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Anthocyanins are natural pigments belonging to the flavonoid family that generate the red, blue, and purple colors of fruits, vegetables, and flowers. Their structure and color are dependent on various factors, like the pH. Anthocyanins appear red in acidic, purple in neutral, and blue in basic solutions, making them suitable for use as natural pH indicators. Thus, petals of flowers could be an attractive pedagogic tool for laboratory activities due to the high content of anthocyanins, but the presence of copigments such as flavonols and flavones modifies the characteristic anthocyanin colors in pH studies. Therefore, a simple and ecological liquid-liquid extraction was developed for the separation of anthocyaninic and nonanthocyaninic flavonoids, based on the different acid-base properties of these two classes of pigments. Treatment with NaOH allowed the detection of nonanthocyanin flavonoids in the organic phase through the development of a deep yellow color. Colorimetric analysis of the aqueous anthocyaninic fractions enabled visualization of the typical colors from different forms of anthocyanins, demonstrating the efficacy of the separation method. It was also possible to distinguish if the red pigments of the flower were anthocyanins or betalains. Thus, the beautiful colors of flowers make them an accessible and attractive source of pigments that can be used to demonstrate acid-base properties of organic molecules, solid-liquid and liquid-liquid extraction techniques, intermolecular interactions, and solubility properties. This protocol could be implemented in practical classes of chemistry and biochemistry degrees, being particularly useful for teaching fundamentals of organic chemistry and color chemistry.

The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis dot structures, molecular geometry, bond polarity, molecular polarity, resonance and hybridization. This study investigated the conceptual understanding levels and misconceptions held by university students about molecular structures subject. The sample of the study comprised of 88 undergraduate students enrolled in the Department of Mathematics and Science Education, Faculty of Education, Turkey. The participants responded to open-ended and interview questions regarding the subject. Students' responses were analyzed and their conceptual understanding levels were determined. The results indicated that students had lack of knowledge and misconceptions about the subject although they studied it in the university. Especially, they had poor knowledge about the molecular geometry, molecular polarity, resonance, and hybridization in molecular structures except for Lewis dot structures of molecules. Accordingly, implications have been made for more effective teaching approaches to ensure better understanding of the subjects.

The background of the study is that the planar film heterostructures are nowadays the most common objects nanophotonic and nanoelectronic technologies. The authors noted that, among such objects found so-called quantum wells, which are formed by a complex series of nanoscale layers are deposited with differing elemental composition, and simple single-layer coatings. Test heterostructure may be polycrystalline or amorphous sequentially deposited layers, but can be provided epitaxial objects. In addition to the interest in the composition, structure and thickness of the layers of heterostructure itself, it is important and knowing the width and the quality of the interlayer boundaries, as well as the presence-absence of their mutual diffuse infiltration. The results of the article is that of the operating experience of experts are usually quite clearly represent technological equipment, what type of heterostructures and the distribution of elemental composition therein can be expected. However, the intended routing is always in need of an objective independent confirmation. For planar nanoheterostructures most effective method of non-destructive testing of the objective distribution of elements over the depth of the target and the presence-absence is epitaxially ion beam diagnostics.

Learning within the sciences is often considered through a quantitative lens, but acquiring proficiency with the symbolic representations in chemistry is arguably more akin to language learning. Representational competencies are central to successful communication of chemical information including molecular composition, structure, and properties. This article reports on a qualitative study of learner experiences when introduced to new symbolic representations and representational technologies. Participants' descriptions of these resource interactions were collected through semi-structured interviews and surveys, and were analyzed using phenomenography to identify the variety in student experiences. Results illustrate the impact that representational technologies can have on learner development of problem-solving techniques.

We describe a mobile augmented reality (AR) experience called Atom Tracker designed to help middle school students better understand the cycling of matter in ecosystems with a focus on the concept of conservation of matter and the processes of photosynthesis and respiration. Location-based AR allows students to locate virtual "hotspots," where they interact with multiple representations including vision-based AR animations of virtual atoms during ecological processes such as photosynthesis and physical LEGO® -based representations of molecules. This design case describes the design rationale, the iterative design process, the context for implementation, and reflections on the success and limitations of the Atom Tracker AR experience. An augmented reality interface was chosen due to theoretical support for its utility in supporting interaction with multiple representations (both physical and virtual) of atoms and molecules, the ability to condense and expand temporal and spatial scales associated with ecological processes, and its ability to explicitly situate these representations in real-world contexts that could support learning. Two significant design challenges that we recognized were (a) appropriately leveraging narrative, student engagement and agency when designing around the topic of atoms and molecules, which are inanimate and invisible; and (b) designing for engagement with both virtual and physical resources available during the experience

This article makes a case for a positive role of tension in the creative process in chemistry. I begin with an argument that there is an inherent tension in what makes molecules interesting--their positioning along various polar axes. One of these, the age-old differentiation between useful (to society and for personal profit) commercialization and pure understanding of molecules and their reactions is characteristic. The question of whether there are any bad molecules then leads me to ethical concerns in chemistry, and a particular working out of these in interactions of chemists in the Middle East. An analysis is made of the special tensions involved in publishing, especially in citation ethics; chemists publish a lot, so this is situation ethics worked out on a daily basis. I then find in the literature of psychology good evidence for the positive value of moderate stress in stimulating creativity. It is obvious that too much tension leads to distress, and there are some institutional aspects of chemistry that do not come out well here. But all in all, the dynamic middle is alive, and it leads to good new science.

