Fundamental Chemical Concepts Research Articles

Can Aromaticity be Evaluated Using Atomic Partitions based on the Hilbert-space?

Aromaticity is a fundamental concept in chemistry that explains the stability and reactivity of many compounds by identifying atoms within a molecule that form an aromatic ring. Reliable aromaticity indices focus on electron delocalization and depend on atomic partitions, which give rise to the concept of an atom-in-the-molecule(AIM). Real-space atomic partitions present two important drawbacks: a high computational cost and numerical errors, limiting aromaticity measures to medium-sized molecules with rings up to 12 atoms. This restriction hinders the study of large conjugated systems like porphyrins and nanorings. On the other hand, traditional Hilbert-space schemes are free of the latter limitations but can be unreliable for the large basis sets required in modern computational chemistry. This paper explores AIMs based on three robust Hilbert-space partitions --meta-Löwdin, Natural Atomic Orbitals (NAO), and Intrinsic Atomic Orbitals (IAO)--which combine the advantages of real-space partitions without their disadvantages. These partitions can effectively replace real-space AIMs for evaluating the aromatic character. For the first time, we report multicenter index (MCI) and \iring values for large rings and introduce ESIpy, an open-source Python code for aromaticity analysis in large conjugated rings.

Tools to investigate the cell surface: Proximity as a central concept in glycoRNA biology.

Proximity is a fundamental concept in chemistry and biology, referring to the convergence of molecules to facilitate new molecular interactions or reactions. Hybrid biopolymers like glycosylphosphatidylinositol (GPI)-anchored proteins, ubiquitinated proteins, glycosylated RNAs (glycoRNAs), and RNAylated proteins exemplify this by covalent bonding of moieties that are often orthogonally active. Hybrid molecules like glycoRNAs are localized to new physical spaces, generating new interfaces for biological functions. To fully investigate the compositional and spatial features of molecules like glycoRNAs, flexible genetic and chemical tools that encompass different encoding and targeting biopolymers are required. Here we discuss concepts of molecular proximity and explore newer proximity labeling technologies that facilitate applications in RNA biology, cell surface biology, and the interface therein with a particular focus on glycoRNA biology. We review the advantages and disadvantages of methods pertaining to cell surface RNA identification and provide insights into the vast opportunities for method development in this area.

Game-based learning in metaverse: Virtual chemistry classroom for chemical bonding for remote education

AbstractVirtual classrooms based on the metaverse or virtual reality are useful and effective for imparting basic chemistry concepts. Interactive and immersive environments can effectively teach fundamental chemistry concepts, such as chemical bonding and formulas, thereby making these otherwise abstract and intangible ideas more accessible and understandable. With the outbreak of Covid-19, e-learning platforms have also been developed for chemistry education. However, these platforms are unable to make learning chemistry interactive and enjoyable. Therefore, there is a need to motivate students to learn basic chemistry concepts in an immersive and interactive environment. In this paper, we propose an immersive virtual reality-based Virtual Chemistry Classroom for Chemical Bonding (VC3B) to facilitate the learning of chemical bonding and formulas through a game-based learning approach. It includes two different games for learning chemical bonding and formulas. In the first game, molecule construction, students reconstruct the structure of molecules by rearranging the atoms in order to learn about chemical bonding. In the second game, chemical formula, students compose the chemical formula of a given compound to help them memorize chemical formulas. The study, conducted on 90 middle school students, employed a randomized controlled study design, dividing participants into three groups. Each group learned about chemical bonding and formulas through three different mediums. After conducting the experiment, the students were given a questionnaire to evaluate the usability of VC3B. The results of the study were positive, with participants finding the VC3B to be more interactive than traditional book and online lecture methods. Participants were also motivated to learn and enhance their knowledge of chemistry.

Linking Waterbody Acidification and Aquatic Plant Metabolism: A Lesson Plan for Middle School Students

Ocean acidification, the lowering of seawater pH due to increased concentrations of carbon dioxide in the atmosphere, is an emerging environmental challenge associated with climate change. This publication is intended for Florida grade eight educators and other environmental educators of middle school students. We designed a lesson plan to reinforce fundamental concepts in acid-base chemistry, including the pH scale, and to introduce students to waterbody acidification, its negative effects on shell-forming organisms, and the potential role of aquatic plant metabolism (i.e., photosynthesis and respiration) in mitigating these effects. The goal of the lesson plan is to encourage students to link water chemistry and biological processes while learning about the challenges and potential solutions to acidification within a local context. This lesson plan will contribute to state learning standards while generating appreciation for the complexity of the natural environment.

