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.

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.

Pillar[4]arene[1]thioarene: Synthesis and Host-Guest Binding Properties

The synthesis and characterisation of novel class of pillar[4]arene[1]thioarenes (P[4]A[1]SMe) are reported. Synthesised via an oxidation-thionation strategy, the replacement of a single dialkoxybenzene panel from parent pillar[5]arene (P[5]A) is achieved. 1H-NMR spectroscopic titration experiments, supported by DFT computational studies, revealed that P[4]A[1]SMe show starkly modulated host-guest binding properties for electron deficient aliphatic guests.

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.

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.

The prevalence of a chemical formula in which its Z configuration, gauche conformation or meta isomer is the most stable form is derived from over ten thousand chemical structures. The instance of steric prediction failure is surprisingly common.

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.

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.

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.

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.

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.

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.

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.].

Geometric and energetic data from ab initio calculations of haloethene, haloimine, halomethylenephosphine, haloiminophosphine, halodiazene, halodiphosphene and halocyclopropane

This article presents theoretical data on geometric and energetic features of halogenated compounds of ethene (C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]>C), imine (CN), methylenephosphine (CP), iminophosphine (NP), diazene (NN), diphosphene (PP) and cyclopropane (Δ). The data were obtained from ab initio geometric optimization and frequency calculations at HF, B3LYP, MP2 and CCSD levels of theory on 6–311++G(d,p) basis set. Input structures were generated by shell scripts and run by Q-Chem quantum chemical package. The output files were processed to extract geometric and energetic information by Wolfram Mathematica.

An in silico investigation of menthol metabolism

Prevalence of mentholated products for consumption has brought great importance to studies on menthol’s metabolic pathways to ensure safety, design more potent derivatives, and identify therapeutic benefits. Proposed pathways of (-)-menthol metabolism based on metabolites found experimentally in previous works by Yamaguchi, Caldwell & Farmer, Madyastha & Srivatsan and Hiki et al. were not in agreement. This in silico approach is based on the three in vivo studies and aims to resolve the discrepancies. Reactions in the pathways are conjugation with glucuronic acid/sulfate, oxidation to alcohol, aldehyde & carboxylic acid, and formation of a four-membered/five-membered ring. Gas-phase structures, standard Gibbs energies and SMD solvation energies at B3LYP/6-311++G(d,p) level were obtained for 102 compounds in the pathways. This study provides a more complete picture of menthol metabolism by combining information from three experimental studies and filling missing links in previously published pathways.

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.

Electronic supplementary material

The online version of this article (10.1186/s13104-019-4461-3) contains supplementary material, which is available to authorized users.

Chemical Patterns in Autoxidations Catalyzed by Redox Dyes

We present simple and effective experiments to produce intricate chemical patterns from common chemicals in a classroom setting. Students selected an independent variable of their interest, designed their experiment, and investigated its effect on chemical patterns in a four-hour activity. Photographs and videos were taken, while the identity and the concentration of chemicals in the reaction mixture, the concentration of oxygen gas above the solution, the depth of the solution, the shape and the total area of container's cross section, and the temperature were varied. Students discussed their results and presented their investigation to the class. Our experiments enable students to conduct inquiries with open-ended discussion and also open possibilities for a chemical art competition.

A DFT investigation of the blue bottle experiment: E∘half-cell analysis of autoxidation catalysed by redox indicators

The blue bottle experiment is a collective term for autoxidation reactions catalysed by redox indicators. The reactions are characterized by their repeatable cycle of colour changes when shaken/left to stand and intricate chemical pattern formation. The blue bottle experiment is studied based on calculated solution-phase half-cell reduction potential of related reactions. Our investigation confirms that the reaction in various versions of the blue bottle experiment published to date is mainly the oxidation of an acyloin to a 1,2-dicarbonyl structure. In the light of the calculations, we also propose new non-acyloin reducing agents for the experiment. These results can help guide future experimental studies on the blue bottle experiment.

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.170708.].

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.

Resolutions of the Coulomb Operator: VII. Evaluation of Long-Range Coulomb and Exchange Matrices

Use of the resolution of Ewald operator method for computing long-range Coulomb and exchange interactions is presented. We show that the accuracy of this method can be controlled by a single parameter in a manner similar to that used by conventional algorithms that compute two-electron integrals. Significant performance advantages over conventional algorithms are observed, particularly for high quality basis sets and globular systems. The approach is directly applicable to hybrid density functional theory.

A remarkable identity involving Bessel functions

We consider a new identity involving integrals and sums of Bessel functions. The identity provides new ways to evaluate integrals of products of two Bessel functions. The identity is remarkably simple and powerful since the summand and the integrand are of exactly the same form and the sum converges to the integral relatively fast for most cases. A proof and numerical examples of the identity are discussed.

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.

Resolutions of the Coulomb Operator: V. The Long-Range Ewald Operator

We show that the long-range Ewald operator can be resolved as erf(ωr12)/r12 = ∑k ϕk*(r1) ϕk(r2), where ϕk is proportional to the product of a spherical Bessel function and a spherical harmonic. We demonstrate the use of this new resolution by calculating the long-range Coulomb energy of the nanodiamond crystallite C84H64 and the long-range exchange energy of the graphene C96H24. The resolution appears particularly effective for long-range exchange calculations.