Fundamental Chemical Concepts Research Articles

Key Factors Determining Efficiency of Liquid-Liquid Extraction: Implications from Molecular Dynamics Simulations of Biphasic Behaviors of CyMe4-BTPhen and Its Am(III) Complexes.

CyMe4-BTPhen (2,9-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-1,2,4-benzotriazin-3-yl)-1,10-phenanthroline, denoted as L) has been considered as a promising extractant in lanthanide(III)/actinide(III) separation. Vast endeavors in its application put forward a compelling need on the understanding of the underlying mechanism in the liquid-liquid extraction. To address the issue of its dynamics in biphasic systems, we carried out molecular dynamics (MD) simulations of L and its complexes with a heavy f-block metal ion, americium(III) (Am3+) in "oil"/water binary solvents. Two types of organic phases have been considered, differing in the presence of octanol in the bulk n-dodecane or not, and the distribution of the solutes and their interfacial behaviors have been investigated. Two of the key factors that determine the efficiency of a liquid-liquid extraction protocol were delineated and discussed, that is, the appropriate ligand to enhance the lipophilicity of AmL complexes and appropriate way to form ion pairs to minimize the attraction between the complexes and aqueous phase. The simulations showed that the charge states of both ligand and AmL complexes were strongly correlated with their phase behavior, and the migration of neutral species was driven by van der Waals interactions while that of charged species by electrostatic interactions, indicating stronger lipophilicity of the former than the latter. The presence of octanol facilitated the migration of the ligand from the interface to the organic phase via hydrogen bond between its polar head and the ligand or the AmL complexes and constituted a polar core in the organic phase. This work bridged the widely used liquid-liquid extraction technique in chemistry to a fundamental chemical concept, that is, minimization of hydrophilicity and maximization of lipophilicity to facilitate phase transfer from the aqueous phase to the organic phase, and is expected to improve the understanding of dynamics of ligands and their complexes with metal ions and to contribute to the development of efficient protocols for phase transfer of target species.

Essential learning outcomes for delocalization (resonance) concepts: How are they taught, practiced, and assessed in organic chemistry?

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.

Taming quantum interference in single molecule junctions: induction and resonance are key.

We have joined two fundamental concepts of organic chemistry to provide a deep, yet intuitive, understanding of how side groups influence destructive quantum interference (DQI) in the transport through conjugated molecules. Using density functional theory combined with Green's function techniques, and employing tight-binding models in which all the π-systems are considered, we elucidate the separate roles of bond-resonance and induction in tuning DQI. We show that the position of the anti-resonances produced by DQI is sensitive to the number of side groups, but not in a simple additive way. Instead, addition of multiple groups results in a weaker overall contribution per group, and this can be understood using a straight forward graphical analysis. Furthermore, we show that additional fine tuning of DQI is possible via attachment of a chain of atoms to a second site around the ring. DQI is controlled by modifying the length of the chain, thus providing exquisite control over the anti-resonance position. This insight provides chemists with a large number of options to tune DQI for unprecedented device optimization.

Fundamental physical and chemical concepts behind “drug-likeness” and “natural product-likeness”

Abstract The discovery of a drug is known to be quite cumbersome, both in terms of the microscopic fundamental research behind it and the industrial scale manufacturing process. A major concern in drug discovery is the acceleration of the process and cost reduction. The fact that clinical trials cannot be accelerated, therefore, emphasizes the need to accelerate the strategies for identifying lead compounds at an early stage. We, herein, focus on the definition of what would be regarded as a “drug-like” molecule and a “lead-like” one. In particular, “drug-likeness” is referred to as resemblance to existing drugs, whereas “lead-likeness” is characterized by the similarity with structural and physicochemical properties of a “lead”compound, i.e. a reference compound or a starting point for further drug development. It is now well known that a huge proportion of the drug discovery is inspired or derived from natural products (NPs), which have larger complexity as well as size when compared with synthetic compounds. Therefore, similar definitions of “drug-likeness” and “lead-likeness” cannot be applied for the NP-likeness. Rather, there is the dire need to define and explain NP-likeness in regard to chemical structure. An attempt has been made here to give an overview of the general concepts associated with NP discovery, and to provide the foundational basis for defining a molecule as a “drug”, a “lead” or a “natural compound.”