Physical molecular models have played a valuable role in our understanding of the invisible nano-scale world. We discuss 3D printing and its use in producing models of the molecules of life. Complex biomolecular models, produced from 3D printed parts, can demonstrate characteristics of molecular structure and function, such as viral self-assembly, protein folding, and DNA structure. Advances in computer and user interface technology have enabled physical molecular models to combine with augmented reality to bridge the physical with the computational world. [This article was published in "Journal of Biocommunication," v40 n1 p15-21 2016.]

Protein structure-function relationship serves as the primary learning outcome in any undergraduate biochemistry course. We expanded the protein structure-function exploration, PSFE initiative during COVID-19 to provide more effective and engaging experience to our undergraduates in biochemistry and independent research courses. Multiple alignments of protein sequences provided crucial insight into sequence conservation across many species and thus allow identification of those sections of the sequence most critical to protein function. We used Anabaena Sensory Rhodopsin, ASR its transducer, ASRT and downstream novel kinase gene products of Anabaena PCC 7120 to seek their alignment with homologs in available database. Pymol served an opportunity to achieve this goal (interactive learning during lab session and stimulation of course content discussion) in interesting ways. The PSFE initiative expansion continued during pandemic using online/hybrid modality. Initially model examples all helical ASR and beta-sheet ASRT were introduced to connect and integrate our ongoing research interest into classroom activities. Subsequently, undergraduates in biochemistry course were assigned a homolog of model proteins any particular protein of students choice to study and characterize using Pymol in semester. During first phase, each undergraduate worked independently using established guidelines. Student's exploration progress was periodically reviewed in pilot phase with majority of students who perceived it as challenging task successfully completed the assignment. Using the PyMol application to reinforce visual understanding of protein structure was highly satisfying experience that greatly enriched undergraduates understanding and appreciation. This article reports a session from the virtual international 2021 IUBMB/ASBMB workshop, "Teaching Science on BigData."

We have developed a semester-long laboratory project for an undergraduate immunology course in which students study multiple aspects of macrophage biology including differentiation from progenitors in the bone marrow, activation upon stimulation with microbial ligands, expression of cell surface markers, and modulation of cytokine production. In the first part of the semester, students differentiate macrophages from mouse bone marrow stem cells and perform immunophenotyping on their macrophages using myeloid markers that are either constitutively expressed or expressed upon activation with microbial ligands. Students use a low-cost image cytometer to both visualize and quantify cellular expression of myeloid markers. Students then perform literature research, design, and execute a series of experiments aimed at investigating the role of natural anti-inflammatory compounds on TNF- production in these macrophages. The soup-to-nuts investigative approach in which students generate "their own" macrophages and study their functions over the course of the semester fostered a sense of ownership and accomplishment

A research-style laboratory experiment for advanced undergraduate students is described, which includes the synthesis, characterization, and properties (porosity, stability, amphipathy) testing of the composite [Cu[subscript 2](BTC)[subscript 4/3](H[subscript 2]O)[subscript 2][subscript 6][HPW[subscript 12]O[subscript 40]·(C[subscript 4]H[subscript 12]N)[subscript 2]·25H[subscript 2]O (denoted as NENU-3, H[subscript 3]BTC = 1,3,5-benzenetricarboxylic acid). This experiment lets students experience the universal procedure of hydro(solvo)-thermal synthesis and get knowledge of general scientific research approaches as well as have hands-on experiences in diverse modern instrumental techniques (PXRD, IR and UV--vis spectroscopy, N[subscript 2] adsorption, and TG analysis) extensively used in chemical research. Most importantly, this laboratory experiment exposes students to explore the structure-property-application relationship in NENU-3 composite material through comparing the structure and properties of NENU-3 with those of its individual component materials (H[subscript 3]PW[subscript12]O[subscript 40] and Cu[subscript 3](BTC)[subscript 2]) and consulting the related literature about NENU-3 catalysis. This experiment is helpful for developing the scientific thinking of students in chemistry through completing the analysis and discussion about the structure-property-application relationship in POM@MOF.

Three-dimensional visualization of molecular simulations in virtual reality (VR) is an emerging teaching tool in chemical education. This work describes a VR application which can generate a 3D molecular dynamics (MD) simulation from arbitrary molecular structures and renders that MD simulation trajectory on a VR headset in real-time. This system uses the ZeroMQ (ZMQ) message passing framework for multisimulation to multiclient VR visualization of MD simulation. All MD simulations are done in the HOOMD-blue simulation engine, and the graphics for the VR are rendered in Unity3D. The key feature that sets this software apart from previous 3D viewer programs is the real-time simulation and thus the ability to manipulate thermodynamic variables like temperature on the fly. This allows viewers to build an intuitive understanding of the effects of thermodynamics state variables in a hands-on way. This application was used as a pedagogical tool with high school students, and the curriculum used, along with outcomes of the activity, has been presented here. This application can provide an interactive tool for teaching thermodynamics and statistical mechanics, and even as a diagnostic tool for MD simulations for research purposes.

According to the definition, surface tension could be affected not only by intermolecular interaction but also by molecular area. However, in chemistry textbooks, surface tension is mainly explained only in terms of intermolecular interaction. Although the existing surface tension concept in the textbooks can lead to a variety of counterexamples, research on undergraduates' responses to surface tension anomalies is rare. In this study, we had 16 undergraduates experience an anomalous surface tension experiment and analyzed how they responded to the anomalous data and whether their explanations had met conditions for accommodation. As a result, among the 16 participants, only one student (rejection response) retained her existing conception (i.e., surface tension is proportional only to the intermolecular interaction), and the rest of the students tried to explain the anomaly in their own ways (theory change, peripheral theory change, and abeyance responses). In particular, only the six students who considered both intermolecular interaction and molecular area properly showed a theory change response that matched conditions for accommodation (dissatisfaction, intelligibility, and plausibility). The results of the study imply that the surface tension concept considering both intermolecular interaction and molecular area might be an alternative to the existing concept in chemistry education.

