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Concept: Stereochemistry


A new antibacterial chlorinated benzophenone derivative, (±)-pestalachloride D (1), along with a related analog, (±)-pestalachloride C (2), was recently isolated from the marine-derived fungus Pestalotiopsis sp. isolated from a soft coral Sarcophyton sp. collected from Yongxing Island in the South China Sea. Both chiral HPLC analysis and single-crystal X-ray data indicated that 1 is a racemic mixture. Interestingly, 1 did not exhibit any effect in the zebrafish embryo teratogenicity assay, while 2 led to abnormal growth. The potential impact on zebrafish embryo growth is discussed based on their crystal structures. The main difference of crystal structures between 1 and 2 is that the six-member non-aromatic ring (O4, C10, C9, C8, C2', and C3') in 1 exhibits a distorted chair conformation, while 2 shows a distorted boat conformation. Moreover, compounds 1 and 2 both exhibited moderate antibacterial activity.

Concepts: Stereochemistry, Enantiomer, Solid, South China Sea, Racemic mixture, Cyclohexane conformation, East China Sea, Adderall


Synthetic control over chirality and function is the crowning achievement for metal-organic frameworks, but the same level of control has not been achieved for covalent organic frameworks (COFs). Here we demonstrate chiral COFs (CCOFs) can be crystallized from achiral organic precursors by chiral catalytic induction. A total of nine two-dimensional CCOFs are solvothermally prepared by imine condensations of the C3-symmetric 1,3,5-triformylphloroglucinol (Tp) with diamine or triamine linkers in the presence of catalytic amount of ®- or (S)-1-phenylethylamine. Homochirality of these CCOFs results from chiral catalyst-induced immobilization of threefold-symmetric tris(N-salicylideneamine) cores with a propeller-like conformation of one single handedness during crystallization. The CCOF-TpTab showed high enantioselectivity toward chiral carbohydrates in fluorescence quenching and, after postsynthetic modification of enaminone groups located in chiral channels with Cu(II) ions, it can also be utilized as a heterogeneous catalyst for the asymmetric Henry reaction of nitroalkane with aldehydes.

Concepts: Amino acid, Catalysis, Stereochemistry, Hydrogenation, Enantiomer, Chirality


The prebiotic replication of information-coding molecules is a central problem concerning life’s origins. Here, we report that amyloids composed of short peptides can direct the sequence-selective, regioselective and stereoselective condensation of amino acids. The addition of activated DL-arginine and DL-phenylalanine to the peptide RFRFR-NH2 in the presence of the complementary template peptide Ac-FEFEFEFE-NH2 yields the isotactic product FRFRFRFR-NH2, 1 of 64 possible triple addition products, under conditions in which the absence of template yields only single and double additions of mixed stereochemistry. The templating mechanism appears to be general in that a different amyloid formed by (Orn)V(Orn)V(Orn)V(Orn)V-NH2 and Ac-VDVDVDVDV-NH2 is regioselective and stereoselective for N-terminal, L-amino-acid addition while the ornithine-valine peptide alone yields predominantly sidechain condensation products with little stereoselectivity. Furthermore, the templating reaction is stable over a wide range of pH (5.6-8.6), salt concentration (0-4 M NaCl), and temperature (25-90 °C), making the amyloid an attractive model for a prebiotic peptide replicating system.

Concepts: Protein, Amino acid, Acid, Peptide bond, Stereochemistry, Peptide, Amyloid, Peptide synthesis


Molecular knots remain difficult to produce using the current synthetic methods of chemistry because of their topological complexity. We report here the near-quantitative self-assembly of a trefoil knot from a naphthalenediimide-based aqueous disulfide dynamic combinatorial library. The formation of the knot appears to be driven by the hydrophobic effect and leads to a structure in which the aromatic components are buried while the hydrophilic carboxylate groups remain exposed to the solvent. Moreover, the building block chirality constrains the topological conformation of the knot and results in its stereoselective synthesis. This work demonstrates that the hydrophobic effect provides a powerful strategy to direct the synthesis of entwined architectures.

