Guidelines for publication of research results from force-field calculations

For the publication of research results, the chemical sciences community has had a long history of requiring authors to provide sufficient data so that their research results and procedures can be (1) understood, (2) critically evaluated, and (3) replicated by other competent scientists. The emergence of computational chemistry as a distinct area of research presents new challenges in defining criteria to meet these obligations. While much of the long-standing paradigm for experimental chemistry can be directly transferred to computational chemistry, some differences are apparent. A computational study does not give a product for which one can measure physical properties, nor are percent yields and recoveries available to demonstrate experimental success. Nonetheless, it is imperative that computational results be able to withstand the same scientific scrutiny as experimental ones. Like all fields of scientific endeavor, computational chemistry is also a dynamic science. The continuous and dramatic improvements in computational algorithms and increases in computing power over the last decade have made possible the study of chemical problems for which solutions by computational means previously were unattainable. Moreover, advances in computer technology have also changed the way these computational studies are carried out. For any new study, the traditional search for the nearest energy minimum may no longer be adequate, fewer assumptions and approximations may be acceptable, and even the nature of the data to be stored and reported may have evolved. For example, many computer algorithms have become sufficiently fast and convenient that it is more efficient to repeat some part of the overall calculation than to save and record the corresponding data that it generates. This document has been developed to provide guidance to chemists who employ computations of molecular structure, properties, reactivity, and dynamics as either a part or as the main thrust of a research report. It is derived in part from earlier work carried out by the Provisional Section Committee on Medicinal Chemistry of IUPAC (Gund, P.; Barry, D. C.; Blaney, J. M.; Cohen, C. N. J. Med. Chem., 1988, 31 , 2230–2234). ©1998 IUPAC     

Parallelism in computational chemistry

Summary An account is given of experience gained in implementing computational chemistry application software, including quantum chemistry and macromolecular refinement codes, on distributed memory parallel processors. In quantum chemistry we consider the coarse-grained implementation of Gaussian integral and derivative integral evaluation, the direct-SCF computation of an uncorrelated wavefunction, the 4-index transformation of two-electron integrals and the direct-CI calculation of correlated wavefunctions. In the refinement of macromolecular conformations, we describe domain decomposition techniques used in implementing general purpose molecular mechanics, molecular dynamics and free energy perturbation calculations. Attention is focused on performance figures obtained on the Intel iPSC/2 and iPSC/860 hypercubes, which are compared with those obtained on a Cray Y-MP/464 and Convex C-220 minisupercomputer. From this data we deduce the cost effectiveness of parallel processors in the field of computational chemistry.     

在分析化学实验中渗透马克思主义哲学思想的探讨

分析化学实验中蕴含着丰富的马克思主义哲学思想,如对立统一规律、质量互变规律等。如果教师注重从辩证唯物主义的视角来分析问题,并将哲学观点渗透、融入到日常教学中去,不仅有利于学生掌握科学知识,训练科学思维,更有利于学生形成马克思主义哲学观,提高综合素质。笔者结合自己的教学经验,对分析化学实验教学中马克思主义哲学原理的应用进行简要阐述。     

Combinatorial invariants and covariants as tools for conical intersections

The combinatorial invariant and covariant are introduced as practical tools for analysis of conical intersections in molecules. The combinatorial invariant is a quantity depending on adiabatic electronic states taken at discrete nuclear configuration points. It is invariant to the phase choice (gauge) of these states. In the limit that the points trace a loop in nuclear configuration space, the value of the invariant approaches the corresponding Berry phase factor. The Berry phase indicates the presence of an odd or even number of conical intersections on surfaces bounded by these loops. Based on the combinatorial invariant, we develop a computationally simple and efficient method for locating conical intersections. The method is robust due to its use of gauge invariant nature. It does not rely on the landscape of intersecting potential energy surfaces nor does it require the computation of nonadiabatic couplings. We generalize the concept to open paths and combinatorial covariants for higher dimensions obtaining a technique for the construction of the gauge-covariant adiabatic-diabatic transformation matrix. This too does not make use of nonadiabatic couplings. The importance of using gauge-covariant expressions is underlined throughout. These techniques can be readily implemented by standard quantum chemistry codes.     

Unser tägliches Brot. Zum Erntedank

Bread is regarded as an ultimate “bioproduct without any chemistry.” This is simply not true because chemistry is the basis for the entire bread-manufacturing process from the grain right up to the freshly baked loaf. Its chemical reactions are very complex and we only have a rough idea of what's really going on when kneading the dough and baking the bread. Therefore, attempts of chemists with laboratory but not cuisine experience to produce bread according to scientific principles may lead to more or less edible and digestible products but they cannot compete with the masterpieces of a trained and experienced baker. But that's how it is. Chemistry is necessary for a culinary wonder but sometimes though it is better to let craftspeople with professional experience create the chemical masterpieces and then lean back and simply enjoy things!     

Odorless Chemistry: A Gentle Reductionist Companion to Experiment

Computational quantum chemistry has advanced over the past two decades to the point of recognition as a valuable co-laborer with experiment. Several examples demonstrate this point. For each of the next 40 years, we predict that an additional 1% of chemical research will shift from experiment to computation. Thus by the year 2036 we foresee a picture of chemical research in which 50% of the effort is computational in nature.     

