GPU引发的计算化学革命

综述了图形处理器(GPU)在计算化学中的应用和进展.首先简单介绍了GPU在科学计算中应用的发展,然后分别详细讲述了迄今几个使用GPU和CUDA(compute unified device architecture,显卡厂商Nvidia推出的计算平台)开发工具设计的量子化学计算和分子动力学(MD)模拟的算法和程序,尤其对目前唯一完全使用GPU技术开发的量子化学计算软件TeraChem做了完备的介绍,包括算法、实现的细节和程序目前的功能.此外,本文还对GPU在计算化学上将会发挥的作用做出了极为乐观的展望.     

The Mechanism of Flex-Activation in Mechanophores Revealed By Quantum Chemistry

Flex-activated mechanophores can be used for small-molecule release in polymers under tension by rupture of covalent bonds that are orthogonal to the polymer main chain. Using static and dynamic quantum chemical methods, we here juxtapose three different mechanical deformation modes in flex-activated mechanophores (end-to-end stretching, direct pulling of the scissile bonds, bond angle bendings) with the aim of proposing ways to optimize the efficiency of flex-activation in experiments. It is found that end-to-end stretching, which is a traditional approach to activate mechanophores in polymers, does not trigger flex-activation, whereas direct pulling of the scissile bonds or displacement of adjacent bond angles are efficient methods to achieve this goal. Based on the structural, energetic and electronic effects responsible for these observations, we propose ways of weakening the scissile bonds experimentally to increase the efficiency of flex-activation.     

计算化学辅助无机化学课堂教学模式的探索

根据无机化学教学的特点,针对目前无机化学课堂教学的问题,研究了以计算化学为辅助教学,促进无机化学课堂教学的方法。该创新模式的实施,不仅有利于学生理解无机化学知识难点,发挥主观能动性,也普及了计算化学的实践应用,为高校化学大数据平台的建立提供了契机。     

计算化学数据与图形在普通化学教学中的运用

In view of the fact that there are no physical chemistry and structural chemistry courses in most of the non-chemistry department, the knowledge of computational chemistry of the college students is very limited. It is beneficial to quote some simulation research contents of computational chemistry properly in general chemistry teaching process. This will broaden students' vision, promote students' enthusiasm for learning, update the content of general chemistry teaching, cultivate the thinking ability, and finally improve the quality of teaching.     

Trialkoxysilane Exchange: Scope,Mechanism, Cryptates and pH-Response

The dynamic covalent chemistry (DCvC) of the Si−O bond holds unique opportunities, but has rarely been employed to assemble discrete molecular architectures. This may be due to the harsh conditions required to initiate exchange reactions at silicon in aprotic solvents. Herein, we provide a comprehensive experimental and computational account on the reaction of trialkoxysilanes with alcohols and identify mild conditions for rapid exchange in aprotic solvents. Substituent, solvent and salt effects are uncovered, understood and exploited for the construction of sila-orthoester cryptates. A sharp, divergent pH-response of the obtained cages renders this substance class attractive for future applications well beyond host-guest chemistry, for instance, in drug delivery.     

计算化学实验的课程建设

With the fast development of theoretical chemistry methodologies and computer hardware and software technologies, computational chemistry has become more and more imperative in chemical science. Accordingly, we have initiated "Computational Chemistry Experiments" course based on "Introductory Computational Chemistry" course developed in the Department of Chemistry, Tsinghua University since 2013, to provide basic training and computational chemistry practices for undergraduate students. The popular quantum chemistry software Gaussian is used as the major tool in the course. We focus on the exploratory feature of computational chemistry, creating initial structures and optimizing geometries, to provide fundamental training for students to comprehend the difference of traditional experimental chemistry and modern computational chemistry. Systematic research training is offered to develop the creative thinking capacity of students in using computational chemistry methods in chemistry education and research.     

Acknowledging User Requirements for Accuracy in Computational Chemistry Benchmarks

Computational chemistry has become an important complement to experimental measurements. In order to choose among the multitude of the existing approximations, it is common to use benchmark data sets, and to issue recommendations based on numbers such as mean absolute errors. We argue, using as an example bandgaps calculated with density functional approximations, that a more careful study of the benchmark data is needed, stressing that the user's requirements play a role in the choice of an appropriate method. We also appeal to those who measure data capable of being used as a reference, to publish error estimates. We show how the latter can affect the judgment of approximations used in computational chemistry.     

在有机化学实验中设置计算化学模块

The development of computer technology has promoted the application of computational chemistry teaching in undergraduate Laboratory. We have introduced computation module into our "organic chemistry laboratory", which, as one of the core courses, is set up for fresh undergraduate students. The calculation is carried out by Gaussian and Gauss View, and the results are used in understanding the experimental phenomena. Canvas teaching platform was applied to organize the materials, including videos, handouts, quiz, homework and discussion, and a flipping teaching type was adopted to improve the study efficiency. A course survey showed that the combination of the computation with lab work are very welcome by the students and obtained a satisfactory result.     