“Drug-likeness” properties of natural compounds

Abstract Our previous work was focused on the fundamental physical and chemical concepts behind “drug-likeness” and “natural product (NP)-likeness”. Herein, we discuss further details on the concepts of “drug-likeness”, “lead-likeness” and “NP-likeness”. The discussion will first focus on NPs as drugs, then a discussion of previous studies in which the complexities of the scaffolds and chemical space of naturally occurring compounds have been compared with synthetic, semisynthetic compounds and the Food and Drug Administration-approved drugs. This is followed by guiding principles for designing “drug-like” natural product libraries for lead compound discovery purposes. In addition, we present a tool for measuring “NP-likeness” of compounds and a brief presentation of machine-learning approaches. A binary quantitative structure–activity relationship for classifying drugs from nondrugs and natural compounds from nonnatural ones is also described. While the studies add to the plethora of recently published works on the “drug-likeness” of NPs, it no doubt increases our understanding of the physicochemical properties that make NPs fall within the ranges associated with “drug-like” molecules.

Electronegativities of Pauling and Mulliken in Density Functional Theory.

Electronegativity is a fundamental concept in chemistry that allows one to infer important aspects about the interactions between chemical species. In the present work we make use of the framework provided by the density functional theory of chemical reactivity, to discuss in a unified way the approaches to the concept of electronegativity developed by Pauling and by Mulliken. Our analysis starts by making use of the identification of the electronegativity of Mulliken with the chemical potential of density functional theory, and continues to show that the ionic correction proposed by Pauling can be derived, with certain approximations, from the quadratic smooth interpolation of the energy as a function of the number of electrons in terms of the chemical potentials and the hardnesses of the interacting species, from which one can infer the close qualitative relationship between Pauling's electronegativity and the electrophilicity concept.

Approximating Periodic Potential Energy Surfaces with Sparse Trigonometric Interpolation.

The potential energy surface (PES) describes the energy of a chemical system as a function of its geometry and is a fundamental concept in computational chemistry. A PES provides much useful information about the system, including the structures and energies of various stationary points, such as local minima, maxima, and transition states. Construction of full-dimensional PESs for molecules with more than 10 atoms is computationally expensive and often not feasible. Previous work in our group used sparse interpolation with polynomial basis functions to construct a surrogate reduced-dimensional PESs along chemically significant reaction coordinates, such as bond lengths, bond angles, and torsion angles. However, polynomial interpolation does not preserve the periodicity of the PES gradient with respect to angular components of geometry, such as torsion angles, which can lead to nonphysical phenomena. In this work, we construct a surrogate PES using trigonometric basis functions, for a system where the selected reaction coordinates all correspond to the torsion angles, resulting in a periodically repeating PES. We find that a trigonometric interpolation basis not only guarantees periodicity of the gradient but also results in slightly lower approximation error than polynomial interpolation.

Introducing Students to Fundamental Chemistry Concepts and Basic Research through a Chemistry of Fashion Course for Nonscience Majors

