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Possibilities and Challenges of Using Educational Cheminformatics for STEM Education: A SWOT Analysis of a Molecular Visualization Engineering Project
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Journal of Chemical Education

Cite this: J. Chem. Educ. 2022, 99, 3, 1190–1200
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https://doi.org/10.1021/acs.jchemed.1c00683
Published February 3, 2022

Copyright © 2022 The Author. Published by American Chemical Society and Division of Chemical Education, Inc. This publication is licensed under

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Abstract

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This perspective paper analyses the possibilities and challenges of using cheminformatics as a context for STEM education. The objective is to produce theoretical insights through a SWOT analysis of an authentic educational cheminformatics project where future chemistry teachers engineered a physical 3D model using cheminformatics software and a 3D printer. In this article, engineering is considered as the connective STEM component binding technology (cheminformatics software and databases), science (molecular visualizations), and mathematics (graph theory) together in a pedagogically meaningful whole. The main conclusion of the analysis is that cheminformatics offers great possibilities for STEM education. It is a solution-centered research field that produces concrete artifacts such as visualizations, software, and databases. This is well-suited to STEM education, enabling an engineering-based approach that ensures students’ active and creative roles. The main challenge is a high content knowledge demand, derived from the multidisciplinary nature of cheminformatics. This challenge can be solved via training and collaborative learning environment design. Although the work with educational cheminformatics is still in its infancy, it seems a highly promising context for supporting chemistry learning via STEM education.

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Introduction

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Cheminformatics is an applied field of chemistry that blends theoretical chemistry, molecular modeling, computer sciences, and statistical methods to address chemistry-related information science questions. (1,2) Cheminformatics research requires multidisciplinary knowledge, which strongly suggests that it can offer many possibilities for STEM learning. STEM is an acronym referring to the STEM subjects: Science, Technology, Engineering, and Mathematics. STEM learning is a pedagogical approach aimed at supporting the understanding of systems and connections. (3,4) It has spread widely across the world, and many scholars suggest that it has great pedagogical potential to support learners’ interest in STEM subjects. (5,6) From the chemistry education perspective, this is important because, according to many authors, young people often do not find chemistry interesting or relevant. (7−12) This leads to major challenges, such as the small number of applicants to study the field and significant dropout rates even among those who do start their studies. (13−16)
The STEM approach has been applied in chemistry education for over a decade. Chemistry educators and researchers have been developing learning materials, pedagogical models, and contexts that offer possibilities to engage and inspire students to learn chemistry through multidisciplinary STEM projects. (17−25) However, there has been no STEM research carried out in the context of cheminformatics. This is the knowledge gap that this perspective paper aims to address.
In the STEM model, chemistry is placed under the science component, and cheminformatics applies chemical knowledge in a diverse technological context, utilizing mathematics and engineering expertise. Therefore, the aim of this article is to produce theoretical insights into the possibilities and challenges that cheminformatics can offer for STEM education. The evaluation is carried out via the SWOT analysis of an example molecular visualization engineering project designed for chemistry teacher training purposes.
To fulfill the aim outlined above, I will first review the earlier STEM research conducted in the field of chemistry education research (CER). The purpose of this section is to explore what kind of outcomes CER scholars have tried to achieve via STEM learning. After establishing an understanding of the earlier research, I will build new insights for chemistry-educational STEM learning by introducing cheminformatics as a field and analyzing its possibilities and challenges using a SWOT analysis.

STEM Learning in Chemistry Education

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There are several models for defining STEM education. (26) The traditional approach emphasizes all of the STEM subjects as individual fields. Critical opinions claim that this traditional approach is a disconnected model not supporting multidisciplinary collaboration. (3,5) More recent developments in STEM education encourage educators to design learning environments that integrate different STEM components, for example, implementing project-oriented integrated learning models but at the same time concentrating purposefully on teaching a few specific science or mathematics topics. (5) Studies show that such integration can provide more relevant and less fragmented learning experiences, but the challenge is that the integrated approach can be expensive and time-consuming to implement. Integrated STEM implementation requires materials (e.g., wood, plastic, metals, etc.) and other resources (e.g., tools, software, devices, etc.), and teachers need time to design well-structured projects. (27) In addition, the content knowledge demand for teachers is extensive; they have to master all of the subject aspects of the project to some extent. (28)
Taken together, these matters make the designing of integrated STEM learning a challenging task. A recent review (27) has contributed to decreasing this complexity by presenting a framework of instructional practices suitable for integrated STEM projects. According to this systematic literature analysis, integrated STEM learning is often a student-centered process that offers hands-on experiences. STEM learning environments can include features such as
1.

integration of STEM contents

2.

problem-based learning (PBL) approaches

3.

inquiry-based learning (IBL) approaches

4.

cooperative learning (CL) processes

5.

the designing of artifacts (27)

When the earlier STEM research conducted in the CER field is viewed through these design principles, it can be seen that many projects have engaged them in a comprehensive manner (see Table 1). For example, a learning environment can be constructed to encompass a vertical integration of subjects and include cooperative group work conducted in a PBL context. Projects that engage learners with inquiry-based processes often result in the creation of a concrete artifact. However, in many cases, the artifacts are built by the instructor, and the learners use it solely for learning purposes. As mentioned in the introduction, one important objective for STEM education is to support learners’ interests. This is clearly seen in the CER STEM projects, as most of the earlier research built their rationale around supporting learners’ interest in and attitudes toward science.
Table 1. Overview of STEM Projects in the CER Field
topic/themeintegrationaim/rationalepedagogical approachesoutcome/artifact
authentic research and quantitative analysis (23)chemistry and nanotechnologyincrease the relevance via linking topics to students’ personal livesIBL, CLincreased enjoyment
biodisel (17)chemistry and biologysupport meaningful learning and attitudesPBL, IBL, CLinterest in science increased
determining mole ratios (18)chemistry and engineeringdeveloping students’ interest and engage with higher-order thinkingIBLa small lab kit
modular science kit (24)chemistry and engineeringengage young kids with scientific thinking via a safe hands-on environmentIBL3D printed science kit
polymer semiconductors (20)chemistry, technology, and engineeringto improve polymer education via bridging the gap between 9–12 education and university-level chemistry research and educationIBL, interaction with researcherspolymeric semiconductor education kit
STEM gender gap (22) addressing the STEM gender gap via “chemistry camps” for girlsIBL, role modelsinterest in science and science careers increased
STEM summer camp (19)chemistry and biologydeepen the chemistry knowledge gained in high-schools and become familiar with study and career opportunitiesIBL, role modelsincreased content knowledge and interested in a science career
S-STEM program (21) To increase the number of students completing a major in chemistry via authentic research experiencesPBL, intensive courses, mentoringa model for supporting early professional development

Introducing Cheminformatics through the STEM Framework

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The primary goal of cheminformatics is to produce solutions for handling chemical information with computers, for example, mining, processing, storing, searching, and visualizing chemical information in 2D and 3D formats from/in databases, documents, patents, web sites, etc. The amount of data involved varies from small to massive, and the type of information required ranges from the specific to the abstract. Examples of active cheminformatics research topics are the development of chemical information systems, algorithms, software, databases, file formats, and all kinds of other applications derived from those (e.g., molecular visualizations, machine learning, etc.). (29,30) A more detailed description of cheminformatics research can be found in any of the cheminformatics specific journals (e.g., Journal of Chemical Information and Modeling (31) or Journal of Cheminformatics (32)). For those interested in learning cheminformatics through detailed handbooks, there are at least two options: An Introduction to Chemoinformatics (33) from 2007 or Chemoinformatics: A Textbook (34) published in 2003.
The history of cheminformatics dates to the 1950s, when chemists started to apply computers in their research. (1) The first cheminformatics publication was a description of a chemical substructure algorithm by Ray and Kirsch in 1957. (35) The development of statistical methods such as quantitative structure–activity relationship (QSAR) started a few years later. (36) QSAR is a widely applied cheminformatics method that enables exploring the relation of observed activities and molecular structures. (33)
In the 1970s, the pharmaceutical industry became interested in cheminformatics, as it needed more efficient methods to apply to computational drug discovery research. This interest provided more resources, and the field started to develop rapidly. (1) Pharmaceutical companies are interested in cheminformatics because the discovery of new drugs is expensive and time-consuming. Cheminformatics offers tools and methods that enable shortening this timeline. The approaches have evolved from library design to methods enabling the prediction of complex biological activities and structure relationships. (37) In addition, industries are interested in cheminformatics advances in the patent field. (33)
Even though cheminformatics has a decades-long history of being an integral part of chemistry, it has only been recognized as an independent research field since the late 1990s. (2,29) A recent review shows that cheminformatics-related articles have been published for decades but that the number of papers using the term “cheminformatics” or “chemoinformatics” started to grow steadily from the year 2001. (30)
The field of cheminformatics is currently developing quickly, but at the same time, it is a relatively young field and still not widely known. (30,38) In addition, there is only a small amount of earlier research on the role of cheminformatics in education. Although it is integrated into most CER focusing on chemistry software through the data processing and visualizations, (39−42) there are only a few articles focusing directly on cheminformatics. Jirat et al. (43) developed a cheminformatics curriculum for bachelor and master’s level chemistry studies, a pioneering work that integrates various cheminformatics skills into basic chemistry studies. Kamijo et al. (44) developed an adaptive cheminformatics system to read aloud chemical compound names, in order to support students with visual disabilities. Lohning et al. (45) studied students’ perceptions of using cheminformatics software and 3D printing in order to support biochemistry learning. According to their study, the use of cheminformatics software increased learning results related to molecular interactions.
This article seeks to contribute to the same domain as the work of Lohning et al. (45) by expanding earlier knowledge through an exploration of the role of cheminformatics in the STEM framework. For this purpose, an example cheminformatics-based learning module was designed. According to the mentioned recent review, cheminformatics research has a very strong focus on databases, web sites, and software. (30) In this regard, pedagogical activity involving the use of software and databases would represent a general example of cheminformatics research (technology). Reflecting on the earlier educational cheminformatics research done by Lohning et al., (45) 3D printing was selected to represent the aspect of engineering. Other authors have also used 3D printing as a practical context for chemistry-educational STEM learning. An example chemistry education topic that combines cheminformatics software and 3D printing is molecular visualizations. (46) In this article, molecular visualizations represent the science component. Finally, an example of a mathematics topic related to all the above is graph theory. Rationale for selecting the graph theory is that it is widely applied in cheminformatics; for example, according to Rassokhin, (47) practically all cheminformatics software support computer-based 2D and 3D visualizations based on graph theory.

Mathematics: Graph Theory

The objective of this section is to provide background information on graph theory and explain its crucial role in cheminformatics. Even though future chemistry teachers do not use graph theory on a hands-on level in the designed project, it is useful to understand that mathematics has a central role in the development of cheminformatics solutions. Graph theory is an example of this.
Chemical information is communicated through an expression of chemical language (e.g., trivial name, chemical formula, systematic name, or 2D structure diagram). For computers, the best data type would be a text string, which is easy to convert to a “0” and “1” string. This need inspired cheminformatics to develop canonical line notations such as Simplified Molecular Input Line Entry System (SMILES) and International Chemical Identifier (InChI). The use of graph theory in cheminformatics stems from the same tradition. Cheminformatics applies mathematical graph theory to represent molecules. The atoms are considered nodes, and the bonds are the edges linking atoms to together. This enables the processing of chemical structures as mathematical graphs (see Figure 1). (1)

Figure 1

Figure 1. Molecular graph corresponding to the carbon skeleton of 2,3,4-trimethylhexane (the graph is redrawn from ref (48)).

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In addition to atoms and bonds, nodes can represent electrons, molecules, molecular fragments, intermediates, etc., and the edges can represent reaction steps, van der Waals forces, etc. This versatility allows for the use of graphs to represent a wide range of chemical objects, such as molecules, reactions, crystals, polymers, and clusters. (48−52)
Another important use case for graph theory is chemical similarity analysis. (53) Graph-based similarity analysis is based on a graph-isomorphism procedure, which takes a lot computational resources. (54) The graph-based approach is under active development, and researchers have developed efficient algorithms that enable the virtual screening of structures from very large high-dimensional data sets. (51)
From the education perspective, however, graph theory knowledge is not common for chemists. It is a mathematical concept that is not taught in university-level chemistry programs but is a central concept in mathematics and computer sciences studies. Mathematics studies focus on the theoretical aspect of graphs, while computer scientists approach the topic through their algorithmic nature. If one wishes to implement graph theory on a more practical level to chemistry teaching, it is important to know that the graph theory has been found to be an abstract concept to learn. Fortunately, there are some studies on how to reduce this abstraction. For example, it can be reduced by thinking of graphs as processes rather than objects. (55)

Technology: Cheminformatics Software and Databases

The implementation of graph theory has led to the development of many applications, of which one concrete example is cheminformatics software. As mentioned, according to Rassokhin, (47) all cheminformatics toolkits support chemical structure representations based on graph theory. Software are written via programming languages such as C++, (47) JavaScript, (56) and Java. (57) Toolkits can be standalone software packages (e.g., Avogadro (58)) or frameworks that can be used to develop other software (e.g., JSmol (59) or ChemDoodle Web Components (60)). Many of the frameworks and software are licensed under open source licenses, allowing anyone to extend them or build chemistry software with ready-made cheminformatics tools. (58,61,62) Cheminformatics toolkits implement various types of chemical knowledge and cheminformatics applications, such as databases, molecular graphics, and data processing (e.g., retrieval, converting, storing, etc.). In addition, many of them support computational chemistry features like molecular calculations.
In the cheminformatics research field, software development is a highly published and cited topic. The most cited software development project is Open Babel, with over 1500 citations. (30) Open Babel is an open chemical toolkit that allows users to search, convert, analyze, or store data from different chemistry areas. The data can be imported into Open Babel, where it can be processed and finally exported in the required format (see an example workflow in Figure 2). The software reads, converts, and writes over 110 chemical file formats, which makes it extremely flexible from a data perspective. Open Babel is an open software package and has been integrated into dozens of other software systems, for example, Avogadro. (63)

Figure 2

Figure 2. Example of an interconversion of 0D, 2D, and 3D structures using Open Babel. All these data types can be converted to each other, exported, and finally imported into another software package for calculations or visualizations. For example, the 0D notation was retrieved from a database, converted, and exported into a 2D coordinate file for ChemDraw editing. Then, the 2D file was converted into 3D coordinates and exported to a mol2 format, which was imported to Avogadro for geometrical optimization and 3D image production.

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According to many CER scholars, molecular modeling software have an integrated role in chemistry education. Software often include both computational and cheminformatical features, and they can be of use in many ways, e.g., data gathering, extracting relevant data from large data sets, visualizing data, and applying computational methods. (64,65) The challenge is how to choose the most suitable software from the dozens of available options. For example, in a real-world computational chemistry-based PBL module developed by Rodríguez-Becerra et al., (64) pre-service chemistry teachers studied intermolecular forces in protein–ligand context by evaluating different molecular conformations of β-carboline derivatives into the Trypanothione Reductase active-site. This PBL project is an example of an authentic chemistry research problem that requires the use of multiple software solutions. In this case, Avogadro was used to build and visualize molecules, Autogrid to generate grid maps from lattice data, AutoDock to explore conformational states in the docking process, Discovery Studio to analyze the protein–ligand complexes, and finally Excel for the data processing and plotting. To support this decision making process, Rodríguez-Becerra et al. (64) assembled a comprehensive overview of available software packages and their primary use cases.
The use of databases is also central to cheminformatics, and they are the subject of the most active research in the field. (30) Content specific, systematically organized databases are important because the amount of available information is growing exponentially. There are both free and commercial database systems well-suited to use in chemistry. The most frequently used free structural databases are PubChem (pubchem.ncbi.nlm.nih.gov), Crystallography Open Database (crystallography.net), ZINC (zinc.docking.org), ChemSpider (chemspider.com), and Protein Data Bank (PDB) (rcsb.org). Google Scholar, PubMed, Scopus, Web of Science, and SciFinder are examples of popular literature databases and information software. (66)

Science: Molecular Visualizations

Molecular visualizations support the understanding of macroscopic level materials and processes via molecular level explanations. In this paper, molecular visualizations are viewed as the science component binding mathematics and technology together. Molecular visualizations can be physical (e.g., plastic model or 3D print), verbal, symbolic, gestural, or visual. If they are produced via computers, they are called computer-based molecular visualizations (CBMVs). (67) All CBMVs are produced with tools based on cheminformatics research. This is a great achievement, and the cheminformatics field can cite the work done on 2D and 3D molecular visualizations as one of its success stories. (1) In general, molecular visualizations are considered highly important for both chemistry as a science (68) and chemical education. (67,69,70) For example, they support learning by enabling the illustration of the submicroscopic world of chemistry, (71) which in turn supports understanding (72) and facilitates meaningful communication. (73)
In the CER field, the justifications for using CBMVs have remained the same for the last 30 years. Already in the 1990s, Aduldecha et al. (74) reported that university students appreciated the ability to produce professional-level molecular graphics via computers for their reports and essays. A few years later, Barnea and Dori (75) wrote that the use of plastic molecular models was a widespread method in chemistry education but that the challenge was the limited number of ball sizes and colors and the inaccuracies in portraying bond lengths and angles. They saw a great advantage in using molecular modeling software, where learners can build any size of molecules, switch to different representational types, and use visualizations that better support understanding (e.g., atom labels, name generation).
If CBMV are looked at from the chemistry learning perspective, many authors have constructed rationales for their research papers using the Johnstone’s triangle model. (71,76) The central idea behind Johnstone’s work is that chemistry is a difficult science for novices, because learners encounter strange new terms all the time and the knowledge structure of chemistry is complex in general. Chemical information can be represented simultaneously at multiple levels, i.e., the visible macro level (description), the unseen submicro level (explanation), and the abstract symbolic level (representation). For an expert (chemistry teacher), it is easy to work inside of this perceptual triangle and change between levels. For a novice (student), the level change can be much harder. As a solution, Johnstone suggested that teachers work on one level at the time in order to avoid the possible cognitive overload of a learner’s working memory, which could in turn hinder the systematic information storage to long-term memory. (77) In the context of the perceptual triangle, CBMV especially benefits learning at the submicro level, which is the most important because it explains at the molecular level why some chemical phenomena occur. In other words, previously, the CBMM submicrolevel was illustrated through written text, verbal explanations, and static images. Through CBMM, the submicrolevel can be explored actively through translating and manipulating molecules and molecular simulations, and the dynamic nature of chemical phenomena is thus made easier to grasp. CBMV effectively added a representational layer to the submicro level that was previously more of a symbolic level feature (Figure 3).

Figure 3

Figure 3. Possibilities that CBMV offers for teaching and learning submicrolevel chemistry.

