极膜电渗析的集成操作——介绍一个分离与反应技术一体化的化学工程实验

介绍一个分离与反应技术一体化的化学工程实验,实验中需进行发酵过程与双极膜电渗析过程的集成操作,可使学生在了解分离与反应技术一体化基本理论的基础上,改变传统的化学工程反应观念,激发对新型化学工程学科的学习兴趣。     

Automatic identification of model reductions for discrete stochastic simulation

Multiple time scales in cellular chemical reaction systems present a challenge for the efficiency of stochastic simulation. Numerous model reductions have been proposed to accelerate the simulation of chemically reacting systems by exploiting time scale separation. However, these are often identified and deployed manually, requiring expert knowledge. This is time-consuming, prone to error, and opportunities for model reduction may be missed, particularly for large models. We propose an automatic model analysis algorithm using an adaptively weighted Petri net to dynamically identify opportunities for model reductions for both the stochastic simulation algorithm and tau-leaping simulation, with no requirement of expert knowledge input. Results are presented to demonstrate the utility and effectiveness of this approach.     

利用减秩因子分析法同时优化确定化学反应级数和速率常数

通过对反应过程中在线测得的动力学谱-光谱二维数据矩阵进行主成分分析，可确定化学反应过程存在的组分数。提出用优化动力学参数-减秩因子分析法解析二维数据矩阵，对未知动力学模型的复杂反应可同时优化求解第一步反应的级数和速率常数。模拟二维数据验证了该方法的可行性。该方法用于高锰酸钾氧化溴化钠的反应过程中测得的二维数据的解析，结果表明：高锰酸钾的还原过程符合0级反应模型。     

The simulation of molecular weight distributions in polyreaction kinetics by discrete Galerkin methods

This article describes the development of a comprehensive solver for the differential equations arising from the modeling of molecular weight distributions in polyreactions. Based on a series of numerical developments, the software package PREDICI combines new directions in mathematics, chemical computing and implementation. The algorithm is based on a so-called discrete Galerkin h-p-method, which allows the efficient treatment of numerous polymerization reaction types. The abilities of the new concept are demonstrated on challenging examples.     

一种判断电化学/化学反应体系热力学自洽性的新方法

介绍了一种判断电化学/化学反应体系热力学自洽性的新方法-“秩法”。结合 实际例子描述了该方法的原理、计算步骤。该方法充分利用矩阵“秩”的概念,由 反应系数矩阵的“秩”直接判断出其中的独立组分数,并且仅当寻找到依赖反应时 才需对有关方程进行求解。因此,“秩法”概念上清晰、直观,且由于可以直接调 用矩阵变换的子程序,程序实现也极为容易。该方法对于电化学、化学及化工反应 过程的模拟将非常有意义。     

烟花中绽放北京奥运理念——绿色化学诠释新北京新奥运

介绍了中国烟花发生和发展的历史梗概,以及烟花中的化学知识和化学反应原理,阐述了北京奥运会和残奥会上烟花所体现出来的“科技奥运”、“绿色奥运”和“人文奥运”,诠释并展现了绿色化学的新视野。     

An automated method for graph-based chemical space exploration and transition state finding

Algorithms that automatically explore the chemical space have been limited to chemical systems with a low number of atoms due to expensive involved quantum calculations and the large amount of possible reaction pathways. The method described here presents a novel solution to the problem of chemical exploration by generating reaction networks with heuristics based on chemical theory. First, a second version of the reaction network is determined through molecular graph transformations acting upon functional groups of the reacting. Only transformations that break two chemical bonds and form two new ones are considered, leading to a significant performance enhancement compared to previously presented algorithm. Second, energy barriers for this reaction network are estimated through quantum chemical calculations by a growing string method, which can also identify non-octet species missed during the previous step and further define the reaction network. The proposed algorithm has been successfully applied to five different chemical reactions, in all cases identifying the most important reaction pathways.     

Gold-catalyzed direct amination of arenes with azodicarboxylates

Gold(III) chloride catalyzed direct amination of arenes with azodicarboxylates was developed. The new catalytic system was active to a broad range of substrates, and the reaction was carried out under mild conditions. It represents the first catalytic system for the direct amination of electron-deficient arenes with azodicarboxylates to the best of our knowledge. This reaction provides an important approach for the synthesis of heterocyclic compounds in pharmaceutical and chemical industries.     

Chemical process optimization by computer — a self-directed chemical synthesis system

A closed-loop automated chemical synthesis system has been designed for the purpose of optimizing chemical reaction parameters. This system uses a time-sharing computer with the simplex algorithm for optimization programmed in extended BASIC language. Strings of ASCII characters from the computer are trapped by terminal hardware at the reaction and analysis sites and are used to control all phases of the system.     