The combined lab and lecture course is designed around the themes of colorants (dyestuffs and pigments) and fibers (natural and human-made) for nonscience majors. Students dye natural and synthetic fibers with natural dyes such as turmeric, raspberries, tea, and cochineal insects as well as synthetic dyes. The students observe the colorfast properties of a dye and the changes made to a fiber during the dyeing process. Some chemical concepts introduced over the semester are light energy and color, solution chemistry, chemical bonding and bond polarity, acids and bases, and oxidizing and reducing agents. An important component of this class is introducing students to primary literature. The students, throughout the semester, read and discuss research articles on topics relevant to the coursework. The course culminates with students applying all they learned through a self-designed inquiry project. Students, in groups, write a research proposal using science research literature. At the end of the semester, the students in the lab conduct original research, which culminates with the students sharing their findings with the class in a conference-like setting. Students from two classes (N = 34) completed a SALG (student assessment of their learning gains) survey; SALG is a web-based instrument that allows students to assess their perceptions of learning gains made over the duration of the course. The students were asked about the gains they experienced from this course in collaborative work, scientific literacy skills, science attitudes, and connecting science to other situations. The students showed good gains in working in collaborative settings and knowing how to gather and use data. The students also reported a better understanding of how chemistry relates to other classes and how it can apply to other situations. The students were also taught how to critically read scientific research articles. While the improvement in critical reading was not as robust, it did indicate an improvement in the students’ understanding of how to read scientific studies. This lab and lecture course, designed to increase interdisciplinary learning at the school—particularly with the school’s fashion, marketing, and communication majors—piqued students’ interest in chemistry, improved their understanding of scientific processes, and helped them understand the role of chemistry in other subjects.

Is It Possible To Determine Oxidation States for Atoms in Molecules Using Density-Based Quantities? An Information-Theoretic Approach and Conceptual Density Functional Theory Study.

The oxidation state, also called oxidation number, of atoms in molecules is a fundamental chemical concept. It is defined as the charge of an atom in a molecule after the ionic approximation of its heteronuclear bonds is applied. Even though for simple molecules the assignment of oxidation states is straightforward, redundancy and ambiguity do exist for others. In this work, we present a density-based framework to determine the oxidation state using the quantities from the information-theoretic approach. As a proof of concept, we examined six elements for a total of 49 molecules. Strong linear correlations were obtained with Shannon entropy, Ghosh-Berkowitz-Parr entropy, information gain, relative Rényi entropy of orders 2 and 3, and Hirshfeld charge. We also discovered that the crystal radius of elements plays the key role in rationalizing the system dependent nature of these strong linear correlations. The validity and effectiveness of our results were demonstrated by the examples of molecules containing elements with two or more oxidation states. Our results should be applicable to more complicated systems in assigning different oxidation states.

Astrochemistry as a Gateway to Teaching and Learning Threshold Concepts in Physical Chemistry

The purpose of this paper is to examine the use of astrochemistry examples in teaching the potential threshold concepts (TCs) of physical chemistry that are contained in the recently published Physical Chemistry Anchoring Concepts Content Map (PChem-ACCM). The paper provides a brief overview of how selected astrochemical examples can be utilized to teach and learn suggested TCs that are commonly encountered in the three main overarching areas of physical chemistry curriculum, namely: chemical kinetics, quantum chemistry, and thermodynamics. Using astrochemical examples to decipher the abstract nature of the many fundamental physical chemistry concepts, which are usually accompanied by rigorous mathematical treatments, provides a rich ground in which to implement alternative teaching pedagogies and practices that can help the learner master the associated TCs.

Dramatisering i spänningsfältet mellan som om och som är och sexåringars meningsskapande av kemiska begrepp och processer

In this study, we discuss dramatizing as a form of play-responsive teaching in early childhood education. Based on empirical observation, the purpose of the study is to contribute to knowledge-building through offering possibilities for children to make sense of scientific knowledge by engaging in mutual fantasizing about certain fundamental processes and concepts in chemistry. The empirical foundation consists of interviews conducted with eleven 6-year-old children after they had participated in a workshop at a culture center for children where they dramatized certain chemistry concepts and processes. Theoretically, dramatizing is understood as role play in an imaginary dimension (as if) and learning is conceptualized in terms of the appropriation of cultural tools and practices. Based on our analysis, we argue that central to dramatizing (and in general, play-responsive teaching) is how participants distinguish, relate and shift between engaging with the phenomena and the processes of as if and as is.