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There is some evidence that strengthening submicro level visualizations using interactive 3D molecular models, simulations, and animations helps students to better navigate the perceptual triangle. But, even when using carefully designed visualizations, the danger of overloading the working memory is present, and the effective use of these visualizations in education still requires detailed instructions. (78−80) According to Kozma and Russell, (81) developing visualization skills is extremely important for vocational relevance, as representational competence is essential to a chemist’s work. All types of visualizations have their own strengths and limitations. Justi and Gilbert (82) state that it is important for teachers to discuss the nature of these models, in order to allow learners to build their own models and to compare them to other scientific models. This process would give them an understanding of how chemical models are produced and how chemistry as a science progress. In addition, analyzing, evaluating, and creating visualizations would develop higher-order thinking skills. (83)
Cheminformatics toolkits described earlier make the production of 3D molecular visualizations available to all learners, so that drawing skills do not limit the learning process. According to chemistry teachers, working with CBMV is motivating for students. In the research conducted by Aksela and Lundell, (65) teachers felt that CBMVs helped to illustrate difficult concepts, developed students’ visualization skills, and aroused students’ interest in chemistry. CBMVs were also experienced as a modern chemistry tool that students would find interesting, and teachers thought it could encourage them to study chemistry further.
The data from students backs up the teachers’ beliefs. For example, Dori and Barnea (75) reported that the majority of the high school students enjoyed working with CBMVs. Students felt that it developed their spatial skills and content knowledge. Similar observations were made by Rodríguez-Becerra et al. (64) when they investigated pre-service chemistry teachers’ perceptions of educational computational chemistry (the cheminformatics workflow of Rodríguez-Becerra et al. was described in the previous section). According to Barnea, (84) graduate students liked combining computers and chemistry because it developed their chemistry and computer skills at the same time. There is also pre- and post-test data that supports the teachers’ perceptions. Dori and Kaberman (85) studied quantitatively how molecular modeling affected high school chemistry students visualization skills. They reported seeing statistically significant improvements in their comprehensive 600-student data set, but their research design did not include test/control groups and therefore gives no indication of the efficiency of CBMV compared to learning without CBMVs. Savec et al. (69) tested the efficiency of CBMV in solving spatial chemistry tasks compared to the use of plastic models. According to their research, CBMVs were as effective as plastic models, but using plastic models and CBMVs together was less effective than using the methods separately because the combined use may split students’ attention. This observation should be considered in designing pedagogical modules including models. Lastly, Barnea and Dori (86) determined that gender does not affect learning outcomes when CBMV is implemented.
Nowadays, there is no need for comparing CBMV supported learning to learning without it. Through modern web visualization technologies such as HTML5 and JavaScript, the field of cheminformatics has managed to transform CBMV activities from separate learnings tasks to an integral part of modern learning materials, textbooks, and mobile applications. (59,62,87,88) Textbooks can be made in HTML5 format, and molecular models can then be embedded inside the web pages. These models can be used on all types of devices, from mobile phones to desktop computers. For basic features such as molecular visualizations or energy minimization calculations, there is no need to use commercial software or install special products. Such HTML5/JavaScript technologies suitable for chemistry have been reviewed extensively by Theisen. (56)

Engineering: 3D-Printing

3D printing is an additive manufacturing technology where objects are built by adding material layer by layer. It is a growing industrial field. Earlier 3D printing was used more for prototyping, but currently, it is developing into a common manufacturing method. (89) This growth has created a demand for more experts in the field, a fact which is recognized in education contexts, and many schools are adding 3D printing to their curricula. (90) The use of 3D printing in schools requires technology (3D printers) and its mastery, but in addition, 3D printing requires knowledge of the printing context. Depending on the context, this knowledge can be based on science or mathematics. In this research, the context is molecular visualizations, which emphasizes the science knowledge aspect. From the STEM perspective, engineering can be considered a connective domain that offers science, mathematics, and technology, a meaningful learning context. Engineering can be viewed as the process used for creating new and improved artifacts. (91) The relation of engineering and 3D printing is that in STEM education 3D printing is often used as the engineering component. (92)
3D printing offers many possibilities for chemistry education. However, the implementation of new technology can involve many challenges and requires careful research-based development. This has inspired dozens of CER scholars to develop pedagogical models for using 3D printing in chemistry education. (93) The 3D printing focus in this article is printing physical molecular visualizations, which is the most common 3D printing activity in chemistry education. The reasons for printing molecular visualizations include the lack or high cost of suitable molecular models, the limitations of current models, and the possibilities that concrete models offer for chemistry learning. (46,93) There is clear evidence that such concrete models support chemistry learning. They enable physical hands-on experience in rotating and translating the structures, (94) but according to pre-/post-data, concrete models are not significantly more efficient than virtual models. (69,95) 3D printing combines virtual and physical visualization, which strengthens the illustration of the submicroscopic level (see Figure 3). For example, traditional plastic model kits do not enable the building of complex compounds or larger structures, which can however be easily visualized via cheminformatics software and 3D printed. (96,97)
Even though the price of 3D printers is constantly decreasing, making it possible for more and more schools to purchase them, it is still a rare technology for schools. It is also noteworthy that 3D printing may take several hours (45,98) and includes many safety issues to consider. (99) These concerns may be the reason most 3D printing-related CER do not engage students actively in the printing process; instead, they usually work with the already printed models. However, there have been some attempts to utilize makerspace facilities (an open collaborative work space including tools and technology) in large-scale chemistry courses, in order to provide all students with a 3D printing experience. (98)

SWOT Analysis

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The challenges and possibilities of using cheminformatics for STEM education will be analyzed via a SWOT analysis. SWOT is an analytical framework focusing on exploring internal Strengths and Weaknesses and external Opportunities and Threats. SWOT is often used in strategic planning and is therefore well-suited to mapping the possibilities (strengths and opportunities) and challenges (weaknesses and threats) of the selected context. (100)
The analysis will be carried out by first presenting an example cheminformatics-based engineering activity, on the basis of the perspectives introduced in the theoretical framework. Then, the example will be used in conducting the analysis. The exact research question guiding the analysis was: What kind of possibilities and challenges does educational cheminformatics, applied in the context of 3D printing, offer to STEM education?

Educational Cheminformatics Engineering Project

On the basis of the literature review, an example cheminformatics engineering activity for future chemistry teachers has been designed. The activity consists of three parts:
1.

First, students read a research article addressing 3D printing in chemistry education. (93) This phase ensures a research-based approach.

2.

After reading the theory, they carry out a hands-on experiment by selecting a molecule they want to print and print it using the department’s 3D printers or devices found in public libraries. The goal is to design a model that improves the available physical models. This phase ensures that the students will have an active role in the printing process. The engineering aspect is to solve a challenge of not having suitable physical models available.

3.

After printing they will: (1) write a short essay where they reflect on how 3D printing or printed models could be used to support chemistry teaching and learning and (2) post an image of the printed model on a discussion forum, along with a short description, for peer commentary.

This activity has been part of master’s level chemistry education course called Models and Visualization in Chemistry Education (5 ECTS) since 2017 in the University of Helsinki, Finland. It is a mandatory course for the chemistry education majors, and in the past five years, altogether 30 future chemistry teachers have carried out the activity. The course is held once a year, and the cheminformatics module is developed on a yearly basis after student feedback and the latest CER are reviewed.
From the STEM perspective, the activity applies science, mathematics, and technology in a chemistry educational engineering context based on applications produced by cheminformatics (see Figure 4). The hands-on phase starts by designing a molecular context, which will be retrieved from a database or build via freely selectable software. Students usually choose to use Avogadro with Open Babel or JSmol-based web applications. Using the software, the model is manipulated and visualized in the needed form and exported or converted to a 3D printable STL format. Therefore, the cheminformatics software is used as a tool in processing the chemical structure from line notation to a CBMV and finally to a printed file format, using algorithms based on the graph theory (see Figure 2). Next, the resolution and size will be adjusted according the available printing time. The final product is a printed physical molecular visualization.

Figure 4

Figure 4. Overview of the designed cheminformatics activity and its relation to the STEM framework.

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It is noteworthy that the students’ perceptions are not the focus of this analysis. The goal is to analyze the possibilities and challenges of cheminformatics as a context for STEM education. The designed activity is used as a practical case for conducting the analysis. The strategy is to use a real pedagogical model as an example and then to generate theoretical insights into the possibilities and challenges of implementing cheminformatics as a context for STEM education. Thus, the goal of using the real pedagogical model is to increase the credibility of the theoretical analysis.

Results and Discussion

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The SWOT analysis will be reported by first writing an overview covering all SWOT components and then looking the individual components. The goal is to focus first on the possibilities, then introduce the challenges, and lastly the potential solutions. The reason for this structure is that the strengths, weaknesses, opportunities, and threats are often connected. To improve the overall clarity, the results are summarized in Table 2, at the end of this section.
Table 2. Summary of the SWOT Analysis
 possibilitieschallenges
internalstrengthsweaknesses
 - Multidisciplinary field offers many possibilities for subject level integration of chemistry and mathematics.- High content knowledge demand. For example, the connection of graph theory and cheminformatics software is clear but abstract for the user at the same time.
 - The engineering approach supports multiple pedagogical models stimulating higher-order thinking skills.- Addressing the diverse content knowledge is a time-consuming and challenging learning environment design task.
 - The visualization perspective can be used in improving chemistry learning (e.g., submicrolevel understanding and knowledge of models).- Need for collaborative learning environment design. This takes time but can also be an opportunity.
  - A long printing time. Can be supported by reducing the resolution or size.
  - Possible work safety hazards. (99)
externalopportunitiesthreats
 - Emerging field could inspire young people to follow science careers. For example, this article can be offered for students as an inspiration. (103)- Lack of printers and software. This can be aided by collaboration with public libraries.
 - Enables engaging leaners with makerspace culture, which supports interest, networking, engagement, and career choices.- Oversized curriculum, (101) no time for projects.
 - Enables introducing open-source culture and open science. 
Cheminformatics is a multidisciplinary field of chemistry. This multidisciplinary nature offers versatile internal possibilities for STEM education, viewed from the subject integration perspective. (27) For example, it incorporates a mathematical base through graph theory, (47) which is used to produce a wide range of technological solutions such as software and databases. (30) These solutions offer great value to both chemistry research and education. (67,68) Software packages are used to produce molecular visualizations that, in general, are needed in all chemistry learning. Such visualizations facilitate communication in general and enable the integration of different science subjects (e.g., physics, biology, geography, etc.) and mathematics (e.g., geometry, shapes, etc.). (73) This also shows learners how mathematical knowledge is applied in cheminformatics software design and how cheminformatics tools are used to support scientific communication.
However, even though the connection between graph theory and software is clearly present, it can also be experienced abstract. The software user seldom looks at the algorithmic level documentation of how the graph theory is used inside the software code. In this sense, the implementation of graph theory is an extra-situational mathematical background information for the whole project. (101) Cheminformatics context also includes mathematics that can be applied on a practical level in education, for example, comparing Tanimoto similarity of two or more molecules, working with QSAR models, or performing geometrical measurements for a molecule. These examples could be an interesting pedagogical development focus for future research.
As the literature suggests, engineering can be used as the connective STEM component that enables the design of pedagogically meaningful learning environments. (91) In this article, the example case was an educational cheminformatics engineering project that resulted in an improved physical model. From the chemistry learning perspective, this can be used in strengthening the submicrolevel visualizations (71,76) and supporting model- and modeling-based chemistry learning. (82) The process produces both computer-based and physical artifacts. Looking at it from a pedagogical perspective, an engineering-based activity supports multiple approaches used in STEM education. For example, it is constructed around a design problem, and solving the design challenge requires an inquiry-based approach, which activates higher-order thinking skills. If needed, students have the option of performing the activity in teams and using external experts in problem solving, which would emphasize collaborative learning. (27,83)
The design context can also be something other than an improved physical model. For example, the chemistry topic could be almost anything, because information retrieval from databases, data processing, and molecular visualizations are used widely in all chemistry studies. From the 3D printing perspective, there are dozens of examples found from the literature. (93) The cheminformatics engineering challenge could also be a software development project, because many cheminformatics solutions are published under an open source license. (58,59,63) This would introduce learners to both open source culture and open science thinking.
The primary challenge to this approach is that designing a holistic cheminformatics learning environment demands advanced level content knowledge, technical knowledge, and basic level programming skills. Individual teachers do not usually have the competences to cover all of these aspects, especially because cheminformatics is not formally taught in chemistry or chemistry teacher training programs. (43) A potential solution to this challenge is to use a collaborative learning environment design approach. (102) When teachers and researchers plan learning environments together, they support each other’s strengths and weaknesses. However, collaborative design can be time-consuming and requires careful planning. Another potential solution is to use makerspaces with external mentors from academia or the chemical industry who have an in-depth understanding of cheminformatics. (98) Such mentors could also inspire the students as role models and discuss their daily work in order to strengthen their professional relevance. (20−22) This could help address the interest challenge faced by science studies. (7−12) Another content challenge is a possible oversized curriculum, where there are so much concepts to teach that it takes all the teaching time. At the same time, conducting STEM projects can also require a large amount of teaching time, which might not encourage teachers to design and implement larger projects. (27)
Time-related challenges can be both internal and external. An oversized curriculum is an external threat that derives from the national level curriculum instructions. A long printing time is an internal weakness, which can be reduced by downgrading the print resolution. (98) Safety hazards related to 3D printing are another internal weakness that requires careful attention from the teachers, (99) however safety planning challenges can be addressed via training. The lack of printers and software is an external threat.
Even though cheminformatics has a long history, it is still considered a young field. It has its own research tradition for basic research on databases, algorithms, software etc., but at the same time, it produces solutions for other fields of chemistry to use. This project example works on the traditional cheminformatics related to structural data retrieving and file conversion technology. But, examples could also be taken from the current research that focuses on machine learning and deep learning neurons. (30) The field is advancing quickly and could offer interesting examples for students to see how chemistry as a science progresses, as well as promoting students’ scientific and technologic literacy. In addition, cheminformatics employs people with different backgrounds, offering alternative examples of possible chemistry related careers. (19)

Conclusions

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This perspective paper introduced cheminformatics using the STEM framework and analyzed its educational possibilities and challenges through a SWOT analysis. The objective was to produce theoretical insights for STEM education through the analysis of an authentic educational cheminformatics project. The main conclusion is that cheminformatics offers significant possibilities for STEM education, which are due to its multidisciplinary nature. Cheminformatics can be used in teaching many central chemistry topics like functional groups, structure–property relationships, reactions, or creating new artifacts such as molecular visualizations and software packages supporting multiple pedagogical approaches. If the required devices and software are available, the main challenges are the high content knowledge demand and the fact that schools may not have time for larger projects. (27) This challenge can be solved via a collaborative learning environment design. It is noteworthy that earlier STEM literature in CER do not emphasize the students’ active role in creating artifacts (see Table 1). The solution is to emphasize the engineering component and engage learners throughout the whole design process, (91) as was implemented in the example project.
There are multiple possible research questions to address in the future. For example: Is cheminformatics experienced as a relevant context by learners and teachers? (8,10) What kind of learning materials are suitable for using cheminformatics in different levels of education, from lower-secondary level to higher education, and in different subjects? (9) Which topics from different subjects can be taught via educational cheminformatics engineering STEM projects? How can the role of mathematics in cheminformatics-based STEM education made clearer? Answering these questions will require collaborative design-based research methods for learning environment design. (102) In conclusion, even though educational cheminformatics is still in its beginning stages, it seems to be a highly promising context for supporting chemistry learning via STEM education.

Author Information

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    • Notes
      The author declares no competing financial interest.

