The properties and stereochemical reactivity of cyclobutadiene, benzene, cyclooctatetraene, and the [10]- to [14]annulenes can be uniformly rationalized through the bent bond/antiperiplanar hypothesis (BBAH). This new orbital model considers electronic delocalization between pyramidal diradical resonance structures and associated bent bonds, as it applies to aromatic, nonaromatic, and antiaromatic molecules.
Glycosylation reactions were performed on a series of bicyclic C2-substituted pyranoside models to isolate and analyze factors that control the glycosylation stereoselectivities observed in carbohydrates. The bent bond/antiperiplanar hypothesis (BBAH) orbital model rationalizes all of these results by considering hyperconjugation interactions between groups at C2 and the two τ bonds (bent bonds) of oxocarbenium ion intermediates formed under the glycosylation conditions. According to the BBAH, nucleophiles add to oxocarbenium intermediates by SN2-like antiperiplanar displacement of the weaker of their two τ bonds.
Hypoxia induces precocious hatching in zebrafish, but we do not have a clear understanding of the molecular mechanisms regulating the activation of the hatching enzyme or how these mechanisms trigger precocious hatching under unfavorable environmental conditions. Using immunohistochemistry, pharmacological inhibition of matrix metalloproteinase 13 (Mmp13), and in vivo zymography, we show that Mmp13a is present in the hatching gland just as embryos become hatching competent and that Mmp13a activity is required for both normal hatching and hypoxia-induced precocious hatching. We conclude that Mmp13a likely functions in activating the hatching enzyme zymogen and that Mmp13a activity is necessary but not sufficient for hatching in zebrafish. This study highlights the broad nature of MMP function in development and provides a non-mammalian example of extra-embryonic processes mediated by MMP activity.
The glycosylation stereoselectivities for a series of bicyclic furanoside models have been carried out in the presence of weak nucleophiles. These results were analyzed through the bent bond/antiperiplanar hypothesis (BBAH) orbital model to test its validity. According to the BBAH, incoming nucleophiles displace one of the two bent bonds of bicyclic oxocarbenium ion intermediates in an antiperiplanar fashion. The glycosylation stereoselectivity is then governed by the displacement of the weaker bent bond as determined by the presence of electron-withdrawing or -donating substituents at C2. Overall, the BBAH analysis expands Woerpel's "inside/outside attack" glycosylation model by considering the stereoelectronic influence of neighboring electron-withdrawing and -donating groups on the nucleophilic addition to oxocarbenium ion intermediates.
The thermolysis of an optically active tetradeuterated 2-methoxymethyl methylenecyclopropane produces a specific ratio of eight possible rearrangement stereoisomers. Despite numerous efforts, this reaction and other similar transformations have defied mechanistic interpretation until now. The direct application of the bent bond/antiperiplanar hypothesis (BBAH) to this reaction produces a mechanistic model that rationalizes all the observed reaction kinetics and products. The BBAH dictates that allyl diradical intermediates, produced during methylenecyclopropane thermolysis, retain pyramidal character due to antiperiplanar delocalization into their respective bent bond.
The bent bond/antiperiplanar hypothesis (BBAH) is used to propose a mechanism-based orbital model for the facial selectivity of sigmatropic hydrogen shifts under both thermal and photochemical conditions. The BBAH analysis of these concerted rearrangements invokes transient vibrationally excited singlet diradicals in both 4 n and 4 n+2 polyenes.
The bent bond/antiperiplanar hypothesis (BBAH) has been applied to the thermal rearrangements of cyclooctatetraene and related C8H8 isomers. This novel orbital model shows that pyramidal singlet diradical intermediates produced from thermal vibrational states of C8H8 isomers account for their chemical reactivity.
The bent bond/antiperiplanar (BBA) hypothesis has been applied to the analysis of [1,3]-sigmatropic alkyl shifts. These thermal rearrangements, for which there is evidence that they proceed through diradical intermediates, can be interpreted by considering their transient allyl radical structures. For the thermolysis of cyclic molecules, the preferred generation of pyramidal allyl radicals in staggered conformations is postulated on the basis of the BBA hypothesis. This accounts for the preference of suprafacial rearrangement pathways as well as the extent of inversion or retention of configuration at the migrating carbons.
The design of molecular catalysts that mimic the behavior of enzymes is a topical field of activity in emerging technologies, and can lead to an improved understanding of biological systems. Herein, we report how the bulky arms of the cations in [(n C4 H9 )4 N](+) [HCO3 ](-) give rise to a host scaffold that emulates the substrate binding sites in carbonic anhydrase enzymes, affording a unique glimpse of an arrested intermediate in the base-mediated binding and activation of CO2 .
