From Plastic Models to Virtual Reality Headsets: Enhancing Molecular Structure Education for Undergraduate Students.

The comprehension of molecular structure is pivotal in chemistry education. Over the past decade, Mahidol University International College has employed various teaching tools for the introductory chemistry laboratory class. This paper outlines our evolutionary shift from traditional tools, such as plastic and plasticine models, to the integration of computer software, and ultimately to augmented reality (AR) and virtual reality (VR) tools-specifically, MoleculARweb and MolecularWebXR developed by École Polytechnique Fédérale de Lausanne researchers. In this paper, we detail the implementation of these tools in our classes and present the outcomes of student surveys. Our instructional focus encompasses VSEPR, Atomic Orbitals, Molecular Orbitals, Skeletal Formula, and Enantiomers. This paper not only serves as a model for educators in general chemistry at secondary school or university levels to incorporate technology into their classrooms but also showcases a collaborative endeavor between Swiss and Thai researchers.

Terahertz Spectroscopic Analysis of Lactose in Infant Formula: Implications for Detection and Quantification.

Lactose plays a significant role in daily lives as a constituent of various food and pharmaceutical products. Yet, lactose intolerance conditions demand low-lactose and lactose-free products in the market. These increasing nutritional claims and labels on food products entail simple and reliable methods of analysis that can be used for meeting quality standards, nutritional claims and legal requirements. In this study, terahertz time-domain spectroscopy (THz-TDS) was employed to analyse α-lactose monohydrate qualitatively and quantitatively in food products. Both absorption spectra and absorption coefficient spectra were investigated for their prediction performance. Regression models for lactose quantification using peak area and height of the absorption peaks 0.53 and 1.37 THz were developed and assessed in infant formula samples. Satisfactory prediction results were achieved in ideal conditions with pure standards, but not in all predictions of infant formula samples. Reasons and further implications are discussed.

The prevalence of anconeus epitrochlearis muscle and Osborne's ligament in cubital tunnel syndrome patients and healthy individuals: An anatomical study with meta-analysis.

BACKGROUND: Anconeus epitrochlaeris muscle and Osborne's ligament are anatomical variants that are occasionally found at the cubital tunnel of the elbow. In certain individuals, these two structures may compress the ulnar nerve resulting in a cubital tunnel syndrome. Although these variants have been reported extensively, its prevalence is still unclear and its contribution to cubital tunnel syndrome is debatable. The aim of this study is to generate weighted frequency values of the anconeus epitrochlearis and Osborne's ligament, as well as to identify any association of these two structures with gender, side, ethnicity and the development of cubital tunnel syndrome. METHODS: An anatomical study and a meta-analysis were performed to more accurately study the prevalence of anconeus epitrochlearis and Osborne's ligament. A total of 40 original studies including the present study met the inclusion criteria for meta-analysis and 6 case reports for descriptive analysis. RESULTS: Crude pooled prevalence estimate of the anconeus epitrochlearis was significantly higher (p < 0.001) in healthy subjects (14.2%) than in subjects diagnosed with cubital tunnel syndrome (4.5%). No significant difference was found for gender, side or laterality. The anconeus epitrochlearis was significantly more common in Europeans populations (18.2%) when compared with North American (6.8%) (p = 0.012) and Asian populations (7.5%) (p < 0.001). Anconeus epitrochlearis had a tendency to be hypertrophied when associated with cubital tunnel syndrome. The definition of Osborne's ligament is unclear, resulting in inconsistent reported prevalence across studies. CONCLUSION: The present study provides a more accurate estimate of anconeus epitrochlearis across the populations. There was a negative correlation between the presence of anconeus epitrochlearis and the development cubital tunnel syndrome, supporting the idea that the muscle may be protective against cubital tunnel syndrome. Future studies are needed to give proper definition of Osborne's ligament and accurately study its prevalence across populations.

The prevalence of the azygos lobe: A meta-analysis of 1,033,083 subjects.

The azygos lobe (AL) is an accessory lobe of the right lung with prevalence between 0.4 and 1.2%. The aim of the present review is to provide a better estimate of the frequency of the AL and to examine its relationships with other variables such as population, diagnostic methods, and co-occurring illnesses. Studies published between 1899 and October 2020 were searched through three electronic databases; Google Scholar, PubMed, and JSTOR. Titles, abstracts, and full texts of the retrieved entries were screened to determine their appropriateness for inclusion. A total of 88 studies relating to 1,033,083 subjects met the inclusion criteria. A random-effects meta-analysis yielded an overall prevalence of 0.30% (95% CI: 0.0024-0.0035, I2  = 97.9%). Linear regression and subgroup analysis revealed a negative correlation (ρ = -0.540, p <0.001) between AL prevalence and sample size; studies with smaller sample sizes had higher prevalences. The AL prevalence in individuals with congenital pulmonary defects, 5.2% (95% CI: 0.0018-0.0086, I2  = 0%), was 17 times higher than the overall prevalence (z = 6.65, p <0.001), suggesting associations with other abnormalities and possibly a genetic predisposition. In addition to an evidence-based synthesis of AL prevalence, this study demonstrates publication bias and small-study effects in the anatomy literature. Awareness of the AL is crucial for radiologists when they interpret unusual radiological findings and for surgeons when they operate in the region.