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      A review. There is a growing need for workers with STEM-aligned training in the modern global economy, but a paucity of workers to fill these positions. One important contributor to this issue is low student persistence in STEM. Nontraditional science courses that utilize more active-participation and learning are attractive as tools to increase student persistence and engender more interest in STEM. Herein is described the content and implementation of the undergraduate chem.-based service-learning course, Chem. 1898: Service Learning, that was offered in Spring 2019 at Tulane University. The goal of the course was to increase self-efficacy in chem. and sustain undergraduate interest in STEM. The course also serves to increase STEM interest in the New Orleans public-school students. Chem. 1898 features a well-rounded curriculum and diverse activities. The enrolled undergraduate students were not only taught chem. concepts (general chem. and supramol. chem.) but also asked to present the chem. concepts using attention-grabbing demonstrations to public-school students in the New Orleans area. In addn., the course covered multiple nonscience topics, including the pedagogy of service-learning, background on the New Orleans public-school system, and a guide for how to work with the community. The course also involved student reflection activities/surveys and interfaced with the Tulane Center for Public Service. Preliminary qual. results from a set of anonymous pre- and poststudent surveys indicated that the undergraduate students gained self-efficacy in the general chem. concepts covered in the course. Although the course did not have an effect on the career choices of the undergraduate students, the majority of the students were already very interested in a STEM career. Further, some students mentioned gaining a benefit in public speaking skills, and some considered the possibility of teaching and working with children in the future.
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      White, D.; Delaney, S. Full STEAM Ahead, but Who Has the Map? - A PRISMA Systematic Review on the Incorporation of Interdisciplinary Learning into Schools. LUMAT Int. J. Math Sci. Technol. Educ. 2021, 9 (2), 9– 32,  DOI: 10.31129/LUMAT.9.2.1387
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      Thibaut, L.; Ceuppens, S.; Loof, H. D.; Meester, J. D.; Goovaerts, L.; Struyf, A.; Pauw, J. B.; Dehaene, W.; Deprez, J.; Cock, M. D.; Hellinckx, L.; Knipprath, H.; Langie, G.; Struyven, K.; Velde, D. V. de; Petegem, P. V.; Depaepe, F. Integrated STEM Education: A Systematic Review of Instructional Practices in Secondary Education. Eur. J. STEM Educ. 2018, 3 (1), 02,  DOI: 10.20897/ejsteme/85525
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      Willett, P. Chemoinformatics: A History. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2011, 1 (1), 46– 56,  DOI: 10.1002/wcms.1
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      Chemoinformatics: a history
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      This paper gives a brief history of the development of chemoinformatics since the first studies in the late 1950s and early 1960s of methods for searching databases of chem. mols. and for predicting their biol. and chem. properties. Topics, and assocd. key papers, that are discussed include: structure, substructure, and similarity searching; the processing of generic chem. structures and of chem. reactions; chem. expert systems; the identification of qual. and quant. structure-activity relationships in both two and three dimensions; pharmacophore anal.; ligand-protein docking; mol. diversity anal.; and drug-likeness studies. Brief mention is also made of other important areas such as computer-assisted synthesis design and computer-assisted structure elucidation.
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      Willett, P. The Literature of Chemoinformatics: 1978–2018. Int. J. Mol. Sci. 2020, 21 (15), 5576,  DOI: 10.3390/ijms21155576
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      Journal of Chemical Information and Modeling. About the Journal. https://pubs.acs.org/page/jcisd8/about.html (accessed 2021-05-21). DOI: 10.1021/jcisd8
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      Journal of Cheminformatics. Aims and scope. https://jcheminf.biomedcentral.com/submission-guidelines/aims-and-scope (accessed 2020-08-28).
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      Leach, A. R.; Gillet, V. J. An Introduction to Chemoinformatics; Springer: Dordrecht; London, 2007.
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      Chemoinformatics: A Textbook; Gasteiger, J., Engel, T., Eds.; Wiley-VCH: Weinheim, Germany, 2003.
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      Ray, L. C.; Kirsch, R. A. Finding Chemical Records by Digital Computers. Science 1957, 126 (3278), 814– 819,  DOI: 10.1126/science.126.3278.814
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      Finding Chemical Records by Digital Computers
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      Li, L.; Hu, J.; Ho, Y.-S. Global Performance and Trend of QSAR/QSPR Research: A Bibliometric Analysis. Mol. Inform. 2014, 33 (10), 655– 668,  DOI: 10.1002/minf.201300180
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      Global Performance and Trend of QSAR/QSPR Research: A Bibliometric Analysis
      Li, Li; Hu, Jianxin; Ho, Yuh-Shan
      Molecular Informatics (2014), 33 (10), 655-668CODEN: MIONBS; ISSN:1868-1743. (Wiley-VCH Verlag GmbH & Co. KGaA)
      A bibliometric anal. based on the Science Citation Index Expanded was conducted to provide insights into the publication performance and research trend of quant. structure-activity relationship (QSAR) and quant. structure-property relationship (QSPR) from 1993 to 2012. The results show that the no. of articles per yr quadrupled from 1993 to 2006 and plateaued since 2007. Journal of Chem. Information and Modeling was the most prolific journal. The internal methodol. innovations in acquiring mol. descriptors and modeling stimulated the articles' increase in the research fields of drug design and synthesis, and chemoinformatics; while the external regulatory demands on model validation and reliability fueled the increase in environmental sciences. "Prediction endpoints", "statistical algorithms", and "mol. descriptors" were identified as three research hotspots. The articles from developed countries were larger in no. and more influential in citation, whereas those from developing countries were higher in output growth rates.
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      Martinez-Mayorga, K.; Madariaga-Mazon, A.; Medina-Franco, J. L.; Maggiora, G. The Impact of Chemoinformatics on Drug Discovery in the Pharmaceutical Industry. Expert Opin. Drug Discovery 2020, 15 (3), 293– 306,  DOI: 10.1080/17460441.2020.1696307
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      The impact of chemoinformatics on drug discovery in the pharmaceutical industry
      Martinez-Mayorga, Karina; Madariaga-Mazon, Abraham; Medina-Franco, Jose L.; Maggiora, Gerald
      Expert Opinion on Drug Discovery (2020), 15 (3), 293-306CODEN: EODDBX; ISSN:1746-0441. (Taylor & Francis Ltd.)
      A review. Even though there have been substantial advances in our understanding of biol. systems, research in drug discovery is only just now beginning to utilize this type of information. The single-target paradigm, which exemplifies the reductionist approach, remains a mainstay of drug research today. A deeper view of the complexity involved in drug discovery is necessary to advance on this field.: This perspective provides a summary of research areas where cheminformatics has played a key role in drug discovery, including of the available resources as well as a personal perspective of the challenges still faced in the field.: Although great strides have been made in the handling and anal. of biol. and pharmacol. data, more must be done to link the data to biol. pathways. This is crucial if one is to understand how drugs modify disease phenotypes, although this will involve a shift from the single drug/single target paradigm that remains a mainstay of drug research. Moreover, such a shift would require an increased awareness of the role of physiol. in the mechanism of drug action, which will require the introduction of new math., computer, and biol. methods for chemoinformaticians to be trained in.
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      Wild, D. J. Cheminformatics for the Masses: A Chance to Increase Educational Opportunities for the next Generation of Cheminformaticians. J. Cheminformatics 2013, 5, 32,  DOI: 10.1186/1758-2946-5-32
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      Cheminformatics for the masses: a chance to increase educational opportunities for the next generation of cheminformaticians
      Wild, David J.
      Journal of Cheminformatics (2013), 5 (), 32CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
      A review. This paper describes the cheminformatics for masses and a chance to increase educational opportunities for next generation of cheminformaticians.
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      Romero, R. M.; Bolger, M. B.; Morningstar-Kywi, N.; Haworth, I. S. Teaching of Biopharmaceutics in a Drug Design Course: Use of GastroPlus as Educational Software. J. Chem. Educ. 2020, 97 (8), 2212– 2220,  DOI: 10.1021/acs.jchemed.0c00401
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      Teaching of Biopharmaceutics in a Drug Design Course: Use of GastroPlus as Educational Software
      Romero, Rebecca M.; Bolger, Michael B.; Morningstar-Kywi, Noam; Haworth, Ian S.
      Journal of Chemical Education (2020), 97 (8), 2212-2220CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
      In early-stage drug design, establishment of promising drug candidates requires integration of structure-based mol. design with biopharmaceutics and ADMET. Thus, students in a drug design course should learn the basis for and effects of candidate small mols. binding to therapeutic targets and the importance of simultaneous understanding of ADMET characteristics that will largely det. if the mol. can achieve a therapeutically relevant concn. at the target site and become an orally deliverable drug. This second aspect of education in drug design has been relatively overlooked compared to structure-based design. Here, we describe a course using sophisticated simulation and modeling software, GastroPlus and ADMET Predictor, which are commonly used in the pharmaceutical industry. We use a combination of short lectures, software demonstration, and hands-on use, which allows students to "design a drug" with incorporation of structural and ADMET considerations. Student feedback indicated that the use of the software and the course design were helpful in enhancing their understanding of the importance of biopharmaceutics properties and ADMET in drug design. GastroPlus and ADMET Predictor have recently become more accessible to educators, and our experience using this software in an educational setting may be helpful for instructors who wish to develop a similar course.
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      D’Ambruoso, G. D.; Cremeens, M. E.; Hendricks, B. R. Web-Based Animated Tutorials Using Screen Capturing Software for Molecular Modeling and Spectroscopic Acquisition and Processing. J. Chem. Educ. 2018, 95 (4), 666– 671,  DOI: 10.1021/acs.jchemed.7b00511
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      Evans, M. J.; Moore, J. S. A Collaborative, Wiki-Based Organic Chemistry Project Incorporating Free Chemistry Software on the Web. J. Chem. Educ. 2011, 88 (6), 764– 768,  DOI: 10.1021/ed100517g
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      A Collaborative, Wiki-Based Organic Chemistry Project Incorporating Free Chemistry Software on the Web
      Evans, Michael J.; Moore, Jeffrey S.
      Journal of Chemical Education (2011), 88 (6), 764-768CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
      In recent years, postsecondary instructors have recognized the potential of wikis to transform the way students learn in a collaborative environment. However, few instructors have embraced in-depth student use of chem. software for the creation of interactive chem. content on the Web. Using currently available software, students are able to design, build, and describe computational mol. models with a high degree of independence. For a second-semester org. chem. course with biochem. applications, we designed and implemented a wiki-based project that involved student development of Web pages presenting the mechanism of action of a mol. of their choice. Student feedback supports the value of the project as a means to help students apply course content to biochem. applications. Org. chem. instructors may benefit from the experience we gained while designing and implementing an org. chem. wiki project.
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      Marson, G. A.; Torres, B. B. Fostering Multirepresentational Levels of Chemical Concepts: A Framework To Develop Educational Software. J. Chem. Educ. 2011, 88 (12), 1616– 1622,  DOI: 10.1021/ed100819u
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      Fostering Multirepresentational Levels of Chemical Concepts: A Framework To Develop Educational Software
      Marson, Guilherme A.; Torres, Bayardo B.
      Journal of Chemical Education (2011), 88 (12), 1616-1622CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
      This work presents a convenient framework for developing interactive chem. education software to facilitate the integration of macroscopic, microscopic, and symbolic dimensions of chem. concepts-specifically, via the development of software for gel permeation chromatog. The instructional role of the software was evaluated in a study involving 237 undergraduates. The results suggest that the software fostered transition from lower- to higher-order cognitive reasoning. Common misconceptions regarding microscopic phenomena were also detected and addressed.
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      Jirat, J.; Cech, P.; Znamenacek, J.; Simek, M.; Skuta, C.; Vanek, T.; Dibuszova, E.; Nic, M.; Svozil, D. Developing and Implementing a Combined Chemistry and Informatics Curriculum for Undergraduate and Graduate Students in the Czech Republic. J. Chem. Educ. 2013, 90 (3), 315– 319,  DOI: 10.1021/ed3001446
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      Developing and Implementing a Combined Chemistry and Informatics Curriculum for Undergraduate and Graduate Students in the Czech Republic
      Jirat, Jiri; Cech, Petr; Znamenacek, Jiri; Simek, Miroslav; Skuta, Ctibor; Vanek, Tomas; Dibuszova, Eva; Nic, Miloslav; Svozil, Daniel
      Journal of Chemical Education (2013), 90 (3), 315-319CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
      Experience developing multidisciplinary bachelor's and master's curricula involving intertwined chem., informatics, and librarianship-editorship skills is described. The bachelor's curriculum was created in close cooperation of academic staff, library staff, and the publishing house staff (Institute of Chem. Technol. Prague: a sole publisher of chem. literature in Czech Republic), with the aim to educate a new generation of information retrieval and e-publishing professionals in the science-technol.-medicine (STM) field. This cooperation together with a set of specifically tailored courses gave students the insights into real-world issues of STM publishing. The master's curriculum, heavily relying on the bachelor's stage, inclines towards cheminformatics and deepens software engineering skills. Successes, pitfalls, and failures are described, together with proposed changes and future directions.
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      Kamijo, H.; Morii, S.; Yamaguchi, W.; Toyooka, N.; Tada-Umezaki, M.; Hirobayashi, S. Creating an Adaptive Technology Using a Cheminformatics System To Read Aloud Chemical Compound Names for People with Visual Disabilities. J. Chem. Educ. 2016, 93 (3), 496– 503,  DOI: 10.1021/acs.jchemed.5b00217
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      Creating an Adaptive Technology Using a Cheminformatics System To Read Aloud Chemical Compound Names for People with Visual Disabilities
      Kamijo, Haruo; Morii, Shingo; Yamaguchi, Wataru; Toyooka, Naoki; Tada-Umezaki, Masahito; Hirobayashi, Shigeki
      Journal of Chemical Education (2016), 93 (3), 496-503CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
      Various tactile methods, such as Braille, have been employed to enhance the recognition ability of chem. structures by individuals with visual disabilities. However, it is unknown whether reading aloud the names of chem. compds. would be effective in this regard. There are no systems currently available using an audio component to assist in the recognition of chem. structures. This study aims to establish the essential requirements for the prototype Chem. Literature Extn. and Aloud-reading System (CLeArS) that enables visually impaired people to recognize a depicted chem. structure after hearing its name, which complies with the nomenclature adopted by the International Union of Pure and Applied Chem. Details of the methods employed in CLeArS and its execution are presented, in addn. to the fundamental requirements for recognizing chem. structures using CLeArS. Exptl. results on 450 images comprising both simple and complex chem. structures show a high recognition rate of 90% among subjects with visual disabilities. Thus, we conclude that reading aloud the names of chem. compds. is an effective method enabling students with impaired vision to recognize chem. structures.
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      Lohning, A. E.; Hall, S.; Dukie, S. Enhancing Understanding in Biochemistry Using 3D Printing and Cheminformatics Technologies: A Student Perspective. J. Chem. Educ. 2019, 96 (11), 2497– 2502,  DOI: 10.1021/acs.jchemed.8b00965
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      Enhancing Understanding in Biochemistry Using 3D Printing and Cheminformatics Technologies: A Student Perspective
      Lohning, Anna E.; Hall, Susan; Dukie, Shailandra
      Journal of Chemical Education (2019), 96 (11), 2497-2502CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
      Students often approach biochem. with a degree of trepidation with many considering it one of the more difficult subjects. This is, in part, due to the necessity of making visual images of submicroscopic concepts. Mol. interactions underpin most biol. processes; therefore, mastering these concepts is essential. Understanding the forces and mechanisms that underpin protein-ligand interactions is a key learning goal for mastering the protein structure-function relationship. We intended to overcome such learning barriers by implementing assignment-based activities across three successive biochem. cohorts. The activities involved 3D printed proteins and cheminformatics/mol. modeling software activities which had the advantage of targeting students' visual-spatial ability. Learning activities, conducted in small groups, were specifically designed to enhance understanding of the protein structure-function relationship through a detailed anal. of mol.-level interactions between proteins and ligands. Here we describe the methodol. for prepn. of the learning tools and how they were incorporated in the learning exercises in the form of both formative and summative assessments. We compared their perceived effectiveness via student feedback surveys conducted over three consecutive cohorts. Survey results showed students were pos. engaged with these technologies with a slight preference for cheminformatics. From an instructor's perspective, we found significantly improved overall grade avs. for the subjects following implementation of the assignments which may suggest these tools contributed to enhanced understanding. While print resoln. could not match that of cheminformatics software, we present evidence to support their continued incorporation in the course. Feedback obtained will inform future curriculum development.
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      Pinger, C. W.; Geiger, M. K.; Spence, D. M. Applications of 3D-Printing for Improving Chemistry Education. J. Chem. Educ. 2020, 97 (1), 112– 117,  DOI: 10.1021/acs.jchemed.9b00588
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      Applications of 3D-Printing for Improving Chemistry Education
      Pinger, Cody W.; Geiger, Morgan K.; Spence, Dana M.
      Journal of Chemical Education (2020), 97 (1), 112-117CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
      A review. Wide accessibility and a broad range of applications have made 3D-printers a commonplace tool in the science community. From tier-one research institutions to community public libraries and high schools, 3D-printers are being used to enrich STEM education through a variety of learning techniques and experiences. Reports of 3D-printed models for improved visualization of chem. phenomena, as well as the educational use of 3D-printed lab. devices, are rapidly increasing. The objective of this review is to provide a resource for educators interested in incorporating 3D-printing into their chem. classrooms by evaluating recent peer-reviewed reports that used this technol. to enhance chem. education.
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      Rassokhin, D. The C++ Programming Language in Cheminformatics and Computational Chemistry. J. Cheminformatics 2020, 12 (1), 10,  DOI: 10.1186/s13321-020-0415-y
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      The C++ programming language in cheminformatics and computational chemistry
      Rassokhin Dmitrii
      Journal of cheminformatics (2020), 12 (1), 10 ISSN:1758-2946.
      This paper describes salient features of the C++ programming language and its programming ecosystem, with emphasis on how the language affects scientific software development. Brief history of C++ and its predecessor the C language is provided. Most important aspects of the language that define models of programming are described in greater detail and illustrated with code examples. Special attention is paid to the interoperability between C++ and other high-level languages commonly used in cheminformatics, machine learning, data processing and statistical computing.
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      A graph-theoretical approach to structure-property relationships
      Mihalic, Zlatko; Trinajstic, Nenad
      Journal of Chemical Education (1992), 69 (9), 701-12CODEN: JCEDA8; ISSN:0021-9584.
      A graph theor. approach using topol. indexes is presented for describing QSPR. Various types of indexes are used.
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      Hansen, P. J.; Jurs, P. C. Chemical Applications of Graph Theory. Part I. Fundamentals and Topological Indices. J. Chem. Educ. 1988, 65 (7), 574,  DOI: 10.1021/ed065p574
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      Chemical applications of graph theory. Part I. Fundamentals and topological indices
      Hansen, Peter J.; Jurs, Peter C.
      Journal of Chemical Education (1988), 65 (7), 574-80CODEN: JCEDA8; ISSN:0021-9584.
      Some basic terms and concepts of graph theory are presented along with a discussion of 1 of the applications of graph theory to chem., namely, the use of topol. indexes in QSAR studies and quant. structure-property activity (QSPR) studies.
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      Krotko, D. G. Atomic Ring Invariant and Modified CANON Extended Connectivity Algorithm for Symmetry Perception in Molecular Graphs and Rigorous Canonicalization of SMILES. J. Cheminformatics 2020, 12 (1), 48,  DOI: 10.1186/s13321-020-00453-4
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      Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES
      Krotko, Dmytro G.
      Journal of Cheminformatics (2020), 12 (1), 48CODEN: JCOHB3; ISSN:1758-2946. (SpringerOpen)
      Abstr.: We propose new invariant (the product of the corresponding primes for the ring size of each bond of an atom) as a simple unambiguous ring invariant of an atom that allows distinguishing symmetry classes in the highly sym. mol. graphs using traditional local and distance atom invariants. Also, we propose modifications of Weininger's CANON algorithm to avoid its ambiguities (swapping and leveling ranks, incorrect detn. of symmetry classes in non-arom. annulenes, arbitrary selection of atom for breaking ties). The at. ring invariant and the Modified CANON algorithm allow us to create a rigorous procedure for the generation of canonical SMILES which can be used for accurate and fast structural searching in large chem. databases.