In multielectron atoms or molecules, quantized electronic energy states known as term states provide a framework for interpreting absorption and emission spectra. Enumerating the term states associated with any particular electron configuration is possible using time-honored procedures, but the underpinnings of the methods do not always receive the attention they deserve. Rounding out the discussion with another approach to term states would provide added perspective. In particular, for systems involving two electrons distributing among two orbitals one can begin by identifying plausible wave functions. The states generated are few in number but noteworthy in that analogous states occur in a host of systems, including helium, titanocene, and molecular hydrogen. Parallels among the systems become evident from the forms of the wave functions.

Classroom response systems are an important tool in many active learning pedagogies. They support real-time feedback on student learning and promote student engagement, even in large classrooms, by allowing instructors to solicit an answer to a question from all students and show the results. Existing classroom response systems are general purpose and not tailored to the specific needs of a chemistry classroom. In particular, it is not easy to deploy molecular representations except as static images. Here we present the 3Dmol.js learning environment, a classroom response system that uses the open-source web-based 3Dmol.js JavaScript framework to provide interactive viewing and querying of 3D molecules. 3Dmol.js is available under a BSD 3-clause open-source license, and the learning-environment features are all available through http://3dmol.csb.pitt.edu/ without any software installation required.

Visualization of three-dimensional (3D) elements has always played a huge role in chemistry education. At the same time, it is a challenge to teach with most representations being shown in two-dimensional (2D) media. With the recent rise of extended reality (XR) that includes virtual and augmented reality (VR/AR) technology in higher education, attempts have been made at presenting 2D representations to students in a manner that is easier to understand. However, the effectiveness of said attempts has limitations. Our AR project has developed a free-to-use mobile application "Nucleophile's Point of View" (NuPOV) that aims to address these limitations. By allowing users to not only view chemistry concepts in an AR setting but also interact with them by hand, they are able to learn and understand at a deeper level through an individualized and self-directed learning experience. Our study has shown that such an approach proved to be relatively well-received by students.

An application for visualizing the dynamic properties of an equimolar binary mixture of isotropic reactive particles is presented. By introducing a user selectable choice for the activation energy, the application is useful to demonstrate qualitatively that the reaction rate depends on the above choice and on temperature. The application is based on a 2D realistic dynamic model where atoms move because of their thermal energies and the trajectories are determined by solving numerically Newton's laws according to a Molecular Dynamics (MD) scheme. Collisions are monitored as time progresses, and every time the collision energy is larger than the selected activation energy, a reactive event occurs. By examining the time evolution of the configurations, it is possible to observe that the number of reactive collisions is always smaller than the total number of collisions. However, the number of reactive events increases on raising the temperature and/or by decreasing the activation energy. The above observations, as well as more quantitative analyses of the simulation data, are useful in elucidating the connections existing among particle kinetic energy, temperature, and activation energy of the reaction. The application can be used at different levels of detail and in different instruction levels. Qualitative visual observations of the progress of the reaction are suitable at all levels of instruction. Systematic investigations on the effect of changes of temperature and activation energy, suitable for senior high school and college courses and useful to gain insight into kinetic models and Arrhenius' law, are also reported.

An introduction to the Quantum Chemistry Package (QCP), implemented in the computer algebra system Maple, is presented. The QCP combines sophisticated electronic structure methods and Maple's easy-to-use graphical interface to enable computation and visualization of the electronic energies and properties of molecules. Here we describe how the QCP can be used in the chemistry classroom using lessons we developed that have been incorporated within the package. In this work, we present four illustrative lessons that showcase the potential implementation of the QCP: the calculation and visualization of molecular orbitals of hydrogen fluoride, the application of the particle in a box to conjugated dyes, the use of geometry optimization and normal-mode analysis for hypochlorous acid, and the thermodynamics of combustion of methane. While these topics are typically encountered at the undergraduate level, we have developed a wide range of lessons for the QCP appropriate for high school advanced placement, undergraduate, and advanced graduate curricula. A summary of implementation and student experience at our respective institutions is also provided.

The concept of an atom with an expanded octet, known as hypervalency, has persisted in the general chemistry curriculum, despite abundant theoretical work disputing its veracity. Here, the electronic structure of traditionally hypervalent molecules (H[subscript 2]SO[subscript 3], H[subscript 2]SO[subscript 4], PF[subscript 5], and SF[subscript 6]) is explored through quantum chemical calculations to illustrate the inaccuracies of hypervalency. Through the framing of ionic and dative bonding, an alternative way to conceptualize bonding in such molecules is introduced based on the octet rule already canonized in the general chemistry curriculum. These results are used to construct new Lewis structures that more accurately describe their chemical nature while simultaneously reducing the complexity of drawing Lewis structures. Teaching applications and heuristics are discussed with the hope that these models may eventually supplant hypervalency in the curriculum.