High-pressure stabilization of open-shell bromine fluorides.

Halogen fluorides are textbook examples of how fundamental chemical concepts, such as molecular orbital theory or the valence-shell electron-repulsion (VSEPR) model, can be used to understand the geometry and properties of compounds. However, it is still an open question whether these notions are applicable to matter subject to high pressure (>1 GPa). In an attempt to gain insight into this phenomenon, we present a computational study on the phase transitions and reactivity of bromine fluorides at pressures of up to 100 GPa (≈106 atm). We predict that at a moderately high pressure of 15 GPa, the bonding preference in the Br/F system should change considerably with BrF3 becoming thermodynamically unstable and two novel compounds emerging as stable species: BrF2 and BrF6. Calculations indicate that both these compounds contain radical molecules while being non-metallic. We propose a synthetic route for obtaining BrF2 which does not require the use of highly reactive elemental fluorine. Finally, we show how molecular orbital diagrams and the VSEPR model can be used to explain the properties of compressed bromine fluorides.

Ein Lernposter zum Aufbau von Reinstoffen

Pure chemical substances present a clearly defined area for teaching in which fundamental chemistry concepts can be treated didatically. However, the multitude of concepts involved can easily lead to misunderstandings. A graphical visualisation is presented that can help the students to understand the structure and the scope of the different concepts.

Phase-Dependence of Molecular Structures Arising from Weak London Dispersion Interactions.

ConspectusThe structures of molecules can be different in different phases. Intermolecular forces, even those of weak noncovalent interactions (WNCIs), can lead to a preference for quite different conformations in the solid, the gas, and the liquid phases. WNCIs can cause variations in bond lengths, angles, and torsional angles. Since structure is a fundamental concept in chemistry, the knowledge of structural changes with phase is important to understand the source and effects of distorting contributions from WNCIs but also as a predictive tool for the design and stabilization of new bonding situations.X-ray crystallography is ubiquitous and now mostly straightforward to perform, but facilities for the determination of accurate gas-phase structure determination are rare, and gas-phase work is laborious and time-consuming. There are currently about 1.25 million crystal structures and more than 12 500 experimental gas-phase structures, but the intersection of the two data sets that can tell us about the structural differences of the same molecule in different phases is surprisingly small.In this Account, we describe several cases of WNCI-dominated systems for which accurate experimental structure determinations exist for both the gas phase and the solid state and, in one case, also for solution. The examples include aryl-aryl, aryl-alkyl, and alkyl-alkyl interactions; systems with chalcogen and halogen bonding; and fluorine-based interactions in arylboranes. We work out the role of WNCIs in stabilizing large, strained, or sterically overloaded molecules. We will show how flexible molecules will fold under the action of WNCIs when isolated in the gas and how they fold or unfold when they are embedded in an environment of neighbors in crystals. We will show how they can vary in strength when the substitution patterns in aryl groups are changed by different halogens and how intramolecular WNCIs, such as those forming rings, change when such systems experience additional intermolecular WNCIs.Overall, we hope that this Account will give the reader an idea of the type and magnitude of structural changes that can be expected from a free molecule in the gas phase or a single molecule calculated by quantum chemistry compared with one embedded in a crystal. This should define the limits of comparability and provide some predictive concepts of the distortions and variations to be expected.

Experimental teaching of the Avogadro constant

Although Avogadro’s number is a fundamental concept in chemistry, it is often overlooked in secondary education textbooks in Greece. Students are taught about mol, the number Avogadro, the molar volumes, and the equation of the state of gases. However, in no case is a detailed examination held about the importance of this number and the connection of macroscopic and microscopic quantities through the Avogardo constant. Also, the references related to the topic fail to raise students’ awareness of the atomic and molecular structure and the procedure with which the matter becomes quantic. Furthermore, the experimental approach is non-existent. To address these shortcomings, this project proposes a new and straightforward experimental method for students to determine the value of Avogadro’s number. The carefully designed experimental procedure can be completed within one teaching hour, encouraging active student participation. More importantly, the proposed experimental setup does not require sophisticated instruments and poses no risks, making it feasible for students to conduct it themselves.