Algorithm to infer the structures of molecular formulas within a reaction pathway

MECHEM is a computer aid for elucidation of reaction pathways that was developed over the last 5 years. The program searches systematically and comprehensively for the simplest multistep reaction pathways (or mechanisms) that are consistent with the experimental constraints formulated by the experimentalist, any ad hoc assumptions, and the program's internal theory. Previous articles have reported the basic pathway-generation algorithm and another algorithm that tests the structural soundness of individual steps. This article introduces an algorithm to solve another basic problem: Given a multistep pathway containing a mixture of molecular structures and formulas, assign possible structures to the formulas while obeying (and exploiting) the constraint imposed by the pathway steps. With this new algorithm, MECHEM is now approaching competence as an interactive tool for elucidating some catalytic reaction pathways, which is the current chemical focus. © 1994 by John Wiley & Sons, Inc.     

含芴共轭高分子的合成、表征及性能研究——推荐一个高分子化学综合实验

推荐了一个高分子化学综合实验——含芴共轭高分子的合成、表征及性能研究。实验内容包括利用Sonogashira偶联反应合成共轭高分子,采用核磁共振和红外光谱等检测手段对其结构进行表征,并利用紫外-可见光谱、荧光和热重分析对其性能进行研究。本实验结合了高分子化学和聚合物仪器分析与表征的知识点,建议纳入高分子专业高年级综合实验课程。     

Algorithm for error-compensated kinetic determinations without prior knowledge of reaction order or rate constant

The development and evaluation of a new algorithm for error-compensating predictive kinetic determinations are described. With the new algorithm it is possible to fit kinetic data without prior knowledge of the rate constant, reaction order or initial and final values of the detector signal. A curve-fitting method is used to obtain values of these parameters that give the best fit of the model to the data. Although intended to be used primarily to compute signal changes between t=0 and ∞, the method can also be used to determine reaction orders. Although the algorithm fails for reaction orders of zero and unity, it works well for orders between these values and orders greater than unity. Simulated data are used to evaluate the effects of reaction order, signal noise and data range on computed values of signal change and, to a lesser extent, reaction order.     

Toward De Novo Catalyst Discovery: Fast Identification of New Catalyst Candidates for Alcohol-Mediated Morita–Baylis–Hillman Reactions**

Recently we have demonstrated how a genetic algorithm (GA) starting from random tertiary amines can be used to discover a new and efficient catalyst for the alcohol-mediated Morita–Baylis–Hillman (MBH) reaction. In particular, the discovered catalyst was shown experimentally to be eight times more active than DABCO, commonly used to catalyze the MBH reaction. This represents a breakthrough in using generative models for catalyst optimization. However, the GA procedure, and hence discovery, relied on two important pieces of information; 1) the knowledge that tertiary amines catalyze the reaction and 2) the mechanism and reaction profile for the catalyzed reaction, in particular the transition state structure of the rate-determining step. Thus, truly de novo catalyst discovery must include these steps. Here we present such a method for discovering catalyst candidates for a specific reaction while simultaneously proposing a mechanism for the catalyzed reaction. We show that tertiary amines and phosphines are potential catalysts for the MBH reaction by screening 11 molecular templates representing common functional groups. The method relies on an automated reaction discovery workflow using meta-dynamics calculations. Combining this method for catalyst candidate discovery with our GA-based catalyst optimization method results in an algorithm for truly de novo catalyst discovery.     

The use of quantum molecular calculations to guide a genetic algorithm: a way to search for new chemistry

The process of gene-based molecular evolution has been simulated in silico by using massively parallel density functional theory quantum calculations, coupled with a genetic algorithm, to test for fitness with respect to a target chemical reaction in populations of genetically encoded molecules. The goal of this study was the identification of transition-metal complexes capable of mediating a known reaction, namely the cleavage of N(2) to give the metal nitride. Each complex within the search space was uniquely specified by a nanogene consisting of an eight-digit number. Propagation of an individual nanogene into successive generations was determined by the fitness of its phenotypic molecule to perform the target reaction and new generations were created by recombination and mutation of surviving nanogenes. In its simplest implementation, the quantum-directed genetic algorithm (QDGA) quickly located a local minimum on the evolutionary fitness hypersurface, but proved incapable of progressing towards the global minimum. A strategy for progressing beyond local minima consistent with the Darwinian paradigm by the use of environmental variations coupled with mass extinctions was therefore developed. This allowed for the identification of nitriding complexes that are very closely related to known examples from the chemical literature. Examples of mutations that appear to be beneficial at the genetic level but prove to be harmful at the phenotypic level are described. As well as revealing fundamental aspects of molecular evolution, QDGA appears to be a powerful tool for the identification of lead compounds capable of carrying out a target chemical reaction.     