Bicarbonates/chemistry , Biomimetic Materials/chemistry , Carbon Dioxide/metabolism , Carbonic Anhydrases/chemistry , Quaternary Ammonium Compounds/chemistry , Bicarbonates/metabolism , Binding Sites , Biomimetic Materials/metabolism , Biomimetics , Carbonic Anhydrases/metabolism , Crystallography, X-Ray , Models, Molecular , Quaternary Ammonium Compounds/metabolism
Spatial visualization abilities are positively related to performance on science, technology, engineering, and math tasks, but this relationship is influenced by task demands and learner strategies. In two studies, we illustrate these interactions by demonstrating situations in which greater spatial ability leads to problematic performance. In Study 1, chemistry students observed and explained sets of simultaneously presented displays depicting chemical phenomena at macroscopic and particulate levels of representation. Prior to viewing, the students were asked to make predictions at the macroscopic level. Eye movement analyses revealed that greater spatial ability was associated with greater focus on the prediction-relevant macroscopic level. Unfortunately, that restricted focus was also associated with lower-quality explanations of the phenomena. In Study 2, we presented the same displays but manipulated whether participants were asked to make predictions prior to viewing. Spatial ability was again associated with restricted focus, but only for students who completed the prediction task. Eliminating the prediction task encouraged attempts to integrate the displays that related positively to performance, especially for participants with high spatial ability. Spatial abilities can be recruited in effective or ineffective ways depending on alignments between the demands of a task and the approaches individuals adopt for completing that task.
Attention/physiology , Comprehension/physiology , Learning/physiology , Space Perception/physiology , Eye Movements , Female , Humans , Male , Pattern Recognition, Visual , Photic Stimulation , Predictive Value of Tests , Rotation , Students , Universities , Video Recording
By taking into consideration bent bonds (τ-bonds, tau-bonds), the antiperiplanar hypothesis, the classic theory of resonance, and the preference for staggered bonds over eclipsed bonds in tetrahedral systems, a simple qualitative model is presented to rationalize the conformation and reactivity for a wide range of compounds containing double bonds and/or carbonyl groups. Alkenes, carbonyl and carboxyl derivatives, conjugated systems as well as other functional groups are revisited. This also leads to a simple model to understand aromaticity, and electrocyclic reactions. The bent bond model and the antiperiplanar hypothesis provide a qualitative model for better understanding the electron delocalization and the reactivity inherent to unsaturated organic systems by an alternative view of the classic resonance theory.
The reverse-docking of a TADDOL catalyst to rigid transition-state (TS) representations of an asymmetric hetero-Diels-Alder reaction is described. The resulting docking poses represent a simplified geometric model of the TS for the catalyzed reaction. The conformational space of the catalyst in proximity to the catalyst-free TS models is sampled stochastically and the energetically favored poses are subjected to a clustering procedure to highlight structural attributes compatible with organocatalysis. Each pose is scored and ranked based on its molecular-mechanics docking energy. The reverse-docking procedure reveals a clear energetic trend in favor of the experimentally preferred product enantiomers. Analysis of the best poses suggests a geometric model that is consistent with principles of molecular recognition, catalysis, and experimental data.
Catalysis , Organic Chemicals/chemistry , Molecular Conformation
A novel methodology for 'reverse-docking' a cationic peptide-based organocatalyst to a rigid anionic transition state (TS) model for the conjugate addition of azide to alpha,beta-unsaturated carbonyl substrates is described. The resulting docking poses serve as simplified TS models for enantioselective catalysis. Molecular mechanics-based scoring and ranking of the docking poses, followed by clustering and structural analysis, reveal a clear energetic preference for docking to the S-enantiomeric azidation TS model, in agreement with experiment. Clear energetic trends emerged from docking the catalyst to both enantiomers of all six azidation TS models of this study. Structural analysis of the most favorable pose suggests a mechanism for enantioselective catalysis that is consistent with principles of molecular recognition, catalysis, and experimental data.
Azides/metabolism , Computational Biology , Enzymes/physiology , Peptides/physiology , Catalysis , Ligands , Models, Molecular
A series of tripodal amidopyridine receptors capable of selective recognition of methylmethanetriacetic acid (MMTA) in organic solvents is described. Intramolecular hydrogen-bonding groups, built into some of the receptors, were designed as preorganization devices. Binding was studied by NMR titration, variable temperature NMR experiments, 2D-NMR, isothermal titration calorimetry, and single-crystal X-ray crystallography. The results reveal that a balancing act between inter- and intramolecular hydrogen-bonding interactions in the complexes governs both the dynamics and the geometry of binding. Receptor 1b (without intramolecular hydrogen-bonding groups) features a simple symmetric MMTA binding geometry with optimal enthalpic interactions. In sharp contrast, receptor 1a (with intramolecular hydrogen-bonding groups) reveals a temperature-dependent dual binding mode where MMTA can bind in two completely different geometries. The two solution binding geometries of 1a.MMTA were unraveled by NMR experiments and correlated to the X-ray structures.