Quantum Chemical Investigation of Polychlorinated Dibenzodioxins, Dibenzofurans and Biphenyls: Relative Stability and Planarity Analysis.

All the possible polychlorinated aromatic compounds in the classes of dibenzodioxins (PCDDs), dibenzofurans (PCDFs), and biphenyls (PCBs) were studied by the quantum chemical methods of HF/6-311++G(d,p), B3LYP/6-311++G(d,p), and MP2/cc-pVTZ. The calculated stabilities and structures of these compounds were compared with the available data on their abundance and toxicity. Prediction models for trends in energy and planarity among these congeners were proposed. The results discussed here can help contribute to the understanding of the role of dioxin-like compounds (DLCs) in the environment.

Resolutions of the Coulomb operator: VIII. Parallel implementation using the modern programming language X10.

Use of the modern parallel programming language X10 for computing long-range Coulomb and exchange interactions is presented. By using X10, a partitioned global address space language with support for task parallelism and the explicit representation of data locality, the resolution of the Ewald operator can be parallelized in a straightforward manner including use of both intranode and internode parallelism. We evaluate four different schemes for dynamic load balancing of integral calculation using X10's work stealing runtime, and report performance results for long-range HF energy calculation of large molecule/high quality basis running on up to 1024 cores of a high performance cluster machine.

Switchable Metal-Ion Selectivity in Sulfur-Functionalised Pillar[5]arenes and Their Host-Guest Complexes.

Nucleophilic substitution of pertosylated pillar[5]arene (P-OTs) with commercially available sulfur containing nucleophiles (KSCN, KSAc, and thiophenol), yields a series of sulfur-functionalised pillar[5]arenes. DLS results and SEM images imply that these pillararene macrocycles self-assemble in acetonitrile solution, while X-ray crystallographic evidence suggests solvent-dependent assembly in the solid state. The nature of the sulfur substituents decorating the rim of the pillararene controls binding affinities towards organic guest encapsulations within the cavity and dictates metal-ion binding properties through the formation of favorable S-M2+ coordination bonds outside the cavity, as determined by 1 H NMR and fluorescence spectroscopic experiments. Addition of a dinitrile guest containing a bis-triazole benzene spacer (btn) induced formation of pseudorotaxane host-guest complexes. Fluorescence emission signals from these discrete macrocycles were significantly attenuated in the presence of either Hg2+ or Cu2+ in solution. Analogous titrations utilizing the corresponding pseudorotaxanes alter the binding selectivity and improve fluorescence sensing sensitivity. In addition, preliminary liquid-liquid extraction studies indicate that the macrocycles facilitate the transfer of Cu2+ from the aqueous to the organic phase in comparison to extraction without pillar[5]arene ligands.

1-(2'-Anilinyl)prop-2-yn-1-ol rearrangement for oxindole synthesis.

A synthetic method that relies on NIS (N-iodosuccinimide)-mediated cycloisomerization reactions of 1-(2'-anilinyl)prop-2-yn-1-ols to gem-3-(diiodomethyl)indolin-2-ones and 2-(iodomethylene)indolin-3-ones has been developed. The reactions were shown to be chemoselective, with secondary and tertiary alcoholic substrates exclusively giving the 3- and 2-oxindole products, respectively. In the case of the latter, the transformation features an unprecedented double 1,2-OH and 1,2-alkyl migration relay. Density functional theory (DFT) calculations based on proposed iodoaminocyclization species provide insight into this unique divergence in product selectivity.

Resolutions of the Coulomb operator. VI. Computation of auxiliary integrals.

We discuss the efficient computation of the auxiliary integrals that arise when resolutions of two-electron operators (specifically, the Coulomb operator [T. Limpanuparb, A. T. B. Gilbert, and P. M. W. Gill, J. Chem. Theory Comput. 7, 830 (2011)] and the long-range Ewald operator [T. Limpanuparb and P. M. W. Gill, J. Chem. Theory Comput. 7, 2353 (2011)]) are employed in quantum chemical calculations. We derive a recurrence relation that facilitates the generation of auxiliary integrals for Gaussian basis functions of arbitrary angular momentum and propose a near-optimal algorithm for its use.