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      Probst, D.; Reymond, J.-L. Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees. J. Cheminformatics 2020, 12 (1), 12,  DOI: 10.1186/s13321-020-0416-x
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      Visualization of very large high-dimensional data sets as minimum spanning trees
      Probst Daniel; Reymond Jean-Louis
      Journal of cheminformatics (2020), 12 (1), 12 ISSN:1758-2946.
      The chemical sciences are producing an unprecedented amount of large, high-dimensional data sets containing chemical structures and associated properties. However, there are currently no algorithms to visualize such data while preserving both global and local features with a sufficient level of detail to allow for human inspection and interpretation. Here, we propose a solution to this problem with a new data visualization method, TMAP, capable of representing data sets of up to millions of data points and arbitrary high dimensionality as a two-dimensional tree (http://tmap.gdb.tools). Visualizations based on TMAP are better suited than t-SNE or UMAP for the exploration and interpretation of large data sets due to their tree-like nature, increased local and global neighborhood and structure preservation, and the transparency of the methods the algorithm is based on. We apply TMAP to the most used chemistry data sets including databases of molecules such as ChEMBL, FDB17, the Natural Products Atlas, DSSTox, as well as to the MoleculeNet benchmark collection of data sets. We also show its broad applicability with further examples from biology, particle physics, and literature.
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    52. 52
      Suzuki, M.; Nagamochi, H.; Akutsu, T. Efficient Enumeration of Monocyclic Chemical Graphs with given Path Frequencies. J. Cheminformatics 2014, 6 (1), 31,  DOI: 10.1186/1758-2946-6-31
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      Efficient enumeration of monocyclic chemical graphs with given path frequencies
      Suzuki, Masaki; Nagamochi, Hiroshi; Akutsu, Tatsuya
      Journal of Cheminformatics (2014), 6 (), 31/1-31/18, 18 pp.CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
      Background: The enumeration of chem. graphs (mol. graphs) satisfying given constraints is one of the fundamental problems in chemoinformatics and bioinformatics because it leads to a variety of useful applications including structure detn. and development of novel chem. compds. Results: We consider the problem of enumerating chem. graphs with monocyclic structure (a graph structure that contains exactly one cycle) from a given set of feature vectors, where a feature vector represents the frequency of the prescribed paths in a chem. compd. to be constructed and the set is specified by a pair of upper and lower feature vectors. To enumerate all tree-like (acyclic) chem. graphs from a given set of feature vectors, Shimizu et al. and Suzuki et al. proposed efficient branch-and-bound algorithms based on a fast tree enumeration algorithm. In this study, we devise a novel method for extending these algorithms to enumeration of chem. graphs with monocyclic structure by designing a fast algorithm for testing uniqueness. The results of computational expts. reveal that the computational efficiency of the new algorithm is as good as those for enumeration of tree-like chem. compds. Conclusions: We succeed in expanding the class of chem. graphs that are able to be enumerated efficiently.
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      Basak, S. C.; Magnuson, V. R.; Niemi, G. J.; Regal, R. R. Determining Structural Similarity of Chemicals Using Graph-Theoretic Indices. Discrete Appl. Math. 1988, 19 (1), 17– 44,  DOI: 10.1016/0166-218X(88)90004-2
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      Raymond, J. W.; Willett, P. Effectiveness of Graph-Based and Fingerprint-Based Similarity Measures for Virtual Screening of 2D Chemical Structure Databases. J. Comput. Aided Mol. Des. 2002, 16 (1), 59– 71,  DOI: 10.1023/A:1016387816342
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      Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases
      Raymond, John W.; Willett, Peter
      Journal of Computer-Aided Molecular Design (2002), 16 (1), 59-71CODEN: JCADEQ; ISSN:0920-654X. (Kluwer Academic Publishers)
      The effectiveness of the graph-based and fingerprint-based measures of structural similarity for virtual screening of sets of 2D mols. drawn from the MDDR ad ID Alert databases was evaluated. The graph-based measures employ a new max. common edge subgraph isomorphism algorithm, called RASCAL. The effectiveness of these graph-based searches is compared with that resulting from similarity searches using BCI, Daylight and Unity 2D fingerprints. The results suggest that graph-based approaches provide an effective complement to existing fingerprint-based approaches to virtual screening.
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      Hazzan, O.; Hadar, I. Reducing Abstraction When Learning Graph Theory. J. Comput. Math. Sci. Teach. 2005, 24 (3), 255– 272
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      Theisen, K. J. Programming Languages in Chemistry: A Review of HTML5/JavaScript. J. Cheminformatics 2019, 11 (1), 11,  DOI: 10.1186/s13321-019-0331-1
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      Programming languages in chemistry: a review of HTML5/JavaScript
      Theisen Kevin J
      Journal of cheminformatics (2019), 11 (1), 11 ISSN:1758-2946.
      This is one part of a series of reviews concerning the application of programming languages in chemistry, edited by Dr. Rajarshi Guha. This article reviews the JavaScript technology as it applies to the chemistry discipline. A discussion of the history, scope and technical details of the programming language is presented.
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      Amani, P.; Sneyd, T.; Preston, S.; Young, N. D.; Mason, L.; Bailey, U.-M.; Baell, J.; Camp, D.; Gasser, R. B.; Gorse, A.-D.; Taylor, P.; Hofmann, A. A Practical Java Tool for Small-Molecule Compound Appraisal. J. Cheminformatics 2015, 7 (1), 28,  DOI: 10.1186/s13321-015-0079-1
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      A practical Java tool for small-molecule compound appraisal
      Amani, Parisa; Sneyd, Todd; Preston, Sarah; Young, Neil D.; Mason, Lyndel; Bailey, Ulla-Maja; Baell, Jonathan; Camp, David; Gasser, Robin B.; Gorse, Alain-Dominique; Taylor, Paul; Hofmann, Andreas
      Journal of Cheminformatics (2015), 7 (), 28/1-28/4CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
      The increased use of small-mol. compd. screening by new users from a variety of different academic backgrounds calls for adequate software to administer, appraise, analyze and exchange information obtained from screening expts. While software and spreadsheet solns. exist, there is a need for software that can be easily deployed and is convenient to use. The Java application cApp addresses this need and aids in the handling and storage of information on small-mol. compds. The software is intended for the appraisal of compds. with respect to their physico-chem. properties, anal. in relation to adherence to likeness rules as well as recognition of pan-assay interference components and crosslinking with identical entries in the PubChem Compd. Database. Results are displayed in a tabular form in a graphical interface, but can also be written in an HTML or PDF format. The output of data in ASCII format allows for further processing of data using other suitable programs. Other features include similarity searches against user-provided compd. libraries and the PubChem Compd. Database, as well as compd. clustering based on a MaxMin algorithm. CApp is a personal database soln. for small-mol. compds. which can handle all major chem. formats. Being a standalone software, it has no other dependency than the Java virtual machine and is thus conveniently deployed. It streamlines the anal. of mols. with respect to physico-chem. properties and drug discovery criteria; cApp is distributed under the GNU Affero General Public License version 3.
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      Hanwell, M. D.; Curtis, D. E.; Lonie, D. C.; Vandermeersch, T.; Zurek, E.; Hutchison, G. R. Avogadro: An Advanced Semantic Chemical Editor, Visualization, and Analysis Platform. J. Cheminformatics 2012, 4 (1), 17,  DOI: 10.1186/1758-2946-4-17
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      Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
      Hanwell, Marcus D.; Curtis, Donald E.; Lonie, David C.; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey R.
      Journal of Cheminformatics (2012), 4 (), 17CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
      Background: The Avogadro project has developed an advanced mol. editor and visualizer designed for cross-platform use in computational chem., mol. modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building mol. structures, formatting input files, and analyzing output of a wide variety of computational chem. packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chem. data types. Results: The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chem., physics, materials science, and biol. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate mol. structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for mol. dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions: Avogadro offers a semantic chem. builder and platform for visualization and anal. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extg. chem. data from a wide variety of formats, including computational chem. output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in org. chem., inorg. complexes, drug design, materials, biomols., and simulations.
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      Hanson, R. M.; Prilusky, J.; Renjian, Z.; Nakane, T.; Sussman, J. L. JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem. 2013, 53 (3–4), 207– 216,  DOI: 10.1002/ijch.201300024
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      JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia
      Hanson, Robert M.; Prilusky, Jaime; Zhou, Renjian; Nakane, Takanori; Sussman, Joel L.
      Israel Journal of Chemistry (2013), 53 (3-4), 207-216CODEN: ISJCAT; ISSN:0021-2148. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Although Java does not run on some handheld devices, e.g., iPads and iPhones, JavaScript does. The development of JSmol, a JavaScript-only version of Jmol, is described, and its use in Proteopedia is demonstrated. A key aspect of JSmol is that it includes the full implementation of the entire set of Jmol functionalities, including file reading and writing, scripting, and rendering. The relative performances of Java-based Jmol and JavaScript-only JSmol are discussed. We can now confirm that the guiding principles of Java programming can be completely and relatively straightforwardly transformed directly into JavaScript, requiring no Java applet, and producing identical graphical results. JSmol is thus the first full-featured mol. viewer, and the first ever viewer for proteins, which can be utilized with an internet browser on handheld devices lacking Java. Since the MediaWiki features of Proteopedia have been modified to optionally use JSmol, the wealth of crowd-sourced content in Proteopedia is now directly available on such devices, without the need to download any addnl. applet.
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      Burger, M. C. ChemDoodle Web Components: HTML5 Toolkit for Chemical Graphics, Interfaces, and Informatics. J. Cheminformatics 2015, 7 (1), 35,  DOI: 10.1186/s13321-015-0085-3
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      ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics
      Burger Melanie C
      Journal of cheminformatics (2015), 7 (), 35 ISSN:1758-2946.
      ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses <canvas> and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.
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      Pernaa, J. Edumol: Avoin Ja Ilmainen Molekyylimallinnussovellus Kemian Opetuksen Tueksi. LUMAT Int. J. Math Sci. Technol. Educ. 2015, 3 (7), 960– 975,  DOI: 10.31129/lumat.v3i7.977
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      Bergwerf, H. MolView: An Attempt to Get the Cloud into Chemistry Classrooms. DivCHED CCCE: Committee on Computers in Chemical Education 2015, 1– 9
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      O’Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: An Open Chemical Toolbox. J. Cheminformatics 2011, 3 (1), 33,  DOI: 10.1186/1758-2946-3-33
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      Open Babel: an open chemical toolbox
      O'Boyle, Noel M.; Banck, Michael; James, Craig A.; Morley, Chris; Vandermeersch, Tim; Hutchison, Geoffrey R.
      Journal of Cheminformatics (2011), 3 (), 33CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
      Background: A frequent problem in computational modeling is the interconversion of chem. structures between different formats. While std. interchange formats exist (for example, Chem. Markup Language) and de facto stds. have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chem. data, differences in the data stored by different formats (0D vs. 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results: We discuss, for the first time, Open Babel, an open-source chem. toolbox that speaks the many languages of chem. data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chem. and mol. data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions: Open Babel presents a soln. to the proliferation of multiple chem. file formats. In addn., it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chem. data in areas such as org. chem., drug design, materials science, and computational chem. It is freely available under an open-source license.
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      Rodríguez-Becerra, J.; Cáceres-Jensen, L.; Diaz, T.; Druker, S.; Bahamonde Padilla, V.; Pernaa, J.; Aksela, M. Developing Technological Pedagogical Science Knowledge through Educational Computational Chemistry: A Case Study of Pre-Service Chemistry Teachers’ Perceptions. Chem. Educ. Res. Pract. 2020, 21 (2), 638– 654,  DOI: 10.1039/C9RP00273A
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      Developing technological pedagogical science knowledge through educational computational chemistry: a case study of pre-service chemistry teachers' perceptions
      Rodriguez-Becerra, Jorge; Caceres-Jensen, Lizethly; Diaz, Tatiana; Druker, Sofia; Bahamonde Padilla, Victor; Pernaa, Johannes; Aksela, Maija
      Chemistry Education Research and Practice (2020), 21 (2), 638-654CODEN: CERPCE; ISSN:1756-1108. (Royal Society of Chemistry)
      The purpose of this descriptive case study was to develop pre-service chem. teachers' Technol. Pedagogical Science Knowledge (TPASK) through novel computational chem. modules. The study consisted of two phases starting with designing a computational chem. based learning environment followed by a case study where students' perceptions toward educational computational chem. were explored. First, we designed an authentic research-based chem. learning module that supported problem-based learning through the utilization of computational chem. methods suitable for pre-service chem. education. The objective of the learning module was to promote learning of specific chem. knowledge and development of scientific skills. Systematic design decisions were made through the TPASK framework. The learning module was designed for a third-year phys. chem. course taken by pre-service chem. teachers in Chile. After the design phase, the learning module was implemented in a course, and students' perceptions were gathered using semi-structured group interviews. The sample consisted of 22 pre-service chem. teachers. Data were analyzed through qual. content anal. using the same TPASK framework employed in the learning module design. Based on our findings, pre-service chem. teachers first acquired Technol. Scientific Knowledge (TSK) and then developed some elements of their TPASK. Besides, they highly appreciated the combination of student-centered problem-based learning and the use of computational chem. tools. Students felt the educational computational learning environment supported their own knowledge acquisition and expressed an interest in applying similar learning environments in their future teaching careers. This case study demonstrates that learning through authentic real-world problems using educational computational methods offers great potential in supporting pre-service teachers' instruction in the science of chem. and pedagogy. For further research in the TPASK framework, we propose there would be significant benefit from developing new learning environments of this nature and evaluating their utility in pre-service and in-service chem. teacher's education.
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      Aksela, M.; Lundell, J. Computer-Based Molecular Modelling: Finnish School Teachers’ Experiences and Views. Chem. Educ. Res. Pract. 2008, 9 (4), 301– 308,  DOI: 10.1039/B818464J
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      Computer-based molecular modelling: Finnish school teachers' experiences and views
      Aksela, Maija; Lundell, Jan
      Chemistry Education Research and Practice (2008), 9 (4), 301-308CODEN: CERPCE ISSN:. (Royal Society of Chemistry)
      Modern-computer-based mol. modeling opens up new possibilities for chem. teaching at different levels. This article presents a case study seeking insight into Finnish school teachers' use of computer-based mol. modeling in teaching chem., into the different working and teaching methods used, and their opinions about necessary support. The study suggests that most of the teachers studied need personally to discover the benefits of mol. modeling in their own work that illustrate on a practical level how mol. modeling can provide added value for teaching and understanding school chem. Teachers state that they need more pedagogical and tech. training in mol. modeling so they can use it more and effectively in their own teaching. Furthermore, there is a need for easily adaptable learning and teaching materials to be made available to teachers in their domestic teaching language.
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      Ghani, S. S. A Comprehensive Review of Database Resources in Chemistry. Eclética Quím. J. 2020, 45 (3), 57– 68,  DOI: 10.26850/1678-4618eqj.v45.3.2020.p57-68
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      Kozlíková, B.; Krone, M.; Falk, M.; Lindow, N.; Baaden, M.; Baum, D.; Viola, I.; Parulek, J.; Hege, H.-C. Visualization of Biomolecular Structures: State of the Art Revisited: Visualization of Biomolecular Structures. Comput. Graph. Forum 2017, 36 (8), 178– 204,  DOI: 10.1111/cgf.13072
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      Vesna Savec, F.; Vrtacnik, M.; Gilbert, J. Evaluating the Educational Value of Molecular Structure Representations. In Visualization in Science Education; Gilbert, J., Ed.; Models and Modeling in Science Education; Springer Netherlands: Dordrecht, Netherlands, 2005; pp 269– 297. DOI: 10.1007/1-4020-3613-2_14
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      Jones, L. L.; Jordan, K. D.; Stillings, N. A. Molecular Visualization in Chemistry Education: The Role of Multidisciplinary Collaboration. Chem. Educ. Res. Pract. 2005, 6 (3), 136– 149,  DOI: 10.1039/B5RP90005K
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      Molecular visualization in chemistry education: The role of multidicisplinary collaboration
      Jones, Loretta L.; Jordan, Kenneth D.; Stillings, Neil A.
      Chemistry Education Research and Practice (2005), 6 (3), 136-149CODEN: CERPCE ISSN:. (Royal Society of Chemistry)
      Visualization tools and high performance computing have changed the nature of chem. research and have the promise to transform chem. instruction. However, the images central to chem. research can pose difficulties for beginning chem. students. In order for mol. visualization tools to be useful in education, students must be able to interpret the images they produce. Cognitive scientists can provide valuable insight into how novices perceive and ascribe meaning to mol. visualizations. Further insights from educators, computer scientists and developers, and graphic artists are important for chem. educators who want to help students learn with mol. visualizations. A diverse group of scientists, educators, developers, and cognitive psychologists have begun a series of international collaborations to address this issue. The effort was initiated at the National Science Foundation supported Mol. Visualization in Science Education Workshop held in 2001 and has continued through a series of mini-grants. These groups are investigating characteristics of mol. representations and visualizations that enhance learning, interactions with mol. visualizations that best help students learn about mol. structure and dynamics, roles of mol. modeling in chem. instruction, and fruitful directions for research on mol. visualization in the learning of chem. This article summarizes the value of collaboration identified by participants in the workshop and subsequent collaborations.
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      Aduldecha, S.; Akhter, P.; Field, P.; Nagle, P.; O’Sullivan, E.; O’Connor, K.; Hathaway, B. J. The Use of the Desktop Molecular Modeller Software in the Teaching of Structural Chemistry. J. Chem. Educ. 1991, 68 (7), 576,  DOI: 10.1021/ed068p576
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      The use of the Desktop Molecular Modeller software in the teaching of structural chemistry
      Aduldecha, S.; Akhter, P.; Field, P.; Nagle, P.; O'Sullivan, E.; O'Connor, K.; Hathaway, B. J.
      Journal of Chemical Education (1991), 68 (7), 576-83CODEN: JCEDA8; ISSN:0021-9584.
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      Barnea, N.; Dori, Y. J. Computerized Molecular Modeling as a Tool to Improve Chemistry Teaching. J. Chem. Inf. Comput. Sci. 1996, 36 (4), 629– 636,  DOI: 10.1021/ci950122o
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      Computerized Molecular Modeling as a Tool To Improve Chemistry Teaching
      Barnea, Nitza; Dori, Yehudit J.
      Journal of Chemical Information and Computer Sciences (1996), 36 (4), 629-636CODEN: JCISD8; ISSN:0095-2338. (American Chemical Society)
      The use of mol. models to illustrate and explore phenomena in chem. teaching is widespread. However, only one type of model is usually used, and not enough emphasis is put on its meaning. The advantage of computerized mol. modeling (CMM) stems from the convenience and simplicity of building mols. of any size and color in a no. of presentations. To expose chem. teachers to the use of CMM we developed a 14 h workshop on models. It consists of an introduction to the model concept, using various types of models (including CMM) and experiencing ways to use them for illustrating chem. structure and bonding via team projects. This workshop has been incorporated into pre- and in-service training at the Department of Education in Technol. and Science at the Technion since 1994. As a final project, teachers were asked to plan a session of 1-2 lessons by building a miniature database of mols. along with working instructions. The new methodol. is based on using CMM through a special booklet, designed in a constructivist approach. During 1995, it was implemented in three tenth grade exptl. classes with two other classes serving as a control group. Overall, teachers' attitudes toward using mol. modeling to improve chem. teaching were favorable. The effect of using mol. modeling on students' understanding and constructing new concepts was investigated in relation to chem. structure and bonding as well as to geometric and symbolic representation. In two representative questions related to three-dimensional mol. structure, the exptl. group performed better than the control group. Students' attitudes toward the use of CMM have also been found to be pos. Most of the students enjoyed using the new methodol. and indicated it helped them understand concepts in mol. geometry and bonding.
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    • Abstract