Nanoscale phenomena are under increasingly intense investigation both in academia and industry. The unique physical and chemical properties stemming from their high surface area and confined space lead to properties that are distinct from atomic and bulk materials. Students need experience in nanoscience to enter this growing field of nanoscience research. This laboratory experiment introduces the optical properties of noble metal nanoparticles and probes the effect that the metal composition has on these properties. An aqueous synthesis is performed, which allows for the control of the alloy composition of Au/Ag nanoparticles, while minimizing costs and hazardous waste. The composition of the synthesized particles is verified by mass analysis. Extinction spectra are recorded experimentally and determined "in silico." The experimental and theoretical spectra are compared, and students are asked to identify causes for discrepancies on the basis of mass and particle size analysis. Students actively engage in identifying how the dielectric function of a nanoparticle affects the optical properties. By performing these experiments, students gain practical knowledge of the synthesis and characterization of metal nanoparticles, as well as an initial introduction to elements of theoretical chemistry. This experiment has been found to be easily reproducible; it utilizes primarily nonhazardous, nontoxic, green materials, and it can be performed with minimal added costs to normal budgets for lab courses.

Research in the past decades repeatedly revealed university students' struggles to properly understand physical chemistry concepts. In contrast to school, tertiary teaching relies heavily on the symbolic level, mainly applying abstract representations such as equations and diagrams. To follow the lessons and generate conceptual understanding, students need to connect those representations with macroscopic and submicroscopic aspects of the scientific concept depicted. For German first-year chemistry students, this increase in abstraction in a major subject of study contributes to excessive demand and demotivation (especially during out-of-class learning) and increases the risk of early dropouts. We designed a simulation-based learning environment (BIRC: Bridging Imagination and Representation in Chemistry) to suit the needs of first-year students and support them when learning physical chemistry at home. Our approach, featuring molecular dynamics simulations, requires students to assess their own mental models on the submicroscopic level and connect them to equations and diagrams on the symbolic level. Prior studies did already highlight the potential of individual BIRC learning units to foster conceptual understanding on specific topics. In this paper, we investigate if and how students of a broader sample use these learning activities as voluntary supplement beside regular coursework. During the term, we used think-aloud protocols, interviews and eight online questionnaires to analyse students' mental and emotional interaction while working on BIRC, assessing whether students perceived BIRC as a suitable, enjoyable and supportive resource to enhance learning. Via two paper & pencil achievement tests we examined students' retention concerning submicroscopic mental models and their ability to connect these mental models with symbolic representations 5-10 weeks later. Our findings indicate a cognitively engaging, comparably enjoyable learning process, which strengthens conceptual understanding and -- despite the necessary time and effort -- induces a broad number of students to voluntarily work on several units at home.

Social distancing during the COVID-19 pandemic presents mental health and academic obstacles for students. As mental health can strongly influence academic performance, addressing the loss of community by transitioning to distance education, midsemester, is imperative. This work draws upon the community and wellness benefits associated with online gaming and applies it to ChemDraw. The goal is to improve the class' wellness and social community while teaching valuable organic chemistry skills. In this paper, a molecule, speed-drawing tournament (Molecule Madness) is presented along with reflections describing the impacts on student wellness and organic chemistry skills. Gamification of ChemDraw is achieved by (1) treating at-home practice as video-game training and (2) using video-conferencing software as a medium for multiplayer gameplay. As the primary focus is placed on education rather than entertainment, ChemDraw is subclassified as a serious educational game. Community is developed by in-game, online chat: observers, announcers, and competitors all interact with each other in real time. The tournament provided students an event to look forward to, helped maintain/improve class community, and developed organic chemistry skills (molecular drawing, history of molecules, and conversational IUPAC) in addition to increased appreciation for IUPAC nomenclature. Although an online community cannot substitute for in-person classroom experiences, this activity supplements the loss of community associated with social distancing and could be extended to enhance community within a face-to-face environment. Additionally, ideas are presented that illustrate how other chemistry classes and topics can be gamified in computer environments (both single- and multiplayer) by drawing upon well-established gaming modes (story mode, maker mode, and speed runs). Overall, this work highlights the supplemental role that chemistry video games can play in learning chemistry: by engaging students in an alternative, yet familiar to many format, classroom community and student confidence are maintained/strengthened.

Individual differences in cognitive decline during normal aging and Alzheimer's disease (AD) are common, but the molecular mechanisms underlying these distinct outcomes are not fully understood. We utilized a combination of genetic, molecular, and behavioral data from a mouse population designed to model human variation in cognitive outcomes to search for the molecular mechanisms behind this population-wide variation. Specifically, we used a systems genetics approach to relate gene expression to cognitive outcomes during AD and normal aging. Statistical causal-inference Bayesian modeling was used to model systematic genetic perturbations matched with cognitive data that identified astrocyte and microglia molecular networks as drivers of cognitive resilience to AD. Using genetic mapping, we identified "Fgf2" as a potential regulator of the astrocyte network associated with individual differences in short-term memory. We also identified several immune genes as regulators of a microglia network associated with individual differences in long-term memory, which was partly mediated by amyloid burden. Finally, significant overlap between mouse and two different human coexpression networks provided strong evidence of translational relevance for the genetically diverse AD-BXD panel as a model of late-onset AD. Together, this work identified two candidate molecular pathways enriched for microglia and astrocyte genes that serve as causal AD cognitive biomarkers, and provided a greater understanding of processes that modulate individual and population-wide differences in cognitive outcomes during AD.

Facile visualization of biomolecules is an essential component of the undergraduate biochemistry curriculum. In the past, a number of tools have been used to display biomolecules. More recently, the advent of greater accessibility to virtual reality (VR) and augmented reality (AR) programs has created a new mechanism to visualize biomolecules. However, creation of VR and AR programs often requires extensive coding experience. In order to expand the utility of AR programs in visualization of biomolecules, we enabled undergraduate students to create their own AR protein visualization tool using an off-the-shelf program running in multiplatform smartphones or tablets to enhance student inclusivity. Assessment of this program shows that students can create their own biomolecule models, were enthusiastic about doing so, and found that their learning was enhanced when this AR module was inserted into their upper level biochemistry class. This activity could be readily adapted for remote and online learning.

