Engaging undergraduate students in computational chemistry research: A tutorial for new assistant professors

In this article, we provide advice and insights, based on our own experiences, for computational chemists who are beginning new tenure-track positions at primarily undergraduate institutions. Each of us followed different routes to obtain our tenure-track positions, but we all experienced similar challenges when getting started in our new position. In this article, we discuss our approaches to seven areas that we all found important for engaging undergraduate students in our computational chemistry research, including setting up computational resources, recruiting research students, training research students, designing student projects, managing the lab, mentoring students, and student conference participation.     

Building capacity for undergraduate education and training in computational molecular science: A collaboration between the MERCURY consortium and the Molecular Sciences Software Institute

The Molecular Sciences Software Institute (MolSSI) is an National Science Foundation (NSF) funded institute that focuses on improving software, education, and training in the computational molecular sciences. Through a collaboration with the Molecular Education and Research Consortium in Undergraduate computational chemistRY (MERCURY), the MolSSI has developed resources for undergraduate and other early career students to lay an educational foundation for the next generation of computational molecular scientists. The resources focus on introducing best practices in software engineering to students from the very start to make their software more useable, maintainable, and reproducible.     

Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery

As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster, and a number of programs (e.g., Prepare, React, Select) with the aim of combining computational chemistry and medicinal chemistry expertise to facilitate drug discovery and development and more specifically to integrate synthesis into computer-aided drug design. In our quest for potent SERMs, this platform was used to build virtual combinatorial libraries, filter and extract a highly diverse library from the NCI database, and dock them to the estrogen receptor (ER), with all of these steps being fully automated by computational chemists for use by medicinal chemists. As a result, virtual screening of a diverse library seeded with active compounds followed by a search for analogs yielded an enrichment factor of 129, with 98% of the seeded active compounds recovered, while the screening of a designed virtual combinatorial library including known actives yielded an area under the receiver operating characteristic (AU-ROC) of 0.78. The lead optimization proved less successful, further demonstrating the challenge to simulate structure activity relationship studies.     

PowerMV: a software environment for molecular viewing, descriptor generation, data analysis and hit evaluation

Ideally, a team of biologists, medicinal chemists and information specialists will evaluate the hits from high throughput screening. In practice, it often falls to nonmedicinal chemists to make the initial evaluation of HTS hits. Chemical genetics and high content screening both rely on screening in cells or animals where the biological target may not be known. There is a need to place active compounds into a context to suggest potential biological mechanisms. Our idea is to build an operating environment to help the biologist make the initial evaluation of HTS data. To this end the operating environment provides viewing of compound structure files, computation of basic biologically relevant chemical properties and searching against biologically annotated chemical structure databases. The benefit is to help the nonmedicinal chemist, biologist and statistician put compounds into a potentially informative biological context. Although there are several similar public and private programs used in the pharmaceutical industry to help evaluate hits, these programs are often built for computational chemists. Our program is designed for use by biologists and statisticians.     

Integrating Molecular Modeling with Semiempirical Quantum Mechanical Calculations into the Upper-Level Inorganic Chemistry Course

The analysis of chemical bonding and reactivity from the perspective of molecular orbital theory is challenging for students at the undergraduate level. In an attempt to improve the instruction of this material in my upper-level inorganic chemistry course I developed a series of computational experiments using a molecular modeling program that can perform semiempirical quantum mechanical calculations. These exercises explore the chemistry of molecular systems through an analysis of the variation in the attractive and repulsive forces in the system as a function of structure or composition. The exercises challenge the analysis skills of the students by requiring them to consider how two or more factors contribute to the properties of the system. Examples of exercises that demonstrate different types of computational experiments are given. These sample exercises examine the structure of simple molecules, the reactivity of Lewis acids, and the bonding in transition metal complexes.     

Nuclear science education in Taiwan, 1956–1992

The nuclear science education has been established in Taiwan at the College of Nuclear Science, National Tsing Hua University since 1956, the only one among 123 universities and colleges in Taiwan where nuclear-related education is offered. The Nuclear/Radiochemistry program, with nine faculty members, offers bachelor's, master's, and doctorate degrees in Nuclear Science. Lectures and lab classes of nuclear chemistry, radiochemistry, and allied branches in health physics, nuclear instruments, nuclear engineering, nuclear medicine, radiation biology, and environmental monitoring are given to the 17 undergraduate students and 33 postgraduate students currently registered. Support from the well-developed local nuclear power industry and government agencies is converged with rapid growth rate toward the Nuclear/Radiochemistry program; the 1992 annual research contracts for the program amounted over one million US dollars. Careerplacement program for graduates is developed to orientate them into the local nuclear power utilities as well as agricultural, medical, industrial, academic, and govemmental sects where nuclear chemists and radiochemists at all levels are desperately needed.     