A Simple Method for Teaching Bragg’s Law in an Undergraduate Teaching Laboratory with the Use of Metal–Organic Frameworks

Metal–organic frameworks (MOFs) are a class of porous materials that are often crystalline with high surface area and structural tunability. In this laboratory experiment designed for inorganic chemistry students at the undergraduate level, students complete a two-step experiment where they will first (i) synthesize two isostructural zirconium-based MOFs, UiO-66 and UiO-67, and then (ii) isolate and characterize the materials using powder X-ray diffraction (PXRD). A simple solvothermal procedure was developed for the synthesis of UiO-66 and UiO-67 using the air/moisture-stable zirconyl chloride octahydrate as a starting reagent. Depending on the equipment available, the MOFs can be further characterized by nitrogen adsorption analysis for surface area determination using Brunauer–Emmett–Teller (BET) theory, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), thermogravimetric analysis (TGA), 1H nuclear magnetic resonance (NMR) spectroscopy, and scanning electron microscopy (SEM). Upon synthesizing the MOFs and collecting the characterization data, students analyze and describe their results by answering a series of questions included in the laboratory manual. This exercise will allow students to develop practical laboratory skills while expanding their knowledge on some fundamental concepts in inorganic chemistry, materials chemistry, MOFs, crystallography, and other characterization techniques as availability allows.

On how some fundamental chemical concepts are correlated by arithmetic, geometric and harmonic means

On how some fundamental chemical concepts are correlated by arithmetic, geometric and harmonic means

Phosphole aromaticity enhancement by electron pumping through Schleyer hyperconjugative aromaticity: A comprehensive DFT study

Combination of aromaticity and hyperconjugation as two fundamental concepts in organic chemistry results hyperconjugative aromaticity. Due to trigonal pyramidal P (III) atom in phosphole ring, it is only slightly more aromatic than cyclopentadiene. In the present work, the hyperconjugative aromaticity of phosphole derivatives, bearing an electron donating group, have been studied at the DFT-B3LYP/6–311++G(d, p) level of theory using various aromaticity indices such as geometric, magnetic, electronic and energetic criteria. Our DFT calculations reveal that an electropositive substituent can enhance phosphole aromaticity through Schleyer hyperconjugative aromaticity. This hyperconjugative electron donation by the substituents results in a partially anionic phosphole ring. Among the electropositive groups, silyl and germanium substituents have the best performance. The excellent correlations are observed between all aromaticity indices. Our findings could help chemists to design novel hyperconjugative aromatic phospholes.

Assessment of the performance of six indices in predicating the aromaticity of planar porphyrinoids.

Aromaticity is a fundamental chemical concept that has been widely used in explaining the reactivity, stability, structure, and magnetic properties of many molecules such as conjugated macrocycles, metal heterocyclic compounds, and certain metal clusters. Porphyrinoids (including porphyrin) are of particular interest in terms of diverse aromaticity. Various indices therefore have been used to predict the aromaticity of porphyrin-like macrocycles. However, the reliability of these indices for porphyinoids is always questionable. In order to assess the performance of the indices, we have selected six representative indices to predict the aromaticity of 35 porphyrinoids. The calculated values were then compared with the corresponding results obtained from experiments. Our studies suggest that the theoretical prediction by nucleus independent chemical shifts (NICS), topology of the induced magnetic field (TIMF), anisotropy of the induced current density (AICD), and gauge including magnetically induced current method (GIMIC) are essentially consistent with experimental evidence in all 35 cases and thus are preferred indices. Based on density functional theory, the performance of the NICS, TIMF, AICD, GIMIC, harmonic oscillator model of aromaticity (HOMA), and multicenter bond order (MCBO) indices were evaluated theoretically. Molecular geometries were optimized at the M06-2X/6-311G** level. NMR calculations using GIAO or CGST method were performed at the M06-2X/6-311G** level. The above calculations were carried out using Gaussian16 suite. The TIMF, GIMIC, HOMA, and MCBO indices were obtained using the Multiwfn program. The AICD outputs were visualized using the POV-Ray software.

Back to the Basics: Developing Advanced Metal-Organic Frameworks Using Fundamental Chemistry Concepts.

Over the past 25 years, metal-organic frameworks (MOFs) have developed into an increasingly intricate class of crystalline porous materials in which the choice of building blocks offers significant control over the physical properties of the resulting material. Despite this complexity, fundamental coordination chemistry design principles provided a strategic basis to design highly stable MOF structures. In this Perspective, we provide an overview of these design strategies and discuss how researchers leverage fundamental chemistry concepts to tune reaction parameters and synthesize highly crystalline MOFs. We then discuss these design principles in the context of several literature examples, highlighting both relevant fundamental chemistry principles and additional design principles required to access stable MOF structures. Finally, we envision how these fundamental concepts may offer access to even more advanced structures with tailored properties as the MOF field looks toward the future.