Concepts: Knot theory, Chemical properties, Knot, Stereochemistry, Intermolecular forces, Chemistry, Hydrophobe, Hydrophobic effect


‘Dibal'lin’ on a budget: The enantioselective total syntheses of transtaganolides A-D are rapidly achieved by a highly diastereoselective Ireland-Claisen/Diels-Alder cascade reaction of an enantioenriched geraniol derivative. Based on X-ray diffraction data, the absolute configuration of these metabolites is established and discussed within the context of existing biosynthetic hypotheses.

Concepts: Diffraction, X-ray, Absolute, Stereochemistry, X-ray crystallography, Cascade reaction


This Account describes how attractive interactions of aromatic rings with other groups can influence and control the stereoselectivity of many reactions. Recent developments in theory have improved the accuracy in the modeling of aromatic interactions. Quantum mechanical modeling can now provide insights into the roles of these interactions at a level of detail not previously accessible, both for ground-state species and for transition states of chemical reactions. In this Account, we show how transition-state modeling led to the discovery of the influence of aryl groups on the stereoselectivities of several types of organic reactions, including asymmetric dihydroxylations, transfer hydrogenations, hetero-Diels-Alder reactions, acyl transfers, and Claisen rearrangements. Our recent studies have also led to a novel mechanistic picture for two classes of (4 + 3) cycloadditions, both of which involve reactions of furans with oxyallyl intermediates. The first class of cycloadditions, developed by Hsung, features neutral oxyallyl intermediates that contain a chiral oxazolidinone auxiliary. Originally, it was thought that these cycloadditions relied on differential steric crowding of the two faces of a planar intermediate. Computations reveal a different picture and show that cycloaddition with furan takes place preferentially through the more crowded transition state: the furan adds on the same side as the Ph substituent of the oxazolidinone. The crowded transition state is stabilized by a CH-π interaction between furan and Ph worth approximately 2 kcal/mol. Attractive interactions with aromatic rings also control the stereoselectivity in a second class of (4+3) cycloadditions involving chiral alkoxy siloxyallyl cations. Alkoxy groups derived from chiral α-methylbenzyl alcohols favor crowded transition states, where a stabilizing CH-π interaction is present between the furan and the Ar group. The cationic cycloadditions are stepwise, while the Hsung cycloadditions are concerted. Our results suggest that this form of CH- π-directed stereocontrol is quite general and likely controls the stereoselectivities of other addition reactions in which one face of a planar intermediate bears a pendant aromatic substituent.

Concepts: Chemical reaction, Transition state, Stereochemistry, Chemistry, Organic reaction, Transition state theory, Aromatic compounds, Thiophene


We report the first in situ and real-time monitoring of the interconversion of L- and D-alanine-d3 by alanine racemase from Bacillus Stearothermophilus directly observed by 2H-NMR spectroscopy in anisotropic phase. The enantiomers are distinguished by the difference of their 2H quadrupolar splittings in a chiral liquid-crystalline environment made of short DNA fragments. The proof-of-principle, the reliability and the robustness of this new method is demonstrated by the determination of the turnover rates of the enzyme using the Michaelis-Menten model.

Concepts: Scientific method, Bacteria, Polymerase chain reaction, Stereochemistry, DNA polymerase, Object-oriented programming, Activation energy