“双一流”建设背景下化学拔尖班学生的国际化培养模式探索与实践

四川大学化学学院于2009年开始实施"化学拔尖学生培养试验计划",致力于培养化学领域领军人才。在化学学科入选教育部"双一流"学科建设的背景下,学院立足本专业特点、依托校院两级资源,从师资、课程、学生、办学等多方面构建拔尖学生国际化培养体系,做出了诸多尝试并取得了良好的成效。本文在对现有国际化建设策略讨论的基础上,进一步对加强拔尖学生全球胜任力进行思考、提出建议。     

Computer-aided drug design platform using PyMOL

The understanding and optimization of protein-ligand interactions are instrumental to medicinal chemists investigating potential drug candidates. Over the past couple of decades, many powerful standalone tools for computer-aided drug discovery have been developed in academia providing insight into protein-ligand interactions. As programs are developed by various research groups, a consistent user-friendly graphical working environment combining computational techniques such as docking, scoring, molecular dynamics simulations, and free energy calculations is needed. Utilizing PyMOL we have developed such a graphical user interface incorporating individual academic packages designed for protein preparation (AMBER package and Reduce), molecular mechanics applications (AMBER package), and docking and scoring (AutoDock Vina and SLIDE). In addition to amassing several computational tools under one interface, the computational platform also provides a user-friendly combination of different programs. For example, utilizing a molecular dynamics (MD) simulation performed with AMBER as input for ensemble docking with AutoDock Vina. The overarching goal of this work was to provide a computational platform that facilitates medicinal chemists, many who are not experts in computational methodologies, to utilize several common computational techniques germane to drug discovery. Furthermore, our software is open source and is aimed to initiate collaborative efforts among computational researchers to combine other open source computational methods under a single, easily understandable graphical user interface.     

Solar-Driven Artificial Carbon Cycle

Constituting the artificial carbon cycle,for example,through recycling CO₂ and converting CH₄ to value-added fuels and chemicals with solar energy,offers a sustainable future for humankind to tackle the global environmental issues and energy crisis.However,significant bottlenecks remain in such photocatalytic conversion,mainly related to the reaction activity and product selectivity.Herein,we share our efforts and systematic research progress on addressing the double bottlenecks for achieving solar-driven artificial carbon cycle,with specifically focusing on the photocatalytic CO₂ and CH₄ conversion.We further elucidate the common fundamentals behind various designed photocatalytic materials systems.Toward future development,we highlight the opportunities and challenges in the research field.     

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.     

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。     

Quality information from the grapevine

A letter by Lucien Herr, a highly regarded leading French intellectual at the time of World War I, provides capsule portraits of chemists such as Gabriel Bertrand, Paul Lebeau, Charles Moureu, and Georges Urbain. It makes us better aware of who they were and of how their contemporaries saw their work, which had much to do with their personalities, whether congenial or abrasive. This article is concerned with the kind of information carried by the so-called grapevine. It can be invaluable to the historian, for the light it sheds on the character of a scientist. The document drawn upon, from World War I (1915), depicts graphically the personalities of some of the French chemists engaged in the rush to design and produce chemical weapons. It is a frank and even brutal appraisal of their strengths and weaknesses. This is the kind of evaluation that scientists routinely engage in, but devoid of the hyperbole, pro or con, which usually flavours it.     

Connecting the philosophy of chemistry,green chemistry,and moral philosophy

This paper aims to connect philosophy of chemistry, green chemistry, and moral philosophy. We first characterize chemistry by underlining how chemists: (1) co-define chemical bodies, operations, and transformations; (2) always refer to active and context-sensitive bodies to explain the reactions under study; and (3) develop strategies that require and intertwine with a molecular whole, its parts, and the surroundings at the same time within an explanation. We will then point out how green chemists are transforming their current activities in order to act upon the world without jeopardizing life. This part will allow us to highlight that green chemistry follows the three aforementioned characteristics while including the world as a partner, as well as biodegradability and sustainability concerns, into chemical practices. In the third part of this paper, we will show how moral philosophy can help green chemists: (1) identify the consequentialist assumptions that ground their reasoning; and (2) widen the scope of their ethical considerations by integrating the notion of care and that of vulnerability into their arguments. In the fourth part of the paper, we will emphasize how, in return, this investigation could help philosophers querying consequentialism as soon as the consequences of chemical activities over the world are taken into account. Furthermore, we will point out how the philosophy of chemistry provides philosophers with new arguments concerning the key debate about the ‘intrinsic value’ of life, ecosystems and the Earth, in environmental ethics. To conclude, we will highlight how mesology, that is to say the study of ‘milieux’, and the concept of ‘ecumeme’ proposed by the philosopher and geographer Augustin Berque, could become important both for green chemists and moral philosophers in order to investigate our relationships with the Earth.     