Selective Extraction, Recovery, and Sensing of Hydroquinone Mediated by a Supramolecular Pillar[5]quinone Quinhydrone Charge-Transfer Complex.

Intermolecular interactions between an electron-rich aromatic hydroquinone (HQ) with its electron deficient counterpart, benzoquinone (BQ), result in the formation of a quinhydrone charge-transfer complex. Herein, we report a novel quinhydrone-type complex between pillar[5]quinone (P[5]Q) and HQ. Characterized by a suite of spectroscopic techniques including 1H NMR, UV-visible, and FTIR together with PXRD, SEM, BET, CV, and DFT modeling studies, the stability of the complex is determined to be due to an electron-proton transfer reaction coupled with a complementary donor-acceptor interaction. The selectivity of P[5]Q toward HQ over other dihydroxybenzene isomers allows for not only the naked-eye detection of HQ but also its selective liquid-liquid extraction and recovery from aqueous media.

Chemometric Analysis of a Ternary Mixture of Caffeine, Quinic Acid, and Nicotinic Acid by Terahertz Spectroscopy.

Caffeine, quinic acid, and nicotinic acid are among the significant chemical determinants of coffee quality. This study develops a chemometric model to quantify these compounds in ternary mixtures analyzed by terahertz time-domain spectroscopy (THz-TDS). A data set of 480 THz spectra was obtained from 80 samples. Combinations of data preprocessing methods, including normalization (Z-score, min-max scaling, Mie baseline removal) and dimensionality reduction (principal component analysis (PCA), factor analysis (FA), independent component analysis (ICA), locally linear embedding (LLE), non-negative matrix factorization (NMF), isomap), and prediction models (partial least-squares regression (PLSR), support vector regression (SVR), multilayer perceptron (MLP), convolutional neural network (CNN), gradient boosting) were analyzed for their prediction performance (totaling to 4,711,685 combinations). Results show that the highest quantification performance was achieved at a root-mean-square error of prediction (RMSEP) of 0.0254 (dimensionless mass ratio), using min-max scaling and factor analysis for data preprocessing and multilayer perceptron for prediction. Effects of preprocessing, comparison of prediction models, and linearity of data are discussed.

Z-matrix template-based substitution approach for enumeration of 3D molecular structures.

The exhaustive enumeration of 3D chemical structures based on Z-matrix templates has recently been used in the quantum chemical investigation of constitutional isomers, diastereomers and rotamers. This simple yet powerful initial structure generation approach can apply beyond the investigation of compounds of identical formula by quantum chemical methods. This paper provides a comprehensive description of the overall concept followed by a practical tutorial to the approach.•The four steps required for Z-matrix template-based substitution are template construction, generation of tuples for substitution sites, removal of duplicate tuples and substitution on the template.•The generated tuples can be used to create chemical identifiers to query compound properties from chemical databases.•All of these steps are demonstrated in this paper by common model compounds and are very straightforward for an undergraduate audience to reproduce. A comparison of the approach in this paper and other options is also discussed.

Steric effects vs. electron delocalization: a new look into the stability of diastereomers, conformers and constitutional isomers.

A quantum chemical investigation of the stability of compounds with identical formulas was carried out on 23 classes of compounds made of C, N, P, O and S atoms as core structures and halogens H, F, Cl, Br and I as substituents. All possible structures were generated and investigated by quantum mechanical methods. The prevalence of a formula in which its Z configuration, gauche conformation or meta isomer is the most stable form is calculated and discussed. Quantitative and qualitative models to explain the stability of the 23 classes of halogenated compounds were also proposed.

A virtual alternative to molecular model sets: a beginners' guide to constructing and visualizing molecules in open-source molecular graphics software.

OBJECTIVE: The application of molecular graphics software as a simple and free alternative to molecular model sets for introductory-level chemistry learners is presented. RESULTS: Based on either Avogadro or IQmol, we proposed four sets of tasks for students, building basic molecular geometries, visualizing orbitals and densities, predicting polarity of molecules and matching 3D structures with bond-line structures. These topics are typically covered in general chemistry for first-year undergraduate students. Detailed step-by-step procedures are provided for all tasks for both programs so that instructors and students can adopt one of the two programs in their teaching and learning as an alternative to molecular model sets.

Geometric and energetic data from quantum chemical calculations of halobenzenes and xylenes.

This article presents theoretical data on geometric and energetic features of halobenzenes and xylenes. Data were obtained from ab initio geometry optimization and frequency calculations at HF, B3LYP, MP2 and CCSD levels of theory on 6-311++G(d,p) basis set. In total, 1504 structures of halobenzenes, three structures of xylenes and one structure of benzene were generated and processed by custom-made codes in Mathematica. The quantum chemical calculation was completed in Q-Chem software package. Geometric and energetic data of the compounds are presented in this paper as supplementary tables. Raw output files as well as codes and scripts associated with production and extraction of data are also provided.