The use of symmetry is widespread in chemistry, as it is used for predictions of the number of allowed and forbidden absorptions in electronic, vibrational, and rotational spectroscopies; for predictions of the combination of atomic orbitals to produce molecular orbitals; and in many other chemical applications. One critical step in these applications is the determination of the irreducible representations contained in a reducible one. To expand the tools available in this area, in addition to providing a new method for addressing irreducible representations in point group theory, an open source language program is presented here. Moreover, this program can even be applied to point groups that have complex characters, avoiding the "doubling problem" which occurs in the treatment of these groups. This software has immediate spectroscopic applications, and as an example, special attention is given here to vibrational spectroscopy. The use of this program, in both undergraduate and graduate classes, has the potential to reduce significantly the difficulty in understanding the applications of group theory in chemistry, especially for molecules which belong to symmetry groups with a large number of elements.

Experimental methods for determining 3-D atomic structures, such as crystallography, are rarely taught in the undergraduate curriculum, yet are considered to be the norm for 3-D structure determination in a research setting. Although a fully physical understanding of crystallography takes years of practice, practical applications and basic interpretation of small-molecule crystallography can be readily integrated into undergraduate curricula to give students a research-like laboratory experience. Three 1-h crystallography laboratory modules were developed using the free Olex[superscript 2] software to determine the structure of (dithiolene)[subscript 2]Co(1,3,5-triaza-7-phosphaadamantane)·dichloroethane, while introducing basic crystallography knowledge, crystal evaluation through microscopy, practical structure determination skills, and spatial awareness through 3-D printing. Following implementation in an advanced instrumental analysis class composed of 14 Master's and undergraduate students, the increase of topical knowledge of small molecule crystallography was 18-30% based on tailored assessment surveys, and student feedback was highly positive. This suggests that students without a prior background in crystallography were able to learn and retain information about small molecule crystallography from these laboratory modules.

Drug design and development requires collaboration among scientists with diverse expertise. In early-stage drug design, establishment of promising drug candidates requires integration of structure-based molecular design with biopharmaceutics and ADMET (absorption, distribution, metabolism, excretion, and toxicity) principles. Much of this work is increasingly computational. Thus, students in a drug design course should learn the basis for and effects of candidate small molecules binding to therapeutic targets and the importance of simultaneous understanding of ADMET characteristics that will largely determine if the molecule can achieve a therapeutically relevant concentration 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. Our teaching approach has evolved over a decade in early graduate and advanced undergraduate settings. 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.

A bachelor's degree program in chemistry typically starts with basic concepts in mathematics, physics, and chemistry. Those principles are very important because they pave the ground for future advanced studies and, therefore, one needs to present them in a clear but rigorous way. One example is provided by the mathematical notion of an iterative process which acquires a significant relevance in chemistry. The popular Newton-Raphson algorithm has been selected to exemplify how iterative methods work as it is highly effective and suitable for undergraduate students. Additionally, this work presents a straightforward and interactive pedagogical tool, created with the widespread Microsoft Office Excel, which can be applied in a classroom to solve nonlinear equations numerically. Four pervasive topics in undergraduate programs are given to illustrate the importance of iterative processes, namely the calculation of pH of a weak acid solution, the molar volume of a real gas, the molecular geometry delivered by VSEPR theory, and the conformational analysis of 1,2-dichloroethane molecule.

The increasing use of information technology in the discovery of new molecular entities encourages the use of modern molecular-modeling tools to help teach important concepts of drug design to chemistry and pharmacy undergraduate students. In particular, statistical models such as quantitative structure--activity relationships (QSAR)--often as its 3D QSAR variant--are commonly used in the development and optimization of a leading compound. We describe how these drug discovery methods can be taught and learned by means of free and open-source web applications, specifically the online platform www.3d-qsar.com. This new suite of web applications has been integrated into a drug design teaching course, one that provides both theoretical and practical perspectives. We include the teaching protocol by which pharmaceutical biotechnology master students at Pharmacy Faculty of Sapienza Rome University are introduced to drug design. Starting with a choice among recent articles describing the potencies of a series of molecules tested against a biological target, each student is expected to build a 3D QSAR ligand-based model from their chosen publication, proceeding as follows: creating the initial data set (Py-MolEdit); generating the global minimum conformations (Py-ConfSearch); proposing a promising mutual alignment (Py-Align); and finally, building, and optimizing a robust 3D QSAR models (Py-CoMFA). These student activities also help validate these new molecular modeling tools, especially for their usability by inexperienced hands. To more fully demonstrate the effectiveness of this protocol and its tools, we include the work performed by four of these students (four of the coauthors), detailing the satisfactory 3D QSAR models they obtained. Such scientifically complete experiences by undergraduates, made possible by the efficiency of the 3D QSAR methodology, provide exposure to computational tools in the same spirit as traditional laboratory exercises. With the obsolescence of the classic Comparative Molecular Field Analysis Sybyl host, the 3dqsar web portal offers one of the few available means of performing this well-established 3D QSAR method.