Unconventional Aromaticity in Organometallics: The Power of Transition Metals.

Aromaticity, one of the most fundamental concepts in chemistry, has attracted considerable attention from both theoreticians and experimentalists. Much effort on aromaticity in organometallics has been devoted to metallabenzene and derivatives. In comparison, aromaticity in other organometallics is less developed. This Account describes how our group has performed quantum chemical calculations to examine aromaticity in recently synthesized novel organometallic complexes. By collaborations with experimentalists, we have extended several aromaticity concepts into organometallics to highlight the power of transition metals. In general, the transition metal could participate in delocalization either out of rings or in the rings. We examined the former by probing the possibility of transition metal substituents in hyperconjugative aromaticity, where the metal is out of the rings. Calculations on tetraaurated heteroaryl complexes reveal that incorporation of the aurated substituents at the nitrogen atom can convert nonaromaticity in the parent indolium into aromaticity in the aurated one due to hyperconjugation, thus extending the concept of hyperconjugative aromaticity to heterocycles with transition metal substituents. More importantly, further analysis indicates that the aurated substituents can perform better than traditional main-group substituents. Recently, we also probed the strongest aromatic cyclopentadiene and pyrrolium rings by hyperconjugation of transition metal substituents. Moreover, theoretical calculations suggest that one electropositive substituent is able to induce aromaticity; whereas one electronegative substituent prompts nonaromaticity rather than antiaromaticity. We also probed the possibility of Craig-type Möbius aromaticity in organometallic chemistry, where the position of the transition metals is in the rings. According to the electron count and topology, aromaticity can be classified as Hückel-type and Möbius-type. In comparison with numerous Hückel aromatics containing 4 n+2 π-electrons, Möbius aromatics with 4 n π-electrons, especially the Craig-type species, are particularly limited. We first examined aromaticity in osmapentalynes. Theoretical calculations reveal that incorporation of the osmium center not only reduces the ring strain of the parent pentalyne, but also converts Hückel antiaromaticity in the parent pentalyne into Craig-type Möbius aromaticity in metallapentalynes. Further studies show that the transition metal fragments can also make both 16e and 18e osmapentalenes aromatic, indicating that the Craig-type Möbius aromaticity in osmapentalyne is rooted in osmapentalenes. In addition, Möbius aromaticity is also possible in dimetalla[10]annulenes, where the lithium atoms are not spectator cations but play an important role due to their bonding interaction with the diene moieties. We then examined the possibility of σ-aromaticity in an unsaturated ring. Traditional π-aromaticity is used to describe the π-conjugation in fully unsaturated rings; whereas σ-aromaticity may stabilize fully saturated rings with delocalization caused by σ-electron conjugation. We found that the unsaturated three-membered ring in cyclopropaosmapentalene is σ-aromatic. Very recently, we extended σ-aromaticity into in a fully unsaturated ring. The concepts and examples presented here show the importance of interplay and union between experiment and theory in developing novel aromatic systems and, especially, the indispensable role of computational study in rationalization of unconventional aromaticity. All these findings highlight the strong power of transition metals originating from participation of d orbitals in aromaticity, opening an avenue to the design of unique metalla-aromatics.

From Current Science to School – the Facets of Green Chemistry on the Example of Ionic Liquids