用竞赛方式促进计算化学课程教学

结合举办"魅力计算·演绎分子"南开大学化学学院计算化学知识技能大赛的教学实践,从竞赛目标、竞赛流程、评分标准、培训内容、考核方式和实施效果等几个方面,阐述了采用竞赛方式丰富计算化学教学内容的一些经验和方法,积累了计算化学课程教学改革的经验。     

化学:人类生存和发展的基础——以诺贝尔化学奖为线索

截止2020年诺贝尔化学奖共颁发了112次,其见证了化学学科的发展历程、化学学科与人类生活密不可分的联系,以及化学学科发展的最前沿。以诺贝尔化学奖为主线,联系诺贝尔化学奖趣闻,讲解化学学科将是人类生存的基础,乃至对人类社会和生存发展做出的重要贡献,可以使大家认识到化学学科的重要性,并且更加了解如何进行化学研究,促进化学学科的长足发展。     

计算化学在分子轨道教学中的应用

分子轨道理论是理解分子电子结构与微观性质的重要理论之一,也是本科生与研究生结构化学教学中的重点与难点。学生对原子轨道组合形成分子轨道、分子轨道能级交叉混合等知识的理解缺乏形象直观、定量的认识。本文通过基于量子化学或密度泛函理论的Gaussian 03计算软件,计算、绘制并分析了F_2、O_2、N_2、HF、CO等的分子轨道能级图,将学生较难理解的内容定量、直观地呈现出来,形象地解释了分子轨道成键原则与电子填充原则等分子轨道理论中的重难点,加深了学生对分子轨道理论的理解,特别是sp轨道混杂导致的σ_(2p_z)与π_(2p)轨道能级交叉这一难点,激发了学生学习的主动性和积极性,提高了教学质量。在此基础上,利用分子轨道理论分析了CO_2的电子结构,使学生学会应用分子轨道理论解决实际问题,巩固了相关课堂理论知识。     

A Dicyanomethyl Radical Conjugated with a Pyridylamino Group: Combining Radical-based Dynamic Covalent Chemistry and Coordination Chemistry

In this work, we aimed to develop a dicyanomethyl radical that undergoes both reversible C−C bond formation/dissociation and metal-ligand coordination reactions to combine dynamic covalent chemistry (DCC) based on organic radicals with coordination chemistry. We have previously reported a dicyanomethyl radical conjugated with a triphenylamine ( 1 ⋅) that exhibits a monomer/dimer equilibrium between the σ-bonded dimer ( 1₂ ). We designed and synthesized a novel dicyanomethyl radical with a pyridyl group as a coordination point ( 2 ⋅) by replacing the phenyl group of 1 ⋅ with a 3-pyridyl group. We showed that 2 ⋅ is also in an equilibrium with the σ-bonded dimer ( 2₂ ) in solution and has suitable thermodynamic parameters for application in DCC. 2₂ coordinates to PdCl₂ in a 2 : 2 ratio to selectively form a metallamacrocycle ( 2₂ )₂(PdCl₂)₂, and its structure was clarified by single crystal X-ray analysis. Variable-temperature NMR, ESR, and electronic absorption measurements revealed that ( 2₂ )₂(PdCl₂)₂ also undergoes the reversible C−C bond formation/dissociation reaction. Ligand-exchange experiment showed that 2₂ was liberated from ( 2₂ )₂(PdCl₂)₂ by the addition of another ligand with a higher affinity for Pd^II. This work demonstrated that DCC based on dicyanomethyl radicals works orthogonally to metal-ligand coordination reactions.     

文物保护领域中的化学

化学基本原理植根于各类材质文物的保护技术中,在文物保护领域有着重要的指导地位。以化学为代表的自然科学新方法与新技术,极大地丰富了文物保护的手段,为文物保护研究提供了广阔的发展空间。     

Photochemical Decarbonylation of Oxetanone and Azetidinone: Spectroscopy,Computational Models,and Synthetic Applications**

Photoexcitation of cyclic ketones leads to the expulsion of carbon monoxide and a mixture of products derived from diradical intermediates. Here we show that synthetic utility of this process is improved if strained heterocyclic ketones are used. Photochemistry of 3-oxetanone and N-Boc-3-azetidinone has not been previously described. Decarbonylation of these 4-membered rings proceeds through a step-wise Norrish type I cleavage of the C−C bond from the singlet excited state. Ylides derived from both compounds are high-energy species that are kinetically stable long enough to undergo [3+2] cycloaddition with a variety of alkenes and produce substituted tetrahydrofurans and pyrrolidines. The reaction has a sufficiently wide scope to produce scaffolds that were either previously inaccessible or difficult to synthesize, thereby providing experimental access to new chemical space.     

Photochemical Decarbonylation of Oxetanone and Azetidinone: Spectroscopy,Computational Models,and Synthetic Applications**

Photoexcitation of cyclic ketones leads to the expulsion of carbon monoxide and a mixture of products derived from diradical intermediates. Here we show that synthetic utility of this process is improved if strained heterocyclic ketones are used. Photochemistry of 3-oxetanone and N-Boc-3-azetidinone has not been previously described. Decarbonylation of these 4-membered rings proceeds through a step-wise Norrish type I cleavage of the C−C bond from the singlet excited state. Ylides derived from both compounds are high-energy species that are kinetically stable long enough to undergo [3+2] cycloaddition with a variety of alkenes and produce substituted tetrahydrofurans and pyrrolidines. The reaction has a sufficiently wide scope to produce scaffolds that were either previously inaccessible or difficult to synthesize, thereby providing experimental access to new chemical space.     

“讲一练二考三”模式建设面向实际应用的计算化学课程

将"讲一练二考三"的新型教学理念应用于大学化学的教学是一种有意义的尝试。本文结合计算化学课程的特点和本人的教学实践,从课程建设思路、教学内容、教学方式、练习方式和考试方式等几个方面阐述了采用"讲一练二考三"模式建设面向实际应用的计算化学课程的一些经验和方法,探讨了计算化学课程授课内容和教学方法的改革。