We present a critical discussion of how chemistry textbooks treat the electrolysis of water and aqueous salt solutions, based on a survey of general chemistry textbooks in English and Korean at secondary and tertiary levels, also informed by the historical background of 19th-century debates. English-language textbooks present various and contradictory accounts of the electrolysis of water; a key point of disagreement is whether hydrogen and oxygen gases originate from pre-existing H[superscript +] and OH[superscript -] ions, or from the direct reduction and oxidation of H[subscript 2]O molecules. School textbooks in South Korea all present the same account, with no indication of alternative views. A vast majority of all texts ignore the possibility that H[subscript 2] and O[subscript 2] may result from secondary reactions, which was a standard view in the late 19th century following the works of Daniell and Miller. Concerning the electrolysis of aqueous salt solutions, all texts give oversimplified views of competing reactions based on standard reduction/oxidation potentials. It is understandable that textbooks try to present sufficiently simple pictures that students at each level can handle; however, this should not be done in a way that shuts down questions. We recommend that students should be made aware that textbook accounts are only models, and encouraged to extend their learning beyond the models. The plausibility of our recommendations is shown in a pilot study we conducted with secondary school students in South Korea.

There has been widespread interest in the study of oxoacids of phosphorus owing to their characteristic structures and uses in various areas of daily life. In this article, a new strategy is recommended to determine their structures. This strategy will help to develop problem-solving skills and creativity among students. The strategy is based on the use of the characteristic bonding features of oxoacids of phosphorus.

Sets of models of molecules (which are of interest for teaching molecular structure, symmetry, and related topics in many chemical disciplines) were prepared and made available either for self-directed 3D-printing or through the 3D-printing company Shapeways providing 3D-printing as a service. This allows teachers to save time on searching for relevant examples and to acquire tangible models of molecules even in the absence of freely available 3D-printing facilities. The use of such models for teaching in classrooms along with idealized ball-and-stick models and computer software is encouraged. Simultaneous employment of all the mentioned resources actuates both visual and haptic perception, and their complementary action enhances the effectiveness of teaching and students' engagement. The prepared sets of models are well-suited to teaching molecular structure and symmetry, for showing differences between idealized and real molecules, for explaining crystallographic and noncrystallographic symmetry, and for showing conformational flexibility. The preassembled sets of 3D-printed models described here can be implemented in many courses, including general chemistry, organic and inorganic chemistry, solid state chemistry, crystal chemistry, and so on, which cover the audience of university students of all years and levels, as well as high school students. Worksheets to use in conjunction with the models in classrooms are provided.

Molecular symmetry plays an important role in many areas of chemistry, and students are generally taught to identify intramolecular symmetries at the undergraduate level. Intermolecular symmetry, the symmetry among groups of molecules, is of great importance in topics such as X-ray crystallography, but it receives substantially less attention. Even when familiar with such symmetries as translations, screw rotations, and glide reflections, students rarely obtain the same level of proficiency in identifying these symmetries via inspection as they do with the proper and improper rotations involved in point group symmetry. We describe a tool designed to scaffold the student's ability to mentally manipulate molecules and identify the presence and nature of intermolecular symmetry. The tool consists of an algorithm that the student follows to generate centroids between atoms in putatively symmetry-related molecules. The easily recognized patterns formed by the centroids provide key information about the presence and nature of any intermolecular symmetry relating the molecules. The theoretical basis for the patterns formed by the centroids is provided along with worked examples, an example problem set, and a prescription for generating new exercises.

The concept of equilibrium vapor pressure plays a key role in the general chemistry curriculum; it is among the first and most easily demonstrated examples of equilibrium and frequently caps off the first semester of general chemistry where it illustrates the properties of liquids and intermolecular forces. We report here simple modifications of Levinson's classic experiment that allow measurement of vapor pressures for organic samples at a variety of temperatures. Data analysis gives heats of vaporization which may be interpreted in terms of intermolecular attractive forces. Equipment needs are simple and readily available: a 10 mL graduated cylinder, a tall 1 L beaker, disposable graduated syringes, and a 10 in. needle or cannula bent into a "J" shape. The method uses 1 mL or less of organic sample per trial and works well for organic liquids that are immiscible with and are less dense than water. Student results are presented for the experiment conducted over three semesters as well as the impact on student learning as assessed by common exam results and end-of-semester student surveys.

We present a simple procedure to make an augmented reality app to visualize any chemical 3D model. The molecular structure may be based on crystallographic data or from computational modeling. This guide is made in such a way that no programming skills are needed, and the procedure uses free software and provides a way to visualize 3D structures that are normally difficult to comprehend in the 2D space of paper. The process can be applied to make a 3D representation of any 2D object, and we envisage the app to be useful when visualizing simple stereochemical problems, when presenting a complex 3D structure on a poster presentation or even in audio-visual presentations. The method works for all molecules including small molecules, supramolecular structures, MOFs, and biomacromolecules.

Nuclear magnetic resonance (NMR) spectroscopy has become a cornerstone tool for studying a variety of molecular features in advanced chemistry laboratories. In this experiment, students prepare a pyrrole-[beta]-amide via a one-pot, three-step synthesis and use NMR spectroscopy to confirm its molecular structure. In addition, variable temperature (VT) [superscript 1]H NMR spectroscopy is used to study the dynamic amide bond, a functional group with restricted rotation about the C-N bond. The VT NMR data allow the students to determine the coalescence temperature associated with the slow equilibrium at room temperature and the corresponding energy barrier (delta G?) for the restricted rotation about the C-N bond.

There is a disconnect between the cutting-edge research done in academic laboratories, such as nanotechnology, and what is taught in undergraduate laboratories. In the current undergraduate curriculum, very few students get a chance to do hands-on experiments in nanotechnology-related fields, most of which are through selective undergraduate research programs. In most cases, complicated synthesis procedures, expensive reagents, and the requirement for specific instrumentation prevent broad adaptation of nanotechnology-based experiments to laboratory courses. DNA, being a nanoscale molecule, has recently been used in bottom-up nanotechnology with applications in sensing, nanorobotics, and computing. In this article, we propose a simple experiment involving the synthesis of a DNA nanoswitch that can change its shape from a linear "off" state to a looped "on" state in the presence of a target DNA molecule. The experiment also demonstrates the programmable topology of the looped state of the nanoswitch and its effect on gel migration. The experiment is easy to adapt in an undergraduate laboratory, requires only agarose gel electrophoresis, has a minimal setup cost for materials, and can be completed in a 3 hour time frame.