Ionic liquids (ILs) are a widely investigated topic in various technical disciplines at the present time. A main focus of the research on ILs lies on applications in the field of a more sustainable, ‘greener’ chemistry that benefits from their unique property combination. This allows for the improvement of existing technologies and the use in novel, innovative processes. Especially the synergistic combination with other concepts of green chemistry is expected to lead to promising application of ILs. Regardless of their presence in current scientific research, they are covered rarely in the didactics of chemistry, although they represent an ideal subject to incorporate fundamental relationships or chemical concepts into teaching. They can also be included in various demonstration or hands-on experiments. Therefore, the topic of ILs is very promising for the transfer of knowledge from chemical research and industry into didactical experiments especially in the greater context of green chemistry. In this contribution, we present some simple experiments that utilize a multifunctional IL as recyclable catalyst in a biphasic homogenous catalysis. The experiments demonstrate the ecological and economic benefits offered by ILs in an intelligent process design compared to the conventional protocols for esterification. It is shown that exploiting the potential offered by the tunability of functional ILs as high-performance chemicals rather than ‘simple solvents’ offers many possibilities for a more sustainable chemical production.

Analysis of copper alloys as an introduction to data analysis and interpretation for General Chemistry courses

The work herein presents a laboratory experience designed to foster clear connections between chemistry concepts, experimental measurements, and laboratory techniques. The experience consists of three different experiments to be completed in sequence over several laboratory sessions. First the density of the samples is determined, then the specific heat capacity is measured, and finally the cooling curves are determined for the analytes. The experimental work covers fundamental concepts in chemistry (i.e., density, calorimetry, and first-order kinetics), and guides students to develop an overarching comprehension of the chemical and physical properties of the analytes. The analytes are copper alloys with other metals (i.e., Sn, Zn, and Al) with variable chemical compositions. These alloys are robust (i.e., thermally stable, durable), and allow for the collection of reproducible data under the proposed experimental design, as shown in the work herein. The discussion of student-gathered data and results supports the feasibility of the laboratory experience for its implementation in General Chemistry laboratory programs.

Stability and Reactivity of Silicon Magic Numbers Doped with Aluminum and Phosphorus Atoms.

The progressive scaling down of the silicon-based electronics has allowed to develop devices at nanometer scale, requiring new engineering techniques guided by fundamental chemical and physical concepts. Particularly, the nanostructured cluster systems are promising materials since their physical-chemical properties are sensitive to its shape, size, and chemical components, such that completely different materials can be produced by the simple addition or removal of a single atom. These size-tunable properties can open a new area in materials science and engineering. In the present work, quantum chemical methods were used to study the chemical substitution effects caused by subvalent (aluminum) and supervalent (phosphorus) atoms in the physical-chemical properties of some small silicon clusters, which demonstrate high stability, called magic numbers. The changes in the electronic structure and chemical acceptance to the dopants were evaluated with respect to ionization potential, electronic excitation energy, stability, and reactivity parameters. Taken together, these results enable to identify the most stable silicon-doped clusters. Regarding electrophilic reactions, Si10P is the most favorable system, while for nucleophilic reactions, none of the doped clusters resulted in higher stability.

Introducing Students to the Medical Applications of Cross-Linked Hydrogels Using Nontoxic Materials and Experiments Suitable for Many Settings

We report a series of three experiments that introduce students at different stages of their academic preparation to the medical applications of hydrogels for controlled drug delivery and wound healing. The laboratory activity bridges the fundamental concepts of chemistry (acids and bases, equilibria, solvation, and reversible esterification) with the chemistry of polymers and cross-linking, which are among the main tools of nanotechnology. The activity is customizable for students ranging from middle school to undergraduate college academic backgrounds. The two simple experiments demonstrate acid- or glucose-triggered release of a dye (model drug) from cross-linked poly(vinyl alcohol)-based gels. This mimics controlled drug delivery to more acidic cancer cells and controlled release of insulin from antidiabetic patches. The third, more technically challenging experiment demonstrates irreversible solidification of a phosphate-cross-linked chitosan gel upon heating from room temperature to body temperature...

Increase of Direct C-C Coupling Reaction Yield by Identifying Structural and Electronic Properties of High-Spin Iron Tetra-azamacrocyclic Complexes.