BASIC SCIENCE CONCEPTS IN THE LENS OF DAVYDOV’S DEVELOPMENTAL INSTRUCTION: INTRODUCTION TO CHEMISTRY FOR 6-7 GRADERS

The Developmental Instruction considers scientific concepts as mental tools with the main function to guide human actions in a certain domain. According to the Developmental Instruction, each concept stems from a goal-oriented activity that should be reconstructed for students from scratch if we want them to learn the concept properly. As Davydov emphasized, this helps students explore all necessary internals and limitations that can hardly be learned in a different way. Fundamental chemistry concepts such as “chemical element” and “chemical reaction” have a long history, and their predecessors underwent several turns and twists on the way to their modern forms. These pre-concepts originated in ancient times and guided the craft of substance transformations, and their modern descendants still do it. The goal-oriented actions of substance transformations are in the focus of our introductory curriculum. Students name the substances they work with using their own words and understanding. Students’ “provisional language” helps them discuss the results of their simple experiments and plan the follow-ups. As the work goes on, students develop their understanding toward the idea of conservation of elements in chemical reactions. Short essays containing no chemical names and formulas describe the relevant chemical transformations and provide the cultural or historical background. Our teaching experience shows that such kind of introduction turns the systematic chemistry course into the answer to the reasonable questions that the students have about substances and their transformations.

Probing the Hyperconjugative Aromaticity of Cyclopentadiene and Pyrroliums Containing Group 7 Transition Metal Substituents

Aromaticity and hyperconjugation are two fundamental concepts in chemistry. Combining them together led to the proposal of the concept of hyperconjugative aromaticity by Mulliken in 1939. Now, it has been attracting considerable attention from both theoretical and experimental chemists. Recently, the concept of hyperconjugative aromaticity has been extended from main-group substituents to transition metal systems including groups 9, 10, and 11 transition metal substituents. Here, we report the hyperconjugative aromaticity in cyclopentadienes and pyrroliums containing group 7 transition metal substituents through density functional theory (DFT) calculations. It is found that the metal–metal bonding interaction can significantly reduce the aromaticity in cyclopentadienes, whereas the stronger σ-donor ligand, bridged hydride, and carbonyls can enhance aromaticity. All these findings expand the scope of the concept of hyperconjugative aromaticity, enriching aromatic organometallic chemistry.

Quantifying energetic information in density functional theory.

Energy and information are two fundamental concepts in physics and chemistry. In density functional theory (DFT), all information pertaining to stability, reactivity, and other properties is encompassed in the ground state electron density. The basic theorems of DFT govern that energy is a universal functional of the density, and thus, it can be regarded as a special kind of information. In this work, we quantify the energetic information in terms of Shannon entropy and Fisher information for energetic distributions of atoms and molecules. Two identities are unveiled for an energetic density, its gradient, and Laplacian to rigorously satisfy. A new partition scheme to decompose atoms in molecules has been proposed using the energetic distribution. We also show that our approach can simultaneously quantify both two-body and many-body interactions. This new framework should provide new analytical tools for us to appreciate electronic properties of molecular systems, including stability and reactivity. More importantly, this work establishes the missing link in DFT between energy and information, the two most fundamental quantities in quantum theory.