The chemistry of metal-organic frameworks (MOFs), a new class of emerging crystalline porous solids with three-dimensional (3D) networks composed of metals and multidentate organic molecules, was introduced by using three differently shaped crystals. We reported new and mild MOF synthesis methods that are simple and devised to be performed in high school or primarily undergraduate school settings. MOF applications were demonstrated by use of our synthesized MOFs in the capture of iodine as a potentially hazardous molecule from solution and as a drug delivery system. These applications can be visually confirmed in minutes. Students can gain knowledge on advanced topics, such as drug delivery systems, through these easy-to-prepare MOFs. Furthermore, students can gain an understanding of powder X-ray analysis and ultraviolet-visible near-infrared spectroscopy. This laboratory experience is practical, including synthesis and application of MOFs. The entire experiment has also been recorded as an educational video posted on YouTube as a free public medium for students to watch and learn. In this paper we first report the steps we took to synthesize and analyze the MOFs, followed by a description of a simple demonstration that we verified to effectively exhibit adsorption by MOFs. We conclude with a description of how the laboratory activity and demonstration were implemented in an undergraduate chemistry laboratory.

The concept of delocalization (i.e., resonance) is fundamental concept in organic chemistry but essential learning outcomes (LOs) have not previously been proposed nor has there been an analysis of how resonance is taught, despite indications in the literature that students have many non-canonical ideas about the concepts. To address this deficit, we first developed a set of ten learning outcomes believed to be essential to the concept of delocalization in organic chemistry, especially for students' later success. Next, we analyzed how these learning outcomes are being taught, practiced and assessed in common textbooks and in a sample of exams. Five themes emerged from the analysis: (1) several of the essential intended LOs we identified are not represented in the textbooks' teaching explanations, practice questions, or professors' assessments; (2) the concepts related to delocalization are often taught, practiced, and assessed without associated justifications; (3) there is a large gap between when delocalization is taught and when it is used in context; (4) the link between delocalization and other concepts (e.g., reactivity) is not explicitly explained in most teaching materials; and (5) the language used around delocalization may be misleading (e.g., resonance, stability). Our analysis identified areas in which delocalization education could be improved, including with respect to teaching, practice opportunities, and assessing the concepts.

Students undertaking courses in the field of chemistry need to integrate their spatial skills and conceptual knowledge. However, model perception along with the understanding of spatial processes and spatial structures of molecules has been a cause of difficulty for students as conventional teaching methods cannot fully aid student comprehension. In this research, we propose a technological solution to aid the spatial learning process by automatically creating a link between two-dimensional (2D) representations of chemical structures and three-dimensional (3D) molecular visualization. The image of a chemical structure is acquired and processed on-the-fly for structure identification and 3D model generation. The 3D molecular model is simplified for real-time interactive rendering. The efficacy of the proposed solution in enhancing spatial ability of individuals is evaluated through an experiment on first year undergraduate students. Our analysis of the results suggests that virtual models and mobile applications are capable of narrowing the performance gap between students with different levels of spatial ability.

Models that are used to predict and explain phenomena related to molecular vibration and rotation are ubiquitous in physical chemistry, and are of importance in many related fields. Yet, little work has been done to characterize student use and application of these models. We describe the results of a multi-year, multi-institutional qualitative study to investigate how students work with and apply models of molecular vibration and rotation. Our findings indicate that a sizable fraction of students (1) struggle to interpret the meaning of wavefunctions, (2) do not appropriately build potential and kinetic energy terms into models, and (3) conflate portions of various model systems. The data suggests that the ordering of content in the quantum chemistry course impacts students' ideas about the rotational and vibrational behavior of molecules. The results are analyzed through the lenses of a two theoretical frameworks: one for scientific modeling, and one for heuristics in the context of chemistry. Implications for research and teaching practice are provided.

NMR spectroscopy is traditionally taught to students during Organic Chemistry as a tool used for the determination of structures after synthesis. However, modern NMR spectroscopy has many important applications beyond structure elucidation, including molecular profiling of complex mixtures as biofluids and food samples. In this experiment, students collect a series of nonselective and selective 1D NMR spectra of natural and supermarket fruit juices and are asked to identify and quantify the sugars present. For the quantitative analysis of the juices, the students must use the ERETIC2 (electronic reference to access in vivo concentrations 2) method embedded in the NMR software.

Polymers and nanochemistry are important facets of chemistry. In this experiment, students synthesize monodispersed poly(methyl methacrylate) nanospheres from the addition or chain polymerization of a rapidly stirred aqueous mini-emulsion of methyl methacrylate. The 2,2'-azobis(2-methylpropionamidine) dihydrochloride serves as a heat activated, water-soluble, free radical initiator to polymerize the emulsion droplets starting from their outer edge. The uniform small diameter particles will appear iridescent if they are close-packed and their size is similar to the wavelength of visible light. Students characterize the size of the poly(methyl methacrylate) spheres by four methods: the settling velocity and Stokes' law, evaporative self-assembly of a photonic material and visible spectroscopy, direct measurement using scanning electron microscopy (SEM), and SEM measurement of the silica inverse opal. This experiment increases student collaboration and provides the opportunity to work on multiple experiments at once.