原位变温X射线衍射虚拟仿真实验建设与实践

原位变温X射线衍射实验是物理、化学等相关专业综合和创新性实验项目,基于“以虚代实,虚实结合”的思想开发原位变温X射线衍射虚拟仿真实验系统非常必要。本系统完整地模拟了仪器认知、样品测试、数据计算及应用等实验实景,教学中采用线上线下虚实结合的教学方法,培养学生利用大型仪器解决复杂问题的综合能力和高级思维。     

供给侧改革视角下高职院校生活化学实验的设计与教学实践*

在供给侧改革背景下,结合高职院校教学实际,分析了生活化学实验课程在实验设计、教学内容、教学方法等方面存在的问题。从精心设计的实验项目、基于实验展示的教学方法和凸显学生专业特色的考核方式等3个方面进行实践,体现了课程的科学性、实用性、趣味性和可操作性,有助于提升高职院校学生的科学素养。     

The evolution of chemometrics

Chemometrics is the application of statistical and mathematical methods to chemical problems to permit maximal collection and extraction of useful information. The development of advanced chemical instruments and processes has led to a need for advanced methods to design experiments, calibrate instruments, and analyze the resulting data. For many years, there was the prevailing view that if one needed fancy data analyses, then the experiment was not planned correctly, but now it is recognized that most systems are multivariate in nature and univariate approaches are unlikely to result in optimum solutions. At the same time, instruments have evolved in complexity, computational capability has similarly advanced so that it has been possible to develop and employ increasing complex and computationally intensive methods. In this paper, the development of chemometrics as a subfield of chemistry and particularly analytical chemistry will be presented with a view of the current state-of-the-art and the prospects for the future will be presented.     

科教融合式本科实验教学初探：4CzIPN的制备、表征及催化性能探究

可见光催化作为当前国际学术研究前沿热点,吸引了化学工作者的广泛关注,而在本科生有机化学教学实验中鲜有涉及。本实验将通过模块设计,将有机光催化剂4CzIPN的制备与表征、光电性能研究及光其催化反应性能研究融入到本科实验教学之中,是对现有碎片化实验课的升级尝试与创新,属于典型的科教融合的教学案例,实验过程中涉及多种实验技能以及仪器分析手段,对于学生系统性熟悉科研流程、理解化学反应过程、提升综合科研素养以及培养创新实验探究能力具有重要意义。     

Fast pH calculations in aqueous solution chemistry

A technique for computation of the neutralization curves of acid-base solutions, based on an optimization search method, has been developed. The criterion function is the absolute value of the calculated difference between the numbers of positive and negative charges present in the solutions. This technique is generally applicable for solution chemistry, but because of its speed of resolution and its accuracy, it is particularly useful in the control of a real-time process by a computer.     

The Big Freeze: Water and the Scientific Process

In recent years there has been increasing movement toward laboratory exercises that are inquiry-based, requiring students to assume more active roles in the learning process. A laboratory experiment was developed in this light, framed around a simple question, “Which freezes faster, hot water or cold water?” The experiment was used at the beginning of the general chemistry year-long course sequence and served as an introduction to the scientific process. Students were each asked to develop a hypothesis and then design a simple experiment to determine which freezes faster, hot water or cold water, using small cold baths to freeze the water. A strength of this experiment is that students not only design and perform the experiments, but at the end they evaluate each other’s methods.     

TUNNEX: An easy-to-use wentzel-kramers-brillouin (WKB) implementation to compute tunneling half-lives

Tunneling in experiments (TUNNEX) is a free open-source program with an easy-to-use graphical user interface to simplify the process of Wentzel-Kramers-Brillouin (WKB) computations. TUNNEX aims at experimental chemists with basic knowledge of computational chemistry, and it offers the computation of tunneling half-lives, visualization of data, and exporting of graphs. It also provides a helper tool for executing the zero-point vibrational energy correction along the path. The program also enables computing high-level single points along the intrinsic reaction path. TUNNEX is available at https://github.com/prs-group/TUNNEX . As the WKB approximation usually overestimates tunneling half-lives, it can be used to screen tunneling processes before proceeding with elaborate kinetic experiments or higher-level tunneling computations such as instanton theory and small curvature tunneling approaches. © 2018 Wiley Periodicals, Inc.     

The need for scientific software engineering in the pharmaceutical industry

Scientific software engineering is a distinct discipline from both computational chemistry project support and research informatics. A scientific software engineer not only has a deep understanding of the science of drug discovery but also the desire, skills and time to apply good software engineering practices. A good team of scientific software engineers can create a software foundation that is maintainable, validated and robust. If done correctly, this foundation enable the organization to investigate new and novel computational ideas with a very high level of efficiency.     

草酸亚铁制备及组分测定综合实验之更新探索

在实验教学中,增加综合性实验内容,开设研究性、探索性和创新性综合实验是化学专业人才培养的重要组成部分。改革更新"草酸亚铁制备及组成测定"的实验方法,并以此创新综合实验为例,引导学生综合运用所学理论知识设计并优选实验方案。通过综合实验的训练,加深学生对实验及科研方法的理解,提高其实验技能及合作交流的能力。     

主族元素AB4型含氧酸根的成键分析——推荐一个研究型计算化学实验

介绍了一个面向高年级本科生的研究型计算化学实验。主族元素AB4型含氧酸根是无机和结构化学理论课程中讨论化学键类型的例子,然而其结果却存在争议。本实验利用常用量子化学软件,通过计算化学方法分析化学成键,验证猜测,并得出结论。旨在通过本实验,锻炼学生对量子化学计算方法的运用,进而加深对化学基础知识的理解。     

无机及分析化学实验课程中学生创新能力培养探索

无机及分析化学实验课程是化学本科生的必修实验课,在本科生科研能力和创新能力培养中有着极其重要的作用。通过对课程内容、教学形式和开放模式进行改革探索,除加强基本操作和基本技能训练外,通过综合性基础实验和开放实验模式,启迪学生的创新思维,激发学生的创新激情,培养学生的科学素养和探索精神。