A highly sensitive, specific and enantioselective assay has been developed and validated for the estimation of TAK-700 enantiomers [(+)-TAK-700 and (-)-TAK-700] in rat plasma on LC-MS/MS-ESI in the positive-ion mode. Liquid-liquid extraction was used to extract (±)-TAK-700 enantiomers and IS (phenacetin) from rat plasma. TAK-700 enantiomers were separated using methanol and 5 mm ammonium acetate (80:20, v/v) at a flow rate of 0.7 mL/min on a Chiralcel OJ-RH column. The total run time was 7.0 min and the elution of (+)-TAK-700, (-)-TAK-700 and IS occurred at 3.71, 4.45 and 4.33 min, respectively. The MS/MS ion transitions monitored were m/z 308.2 → 95.0 for TAK-700 and m/z 180.2 → 110.1 for IS. The standard curves for TAK-700 enantiomers were linear (r(2)  > 0.998) in the concentration range 2.01-2015 ng/mL for each enantiomer. The inter- and intra-day precisions were in the ranges 3.74-7.61 and 2.06-8.71% and 3.59-9.00 and 2.32-11.0% for (+)-TAK-700 and (-)-TAK-700, respectively. Both the enantiomers were found to be stable in a battery of stability studies. This novel method was applied to the study of stereoselective oral pharmacokinetics of (+)-TAK-700 and it was unequivocally demonstrated that (+)-TAK-700 does not undergo chiral inversion to its antipode in vivo. Copyright © 2012 John Wiley & Sons, Ltd.

Concepts: Stereochemistry, Enantiomer, Chirality, Tartaric acid, Enantiomeric excess


A convenient synthesis of natural and synthetic pterocarpans was achieved in three steps. Optical resolution of the respective enantiomers was accomplished by analytical and semi-preparative HPLC on a chiral stationary phase. For medicarpin and its synthetic derivative 9-demethoxymedicarpin, the absolute configuration was confirmed by a combination of experimental LC-ECD coupling and quantum-chemical ECD calculations. (-)-Medicarpin and (-)-9-demethoxymedicarpin are both 6aR,11aR-configured, and consequently the corresponding enantiomers, (+)-medicarpin and (+)-9-demethoxymedicarpin, possess the 6aS,11aS-configuration. A comparative mechanism study for osteogenic (bone forming) activity of medicarpin (racemic versus enantiomerically pure material) revealed that (+)-(6aS,11aS)-medicarpin (6a) significantly increased the bone morphogenetic protein-2 (BMP2) expression and the level of the bone-specific transcription factor Runx-2 mRNA, while the effect was opposite for the other enantiomer, (-)-(6aR,11aR)-medicarpin (6a), and for the racemate, (±)-medicarpin, the combined effect of both the enantiomers on transcription levels was observed.

Concepts: DNA, Genetics, Gene expression, Transcription, Stereochemistry, RNA polymerase, Enantiomer, Racemic mixture


Original mixed selectors were synthesized by coupling a single l-valine diamide moiety on permethylated β-cyclodextrin. The structures of the new selectors were designed to limit the interactions between the l-valine derivative and cyclodextrin by removing the amino acid moiety from the cyclodextrin cavity by means of an amide linkage on mono-6-amino permethylated β-CD or the insertion of a carboxymethyl group. The accessibility of the amino acid group moiety was thus facilitated. The new mixed selectors exhibited better enantioselectivity than Chirasil-l-Val for half (selector based on mono-6-amino permethylated β-CD) or more (selector with the carboxymethyl group) of the 41 amino acid derivatives. Molecular modeling confirmed that these results could be attributed to an increase in the distance between the chiral center of the amino acid and the cyclodextrin cavity allowing better access of the amino acid moiety. These new mixed chiral selectors demonstrated a novel enantioselective capability with the successful separation of more than 90 racemic mixtures among the 105 chiral compounds tested. These mixed selectors exhibited enhanced enantioselectivity in comparison to binary selectors previously described with respect to both enantiomer resolution and the number of separated chiral compounds. Moreover, an improvement of the enantioseparation factors compared to the corresponding ‘parent phases’ for the amino acid derivatives was observed in many cases. These mixed selectors should therefore be considered some of the most versatile selectors for chiral gas chromatography.

Concepts: Amino acid, Amine, Ammonia, Stereochemistry, Enantiomer, Chirality, Carboxylic acid, Racemic mixture