Macrocyclic ligands have been explored extensively as scaffolds for transition metal catalysts for oxygen and hydrogen atom transfer reactions. C-C reactions facilitated using earth abundant metals bound to macrocyclic ligands have not been well-understood but could be a green alternative to replacing the current expensive and toxic precious metal systems most commonly used for these processes. Therefore, the yields from direct Suzuki-Miyaura C-C coupling of phenylboronic acid and pyrrole to produce 2-phenylpyrrole facilitated by eight high-spin iron complexes ([Fe3+L1(Cl)2]+, [Fe3+L4(Cl)2]+, [Fe2+L5(Cl)]+, [Fe2+L6(Cl)2], [Fe3+L7(Cl)2]+, [Fe3+L8(Cl)2]+, [Fe2+L9(Cl)]+, and [Fe2+L10(Cl)]+) were compared to identify the effect of structural and electronic properties on catalytic efficiency. Specifically, catalyst complexes were compared to evaluate the effect of five properties on catalyst reaction yields: (1) the coordination requirements of the catalyst, (2) redox half-potential of each complex, (3) topological constraint/rigidity, (4) N atom modification(s) increasing oxidative stability of the complex, and (5) geometric parameters. The need for two labile cis-coordination sites was confirmed based on a 42% decrease in catalytic reaction yield observed when complexes containing pentadentate ligands were used in place of complexes with tetradentate ligands. A strong correlation between iron(III/II) redox potential and catalytic reaction yields was also observed, with [Fe2+L6(Cl)2] providing the highest yield (81%, -405 mV). A Lorentzian fitting of redox potential versus yields predicts that these catalysts can undergo more fine-tuning to further increase yields. Interestingly, the remaining properties explored did not show a direct, strong relationship to catalytic reaction yields. Altogether, these results show that modifications to the ligand scaffold using fundamental concepts of inorganic coordination chemistry can be used to control the catalytic activity of macrocyclic iron complexes by controlling redox chemistry of the iron center. Furthermore, the data provide direction for the design of improved catalysts for this reaction and strategies to understand the impact of a ligand scaffold on catalytic activity of other reactions.

A new fundamental type of conformational isomerism.

Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term 'akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.

Calcium contained tap water phenomena: students misconception patterns of acids-bases concept

Acids and bases concept is very important and fundamental concept in learning chemistry. It is one of the chemistry subjects considered as an abstract and difficult concept to understand. The aim of this research was to explore student’s misconception pattern about acids and bases phenomena in daily life, such as calcium contained tap water. This was a qualitative research with descriptive methods. Participants were 546 undergraduate students of chemistry education and chemistry program, and graduate students of chemistry education in West Java, Indonesia. The test to explore students’ misconception about this phenomena was essay test. The results showed that there were five patterns of students’ misconception in explaining the phenomena of calcium carbonate precipitation on heating tap water. Students used irrelevant concepts in explaining this phenomena, i.e. temporary hardness, coagulation, density, and phase concepts. No students had right answer in explaining this phenomena. This research contributes to design meaningful learning and to achieve better understanding.

Adaptive aromaticity in S0 and T1 states of pentalene incorporating 16 valence electron osmium

Aromaticity is a fundamental chemical concept of ever-increasing diversity. According to Hückel’s and Baird’s rules, cyclic conjugated species with 4n+2 π-electrons are aromatic in the singlet electronic ground state (S0) and antiaromatic in the lowest triplet state (T1), and vice-versa. Thus, species with aromaticity in both states have not yet been reported. Here we carry out density functional theory calculations on recently synthesized organometallics, namely osmapentalyne and osmapentalenes, and demonstrate the first example (16-electron osmapentalene) of aromaticity in both S0 and T1 states, which we term adaptive aromaticity. Further electronic structure analysis reveals that the excitation pattern for the formation of the T1 state plays a crucial role in the achievement of adaptive aromaticity. Our findings highlight the role of a transition metal in unorthodox excitation behavior, and may aid the design of adaptive aromatics for photochemical and molecular magnetism applications.