The geometrical deviations from planar to folded or from linear to bent structures observed in multiply bonded heavy main group element analogues of ethylene and acetylene are treated from a ...second-order Jahn–Teller (SOJT) perspective. The structural distortions can be regarded as a consequence of a mixing of the filled highest occupied molecular orbital (HOMO) and an unoccupied orbital (LUMO+1). This mixing stabilizes the HOMO and destabilizes the unoccupied LUMO+1 orbital and produces nonbonding electron density, which causes the geometrical distortion through interelectronic repulsion. This occurs more readily in the heavier species because of their generally weaker bonds, which permit a closer approach and hence greater interaction of the molecular levels. Predicting which geometrical distortion enables the HOMO/LUMO+1 mixing requires knowledge of the symmetries of these frontier orbitals and the symmetry of the distortion. For the undistorted structures the product of the symmetries of the interacting orbitals must correspond to the symmetry of the distortion. More formally, the product of the symmetries of the HOMO, of the distortion (which is one of the fundamental vibrational modes of the molecule), and of the LUMO or LUMO+1 must contain the totally symmetric irreducible representation of the molecular point group. This approach is similar to the SOJT treatment of inversion in trigonal-pyramidal main-group species.
Computational chemistry approaches for studying the formation of terpenes/terpenoids in wines are presented, using five particular terpenes/terpenoids (1,8-cineole, α-ylangene, botrydial, rotundone, ...and the wine lactone), volatile compounds (or their precursors) found in wine and/or wine grapes, as representative examples. Through these examples, we show how modern computational quantum chemistry can be employed as an effective tool for assessing the validity of proposed mechanisms for terpene/terpenoid formation.
An ongoing challenge in modern catalysis is to identify and understand new modes of reactivity promoted by earth-abundant and inexpensive first-row transition metals. Herein, we report a mechanistic ...study of an unusual copper(I)-catalyzed 1,3-migration of 2-bromostyrenes that reincorporates the bromine activating group into the final product with concomitant borylation of the aryl halide bond. A combination of experimental and computational studies indicated this reaction does not involve any oxidation state changes at copper; rather, migration occurs through a series of formal sigmatropic shifts. Insight provided from these studies will be used to expand the utility of aryl copper species in synthesis and develop new ligands for enantioselective copper-catalyzed halogenation.
Density functional theory (DFT) calculations are used to probe the validity of mechanistic proposals for the conversion of isozizanoic acid to 12-norisoziza-5-ene, a reaction that occurs during steam ...distillation of vetiver oil. While this conversion corresponds overall to a simple decarboxylation, a multistep mechanism involving carbocation intermediates is supported by the computational results.
Oxidopyrylium-alkene 5 + 2 cycloaddition conjugate addition cascade (C3) sequences are described. Intramolecular cycloadditions involving terminal alkenes, enals, and enones were investigated. ...Substrates with tethers of varying lengths delivered five- and six-membered carbocycles and heterocycles thus demonstrating the scope and limitation of the cycloaddition–conjugate addition cascade. Several experiments and theoretical calculations provide evidence for the proposed mechanistic pathway.
We describe accommodations that we have made to our applied computational–theoretical chemistry laboratory to provide access for blind and visually impaired students interested in independent ...investigation of structure–function relationships. Our approach utilizes tactile drawings, molecular model kits, existing software, Bash and Perl scripts written in-house, and three-dimensional printing in a process that allows a blind or visually impaired student to satisfy her or his curiosity about structure–function relationships with minimal assistance from sighted co-workers.
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Quantum chemical calculations coupled to experiments were used to predict covalent hydration propensities of biologically relevant α-ketoamides. Experimentally determined hydration ...equilibrium constants for related ketones and aldehydes were compared to computationally determined values to develop a method for predicting hydration equilibrium constants. This method was used on six newly synthesized α-ketoamides to experimentally verify computational predictions. A correlation between calculation and experiment was observed and applied to models of several pertinent APIs. Our results indicate that the keto form is favored for practically all α-ketoamides in biological environs.
In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind ...and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX–BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX–BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted—from published articles, via printed results of computational chemistry experiments, to 3D models—is now available to BVI scientists too. The possibilities offered by AsteriX–BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).
Curricula for three chemistry camp experiences for blind and visually impaired (BVI) individuals that incorporated single- and multiday activities and experiments accessible to BVI students are ...described. Feedback on the camps from students, mentors, and instructors indicates that these events allowed BVI students, who in many cases have been discouraged from doing science, to understand that chemistry can be made accessible and that they can think about chemistry on a level comparable to their sighted peers.
Quantum chemical calculations on the isomerization of 24-methylenecycloartanol are described. An energetically viable mechanism, with a rate-determining protonation step, is proposed. This ...rearrangement may find applicability in tests for determining if an olive oil has been refined.
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The results of density functional calculations on the mechanism of a rearrangement of a sterol proposed to occur during olive oil heating are described. These results indicate that this rearrangement can indeed occur at a fast rate under refining conditions, but will not occur at an appreciable rate under conditions for producing extra virgin olive oil.
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