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      Figure 1

      Figure 1. Molecular graph corresponding to the carbon skeleton of 2,3,4-trimethylhexane (the graph is redrawn from ref (48)).

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      Figure 2

      Figure 2. Example of an interconversion of 0D, 2D, and 3D structures using Open Babel. All these data types can be converted to each other, exported, and finally imported into another software package for calculations or visualizations. For example, the 0D notation was retrieved from a database, converted, and exported into a 2D coordinate file for ChemDraw editing. Then, the 2D file was converted into 3D coordinates and exported to a mol2 format, which was imported to Avogadro for geometrical optimization and 3D image production.

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      Figure 3

      Figure 3. Possibilities that CBMV offers for teaching and learning submicrolevel chemistry.

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      Figure 4

      Figure 4. Overview of the designed cheminformatics activity and its relation to the STEM framework.

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        4
        Applications of Systems Thinking in STEM Education
        York, Sarah; Lavi, Rea; Dori, Yehudit Judy; Orgill, MaryKay
        Journal of Chemical Education (2019), 96 (12), 2742-2751CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        A review. Systems thinking is a holistic approach for examg. complex problems and systems that focuses on the interactions among system components and the patterns that emerge from those interactions. Systems thinking can help students develop higher-order thinking skills in order to understand and address complex, interdisciplinary, real-world problems. Because of these potential benefits, there have been recent efforts to support the implementation of systems thinking approaches in chem. education, including the development of the IUPAC Systems Thinking in Chem. Education (STICE) Project and this Special Issue of the Journal of Chem. Education: "Reimagining Chem. Education: Systems Thinking, and Green and Sustainable Chem.". As part of these efforts, our purposes in this paper are to describe some of the potential benefits assocd. with systems thinking approaches, to identify the STEM education fields that have employed systems thinking approaches, to summarize some of the major findings about the applications of systems thinking in STEM education, and to present methods that have been used to assess systems thinking skills in STEM education. We found that, in general, systems thinking approaches have been applied in life sciences, earth sciences, and engineering but not in the phys. or math. sciences. We also found that the primary emphasis of peer-reviewed publications was on the development of students', rather than teachers', systems thinking abilities. Existing tools for the assessment of systems thinking in STEM education can be divided into (a) assessment rubrics, (b) closed-ended tools, and (c) coding schemes, with each type of assessment tool having its own unique advantages and disadvantages. We highlight one particular case in which researchers applied an interdisciplinary framework for comprehensive assessment of systems thinking. Although systems thinking has not been widely researched or applied in chem. education, many of the conceptual frameworks applied to systems thinking in other STEM education disciplines could potentially be applied in chem. education. We argue that the benefits obsd. when applying systems thinking approaches in other STEM education disciplines could facilitate similar results for chem. education. Finally, we provide considerations for future research and applications of systems thinking in chem. education.
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      5. 5
        Sanders, M. STEM, STEM Education, STEMmania. The Technology Teacher 2009, December/January, 20– 26
        There is no corresponding record for this reference.
      6. 6
        Weidman, J.; Wright, G. Promoting Construction Education in K-12 by Using an Experiential, Student-Centered, STEM-Infused Construction Unit. Technol. Eng. Teach. 2019, 79 (1), 8– 12
        There is no corresponding record for this reference.
      7. 7
        Gago, J. M.; Ziman, J.; Caro, P.; Constantinou, C.; Davies, G.; Parchmann, I.; Rannikmae, M.; Sjøberg, S. Europe Needs More Scientists: Report by the High Level Group on Increasing Human Resources for Science and Technology; European Communities: Luxembourg, Belgium, 2005.
        There is no corresponding record for this reference.
      8. 8
        Lavonen, J.; Juuti, K.; Uitto, A.; Meisalo, V.; Byman, R. Attractiveness of Science Education in the Finnish Comprehensive School. Research findings on young people’s perceptions of technology and science education; Technology Industries of Finland: Helsinki, Finland, 2005; pp 5– 30.
        There is no corresponding record for this reference.
      9. 9
        Hofstein, A.; Mamlok-Naaman, R. High-School Students Attitudes toward and Interest in Learning Chemistry. Educ. Quím. 2011, 22 (2), 90– 102,  DOI: 10.1016/S0187-893X(18)30121-6
        There is no corresponding record for this reference.
      10. 10
        Musengimana, J.; Kampire, E.; Ntawiha, P. Factors Affecting Secondary Schools Students’ Attitudes toward Learning Chemistry: A Review of Literature. Eurasia J. Math. Sci. Technol. Educ. 2021, 17 (1), em1931  DOI: 10.29333/ejmste/9379
        There is no corresponding record for this reference.
      11. 11
        Osborne, J.; Simon, S.; Collins, S. Attitudes towards Science: A Review of the Literature and Its Implications. Int. J. Sci. Educ. 2003, 25 (9), 1049– 1079,  DOI: 10.1080/0950069032000032199
        There is no corresponding record for this reference.
      12. 12
        Osborne, J.; Dillon, J. Science Education in Europe: Critical Reflections, Report to the Nuffield Foundation; King’s College London: London, UK, 2008; pp 1– 32.
        There is no corresponding record for this reference.
      13. 13
        Astin, A. W.; Astin, H. S. Undergraduate Science Education: The Impact of Different College Environments on the Educational Pipeline in the Sciences; Final Report; Higher Education Research Institute, Graduate School of Education, University of California: Los Angeles, CA, 1992; p 384.
        There is no corresponding record for this reference.
      14. 14
        Chen, X.; Soldner, M. Statistical Analysis Report NCES 2014-001. STEM Attrition: College Students’ Paths Into and Out of STEM Fields; National Center for Education Statistics, Institute of Education Sciences, U.S. Department of Education: Washington, DC, 2013.
        There is no corresponding record for this reference.
      15. 15
        Hailikari, T. K.; Nevgi, A. How to Diagnose At-Risk Students in Chemistry: The Case of Prior Knowledge Assessment. Int. J. Sci. Educ. 2010, 32 (15), 2079– 2095,  DOI: 10.1080/09500690903369654
        There is no corresponding record for this reference.
      16. 16
        Heublein, U.; Schmelzer, R. Die Entwicklung der Studienabbruchquoten an den deutschen Hochschulen - Berechnungen auf Basis des Absolventenjahrgangs 2016 (Eng. The development of dropout rates at German universities - calculations based on the graduate year 2016); DZHW-Projektbericht; Deutsches Zentrum für Hochschul- und Wissenschaftsforschung (DZHW): Hannover, Germany, 2018.
        There is no corresponding record for this reference.
      17. 17
        Burrows, A. C.; Breiner, J. M.; Keiner, J.; Behm, C. Biodiesel and Integrated STEM: Vertical Alignment of High School Biology/Biochemistry and Chemistry. J. Chem. Educ. 2014, 91 (9), 1379– 1389,  DOI: 10.1021/ed500029t
        17
        Biodiesel and Integrated STEM: Vertical Alignment of High School Biology/Biochemistry and Chemistry
        Burrows, Andrea C.; Breiner, Jonathan M.; Keiner, Jennifer; Behm, Chris
        Journal of Chemical Education (2014), 91 (9), 1379-1389CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        This article explores the vertical alignment of two high school classes, biol. and chem., around the core concept of biodiesel fuel prodn. High school teachers and university faculty members investigated biodiesel as it relates to societal impact through a National Science Foundation Research Experience for Teachers. Using an action research approach, two high school teachers created and implemented biodiesel lessons in both biol. (biochem. algae focus) and chem. (transesterification focus). This article describes the extent to which this integrated STEM biodiesel lesson, which is vertically aligned in one high school, affected the students' skills and attitudes in relation to STEM subjects. The lesson plans used and the student outcomes based on the biodiesel activities are provided on the basis of a year's implementation. Overall, student skill sets and attitudes improved based on pre-posttest data and classroom indicators, such as student questions. One implication of this work includes a stronger integrated STEM vertical curriculum that could be implemented in any biol. and chem. program, esp. in advanced placement (AP) classes such as AP chem., to encourage and engage students in discovery, inquiry-based learning, problem-based learning, engineering design, and creating expts. that have a real-world applicability such as those with socio-scientific issues. The notion that science disciplines are an interconnected web of concepts is highlighted. This contribution is part of a special issue on teaching introductory chem. in the context of the advanced placement chem. course redesign.
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      18. 18
        Chonkaew, P.; Sukhummek, B.; Faikhamta, C. STEM Activities in Determining Stoichiometric Mole Ratios for Secondary-School Chemistry Teaching. J. Chem. Educ. 2019, 96 (6), 1182– 1186,  DOI: 10.1021/acs.jchemed.8b00985
        18
        STEM Activities in Determining Stoichiometric Mole Ratios for Secondary-School Chemistry Teaching
        Chonkaew, Patcharee; Sukhummek, Boonnak; Faikhamta, Chatree
        Journal of Chemical Education (2019), 96 (6), 1182-1186CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        A review. This article provides teachers with a guideline on how to create a science, technol., engineering, and mathematics (STEM) hands-on environment and prep. a small lab kit for detg. stoichiometric mole ratios of the reaction between hydrogen gas and oxygen gas for secondary-school students. This guideline will provide teachers with a low-cost, simple and rapid workstation allowing and encouraging small groups of students to gain hands-on experience. The small lab kit is developed based on the principle of green chem. resulting in less chem. usage, less time consumption and less waste prodn. This article also provides related STEM activities to improve the engagements, aspirations and attitudes of students toward science and technol. These activities provide students with a chance to explore the stoichiometric mole ratio concepts and challenge them toward STEM.
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      19. 19
        Donnelly, J.; Diaz, C.; Hernandez, F. E. OCTET and BIOTEC: A Model of a Summer Intensive Camp Designed To Cultivate the Future Generation of Young Leaders in STEM. J. Chem. Educ. 2016, 93 (4), 619– 625,  DOI: 10.1021/acs.jchemed.5b00664
        19
        OCTET and BIOTEC: A Model of a Summer Intensive Camp Designed To Cultivate the Future Generation of Young Leaders in STEM
        Donnelly, Julie; Diaz, Carlos; Hernandez, Florencio E.
        Journal of Chemical Education (2016), 93 (4), 619-625CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        Herein, we describe an effective and tested model of a week-long summer science intensive program for high school students that aimed to elaborate on concepts covered in a high school chem. or biol. course, and to provide high school students an opportunity to learn about studying and pursuing careers in the sciences. The program was developed to combine instructional sessions, hands-on activities, and lab. tours in order to review and build upon what students learn in high school. Student assessment and feedback confirms the effectiveness of this student-run program to teach and inspire high school students to pursue the sciences in their academic career.
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      20. 20
        Enlow, J. L.; Marin, D. M.; Walter, M. G. Using Polymer Semiconductors and a 3-in-1 Plastic Electronics STEM Education Kit To Engage Students in Hands-On Polymer Inquiry Activities. J. Chem. Educ. 2017, 94 (11), 1714– 1720,  DOI: 10.1021/acs.jchemed.7b00332
        20
        Using Polymer Semiconductors and a 3-in-1 Plastic Electronics STEM Education Kit To Engage Students in Hands-On Polymer Inquiry Activities
        Enlow, Jessica L.; Marin, Dawn M.; Walter, Michael G.
        Journal of Chemical Education (2017), 94 (11), 1714-1720CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        To improve polymer education for 9-12 and undergraduate students, a plastic electronics lab. kit using polymer semiconductors has been developed. The three-module kit and curriculum use polymer semiconductors to provide hands-on inquiry activities with overlapping themes of elec. cond., light emission, and light-harvesting solar energy conversion. Many of these themes are crit. to contemporary polymer mol. electronics research. The kit includes modules to synthesize and evaluate the elec. properties of conductive colloidal polyaniline (PAni), to construct a polymer light-emitting diode using poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV), and to build a polymer solar cell using MEH-PPV and nanoparticulate TiO2. Designed initially for high school science classrooms, the activities developed also meet new ACS undergraduate education requirements for macromol., supramol., and nanoscale systems in the curriculum and can be used in undergraduate teaching labs. The modules and kit have also been implemented in professional development workshops for training 9-12 science educators to help integrate the activities into their classrooms.
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      21. 21
        Graham, K. J.; McIntee, E. J.; Raigoza, A. F.; Fazal, M. A.; Jakubowski, H. V. Activities in an S-STEM Program To Catalyze Early Entry into Research. J. Chem. Educ. 2017, 94 (2), 177– 182,  DOI: 10.1021/acs.jchemed.6b00338
        21
        Activities in an S-STEM Program To Catalyze Early Entry into Research
        Graham, Kate J.; McIntee, Edward J.; Raigoza, Annette F.; Abul Fazal, M.; Jakubowski, Henry V.
        Journal of Chemical Education (2017), 94 (2), 177-182CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        A cohort program to increase retention of under-represented groups in chem. was developed at the College of Saint Benedict/Saint John's University. In particular, this program chose to emphasize early career mentoring and early access to research. This goal was chosen because research has been repeatedly shown to increase scientific identity resulting in increased retention of students in the STEM fields. Several elements of this program have been useful in prepg. students to access research programs early in their college careers including a summer bridge program, career mentoring, advising, and a second year "research bootcamp" course.
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      22. 22
        Levine, M.; Serio, N.; Radaram, B.; Chaudhuri, S.; Talbert, W. Addressing the STEM Gender Gap by Designing and Implementing an Educational Outreach Chemistry Camp for Middle School Girls. J. Chem. Educ. 2015, 92 (10), 1639– 1644,  DOI: 10.1021/ed500945g
        22
        Addressing the STEM Gender Gap by Designing and Implementing an Educational Outreach Chemistry Camp for Middle School Girls
        Levine, Mindy; Serio, Nicole; Radaram, Bhasker; Chaudhuri, Sauradip; Talbert, William
        Journal of Chemical Education (2015), 92 (10), 1639-1644CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        There continues to be a persistent, widespread gender gap in multiple STEM disciplines at all educational and professional levels: from the self-reported interest of preschool aged students in scientific exploration to the percentages of tenured faculty in these disciplines, more men than women express an interest in science, a confidence in their scientific abilities, and ultimately decide to pursue scientific careers. Reported herein is an intensive outreach effort focused on addressing this gender gap: a full-time, week-long chem. camp that was designed and implemented for middle school girls in the state of Rhode Island. The camp schedule included multiple hands-on expts., field trips, and significant interactions with female scientists, all of which were designed to increase the participants' interest in and enthusiasm for science. The success of the program in changing the participants' attitudes toward science was measured through administration of a precamp and postcamp survey, and the survey results demonstrated a strong success in changing the participants' attitudes toward the widespread applicability of science, their perceived level of support for scientific study, and their interest in pursuing STEM-related careers.
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      23. 23
        Mutambuki, J. M.; Fynewever, H.; Douglass, K.; Cobern, W. W.; Obare, S. O. Integrating Authentic Research Experiences into the Quantitative Analysis Chemistry Laboratory Course: STEM Majors’ Self-Reported Perceptions and Experiences. J. Chem. Educ. 2019, 96 (8), 1591– 1599,  DOI: 10.1021/acs.jchemed.8b00902
        23
        Integrating Authentic Research Experiences into the Quantitative Analysis Chemistry Laboratory Course: STEM Majors' Self-Reported Perceptions and Experiences
        Mutambuki, Jacinta M.; Fynewever, Herb; Douglass, Kevin; Cobern, William W.; Obare, Sherine O.
        Journal of Chemical Education (2019), 96 (8), 1591-1599CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        Integrating authentic research-based experiences that mimic real-world scientific practices and relevance to student personal life into a chem. curriculum can make abstr. chem. principles more palpable to students. Unfortunately, many reported research-based experiences chem. lab. expts. lack relevance to a student's personal life. Addnl., the impact of a "relevant" authentic research-based experience curriculum on students' affective outcomes beyond the General Chem. courses has been overlooked. Two authentic research experiences modules developed around nanotechnol. applications were implemented in a Quant. Anal. Chem. lab. course for STEM majors. A follow-up study assessed the STEM majors' perceptions of the learning environment and the organization of lab after exposure to both conventional expts. and authentic research-based experiences modules, as well as their perceived learning gains and the relevance of the lab. expts. Data were collected through validated surveys, and open-ended survey items and classroom observations. There were 55 students who participated in the study. Results showed significant improvements of students' perceptions of learning environment and organization of the lab., favoring authentic research experiences modules over the conventional expts. Self-reported learning gains and relevance of the expts. to students were also assocd. with the authentic research-based expts. Students' perceptions favoring the intervention modules related to learning through scientific inquiry, content relevance to real-world applications and student personal life, and use of real-world materials and a wide array of chem. instruments and techniques. Results imply the need to implement authentic research-based experiences centered on real-world issues and student personal life in the chem. lab. courses.
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      24. 24
        Rogosic, R.; Heidt, B.; Passariello-Jansen, J.; Björnör, S.; Bonni, S.; Dimech, D.; Arreguin-Campos, R.; Lowdon, J.; Jiménez Monroy, K. L.; Caldara, M.; Eersels, K.; van Grinsven, B.; Cleij, T. J.; Diliën, H. Modular Science Kit as a Support Platform for STEM Learning in Primary and Secondary School. J. Chem. Educ. 2021, 98 (2), 439– 444,  DOI: 10.1021/acs.jchemed.0c01115
        24
        Modular Science Kit as a support platform for STEM learning in primary and secondary school
        Rogosic, Renato; Heidt, Benjamin; Passariello-Jansen, Juliette; Bjoernoer, Saga; Bonni, Silvio; Dimech, David; Arreguin-Campos, Rocio; Lowdon, Joseph; Jimenez Monroy, Kathia L.; Caldara, Manlio; Eersels, Kasper; van Grinsven, Bart; Cleij, Thomas J.; Dilien, Hanne
        Journal of Chemical Education (2021), 98 (2), 439-444CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        The need to develop interest for STEM (science, technol., engineering and mathematics) skills in young pupils has driven many educational systems to include STEM as a subject in primary schools. In this work, a science kit aimed to children from 8 to 14 years old is presented as a support platform for an innovative and stimulating approach to STEM learning. The peculiar design of the kit, based on modular components, is aimed to help develop a multitude of skills in the young students, dividing the learning process in two phases. During phase 1 the pupils build the exptl. setup and visualize the scientific phenomena while in phase 2, they are introduced and challenged to understand the principles on which these phenomena are based, guided by handbook. This approach aims at making the experience more inclusive, stimulating the interest and passion of the pupils for scientific subjects.
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      25. 25
        Schmidt, E.; Vik, R.; Brubaker, B. W.; Abdulahad, S. S.; Soto-Olson, D. K.; Monjure, T. A.; Battle, C. H.; Jayawickramarajah, J. Increasing Student Interest and Self-Efficacy in STEM by Offering a Service-Learning Chemistry Course in New Orleans. J. Chem. Educ. 2020, 97 (11), 4008– 4018,  DOI: 10.1021/acs.jchemed.9b01140
        25
        Increasing Student Interest and Self-Efficacy in STEM by Offering a Service-Learning Chemistry Course in New Orleans
        Schmidt, Emily; Vik, Ryan; Brubaker, Benjamin W.; Abdulahad, Sienna S.; Soto-Olson, Diana K.; Monjure, Tia A.; Battle, Cooper H.; Jayawickramarajah, Janarthanan