In silico geometric and energetic data of all possible simple rotamers made of non-metal elements.

This article presents theoretical data on geometric and energetic features of halogenated rotamers of the following backbone structures, C-C, N-N, P-P, O-O, S-S, N-P, O-S, C-N, C-P, C-O, C-S, N-O, N-S, P-O and P-S. The data is considered to be comprehensive combinations of non-metal elements in the form abcx-ydef whereby a,b,c,d,e,f are halogen (fluorine to iodine), hydrogen or a lone pair and x,y are carbon, nitrogen, phosphorus, oxygen and sulfur. Data were obtained from ab initio geometry optimization and frequency calculations at HF, B3LYP, MP2 and CCSD levels of theory on 6-311++G(d,p) basis set. In total, 8535 non-enantiomeric structures were produced by custom-made codes in Mathematica and Q-Chem quantum chemical package. Extracted geometric and energetic data as well as raw output files, codes and scripts associated with the data production are presented in the data repository.

Correction to 'A DFT investigation of the blue bottle experiment: E° half-cell analysis of autoxidation catalysed by redox indicators'.

[This corrects the article DOI: 10.1098/rsos.171563.].

The Quality and Readability of English Wikipedia Anatomy Articles.

Forty anatomy articles were sampled from English Wikipedia and assessed quantitatively and qualitatively. Quantitatively, each article's edit history was analyzed by Wikipedia X-tools, references and media were counted manually, and two readability indices were used to evaluate article readability. This analysis revealed that each article was updated 8.3 ± 6.8 times per month, and referenced with 33.5 ± 24.3 sources, such as journal articles and textbooks. Each article contained on average 14.0 ± 7.6 media items. The readability indices including: (1) Flesch-Kincaid Grade Level Readability Test and (2) Flesch Reading Ease Readability Formula demonstrated that the articles had low readability and were more appropriate for college students and above. Qualitatively, the sampled articles were evaluated by experts using a modified DISCERN survey. According to the modified DISCERN, 13 articles (32.5%), 24 articles (60%), 3 articles (7.5%), were rated as "good," "moderate," and "poor," respectively. There were positive correlations between the DISCERN score and the number of edits (r = 0.537), number of editors (r = 0.560), and article length (r = 0.536). Strengths reported by the panel included completeness and coverage in 11 articles (27.5%), anatomical details in 10 articles (25%), and clinical details in 5 articles (12.5%). The panel also noted areas which could be improved, such as providing missing information in 28 articles (70%), inaccuracies in 10 articles (25%), and lack or poor use of images in 17 articles (42.5%). In conclusion, this study revealed that many Wikipedia anatomy articles were difficult to read. Each article's quality was dependent on edit frequency and article length. Learners and students should be cautious when using Wikipedia articles for anatomy education due to these limitations.

Resolutions of the Coulomb operator. Part III. Reduced-rank Schrödinger equations.

We consider a modified Schrödinger equation wherein the electron-electron repulsion terms r(ij)(-1) are approximated by truncated one-particle resolutions. Numerical results for the He atom and H2 molecule at the Hartree-Fock, second-order Møller-Plesset, and configuration interaction levels show that the solutions of the resulting reduced-rank Schrödinger equations converge rapidly, and that even low-rank approximations can yield energies with chemical accuracy.

In silico investigation of mitragynine and 7-hydroxymitragynine metabolism.

OBJECTIVE: Mitragynine is the main active compound of Mitragyna speciose (Kratom in Thai). The understanding of mitragynine derivative metabolism in human body is required to develop effective detection techniques in case of drug abuse or establish an appropriate dosage in case of medicinal uses. This in silico study is based upon in vivo results in rat and human by Philipp et al. (J Mass Spectrom 44:1249-1261, 2009). RESULTS: Gas-phase structures of mitragynine, 7-hydroxymitragynine and their metabolites were obtained by quantum chemical method at B3LYP/6-311++G(d,p) level. Results in terms of standard Gibbs energies of reaction for all metabolic pathways are reported with solvation energy from SMD model. We found that 7-hydroxy substitution leads to changes in reactivity in comparison to mitragynine: position 17 is more reactive towards demethylation and conjugation with glucuronic acid and position 9 is less reactive towards conjugation with glucuronic acid. Despite the changes, position 9 is the most reactive for demethylation and position 17 is the most reactive for conjugation with glucuronic acid for both mitragynine and 7-hydroxymitragynine. Our results suggest that 7-hydroxy substitution could lead to different metabolic pathways and raise an important question for further experimental studies of this more potent derivative.