Infrared (IR) thermography renders invisible infrared radiation with intuitive coloration in images and videos taken of objects, reactions, and processes. Educators can take advantage of this technology to extend students' sensory perception of chemical reactions or processes that absorb or release heat in rich detail. In theory, IR thermography can be applied essentially universally for such analysis given that any change in thermal energy must result in, or from, the change of potential energy due to the interactions among atoms, molecules, and photons. Through the use of IR thermography, students can visualize otherwise invisible evidence of what is occurring on the molecular level in a variety of chemical process such as evaporative cooling, phase change, dissolution, titration, and enzymatic reactions. While not new, IR cameras are rapidly becoming affordable with models that connect easily with smartphones and tablets. The price decrease has opened the door for large-scale implementation in the chemistry education laboratory. We report here several laboratory activities and best practices that will facilitate the exploration of specific chemistry concepts through the use of infrared thermography, as well as integration of this technique into existing general chemistry laboratory courses.

A simple one-dimensional [superscript 1]H NMR experiment that quantifies protein bound to gold nanoparticles has been developed for upper-division biochemistry and physical chemistry students. This laboratory experiment teaches the basics of NMR techniques, which is a highly effective tool in protein studies and supports students to understand the concepts of NMR spectroscopy and nanoparticle-protein interactions. Understanding the interactions of gold nanoparticles (AuNPs) with biological macromolecules is becoming increasingly important as interest in the clinical use of nanoparticles has been on the rise. Applications in drug delivery, biosensing, diagnostics, and enhanced imaging are all tangible possibilities with a better understanding of AuNP-protein interactions. The ability to use AuNPs as biosensors for drug delivery methods in cellular uptake is dependent on the amount of protein that is able to bind to the surface of the nanoparticle. This laboratory experiment solidifies concepts such as quantitative NMR spectroscopy while reinforcing precision laboratory titrations. Students learn how [superscript 1]H proton NMR spectra can be used to measure free protein in solution and protein bound to AuNPs. A simple formula is used to determine the binding capacity of the nanoparticle. This analysis helps students to understand the impact of nanoparticle-protein interactions, and it allows them to conceptualize macromolecular binding using NMR spectroscopy.

Nanoparticle Zn[subscript 2x] Cu[subscript 1-x] In[subscript 1-x] S[subscript 2] is a promising and safer alternative to lead- and cadmium-containing quantum dots. Students prepare Zn[subscript 0.44] Cu[subscript 0.78] In[subscript 0.78] S[subscript 2] quantum dots in a one-pot synthesis without an inert atmosphere and investigate how the color, visible absorption band edge, and photoluminescence peak wavelength depend on the size of the particle. Octadecene is used as a noncoordinating solvent with a high boiling point. Oleic acid and stearic acid are used as ligands to dissolve the metal salts in the solvent at 150°C. Dodecanethiolate coordinates to the metal ion, and above 200°C, the metal thiolate decomposes to produce metal sulfide nanoparticles, coated in dodecanethiolate. Samples are withdrawn from the hot solution and quenched at room temperature to produce a series of increasing nanoparticle sizes with the same chemical composition.

The abstract nature of physical chemistry and spectroscopy makes the subject difficult to comprehend for many students. However, bridging arts and science has the potential to provide innovative learning methods and to facilitate the understanding of abstract concepts. Herein, we present a high-school project based on the conversion of selected infrared absorbances of well-known molecules into audible frequencies. This process offered students a unique insight into the way molecules and chemical bonds vibrate, as well as an opportunity to develop their creativity by producing musical pieces related to the molecules they synthesized. We believe that experiencing chemistry from an alternative viewpoint opens up new perspectives not only for student learning but also for the decompartmentalization of scientific and artistic disciplines.

Many STEM (science, technology, engineering, and mathematics) disciplines require a two-semester sequence of introductory college chemistry, which are thus critical gateway courses to a variety of majors. Recognizing the benefit to educators of a structure of content learning across the chemistry curriculum, in 2012, the American Chemical Society (ACS) developed the Anchoring Concepts Content Map, or ACCM. The development and subsequent revision of the general chemistry ACCM inspired the restructuring of our first-year chemistry sequence. Thus our CHEM 1001 and 1002 courses, taught in an atoms-first framework, were reorganized into a set of nine modules, each intentionally linked to one (or more) anchoring concept of the ACCM. In this initial effort, we have developed the course modules and subtopics and a set of learning objectives for each module and linked these to the general chemistry ACCM. To facilitate the initial teaching of the courses, the redesign occurred during the academic year, and the courses were taught in summer term 2019 using a flipped classroom design with three weekly 100 min face-to-face discussion meetings and two weekly laboratories for the 6 week long courses. Herein we describe the course design and its mapping onto the ACCM and discuss the results of the initial implementation, with suggestions given for future adaptations.

Electromagnetic radiation can be classified into two major types depending on its ability to detach electrons from atoms: ionising and non-ionising. The aforementioned categorization is significant due to the effects of ionising radiation on human tissue (e.g. carcinogenesis). However, many students around the globe cannot distinguish these two types of electromagnetic radiation and as a result significant misconceptions arise regarding this topic (for example radiation emitted by mobile phones is considered by many students as ionising). Hence, in this paper a teaching approach specifically designed and implemented for the secondary education level is presented, based on the absorbed energy distribution by atoms/molecules in each radiation type. More specifically, the number of atoms/molecules that absorb equal doses of energy per unit mass can be used in order to explain the difference in the effects caused by the two abovementioned radiation types. Also, two analogies from classical mechanics are presented to provide a full insight into the energy distribution concept from a teaching perspective.