        Journal of Chemical Education (2020), 97 (11), 4008-4018CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        A review. There is a growing need for workers with STEM-aligned training in the modern global economy, but a paucity of workers to fill these positions. One important contributor to this issue is low student persistence in STEM. Nontraditional science courses that utilize more active-participation and learning are attractive as tools to increase student persistence and engender more interest in STEM. Herein is described the content and implementation of the undergraduate chem.-based service-learning course, Chem. 1898: Service Learning, that was offered in Spring 2019 at Tulane University. The goal of the course was to increase self-efficacy in chem. and sustain undergraduate interest in STEM. The course also serves to increase STEM interest in the New Orleans public-school students. Chem. 1898 features a well-rounded curriculum and diverse activities. The enrolled undergraduate students were not only taught chem. concepts (general chem. and supramol. chem.) but also asked to present the chem. concepts using attention-grabbing demonstrations to public-school students in the New Orleans area. In addn., the course covered multiple nonscience topics, including the pedagogy of service-learning, background on the New Orleans public-school system, and a guide for how to work with the community. The course also involved student reflection activities/surveys and interfaced with the Tulane Center for Public Service. Preliminary qual. results from a set of anonymous pre- and poststudent surveys indicated that the undergraduate students gained self-efficacy in the general chem. concepts covered in the course. Although the course did not have an effect on the career choices of the undergraduate students, the majority of the students were already very interested in a STEM career. Further, some students mentioned gaining a benefit in public speaking skills, and some considered the possibility of teaching and working with children in the future.
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      26. 26
        White, D.; Delaney, S. Full STEAM Ahead, but Who Has the Map? - A PRISMA Systematic Review on the Incorporation of Interdisciplinary Learning into Schools. LUMAT Int. J. Math Sci. Technol. Educ. 2021, 9 (2), 9– 32,  DOI: 10.31129/LUMAT.9.2.1387
        There is no corresponding record for this reference.
      27. 27
        Thibaut, L.; Ceuppens, S.; Loof, H. D.; Meester, J. D.; Goovaerts, L.; Struyf, A.; Pauw, J. B.; Dehaene, W.; Deprez, J.; Cock, M. D.; Hellinckx, L.; Knipprath, H.; Langie, G.; Struyven, K.; Velde, D. V. de; Petegem, P. V.; Depaepe, F. Integrated STEM Education: A Systematic Review of Instructional Practices in Secondary Education. Eur. J. STEM Educ. 2018, 3 (1), 02,  DOI: 10.20897/ejsteme/85525
        There is no corresponding record for this reference.
      28. 28
        Eckman, E.; Williams, M.; Silver-Thorn, M. An Integrated Model for STEM Teacher Preparation: The Value of a Teaching Cooperative Educational Experience. J. STEM Teach. Educ. 2016, 51 (1), 1,  DOI: 10.30707/JSTE51.1Eckman
        There is no corresponding record for this reference.
      29. 29
        Willett, P. Chemoinformatics: A History. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2011, 1 (1), 46– 56,  DOI: 10.1002/wcms.1
        29
        Chemoinformatics: a history
        Willett, Peter
        Wiley Interdisciplinary Reviews: Computational Molecular Science (2011), 1 (1), 46-56CODEN: WIRCAH; ISSN:1759-0884. (Wiley-Blackwell)
        This paper gives a brief history of the development of chemoinformatics since the first studies in the late 1950s and early 1960s of methods for searching databases of chem. mols. and for predicting their biol. and chem. properties. Topics, and assocd. key papers, that are discussed include: structure, substructure, and similarity searching; the processing of generic chem. structures and of chem. reactions; chem. expert systems; the identification of qual. and quant. structure-activity relationships in both two and three dimensions; pharmacophore anal.; ligand-protein docking; mol. diversity anal.; and drug-likeness studies. Brief mention is also made of other important areas such as computer-assisted synthesis design and computer-assisted structure elucidation.
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      30. 30
        Willett, P. The Literature of Chemoinformatics: 1978–2018. Int. J. Mol. Sci. 2020, 21 (15), 5576,  DOI: 10.3390/ijms21155576
        There is no corresponding record for this reference.
      31. 31
        Journal of Chemical Information and Modeling. About the Journal. https://pubs.acs.org/page/jcisd8/about.html (accessed 2021-05-21). DOI: 10.1021/jcisd8
        There is no corresponding record for this reference.
      32. 32
        Journal of Cheminformatics. Aims and scope. https://jcheminf.biomedcentral.com/submission-guidelines/aims-and-scope (accessed 2020-08-28).
        There is no corresponding record for this reference.
      33. 33
        Leach, A. R.; Gillet, V. J. An Introduction to Chemoinformatics; Springer: Dordrecht; London, 2007.
        There is no corresponding record for this reference.
      34. 34
        Chemoinformatics: A Textbook; Gasteiger, J., Engel, T., Eds.; Wiley-VCH: Weinheim, Germany, 2003.
        There is no corresponding record for this reference.
      35. 35
        Ray, L. C.; Kirsch, R. A. Finding Chemical Records by Digital Computers. Science 1957, 126 (3278), 814– 819,  DOI: 10.1126/science.126.3278.814
        35
        Finding Chemical Records by Digital Computers
        Ray L C; Kirsch R A
        Science (New York, N.Y.) (1957), 126 (3278), 814-9 ISSN:0036-8075.
        There is no expanded citation for this reference.
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      36. 36
        Li, L.; Hu, J.; Ho, Y.-S. Global Performance and Trend of QSAR/QSPR Research: A Bibliometric Analysis. Mol. Inform. 2014, 33 (10), 655– 668,  DOI: 10.1002/minf.201300180
        36
        Global Performance and Trend of QSAR/QSPR Research: A Bibliometric Analysis
        Li, Li; Hu, Jianxin; Ho, Yuh-Shan
        Molecular Informatics (2014), 33 (10), 655-668CODEN: MIONBS; ISSN:1868-1743. (Wiley-VCH Verlag GmbH & Co. KGaA)
        A bibliometric anal. based on the Science Citation Index Expanded was conducted to provide insights into the publication performance and research trend of quant. structure-activity relationship (QSAR) and quant. structure-property relationship (QSPR) from 1993 to 2012. The results show that the no. of articles per yr quadrupled from 1993 to 2006 and plateaued since 2007. Journal of Chem. Information and Modeling was the most prolific journal. The internal methodol. innovations in acquiring mol. descriptors and modeling stimulated the articles' increase in the research fields of drug design and synthesis, and chemoinformatics; while the external regulatory demands on model validation and reliability fueled the increase in environmental sciences. "Prediction endpoints", "statistical algorithms", and "mol. descriptors" were identified as three research hotspots. The articles from developed countries were larger in no. and more influential in citation, whereas those from developing countries were higher in output growth rates.
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      37. 37
        Martinez-Mayorga, K.; Madariaga-Mazon, A.; Medina-Franco, J. L.; Maggiora, G. The Impact of Chemoinformatics on Drug Discovery in the Pharmaceutical Industry. Expert Opin. Drug Discovery 2020, 15 (3), 293– 306,  DOI: 10.1080/17460441.2020.1696307
        37
        The impact of chemoinformatics on drug discovery in the pharmaceutical industry
        Martinez-Mayorga, Karina; Madariaga-Mazon, Abraham; Medina-Franco, Jose L.; Maggiora, Gerald
        Expert Opinion on Drug Discovery (2020), 15 (3), 293-306CODEN: EODDBX; ISSN:1746-0441. (Taylor & Francis Ltd.)
        A review. Even though there have been substantial advances in our understanding of biol. systems, research in drug discovery is only just now beginning to utilize this type of information. The single-target paradigm, which exemplifies the reductionist approach, remains a mainstay of drug research today. A deeper view of the complexity involved in drug discovery is necessary to advance on this field.: This perspective provides a summary of research areas where cheminformatics has played a key role in drug discovery, including of the available resources as well as a personal perspective of the challenges still faced in the field.: Although great strides have been made in the handling and anal. of biol. and pharmacol. data, more must be done to link the data to biol. pathways. This is crucial if one is to understand how drugs modify disease phenotypes, although this will involve a shift from the single drug/single target paradigm that remains a mainstay of drug research. Moreover, such a shift would require an increased awareness of the role of physiol. in the mechanism of drug action, which will require the introduction of new math., computer, and biol. methods for chemoinformaticians to be trained in.
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      38. 38
        Wild, D. J. Cheminformatics for the Masses: A Chance to Increase Educational Opportunities for the next Generation of Cheminformaticians. J. Cheminformatics 2013, 5, 32,  DOI: 10.1186/1758-2946-5-32
        38
        Cheminformatics for the masses: a chance to increase educational opportunities for the next generation of cheminformaticians
        Wild, David J.
        Journal of Cheminformatics (2013), 5 (), 32CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
        A review. This paper describes the cheminformatics for masses and a chance to increase educational opportunities for next generation of cheminformaticians.
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      39. 39
        Romero, R. M.; Bolger, M. B.; Morningstar-Kywi, N.; Haworth, I. S. Teaching of Biopharmaceutics in a Drug Design Course: Use of GastroPlus as Educational Software. J. Chem. Educ. 2020, 97 (8), 2212– 2220,  DOI: 10.1021/acs.jchemed.0c00401
        39
        Teaching of Biopharmaceutics in a Drug Design Course: Use of GastroPlus as Educational Software
        Romero, Rebecca M.; Bolger, Michael B.; Morningstar-Kywi, Noam; Haworth, Ian S.
        Journal of Chemical Education (2020), 97 (8), 2212-2220CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        In early-stage drug design, establishment of promising drug candidates requires integration of structure-based mol. design with biopharmaceutics and ADMET. Thus, students in a drug design course should learn the basis for and effects of candidate small mols. binding to therapeutic targets and the importance of simultaneous understanding of ADMET characteristics that will largely det. if the mol. can achieve a therapeutically relevant concn. at the target site and become an orally deliverable drug. This second aspect of education in drug design has been relatively overlooked compared to structure-based design. Here, we describe a course using sophisticated simulation and modeling software, GastroPlus and ADMET Predictor, which are commonly used in the pharmaceutical industry. We use a combination of short lectures, software demonstration, and hands-on use, which allows students to "design a drug" with incorporation of structural and ADMET considerations. Student feedback indicated that the use of the software and the course design were helpful in enhancing their understanding of the importance of biopharmaceutics properties and ADMET in drug design. GastroPlus and ADMET Predictor have recently become more accessible to educators, and our experience using this software in an educational setting may be helpful for instructors who wish to develop a similar course.
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      40. 40
        D’Ambruoso, G. D.; Cremeens, M. E.; Hendricks, B. R. Web-Based Animated Tutorials Using Screen Capturing Software for Molecular Modeling and Spectroscopic Acquisition and Processing. J. Chem. Educ. 2018, 95 (4), 666– 671,  DOI: 10.1021/acs.jchemed.7b00511
        There is no corresponding record for this reference.
      41. 41
        Evans, M. J.; Moore, J. S. A Collaborative, Wiki-Based Organic Chemistry Project Incorporating Free Chemistry Software on the Web. J. Chem. Educ. 2011, 88 (6), 764– 768,  DOI: 10.1021/ed100517g
        41
        A Collaborative, Wiki-Based Organic Chemistry Project Incorporating Free Chemistry Software on the Web
        Evans, Michael J.; Moore, Jeffrey S.
        Journal of Chemical Education (2011), 88 (6), 764-768CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        In recent years, postsecondary instructors have recognized the potential of wikis to transform the way students learn in a collaborative environment. However, few instructors have embraced in-depth student use of chem. software for the creation of interactive chem. content on the Web. Using currently available software, students are able to design, build, and describe computational mol. models with a high degree of independence. For a second-semester org. chem. course with biochem. applications, we designed and implemented a wiki-based project that involved student development of Web pages presenting the mechanism of action of a mol. of their choice. Student feedback supports the value of the project as a means to help students apply course content to biochem. applications. Org. chem. instructors may benefit from the experience we gained while designing and implementing an org. chem. wiki project.
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      42. 42
        Marson, G. A.; Torres, B. B. Fostering Multirepresentational Levels of Chemical Concepts: A Framework To Develop Educational Software. J. Chem. Educ. 2011, 88 (12), 1616– 1622,  DOI: 10.1021/ed100819u
        42
        Fostering Multirepresentational Levels of Chemical Concepts: A Framework To Develop Educational Software
        Marson, Guilherme A.; Torres, Bayardo B.
        Journal of Chemical Education (2011), 88 (12), 1616-1622CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        This work presents a convenient framework for developing interactive chem. education software to facilitate the integration of macroscopic, microscopic, and symbolic dimensions of chem. concepts-specifically, via the development of software for gel permeation chromatog. The instructional role of the software was evaluated in a study involving 237 undergraduates. The results suggest that the software fostered transition from lower- to higher-order cognitive reasoning. Common misconceptions regarding microscopic phenomena were also detected and addressed.
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      43. 43
        Jirat, J.; Cech, P.; Znamenacek, J.; Simek, M.; Skuta, C.; Vanek, T.; Dibuszova, E.; Nic, M.; Svozil, D. Developing and Implementing a Combined Chemistry and Informatics Curriculum for Undergraduate and Graduate Students in the Czech Republic. J. Chem. Educ. 2013, 90 (3), 315– 319,  DOI: 10.1021/ed3001446
        43
        Developing and Implementing a Combined Chemistry and Informatics Curriculum for Undergraduate and Graduate Students in the Czech Republic
        Jirat, Jiri; Cech, Petr; Znamenacek, Jiri; Simek, Miroslav; Skuta, Ctibor; Vanek, Tomas; Dibuszova, Eva; Nic, Miloslav; Svozil, Daniel
        Journal of Chemical Education (2013), 90 (3), 315-319CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        Experience developing multidisciplinary bachelor's and master's curricula involving intertwined chem., informatics, and librarianship-editorship skills is described. The bachelor's curriculum was created in close cooperation of academic staff, library staff, and the publishing house staff (Institute of Chem. Technol. Prague: a sole publisher of chem. literature in Czech Republic), with the aim to educate a new generation of information retrieval and e-publishing professionals in the science-technol.-medicine (STM) field. This cooperation together with a set of specifically tailored courses gave students the insights into real-world issues of STM publishing. The master's curriculum, heavily relying on the bachelor's stage, inclines towards cheminformatics and deepens software engineering skills. Successes, pitfalls, and failures are described, together with proposed changes and future directions.
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      44. 44
        Kamijo, H.; Morii, S.; Yamaguchi, W.; Toyooka, N.; Tada-Umezaki, M.; Hirobayashi, S. Creating an Adaptive Technology Using a Cheminformatics System To Read Aloud Chemical Compound Names for People with Visual Disabilities. J. Chem. Educ. 2016, 93 (3), 496– 503,  DOI: 10.1021/acs.jchemed.5b00217
        44
        Creating an Adaptive Technology Using a Cheminformatics System To Read Aloud Chemical Compound Names for People with Visual Disabilities
        Kamijo, Haruo; Morii, Shingo; Yamaguchi, Wataru; Toyooka, Naoki; Tada-Umezaki, Masahito; Hirobayashi, Shigeki
        Journal of Chemical Education (2016), 93 (3), 496-503CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        Various tactile methods, such as Braille, have been employed to enhance the recognition ability of chem. structures by individuals with visual disabilities. However, it is unknown whether reading aloud the names of chem. compds. would be effective in this regard. There are no systems currently available using an audio component to assist in the recognition of chem. structures. This study aims to establish the essential requirements for the prototype Chem. Literature Extn. and Aloud-reading System (CLeArS) that enables visually impaired people to recognize a depicted chem. structure after hearing its name, which complies with the nomenclature adopted by the International Union of Pure and Applied Chem. Details of the methods employed in CLeArS and its execution are presented, in addn. to the fundamental requirements for recognizing chem. structures using CLeArS. Exptl. results on 450 images comprising both simple and complex chem. structures show a high recognition rate of 90% among subjects with visual disabilities. Thus, we conclude that reading aloud the names of chem. compds. is an effective method enabling students with impaired vision to recognize chem. structures.
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      45. 45
        Lohning, A. E.; Hall, S.; Dukie, S. Enhancing Understanding in Biochemistry Using 3D Printing and Cheminformatics Technologies: A Student Perspective. J. Chem. Educ. 2019, 96 (11), 2497– 2502,  DOI: 10.1021/acs.jchemed.8b00965
        45
        Enhancing Understanding in Biochemistry Using 3D Printing and Cheminformatics Technologies: A Student Perspective
        Lohning, Anna E.; Hall, Susan; Dukie, Shailandra
        Journal of Chemical Education (2019), 96 (11), 2497-2502CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        Students often approach biochem. with a degree of trepidation with many considering it one of the more difficult subjects. This is, in part, due to the necessity of making visual images of submicroscopic concepts. Mol. interactions underpin most biol. processes; therefore, mastering these concepts is essential. Understanding the forces and mechanisms that underpin protein-ligand interactions is a key learning goal for mastering the protein structure-function relationship. We intended to overcome such learning barriers by implementing assignment-based activities across three successive biochem. cohorts. The activities involved 3D printed proteins and cheminformatics/mol. modeling software activities which had the advantage of targeting students' visual-spatial ability. Learning activities, conducted in small groups, were specifically designed to enhance understanding of the protein structure-function relationship through a detailed anal. of mol.-level interactions between proteins and ligands. Here we describe the methodol. for prepn. of the learning tools and how they were incorporated in the learning exercises in the form of both formative and summative assessments. We compared their perceived effectiveness via student feedback surveys conducted over three consecutive cohorts. Survey results showed students were pos. engaged with these technologies with a slight preference for cheminformatics. From an instructor's perspective, we found significantly improved overall grade avs. for the subjects following implementation of the assignments which may suggest these tools contributed to enhanced understanding. While print resoln. could not match that of cheminformatics software, we present evidence to support their continued incorporation in the course. Feedback obtained will inform future curriculum development.
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      46. 46
        Pinger, C. W.; Geiger, M. K.; Spence, D. M. Applications of 3D-Printing for Improving Chemistry Education. J. Chem. Educ. 2020, 97 (1), 112– 117,  DOI: 10.1021/acs.jchemed.9b00588
        46
        Applications of 3D-Printing for Improving Chemistry Education
        Pinger, Cody W.; Geiger, Morgan K.; Spence, Dana M.
        Journal of Chemical Education (2020), 97 (1), 112-117CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        A review. Wide accessibility and a broad range of applications have made 3D-printers a commonplace tool in the science community. From tier-one research institutions to community public libraries and high schools, 3D-printers are being used to enrich STEM education through a variety of learning techniques and experiences. Reports of 3D-printed models for improved visualization of chem. phenomena, as well as the educational use of 3D-printed lab. devices, are rapidly increasing. The objective of this review is to provide a resource for educators interested in incorporating 3D-printing into their chem. classrooms by evaluating recent peer-reviewed reports that used this technol. to enhance chem. education.
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      47. 47
        Rassokhin, D. The C++ Programming Language in Cheminformatics and Computational Chemistry. J. Cheminformatics 2020, 12 (1), 10,  DOI: 10.1186/s13321-020-0415-y
        47
        The C++ programming language in cheminformatics and computational chemistry
        Rassokhin Dmitrii
        Journal of cheminformatics (2020), 12 (1), 10 ISSN:1758-2946.
        This paper describes salient features of the C++ programming language and its programming ecosystem, with emphasis on how the language affects scientific software development. Brief history of C++ and its predecessor the C language is provided. Most important aspects of the language that define models of programming are described in greater detail and illustrated with code examples. Special attention is paid to the interoperability between C++ and other high-level languages commonly used in cheminformatics, machine learning, data processing and statistical computing.
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      48. 48
        Mihalić, Z.; Trinajstić, N. A Graph-Theoretical Approach to Structure-Property Relationships. J. Chem. Educ. 1992, 69 (9), 701,  DOI: 10.1021/ed069p701
        48
        A graph-theoretical approach to structure-property relationships
        Mihalic, Zlatko; Trinajstic, Nenad
        Journal of Chemical Education (1992), 69 (9), 701-12CODEN: JCEDA8; ISSN:0021-9584.
        A graph theor. approach using topol. indexes is presented for describing QSPR. Various types of indexes are used.
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      49. 49
        Hansen, P. J.; Jurs, P. C. Chemical Applications of Graph Theory. Part I. Fundamentals and Topological Indices. J. Chem. Educ. 1988, 65 (7), 574,  DOI: 10.1021/ed065p574
        49