Beyond mere diversity: tailoring combinatorial libraries for drug discovery

Combinatorial library design attempts to choose the best set of substituents for a combinatorial synthetic scheme to maximize the chances of finding a useful compound, such as a drug lead. Initial efforts were focused primarily on maximizing diversity, perhaps allowing some bias by the inclusion of a small, fixed set of pharmacophoric substituents. However, many factors besides diversity impact good library design for drug discovery. A library can be better "tailored" by assigning the candidate substituents to categories such as polar, pharmacophoric, rigid, low molecular weight, and expensive. Stratified sampling by successive steps of D-optimal design generates diverse designs which are also consistent with desirable profiles of these properties. Comparing the diversity scores among design profiles reveals the tradeoffs between diversity, physical property distributions, synthetic difficulty, expense, and pharmacophoric bias. The diversity scores can be calibrated by scoring the best designs from subsets of the candidates made either from specific classes of substituents or by randomly eliminating candidates. This procedure shows how poor random designs are compared even to highly biased optimal designs. Library design requires a synergistic effort between computational and synthetic medicinal chemists, so specialized interactive software has been developed to integrate substructure searching, display, and statistical experimental design to facilitate this interaction for the effective design of well-tailored libraries.     

Education and training in Analytical Chemistry

Analytical Chemistry is involved in the undergraduate curriculum in the US in many ways. It is one of four required subjects for accreditation of a college or university by the American Chemical Society. However there is much discussion underway in the US about change in the undergraduate training of analytical chemists to more closely reflect the “problem solving” nature of Analytical Chemistry, and to better address the needs of industry. It is suggested that the curriculum should emphasize the fundamentals but also teach applied Analytical Chemistry, the need for teamwork, and the importance of communication skills.     

Fast semiempirical calculations

Most quantum chemists regard semiempirical methods as ephemeral and computationally cost efficient. For this reason, an article dealing with computational efficiency of semiempirical methods is probably very unfashionable. However, experience at a big computer installation, shared by ab-initio and semiempirical quantum chemists shows that the second group actually consumes more computer time than the first. Obviously, the greater size of the molecules in semiempirical calculations outweighs the inherent efficiency of these methods. The present article describes a simple method for accelerating SCF -type semiempirical methods.     

Quality Information from the Grapevine

Abstract

A letter by Lucien Herr, a highly regarded leading French intellectual at the time of World War I, provides capsule portraits of chemists such as Gabriel Bertrand, Paul Lebeau, Charles Moureu, and Georges Urbain. It makes us better aware of who they were and of how their contemporaries saw their work, which had much to do with their personalities, whether congenial or abrasive. This article is concerned with the kind of information carried by the so-called grapevine. It can be invaluable to the historian, for the light it sheds on the character of a scientist. The document drawn upon, from World War I (1915), depicts graphically the personalities of some of the French chemists engaged in the rush to design and produce chemical weapons. It is a frank and even brutal appraisal of their strengths and weaknesses. This is the kind of evaluation that scientists routinely engage in, but devoid of the hyperbole, pro or con, which usually flavours it.     

Who’s Minding the Store?—Or How a Team of Undergraduate Teaching Interns Rejuvenated an ACS Certified Program

Improvements resulted at all levels in an ACS-certified chemistry program when a team of undergraduate teaching interns began consulting in the laboratories. The author describes the problems and teaching philosophies that led to the institution of the Chemistry Instruction Internship Program, the goals of the program with some preliminary assessments, and how to recruit outstanding undergraduate teaching interns.     

World War I, international participation and reorganisation of the Japanese chemical community

What kind of "war" did Japanese chemists fight during World War I, and what impact did their experiences have on Japanese chemistry in its aftermath? By focusing on the role of Jōji Sakurai (1858-1939), this paper attempts to answer these questions by looking at the drastic changes in the international relationships of the Japanese chemical community caused by the war. It examines how the Japanese National Research Council was established in 1920 as part of the International Research Council, a product of the reconfiguration of international scientific powers triggered by World War I. This paper argues that Sakurai advocated the establishment of the National Research Council after the American model of wartime mobilisation of science, coordinated fractured Japanese chemical communities for international functions, and facilitated Japan's participation and increased influence in international scientific associations such as the International Union of Pure and Applied Chemistry, established in 1919.