The Case of the Limit of Detection

Students learn early on in science courses that reliable results can only be achieved from accurate measurements. In some of the first general chemistry classes, but even more intensively in analytical chemistry classes, students are introduced to the concept of significant figures. They learn that a measurement is only as true and precise as the instrument used to carry it out, and that the level of skill of the measurer (and how they interpret and report the measurement) is also important. A classic example to introduce significant figures involves the measurement of an object’s length using a ruler. Let us say that the object is a string, and one has two rulers available to measure it. The first ruler has 1-cm markings, while the second one presents 0.1-cm markings. When performing any measurement, students learn that more accurate results will be achieved if one estimates and includes an additional digit to the measurement. Thus, as an example, let us say that the string’s length is determined to be between 3 and 4 cm using the first ruler. The measurer will then estimate the tenths decimal place and report the string’s length as 3.4 cm, for example. Although considered significant, the tenths place (i.e., 4) is an estimate and, therefore, it is uncertain. The other digit (i.e., 3) is both significant and certain. Using the second ruler, the string’s length falls between 3.4 and 3.5 cm. The measurer will again estimate an additional decimal place and report the length as 3.48 cm. In this example, the digits 3 and 4 are both significant and certain, while the hundredths place (i.e., 8) is significant but uncertain. Now, how does the concept of significant figures relate to limit of detection (LOD)? There are different interpretations for LOD, but it simply is the lowest concentration of analyte generating an instrument response that is statistically different from (and higher than) that recorded for the blank. According to the International Union of Pure and Applied Chemistry (IUPAC), the LOD is calculated as three times the standard deviation of the instrument response for the blank (Sb), divided by the calibration curve slope (m), i.e., LOD = 3Sb/m. The value Sb is calculated from repeated measurements of the blank solution, usually 10 - 20 replicates (n = 10 -20). Considering a normal distribution, 99.86% of the data is < (x ̅+3S) (i.e., < than the value corresponding to three standard deviations above the mean). Therefore, the LOD calculated at 3Sb is statistically different from, and has a 99.86% chance of being larger than the blank.4 At the LOD, the instrument response recorded for the analyte is certainly not due to the random variation of the blank signal (almost 100% certain). However, there is no certainty associated with the analyte concentration. In other words, one knows the analyte is present, but cannot quantify it with an adequate level of confidence. Considering Sb as noise, the analyte’s signal-to-noise ratio (S/N) at the LOD is 3 (i.e., the instrument response recorded for the analyte is three times higher than the noise). Because S/N is the reciprocal of the relative standard deviation (RSD), analyte signal variations higher than 33% (RSD = 1/3) are expected at the LOD. Therefore, the concentration corresponding to the LOD is, by definition, uncertain. Going back to the concept of significant figures, the LOD must be reported with a single digit, which is significant but uncertain. Many researchers fail to follow these fundamental concepts of statistics and analytical chemistry, as LODs are often reported with several significant figures (!). Perhaps, it is due to a natural difficulty to connect concepts learned at different points in one’s education. Nevertheless, “the case of the LOD” may foster an awareness that could facilitate the identification of instances in which the connection between different concepts is essential: from adequate reporting of analytical results to new ideas and discoveries.

Incorporating research literature and chemistry textbooks in 5E instructional model to reveal ambiguous oxidation state formalism of CuS for pre-service science teachers

AbstractThis paper implements the 5E instructional model to reveal authentic concepts in chemistry, in particular the ambiguous oxidation state formalism of copper sulfide (CuS) for pre-service science teachers (PSTs). We discuss the process and outcomes of learning phases of the 5E (engage, explore, explain, elaborate, and evaluate) for authentic chemistry learning. The puzzle activity of engage phase demonstrate PSTs prior-knowledge, understanding, problem-solving skills in the fundamental concepts of chemistry. However, we observed misconceptions in chemistry concepts, in particular the oxidation state formalism of CuS. Next, the explore phase describe how the scientific evidence from research literature give insight into whether the PSTs conceptions are in accordance with research evidence. The research evidence from collaborative literature review revealed the uncertainty in the oxidation state formalism of CuS. In the explain phase, we explained the complex electronic structure of CuS. In the fourth phase, the elaborate phase, we involve the PSTs in the book review to elaborate and analyze the uncertain concept. The results of the book review provide insight into the coverage of oxidation state formalism of CuS in nine chemistry textbooks. Finally, in evaluate phase, the results of questionnaire describe the PSTs perspectives and experiences in the student-centered chemistry learning.

Modern Criteria of Aromaticity for Organometallic Compounds

Aromaticity as one of the most important fundamental concepts in chemistry is an effect of cyclic electron delocalization, which is very multifaceted and difficult to measure. To define the aromaticity degree as a quantitative characteristic, the aromaticity indices are used that can be divided into energetic, structural, electronic, magnetic, and optical. The aromaticity effect went far beyond the class of π-conjugated hydrocarbons a long time ago; therefore, this review critically examines the most important and modern criteria of aromaticity which are universal in the system choice and have been applied to organometallic compounds.

Programmable Matter: The Nanoparticle Atom and DNA Bond.

Colloidal crystal engineering with DNA has led to significant advances in bottom-up materials synthesis and a new way of thinking about fundamental concepts in chemistry. Here, programmable atom equivalents (PAEs), comprised of nanoparticles (the "atoms") functionalized with DNA (the "bonding elements"), are assembled through DNA hybridization into crystalline lattices. Unlike atomic systems, the "atom" (e.g., the nanoparticle shape, size, and composition) and the "bond" (e.g., the DNA length and sequence) can be tuned independently, yielding designer materials with unique catalytic, optical, and biological properties. In this review, nearly three decades of work that have contributed to the evolution of this class of programmable matter is chronicled, starting from the earliest examples based on gold-core PAEs, and then delineating how advances in synthetic capabilities, DNA design, and fundamental understanding of PAE-PAE interactions have led to new classes of functional materials that, in several cases, have no natural equivalent.