        Chemical applications of graph theory. Part I. Fundamentals and topological indices
        Hansen, Peter J.; Jurs, Peter C.
        Journal of Chemical Education (1988), 65 (7), 574-80CODEN: JCEDA8; ISSN:0021-9584.
        Some basic terms and concepts of graph theory are presented along with a discussion of 1 of the applications of graph theory to chem., namely, the use of topol. indexes in QSAR studies and quant. structure-property activity (QSPR) studies.
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      50. 50
        Krotko, D. G. Atomic Ring Invariant and Modified CANON Extended Connectivity Algorithm for Symmetry Perception in Molecular Graphs and Rigorous Canonicalization of SMILES. J. Cheminformatics 2020, 12 (1), 48,  DOI: 10.1186/s13321-020-00453-4
        50
        Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES
        Krotko, Dmytro G.
        Journal of Cheminformatics (2020), 12 (1), 48CODEN: JCOHB3; ISSN:1758-2946. (SpringerOpen)
        Abstr.: We propose new invariant (the product of the corresponding primes for the ring size of each bond of an atom) as a simple unambiguous ring invariant of an atom that allows distinguishing symmetry classes in the highly sym. mol. graphs using traditional local and distance atom invariants. Also, we propose modifications of Weininger's CANON algorithm to avoid its ambiguities (swapping and leveling ranks, incorrect detn. of symmetry classes in non-arom. annulenes, arbitrary selection of atom for breaking ties). The at. ring invariant and the Modified CANON algorithm allow us to create a rigorous procedure for the generation of canonical SMILES which can be used for accurate and fast structural searching in large chem. databases.
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      51. 51
        Probst, D.; Reymond, J.-L. Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees. J. Cheminformatics 2020, 12 (1), 12,  DOI: 10.1186/s13321-020-0416-x
        51
        Visualization of very large high-dimensional data sets as minimum spanning trees
        Probst Daniel; Reymond Jean-Louis
        Journal of cheminformatics (2020), 12 (1), 12 ISSN:1758-2946.
        The chemical sciences are producing an unprecedented amount of large, high-dimensional data sets containing chemical structures and associated properties. However, there are currently no algorithms to visualize such data while preserving both global and local features with a sufficient level of detail to allow for human inspection and interpretation. Here, we propose a solution to this problem with a new data visualization method, TMAP, capable of representing data sets of up to millions of data points and arbitrary high dimensionality as a two-dimensional tree (http://tmap.gdb.tools). Visualizations based on TMAP are better suited than t-SNE or UMAP for the exploration and interpretation of large data sets due to their tree-like nature, increased local and global neighborhood and structure preservation, and the transparency of the methods the algorithm is based on. We apply TMAP to the most used chemistry data sets including databases of molecules such as ChEMBL, FDB17, the Natural Products Atlas, DSSTox, as well as to the MoleculeNet benchmark collection of data sets. We also show its broad applicability with further examples from biology, particle physics, and literature.
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      52. 52
        Suzuki, M.; Nagamochi, H.; Akutsu, T. Efficient Enumeration of Monocyclic Chemical Graphs with given Path Frequencies. J. Cheminformatics 2014, 6 (1), 31,  DOI: 10.1186/1758-2946-6-31
        52
        Efficient enumeration of monocyclic chemical graphs with given path frequencies
        Suzuki, Masaki; Nagamochi, Hiroshi; Akutsu, Tatsuya
        Journal of Cheminformatics (2014), 6 (), 31/1-31/18, 18 pp.CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
        Background: The enumeration of chem. graphs (mol. graphs) satisfying given constraints is one of the fundamental problems in chemoinformatics and bioinformatics because it leads to a variety of useful applications including structure detn. and development of novel chem. compds. Results: We consider the problem of enumerating chem. graphs with monocyclic structure (a graph structure that contains exactly one cycle) from a given set of feature vectors, where a feature vector represents the frequency of the prescribed paths in a chem. compd. to be constructed and the set is specified by a pair of upper and lower feature vectors. To enumerate all tree-like (acyclic) chem. graphs from a given set of feature vectors, Shimizu et al. and Suzuki et al. proposed efficient branch-and-bound algorithms based on a fast tree enumeration algorithm. In this study, we devise a novel method for extending these algorithms to enumeration of chem. graphs with monocyclic structure by designing a fast algorithm for testing uniqueness. The results of computational expts. reveal that the computational efficiency of the new algorithm is as good as those for enumeration of tree-like chem. compds. Conclusions: We succeed in expanding the class of chem. graphs that are able to be enumerated efficiently.
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      53. 53
        Basak, S. C.; Magnuson, V. R.; Niemi, G. J.; Regal, R. R. Determining Structural Similarity of Chemicals Using Graph-Theoretic Indices. Discrete Appl. Math. 1988, 19 (1), 17– 44,  DOI: 10.1016/0166-218X(88)90004-2
        There is no corresponding record for this reference.
      54. 54
        Raymond, J. W.; Willett, P. Effectiveness of Graph-Based and Fingerprint-Based Similarity Measures for Virtual Screening of 2D Chemical Structure Databases. J. Comput. Aided Mol. Des. 2002, 16 (1), 59– 71,  DOI: 10.1023/A:1016387816342
        54
        Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases
        Raymond, John W.; Willett, Peter
        Journal of Computer-Aided Molecular Design (2002), 16 (1), 59-71CODEN: JCADEQ; ISSN:0920-654X. (Kluwer Academic Publishers)
        The effectiveness of the graph-based and fingerprint-based measures of structural similarity for virtual screening of sets of 2D mols. drawn from the MDDR ad ID Alert databases was evaluated. The graph-based measures employ a new max. common edge subgraph isomorphism algorithm, called RASCAL. The effectiveness of these graph-based searches is compared with that resulting from similarity searches using BCI, Daylight and Unity 2D fingerprints. The results suggest that graph-based approaches provide an effective complement to existing fingerprint-based approaches to virtual screening.
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      55. 55
        Hazzan, O.; Hadar, I. Reducing Abstraction When Learning Graph Theory. J. Comput. Math. Sci. Teach. 2005, 24 (3), 255– 272
        There is no corresponding record for this reference.
      56. 56
        Theisen, K. J. Programming Languages in Chemistry: A Review of HTML5/JavaScript. J. Cheminformatics 2019, 11 (1), 11,  DOI: 10.1186/s13321-019-0331-1
        56
        Programming languages in chemistry: a review of HTML5/JavaScript
        Theisen Kevin J
        Journal of cheminformatics (2019), 11 (1), 11 ISSN:1758-2946.
        This is one part of a series of reviews concerning the application of programming languages in chemistry, edited by Dr. Rajarshi Guha. This article reviews the JavaScript technology as it applies to the chemistry discipline. A discussion of the history, scope and technical details of the programming language is presented.
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      57. 57
        Amani, P.; Sneyd, T.; Preston, S.; Young, N. D.; Mason, L.; Bailey, U.-M.; Baell, J.; Camp, D.; Gasser, R. B.; Gorse, A.-D.; Taylor, P.; Hofmann, A. A Practical Java Tool for Small-Molecule Compound Appraisal. J. Cheminformatics 2015, 7 (1), 28,  DOI: 10.1186/s13321-015-0079-1
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        A practical Java tool for small-molecule compound appraisal
        Amani, Parisa; Sneyd, Todd; Preston, Sarah; Young, Neil D.; Mason, Lyndel; Bailey, Ulla-Maja; Baell, Jonathan; Camp, David; Gasser, Robin B.; Gorse, Alain-Dominique; Taylor, Paul; Hofmann, Andreas
        Journal of Cheminformatics (2015), 7 (), 28/1-28/4CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
        The increased use of small-mol. compd. screening by new users from a variety of different academic backgrounds calls for adequate software to administer, appraise, analyze and exchange information obtained from screening expts. While software and spreadsheet solns. exist, there is a need for software that can be easily deployed and is convenient to use. The Java application cApp addresses this need and aids in the handling and storage of information on small-mol. compds. The software is intended for the appraisal of compds. with respect to their physico-chem. properties, anal. in relation to adherence to likeness rules as well as recognition of pan-assay interference components and crosslinking with identical entries in the PubChem Compd. Database. Results are displayed in a tabular form in a graphical interface, but can also be written in an HTML or PDF format. The output of data in ASCII format allows for further processing of data using other suitable programs. Other features include similarity searches against user-provided compd. libraries and the PubChem Compd. Database, as well as compd. clustering based on a MaxMin algorithm. CApp is a personal database soln. for small-mol. compds. which can handle all major chem. formats. Being a standalone software, it has no other dependency than the Java virtual machine and is thus conveniently deployed. It streamlines the anal. of mols. with respect to physico-chem. properties and drug discovery criteria; cApp is distributed under the GNU Affero General Public License version 3.
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      58. 58
        Hanwell, M. D.; Curtis, D. E.; Lonie, D. C.; Vandermeersch, T.; Zurek, E.; Hutchison, G. R. Avogadro: An Advanced Semantic Chemical Editor, Visualization, and Analysis Platform. J. Cheminformatics 2012, 4 (1), 17,  DOI: 10.1186/1758-2946-4-17
        58
        Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
        Hanwell, Marcus D.; Curtis, Donald E.; Lonie, David C.; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey R.
        Journal of Cheminformatics (2012), 4 (), 17CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
        Background: The Avogadro project has developed an advanced mol. editor and visualizer designed for cross-platform use in computational chem., mol. modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building mol. structures, formatting input files, and analyzing output of a wide variety of computational chem. packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chem. data types. Results: The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chem., physics, materials science, and biol. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate mol. structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for mol. dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions: Avogadro offers a semantic chem. builder and platform for visualization and anal. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extg. chem. data from a wide variety of formats, including computational chem. output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in org. chem., inorg. complexes, drug design, materials, biomols., and simulations.
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      59. 59
        Hanson, R. M.; Prilusky, J.; Renjian, Z.; Nakane, T.; Sussman, J. L. JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem. 2013, 53 (3–4), 207– 216,  DOI: 10.1002/ijch.201300024
        59
        JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia
        Hanson, Robert M.; Prilusky, Jaime; Zhou, Renjian; Nakane, Takanori; Sussman, Joel L.
        Israel Journal of Chemistry (2013), 53 (3-4), 207-216CODEN: ISJCAT; ISSN:0021-2148. (Wiley-VCH Verlag GmbH & Co. KGaA)
        Although Java does not run on some handheld devices, e.g., iPads and iPhones, JavaScript does. The development of JSmol, a JavaScript-only version of Jmol, is described, and its use in Proteopedia is demonstrated. A key aspect of JSmol is that it includes the full implementation of the entire set of Jmol functionalities, including file reading and writing, scripting, and rendering. The relative performances of Java-based Jmol and JavaScript-only JSmol are discussed. We can now confirm that the guiding principles of Java programming can be completely and relatively straightforwardly transformed directly into JavaScript, requiring no Java applet, and producing identical graphical results. JSmol is thus the first full-featured mol. viewer, and the first ever viewer for proteins, which can be utilized with an internet browser on handheld devices lacking Java. Since the MediaWiki features of Proteopedia have been modified to optionally use JSmol, the wealth of crowd-sourced content in Proteopedia is now directly available on such devices, without the need to download any addnl. applet.
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      60. 60
        Burger, M. C. ChemDoodle Web Components: HTML5 Toolkit for Chemical Graphics, Interfaces, and Informatics. J. Cheminformatics 2015, 7 (1), 35,  DOI: 10.1186/s13321-015-0085-3
        60
        ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics
        Burger Melanie C
        Journal of cheminformatics (2015), 7 (), 35 ISSN:1758-2946.
        ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses <canvas> and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.
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      61. 61
        Pernaa, J. Edumol: Avoin Ja Ilmainen Molekyylimallinnussovellus Kemian Opetuksen Tueksi. LUMAT Int. J. Math Sci. Technol. Educ. 2015, 3 (7), 960– 975,  DOI: 10.31129/lumat.v3i7.977
        There is no corresponding record for this reference.
      62. 62
        Bergwerf, H. MolView: An Attempt to Get the Cloud into Chemistry Classrooms. DivCHED CCCE: Committee on Computers in Chemical Education 2015, 1– 9
        There is no corresponding record for this reference.
      63. 63
        O’Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: An Open Chemical Toolbox. J. Cheminformatics 2011, 3 (1), 33,  DOI: 10.1186/1758-2946-3-33
        63
        Open Babel: an open chemical toolbox
        O'Boyle, Noel M.; Banck, Michael; James, Craig A.; Morley, Chris; Vandermeersch, Tim; Hutchison, Geoffrey R.
        Journal of Cheminformatics (2011), 3 (), 33CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
        Background: A frequent problem in computational modeling is the interconversion of chem. structures between different formats. While std. interchange formats exist (for example, Chem. Markup Language) and de facto stds. have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chem. data, differences in the data stored by different formats (0D vs. 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results: We discuss, for the first time, Open Babel, an open-source chem. toolbox that speaks the many languages of chem. data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chem. and mol. data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions: Open Babel presents a soln. to the proliferation of multiple chem. file formats. In addn., it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chem. data in areas such as org. chem., drug design, materials science, and computational chem. It is freely available under an open-source license.
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      64. 64
        Rodríguez-Becerra, J.; Cáceres-Jensen, L.; Diaz, T.; Druker, S.; Bahamonde Padilla, V.; Pernaa, J.; Aksela, M. Developing Technological Pedagogical Science Knowledge through Educational Computational Chemistry: A Case Study of Pre-Service Chemistry Teachers’ Perceptions. Chem. Educ. Res. Pract. 2020, 21 (2), 638– 654,  DOI: 10.1039/C9RP00273A
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        Developing technological pedagogical science knowledge through educational computational chemistry: a case study of pre-service chemistry teachers' perceptions
        Rodriguez-Becerra, Jorge; Caceres-Jensen, Lizethly; Diaz, Tatiana; Druker, Sofia; Bahamonde Padilla, Victor; Pernaa, Johannes; Aksela, Maija
        Chemistry Education Research and Practice (2020), 21 (2), 638-654CODEN: CERPCE; ISSN:1756-1108. (Royal Society of Chemistry)
        The purpose of this descriptive case study was to develop pre-service chem. teachers' Technol. Pedagogical Science Knowledge (TPASK) through novel computational chem. modules. The study consisted of two phases starting with designing a computational chem. based learning environment followed by a case study where students' perceptions toward educational computational chem. were explored. First, we designed an authentic research-based chem. learning module that supported problem-based learning through the utilization of computational chem. methods suitable for pre-service chem. education. The objective of the learning module was to promote learning of specific chem. knowledge and development of scientific skills. Systematic design decisions were made through the TPASK framework. The learning module was designed for a third-year phys. chem. course taken by pre-service chem. teachers in Chile. After the design phase, the learning module was implemented in a course, and students' perceptions were gathered using semi-structured group interviews. The sample consisted of 22 pre-service chem. teachers. Data were analyzed through qual. content anal. using the same TPASK framework employed in the learning module design. Based on our findings, pre-service chem. teachers first acquired Technol. Scientific Knowledge (TSK) and then developed some elements of their TPASK. Besides, they highly appreciated the combination of student-centered problem-based learning and the use of computational chem. tools. Students felt the educational computational learning environment supported their own knowledge acquisition and expressed an interest in applying similar learning environments in their future teaching careers. This case study demonstrates that learning through authentic real-world problems using educational computational methods offers great potential in supporting pre-service teachers' instruction in the science of chem. and pedagogy. For further research in the TPASK framework, we propose there would be significant benefit from developing new learning environments of this nature and evaluating their utility in pre-service and in-service chem. teacher's education.
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      65. 65
        Aksela, M.; Lundell, J. Computer-Based Molecular Modelling: Finnish School Teachers’ Experiences and Views. Chem. Educ. Res. Pract. 2008, 9 (4), 301– 308,  DOI: 10.1039/B818464J
        65
        Computer-based molecular modelling: Finnish school teachers' experiences and views
        Aksela, Maija; Lundell, Jan
        Chemistry Education Research and Practice (2008), 9 (4), 301-308CODEN: CERPCE ISSN:. (Royal Society of Chemistry)
        Modern-computer-based mol. modeling opens up new possibilities for chem. teaching at different levels. This article presents a case study seeking insight into Finnish school teachers' use of computer-based mol. modeling in teaching chem., into the different working and teaching methods used, and their opinions about necessary support. The study suggests that most of the teachers studied need personally to discover the benefits of mol. modeling in their own work that illustrate on a practical level how mol. modeling can provide added value for teaching and understanding school chem. Teachers state that they need more pedagogical and tech. training in mol. modeling so they can use it more and effectively in their own teaching. Furthermore, there is a need for easily adaptable learning and teaching materials to be made available to teachers in their domestic teaching language.
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      66. 66
        Ghani, S. S. A Comprehensive Review of Database Resources in Chemistry. Eclética Quím. J. 2020, 45 (3), 57– 68,  DOI: 10.26850/1678-4618eqj.v45.3.2020.p57-68
        There is no corresponding record for this reference.
      67. 67
        Gilbert, J. Visualization: A Metacognitive Skill in Science and Science Education. In Visualization in Science Education; Gilbert, J., Ed.; Models and Modeling in Science Education; Springer Netherlands, 2005; pp 9– 27. DOI: 10.1007/1-4020-3613-2
        There is no corresponding record for this reference.
      68. 68
        Kozlíková, B.; Krone, M.; Falk, M.; Lindow, N.; Baaden, M.; Baum, D.; Viola, I.; Parulek, J.; Hege, H.-C. Visualization of Biomolecular Structures: State of the Art Revisited: Visualization of Biomolecular Structures. Comput. Graph. Forum 2017, 36 (8), 178– 204,  DOI: 10.1111/cgf.13072
        There is no corresponding record for this reference.
      69. 69
        Vesna Savec, F.; Vrtacnik, M.; Gilbert, J. Evaluating the Educational Value of Molecular Structure Representations. In Visualization in Science Education; Gilbert, J., Ed.; Models and Modeling in Science Education; Springer Netherlands: Dordrecht, Netherlands, 2005; pp 269– 297. DOI: 10.1007/1-4020-3613-2_14
        There is no corresponding record for this reference.
      70. 70
        Jones, L. L.; Jordan, K. D.; Stillings, N. A. Molecular Visualization in Chemistry Education: The Role of Multidisciplinary Collaboration. Chem. Educ. Res. Pract. 2005, 6 (3), 136– 149,  DOI: 10.1039/B5RP90005K
        70
        Molecular visualization in chemistry education: The role of multidicisplinary collaboration
        Jones, Loretta L.; Jordan, Kenneth D.; Stillings, Neil A.
        Chemistry Education Research and Practice (2005), 6 (3), 136-149CODEN: CERPCE ISSN:. (Royal Society of Chemistry)
        Visualization tools and high performance computing have changed the nature of chem. research and have the promise to transform chem. instruction. However, the images central to chem. research can pose difficulties for beginning chem. students. In order for mol. visualization tools to be useful in education, students must be able to interpret the images they produce. Cognitive scientists can provide valuable insight into how novices perceive and ascribe meaning to mol. visualizations. Further insights from educators, computer scientists and developers, and graphic artists are important for chem. educators who want to help students learn with mol. visualizations. A diverse group of scientists, educators, developers, and cognitive psychologists have begun a series of international collaborations to address this issue. The effort was initiated at the National Science Foundation supported Mol. Visualization in Science Education Workshop held in 2001 and has continued through a series of mini-grants. These groups are investigating characteristics of mol. representations and visualizations that enhance learning, interactions with mol. visualizations that best help students learn about mol. structure and dynamics, roles of mol. modeling in chem. instruction, and fruitful directions for research on mol. visualization in the learning of chem. This article summarizes the value of collaboration identified by participants in the workshop and subsequent collaborations.