An improved chemical reaction optimization algorithm for solving the shortest common supersequence problem

The shortest common supersequence (SCS) problem is a classical NP-hard problem, which is normally solved by heuristic algorithms. One important heuristic that is inspired by the process of chemical reactions in nature is the chemical reaction optimization (CRO) and its algorithm known as CRO_SCS. In this paper we propose a novel CRO algorithm, dubbed IMCRO, to solve the SCS problem efficiently. Two new operators are introduced in two of the four reactions of the CRO: a new circular shift operator is added to the decomposition reaction, and a new two-step crossover operator is included in the inter-molecular ineffective collision reaction. Experimental results show that IMCRO achieves better performance on random and real sequences than well-known heuristic algorithms such as the ant colony optimization, deposition and reduction, enhanced beam search, and CRO_SCS. Additionally, it outperforms its baseline CRO_SCS for DNA instances, averaging a SCS length reduction of 1.02, with a maximum length reduction of up to 2.1.     

利用目标试验因子分析法确定化学反应的级数及速率常数

利用目标试验因子分析(TTFA)结合数值遗传算法(NGA).解析反应过程中在线测得的动力学谱-光谱数据矩阵,可在未知各组分纯光谱及动力学模型情况下同时求解出各组分的纯光谱、反应级数及速率常数。提出用近似计算法计算各组分的动力学谱,使该方法能适用于任意反应级数的体系。针对两步连续反应模型,对反应物、中间体和最终产物均有吸收及某一种组分没有吸收的体系的模拟实验数据矩阵进行了处理,表明该方法均能适用。利用该方法对邻苯二甲酸二甲酯在碱性介质中的水解反应及日落黄水溶液的电解降解反应过程中测得的数据矩阵进行解析,均获得了可靠结果。     

Measuring splitting and overlapping in molecular systems. A fuzzy set estimation of reaction hazards

An algorithm for assessments of fuzzy molecular structural characteristics has been presented, and its chemical relevance is approved for numerous evidences of reaction mechanisms. Empirical rules pervading the results of chemical synthesis are continuously the source of information efficiently used by experimental chemists and technologists. Approaching them theoretically to broaden areas of applicability and to make them more precise for better prediction is of great importance to reach progress in the chemical information recognition and to steer and control technological processes. Fuzzy sets called splitting and overlapping have been applied for assessments of the reaction hazards. The mathematically grounded properties turned out to underlie well-known empirical rules for preliminary estimations of organic reaction tendencies. Informative quantitative data shown are revealing new ways of understanding basic chemical reaction mechanisms.     

Carbon Dioxide as a Raw Material: The Synthesis of Formic Acid and Its Derivatives from CO2

The use of carbon dioxide as a raw material for chemical syntheses is an ecologically and economically valuable extension to the carbon sources used at the present time. In order to convert the thermodynamically stable and comparatively unreactive CO₂ molecule into the desired product in an efficient manner, suitable reaction conditions and activation mechanisms must be found. The catalytic reduction of CO₂ to formic acid and its derivatives has been intensively studied in recent years. A number of new approaches to the synthesis of formic acid from CO₂ have reached such a state of knowledge that continuing development may well lead to industrial-scale operation in the near future. This can to a large extent be attributed to the fruitful interaction between investigative work into reaction mechanisms and the development of new catalytic systems.     

Understanding the physics and chemistry of reaction mechanisms from atomic contributions: a reaction force perspective

Studying chemical reactions involves the knowledge of the reaction mechanism. Despite activation barriers describing the kinetics or reaction energies reflecting thermodynamic aspects, identifying the underlying physics and chemistry along the reaction path contributes essentially to the overall understanding of reaction mechanisms, especially for catalysis. In the past years the reaction force has evolved as a valuable tool to discern between structural changes and electrons' rearrangement in chemical reactions. It provides a framework to analyze chemical reactions and additionally a rational partition of activation and reaction energies. Here, we propose to separate these energies further in atomic contributions, which will shed new insights in the underlying reaction mechanism. As first case studies we analyze two intramolecular proton transfer reactions. Despite the atom based separation of activation barriers and reaction energies, we also assign the participation of each atom in structural changes or electrons' rearrangement along the intrinsic reaction coordinate. These participations allow us to identify the role of each atom in the two reactions and therfore the underlying chemistry. The knowledge of the reaction chemistry immediately leads us to suggest replacements with other atom types that would facilitate certain processes in the reaction. The characterization of the contribution of each atom to the reaction energetics, additionally, identifies the reactive center of a molecular system that unites the main atoms contributing to the potential energy change along the reaction path.