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      71. 71
        Johnstone, A. H. Why Is Science Difficult to Learn? Things Are Seldom What They Seem. J. Comput. Assist. Learn. 1991, 7 (2), 75– 83,  DOI: 10.1111/j.1365-2729.1991.tb00230.x
        There is no corresponding record for this reference.
      72. 72
        Briggs, M.; Bodner, G. A Model of Molecular Visualization. In Visualization in Science Education; Gilbert, J., Ed.; Models and Modeling in Science Education; Springer Netherlands: Dordrecht, Netherlands, 2005; pp 61– 72. DOI: 10.1007/1-4020-3613-2_5
        There is no corresponding record for this reference.
      73. 73
        Tversky, B. Prolegomenon to Scientific Visualizations. In Visualization in Science Education; Gilbert, J., Ed.; Models and Modeling in Science Education; Springer Netherlands: Dordrecht, Netherlands, 2005; pp 29– 42. DOI: 10.1007/1-4020-3613-2_3
        There is no corresponding record for this reference.
      74. 74
        Aduldecha, S.; Akhter, P.; Field, P.; Nagle, P.; O’Sullivan, E.; O’Connor, K.; Hathaway, B. J. The Use of the Desktop Molecular Modeller Software in the Teaching of Structural Chemistry. J. Chem. Educ. 1991, 68 (7), 576,  DOI: 10.1021/ed068p576
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        The use of the Desktop Molecular Modeller software in the teaching of structural chemistry
        Aduldecha, S.; Akhter, P.; Field, P.; Nagle, P.; O'Sullivan, E.; O'Connor, K.; Hathaway, B. J.
        Journal of Chemical Education (1991), 68 (7), 576-83CODEN: JCEDA8; ISSN:0021-9584.
        The Desktop Mol. Modeller (DTMM) program is described for use in the computer graphics display of mols. in structural chem. education. The software is entirely menu-driven and constructs mols. graphically from smaller mols. or fragments. Display styles and example structures are presented.
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      75. 75
        Barnea, N.; Dori, Y. J. Computerized Molecular Modeling as a Tool to Improve Chemistry Teaching. J. Chem. Inf. Comput. Sci. 1996, 36 (4), 629– 636,  DOI: 10.1021/ci950122o
        75
        Computerized Molecular Modeling as a Tool To Improve Chemistry Teaching
        Barnea, Nitza; Dori, Yehudit J.
        Journal of Chemical Information and Computer Sciences (1996), 36 (4), 629-636CODEN: JCISD8; ISSN:0095-2338. (American Chemical Society)
        The use of mol. models to illustrate and explore phenomena in chem. teaching is widespread. However, only one type of model is usually used, and not enough emphasis is put on its meaning. The advantage of computerized mol. modeling (CMM) stems from the convenience and simplicity of building mols. of any size and color in a no. of presentations. To expose chem. teachers to the use of CMM we developed a 14 h workshop on models. It consists of an introduction to the model concept, using various types of models (including CMM) and experiencing ways to use them for illustrating chem. structure and bonding via team projects. This workshop has been incorporated into pre- and in-service training at the Department of Education in Technol. and Science at the Technion since 1994. As a final project, teachers were asked to plan a session of 1-2 lessons by building a miniature database of mols. along with working instructions. The new methodol. is based on using CMM through a special booklet, designed in a constructivist approach. During 1995, it was implemented in three tenth grade exptl. classes with two other classes serving as a control group. Overall, teachers' attitudes toward using mol. modeling to improve chem. teaching were favorable. The effect of using mol. modeling on students' understanding and constructing new concepts was investigated in relation to chem. structure and bonding as well as to geometric and symbolic representation. In two representative questions related to three-dimensional mol. structure, the exptl. group performed better than the control group. Students' attitudes toward the use of CMM have also been found to be pos. Most of the students enjoyed using the new methodol. and indicated it helped them understand concepts in mol. geometry and bonding.
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      76. 76
        Johnstone, A. H. The Development of Chemistry Teaching: A Changing Response to Changing Demand. J. Chem. Educ. 1993, 70 (9), 701,  DOI: 10.1021/ed070p701
        There is no corresponding record for this reference.
      77. 77
        Reid, N. A tribute to Professor Alex H Johnstone (1930–2017): His unique contribution to chemistry education research. Chem. Teach. Int. 2019, 1 (1), 1,  DOI: 10.1515/cti-2018-0016
        There is no corresponding record for this reference.
      78. 78
        Fleming, S. A.; Hart, G. R.; Savage, P. B. Molecular Orbital Animations for Organic Chemistry. J. Chem. Educ. 2000, 77 (6), 790,  DOI: 10.1021/ed077p790
        78
        Molecular orbital animations for organic chemistry
        Fleming, Steven A.; Hart, Greg R.; Savage, Paul B.
        Journal of Chemical Education (2000), 77 (6), 790-793CODEN: JCEDA8; ISSN:0021-9584. (Division of Chemical Education of the American Chemical Society)
        There are several approaches to teaching org. chem., and a current trend is presentation of the various subjects (alkanes, alkenes, ketones, etc.) with a theme. Students benefit when they can find a common element that ties the subject matter together. One such theme for org. chem. is the use of electrophile + nucleophile for the description of org. reactions. It has been found that students can understand simple MO explanations of electrophile and nucleophile. Teaching methods for such an approach, including an animation package which build upon a fundamental understanding of MO interactions, are described.
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      79. 79
        Tasker, R.; Dalton, R. Research into Practice: Visualisation of the Molecular World Using Animations. Chem. Educ. Res. Pract. 2006, 7 (2), 141– 159,  DOI: 10.1039/B5RP90020D
        79
        Research into practice: Visualization of the molecular world using animations
        Tasker, Roy; Dalton, Rebecca
        Chemistry Education Research and Practice (2006), 7 (2), 141-159CODEN: CERPCE ISSN:. (Royal Society of Chemistry)
        Most chem. teaching operates at the macro (or lab.) level and the symbolic level, but we know that many misconceptions in chem. stem from an inability to visualize structures and processes at the sub-micro (or mol.) level. However, one cannot change a student's mental model of this level by simply showing them a different, albeit better, model in an animation. Mol.-level animations can be compelling and effective learning resources, but they must be designed and presented with great care to encourage students to focus on the intended 'key features', and to avoid generating or reinforcing misconceptions. One misconception often generated is the perception of 'directed intent' in processes at the mol. level, resulting from the tech. imperative to minimize file size for web delivery of animations. An audiovisual information-processing model - based on a combination of evidence-based models developed by Johnstone and Mayer, cognitive load theory, and dual-coding theory - has been used to inform teaching practice with animations, and seed questions for research on student attributes affecting development of mental models using animations. Based on this model, the constructivist VisChem Learning Design probes students' mental models of a substance or reaction at the mol. level before showing animations portraying the phenomenon. Opportunities to apply their refined models to new situations are crit.
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      80. 80
        Venkataraman, B. Visualization and Interactivity in the Teaching of Chemistry to Science and Non-Science Students. Chem. Educ. Res. Pract. 2009, 10 (1), 62– 69,  DOI: 10.1039/B901462B
        80
        Visualization and interactivity in the teaching of chemistry to science and non-science students
        Venkataraman, Bhawani
        Chemistry Education Research and Practice (2009), 10 (1), 62-69CODEN: CERPCE; ISSN:1756-1108. (Royal Society of Chemistry)
        A series of interactive, instructional units have been developed that integrate computational mol. modeling and visualization to teach fundamental chem. concepts and the relationship between the mol. and macro-scales. The units span the scale from atoms, small mols. to macromol. systems, and introduce many of the concepts discussed in a first year undergraduate class, such as at. structure, chem. bonding, the mol. nature of phys. properties and structure-function relations in macromol. systems. The units were used in an introductory level chem. course for non-science majors and students interested in non-traditional science careers. Assessment of these units indicated that the students are successfully learning fundamental concepts, value the computer-based learning aids, and begin to develop mental models of the mol. scale.
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      81. 81
        Kozma, R.; Russell, J. Students Becoming Chemists: Developing Representationl Competence. In Visualization in Science Education; Gilbert, J., Ed.; Models and Modeling in Science Education; Springer Netherlands: Dordrecht, Netherlands, 2005; pp 121– 145. DOI: 10.1007/1-4020-3613-2_8
        There is no corresponding record for this reference.
      82. 82
        Justi, R.; Gilbert, J. Models and Modelling in Chemical Education. In Chemical Education: Towards Research-based Practice; Gilbert, J., de Jong, O., Justi, R., Treagust, D. F., Driel, J. H., Eds.; Springer Netherlands: Dordrecht, Netherlands, 2003; pp 47– 68.
        There is no corresponding record for this reference.
      83. 83
        Krathwohl, D. R. A Revision of Bloom’s Taxonomy: An Overview. Theory Pract. 2002, 41 (4), 212– 218,  DOI: 10.1207/s15430421tip4104_2
        There is no corresponding record for this reference.
      84. 84
        Barnea, N. Teaching and Learning about Chemistry and Modelling with a Computer Managed Modelling System. In Developing Models in Science Education; Gilbert, J. K., Boulter, C. J., Eds.; Springer Netherlands: Dordrecht, Netherlands, 2000; pp 307– 323. DOI: 10.1007/978-94-010-0876-1_16
        There is no corresponding record for this reference.
      85. 85
        Dori, Y. J.; Kaberman, Z. Assessing High School Chemistry Students’ Modeling Sub-Skills in a Computerized Molecular Modeling Learning Environment. Instr. Sci. 2012, 40 (1), 69– 91,  DOI: 10.1007/s11251-011-9172-7
        There is no corresponding record for this reference.
      86. 86
        Barnea, N.; Dori, Y. J. High-School Chemistry Students’ Performance and Gender Differences in a Computerized Molecular Modeling Learning Environment. J. Sci. Educ. Technol. 1999, 8 (4), 257– 271,  DOI: 10.1023/A:1009436509753
        There is no corresponding record for this reference.
      87. 87
        Bienfait, B.; Ertl, P. JSME: A Free Molecule Editor in JavaScript. J. Cheminformatics 2013, 5 (1), 24,  DOI: 10.1186/1758-2946-5-24
        87
        JSME: a free molecule editor in JavaScript
        Bienfait, Bruno; Ertl, Peter
        Journal of Cheminformatics (2013), 5 (), 24CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
        Background: A mol. editor, i.e. a program facilitating graphical input and interactive editing of mols., is an indispensable part of every cheminformatics or mol. processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit mols. directly within the web browser is essential. One of the most popular tools for mol. structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language-JavaScript. Summary: The actual mol. editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by addnl. functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addn. to desktop computers, the editor supports mol. editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new mol. editor is compact, easy to use and easy to incorporate into web pages. Conclusions: A free mol. editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page at online.
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      88. 88
        Ping, G. L. Y.; Lok, C.; Wei Yeat, T.; Cherynn, T. J. Y.; Tan, E. S. Q. Are Chemistry Educational Apps Useful?” - A Quantitative Study with Three in-House Apps. Chem. Educ. Res. Pract. 2018, 19 (1), 15– 23,  DOI: 10.1039/C7RP00094D
        There is no corresponding record for this reference.
      89. 89
        Long, L. 3D Printing Is Poised to Continue Outpacing Growth of Traditional Manufacturing. https://www.engineering.com/AdvancedManufacturing/ArticleID/16873/3D-Printing-Is-Poised-to-Continue-Outpacing-Growth-of-Traditional-Manufacturing.aspx (accessed 2018-10-18).
        There is no corresponding record for this reference.
      90. 90
        Nemorin, S.; Selwyn, N. Making the Best of It? Exploring the Realities of 3D Printing in School. Res. Pap. Educ. 2017, 32 (5), 578– 595,  DOI: 10.1080/02671522.2016.1225802
        There is no corresponding record for this reference.
      91. 91
        Community for Advancing Discovery Research in Education (CADRE). Engineering: Emphasizing the “E” in STEM Education. STEM Smart Brief; Education Development Center, Inc. (EDC), 2013.
        There is no corresponding record for this reference.
      92. 92
        Wisdom, S.; Novak, E. Using 3D Printing to Enhance STEM Teaching and Learning: Recommendations for Designing 3D Printing Projects. In Integrating 3D Printing into Teaching and Learning: Practitioners’ Perspectives; Ali, N., Khine, M. S., Eds.; BRILL, 2019; pp 187– 205. DOI: 10.1163/9789004415133
        There is no corresponding record for this reference.
      93. 93
        Pernaa, J.; Wiedmer, S. A Systematic Review of 3D Printing in Chemistry Education - Analysis of Earlier Research and Educational Use through Technological Pedagogical Content Knowledge Framework. Chem. Teach. Int. 2019, 2 (2), 20190005,  DOI: 10.1515/cti-2019-0005
        There is no corresponding record for this reference.
      94. 94
        Cooper, A. K.; Oliver-Hoyo, M. T. Creating 3D Physical Models to Probe Student Understanding of Macromolecular Structure. Biochem. Mol. Biol. Educ. 2017, 45 (6), 491– 500,  DOI: 10.1002/bmb.21076
        94
        Creating 3D physical models to probe student understanding of macromolecular structure
        Cooper, A. Kat; Oliver-Hoyo, M. T.
        Biochemistry and Molecular Biology Education (2017), 45 (6), 491-500CODEN: BMBECE; ISSN:1470-8175. (John Wiley & Sons, Inc.)
        The high degree of complexity of macromol. structure is extremely difficult for students to process. Students struggle to translate the simplified two-dimensional representations commonly used in biochem. instruction to three-dimensional aspects crucial in understanding structure-property relationships. We designed four different phys. models to address student understanding of electrostatics and noncovalent interactions and their relationship to macromol. structure. In this study, we have tested these models in classroom settings to det. if these models are effective in engaging students at an appropriate level of difficulty and focusing student attention on the principles of electrostatic attractions. This article describes how to create these unique models for four targeted areas related to macromol. structure: protein secondary structure, protein tertiary structure, membrane protein soly., and DNA structure. We also provide evidence that merits their use in classroom settings based on the anal. of assembled models and a behavioral assessment of students enrolled in an introductory biochem. course. By providing students with three-dimensional models that can be phys. manipulated, barriers to understanding representations of these complex structures can be lowered and the focus shifted to addressing the foundational concepts behind these properties. © 2017 by The International Union of Biochem. and Mol. Biol., 2017.
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      95. 95
        Brown, C. E.; Alrmuny, D.; Williams, M. K.; Whaley, B.; Hyslop, R. M. Visualizing Molecular Structures and Shapes: A Comparison of Virtual Reality, Computer Simulation, and Traditional Modeling. Chem. Teach. Int. 2021, 3, 69,  DOI: 10.1515/cti-2019-0009
        There is no corresponding record for this reference.
      96. 96
        Casas, L.; Estop, E. Virtual and Printed 3D Models for Teaching Crystal Symmetry and Point Groups. J. Chem. Educ. 2015, 92 (8), 1338– 1343,  DOI: 10.1021/acs.jchemed.5b00147
        96
        Virtual and Printed 3D Models for Teaching Crystal Symmetry and Point Groups
        Casas, Lluis; Estop, Eugenia
        Journal of Chemical Education (2015), 92 (8), 1338-1343CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        Both virtual and printed 3D crystal models can help students and teachers deal with chem. education topics such as symmetry and point groups. In the present paper, two freely downloadable tools (interactive PDF files and a mobile app) are presented as examples of the application of 3D design to study point-symmetry. The use of 3D printing to produce tangible crystal models is also explored. A series of dissection puzzles that will be esp. useful for teaching crystallog. concepts such as asym. unit and general/special positions is presented. Educators are encouraged to use the presented tools in their classes, and we expect our work to inspire other college educators to design and share similar tools.
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      97. 97
        Van Wieren, K.; Tailor, H. N.; Scalfani, V. F.; Merbouh, N. Rapid Access to Multicolor Three-Dimensional Printed Chemistry and Biochemistry Models Using Visualization and Three-Dimensional Printing Software Programs. J. Chem. Educ. 2017, 94 (7), 964– 969,  DOI: 10.1021/acs.jchemed.6b00602
        97
        Rapid Access to Multicolor Three-Dimensional Printed Chemistry and Biochemistry Models Using Visualization and Three-Dimensional Printing Software Programs
        Van Wieren, Ken; Tailor, Hamel N.; Scalfani, Vincent F.; Merbouh, Nabyl
        Journal of Chemical Education (2017), 94 (7), 964-969CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        Use of color 3D printers as a visualization tool is described in this paper. Starting from any file depicting a chem. structure, multicolor 3D printed chem. structures can be produced. Most structures were printed in hours, making the entire process from file prepn. to tangible model quickly achievable. Chem. structure examples are showcased from org. chem., organometallic chem., and biochem. This paper presents a method of producing multicolor chem. and biochem. tangible models using Chimera and Magics mol. visualization and 3D printing software.
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      98. 98
        Fourches, D.; Feducia, J. Student-Guided Three-Dimensional Printing Activity in Large Lecture Courses: A Practical Guideline. J. Chem. Educ. 2019, 96 (2), 291– 295,  DOI: 10.1021/acs.jchemed.8b00346
        98
        Student-Guided Three-Dimensional Printing Activity in Large Lecture Courses: A Practical Guideline
        Fourches, Denis; Feducia, Jeremiah
        Journal of Chemical Education (2019), 96 (2), 291-295CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        Modern technol. stimulates the development of innovative classroom activities. We designed a 3D printing activity in two sep. Org. Chem. lectures of at least 200 students each. This assignment required students to 3D print a mol. of their choice, relying on services made available through the university libraries. Data obtained through a survey at the end of the semester provided key information on the students' experiences with printing 3D models for the first time. A summary of this feedback and constructive remarks on the best practices regarding 3D printing assignments in large lecture courses are presented.
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      99. 99
        Bharti, N.; Singh, S. Three-Dimensional (3D) Printers in Libraries: Perspective and Preliminary Safety Analysis. J. Chem. Educ. 2017, 94 (7), 879– 885,  DOI: 10.1021/acs.jchemed.6b00745
        99
        Three-Dimensional (3D) Printers in Libraries: Perspective and Preliminary Safety Analysis
        Bharti, Neelam; Singh, Shailendra
        Journal of Chemical Education (2017), 94 (7), 879-885CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)
        As an emerging technol., three-dimensional (3D) printing has gained much attention as a rapid prototyping and small-scale manufg. technol. around the world. In the changing scenario of library inclusion, Makerspaces are becoming a part of most public and academic libraries, and 3D printing is one of the technologies included in Makerspaces. Owing to the ease of availability and cost effectiveness, most libraries use fused-deposition-modeling-based 3D printers compatible with plastic printing materials, such as polylactic acid (PLA) and acrylonitrile butadiene styrene (ABS). During the printing, PLA and ABS emit ultrafine particles (UFPs) and volatile org. compds. (VOCs) that may deteriorate the indoor air quality. In this article, first, we have discussed the background of 3D printing, the most common technologies used for 3D printing and printing materials, its applications in chem. education and sciences, as well as 3D printing health and safety concerns. Second, we measured and analyzed the no. of UFPs (0.02-1.0 μm) in the 3D printing lab in a library and found that the no. of particles/cubic centimeter significantly increased during the printing procedure (36-60 times) and does not return to baseline even 24 h after shutting down the printers. We also provide some recommendations that should be considered when hosting a 3D printing lab in libraries.
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      100. 100
        Gürel, S.; Tat, M. SWOT Analysis: A Theoretical Review. J. Int. Soc. Res. 2017, 10 (51), 994– 1006,  DOI: 10.17719/jisr.2017.1832
        There is no corresponding record for this reference.
      101. 101
        Gilbert, J. On the Nature of “Context” in Chemical Education. Int. J. Sci. Educ. 2006, 28 (9), 957– 976,  DOI: 10.1080/09500690600702470
        There is no corresponding record for this reference.
      102. 102
        Aksela, M. Towards Student-Centred Solutions and Pedagogical Innovations in Science Education through Co-Design Approach within Design-Based Research. LUMAT Int. J. Math Sci. Technol. Educ. 2019, 7 (3), 113– 139,  DOI: 10.31129/LUMAT.7.3.421
        There is no corresponding record for this reference.
      103. 103
        Wegner, J. K.; Sterling, A.; Guha, R.; Bender, A.; Faulon, J.-L.; Hastings, J.; O’Boyle, N.; Overington, J.; Van Vlijmen, H.; Willighagen, E. Cheminformatics. Commun. ACM 2012, 55 (11), 65– 75,  DOI: 10.1145/2366316.2366334
        There is no corresponding record for this reference.