Importance of Equilibrium Fluctuations between Most Stable Conformers in the Control of the Reaction Mechanism

Coordination among Bond Formation/Cleavage in a Bifunctional-Catalyzed Fast Amide Hydrolysis: Evidence for an Optimized Intramolecular N-Protonation Event

A density functional theory (DFT) computational analysis, using the ωB97X-D functional, of a rapid amide cleavage in 2-carboxyphthalanilic acid (2CPA), where the amide group is flanked by two catalytic carboxyls, reveals key mechanistic information: (a) General base catalysis by a carboxylate coupled to general acid catalysis by a carboxyl is not operative. (b) Nucleophilic attack by a carboxylate on the amide carbonyl coupled to general acid catalysis at the amide oxygen can also be ruled out. (c) A mechanistic pathway that remains viable involves general acid proton delivery to the amide nitrogen by a carboxyl, while the other carboxylate engages in nucleophilic attack upon the amide carbonyl; a substantially unchanged amide carbonyl in the transition state; two concurrent bond-forming events; and a spatiotemporal-base rate acceleration. This mechanism is supported by molecular dynamic simulations which confirm a persistent key intramolecular hydrogen bonding. These theoretical conclusions, although not easily verified by experiment, are consistent with a bell-shaped pH/rate profile but are at odds with hydrolysis mechanisms in the classic literature.

Interaction vs Preorganization in Enzyme Catalysis. A Dispute That Calls for Resolution

This essay focuses on the debate between Warshel et al. (proponents of preorganization) and Menger and Nome (proponents of spatiotemporal effects) over the source of fast enzyme catalysis. The Warshel model proposes that the main function of enzymes is to push the solvent coordinate toward the transition state. Other physical-organic factors (e.g., desolvation, entropic effects, ground state destabilization, etc.) do not, ostensibly, contribute substantially to the rate. Indeed, physical organic chemistry in its entirety was claimed to be "irrelevant to an enzyme's active site". Preorganization had been applied by Warshel to his "flagship" enzyme, ketosteroid isomerase, but we discuss troubling issues with their ensuing analysis. For example, the concepts of "general acid" and "general base", known to play a role in this enzyme's mechanism, are ignored in the text. In contrast, the spatiotemporal theory postulates that enzyme-like rates (i.e., accelerations >10⁸) occur when two functionalities are held rigidly at contact distances less than ca. 3 Å. Numerous diverse organic systems are shown to bear this out experimentally. Many of these are intramolecular systems where distances between functionalities are known. Among them are fast intramolecular systems where strain is actually generated during the reaction, thereby excluding steric compression as a source of the observed enzyme-like rates. Finally, the account ends with structural data from four active sites of enzymes, obtained by others, all showing contact distances between substrate analogues and enzyme. To our knowledge, contact distances less than the diameter of water are found universally among enzymes, and it is to this fact that we attribute their extremely fast rates given the assumption that enzymes, whatever their particular mechanism, obey elementary chemical principles.

Nickel-Catalyzed Decarbonylative Alkylation of Aroyl Fluorides Assisted by Lewis-Acidic Organoboranes

Herein, nickel-catalyzed decarbonylative C-F bond alkylation of aroyl fluorides with organoboron reagents is reported. Aroyl fluorides are more chemically stable than the corresponding aroyl chlorides and can be readily synthesized from the corresponding carboxylic acids. The fluoronickel intermediate formed via oxidative addition interacts with Lewis-acidic trialkylboranes, and the subsequent decarbonylative alkylation proceeds. This new synthetic methodology allows 1,2-bifunctionalization of aromatic carboxylic acids via palladium-catalyzed ortho-C-H arylation. In addition, an unprecedented 1,4-nickel migration on ortho-arylated aroyl fluorides was observed. As a demonstration of the synthetic utility of the present reaction, the sequential 1-alkyl-2-arylation of 3-hydroxy-2-naphthoic acid was accomplished via chemoselective alkylation at a fluorocarbonyl moiety and the subsequent C-O bond arylation at an acetoxy group.

Transforming a Stable Amide into a Highly Reactive One: Capturing the Essence of Enzymatic Catalysis

Aspartic proteinases, which include HIV-1 proteinase, function with two aspartate carboxy groups at the active site. This relationship has been modeled in a system possessing an otherwise unactivated amide positioned between two carboxy groups. The model amide is cleaved at an enzyme-like rate that renders the amide nonisolable at 35 °C and pH 4 owing to the joint presence of carboxy and carboxylate groups. A currently advanced theory attributing almost the entire catalytic power of enzymes to electrostatic reorganization is shown to be superfluous when suitable interatomic interactions are present. Our kinetic results are consistent with spatiotemporal concepts where embedding the amide group between two carboxylic moieties in proper geometries, at distances less than the diameter of water, leads to enzyme-like rate enhancements. Space and time are the essence of enzyme catalysis.

Effective targeting of proton transfer at ground and excited states of ortho-(2′-imidazolyl)naphthol constitutional isomers

Besides electronic effects at the excited state, ground and excited state acidities are largely affected by proximity and structural alignment.

1-Carboxynaphthalen-2-yl acetate monohydrate

In the title compound, C13H10O4·H2O, both the carboxylic acid [Car—Car—C—O = −121.1 (2)°, where ar = aromatic] and the ester [Car—Car—O—C = −104.4 (3)°] groups lie out of the mean plane of the conjugated aromatic system. In the crystal, the organic molecule is hydrogen bonded to water molecules through the ester and carboxy moieties, forming chains along thea-axis direction. The methyl H atoms of the acetoxy group are disordered over two equally occupied sites.

Surface modification of anatase nanoparticles with fused ring salicylate-type ligands (3-hydroxy-2-naphthoic acids): a combined DFT and experimental study of optical properties

The surface modification of nanocrystalline TiO2 particles (45 Å) with salicylate-type ligands consisting of an extended aromatic ring system, specifically 3-hydroxy-2-naphthoic acid, 3,5-dihydroxy-2-naphthoic acid and 3,7-dihydroxy-2-naphthoic acid, was found to alter the optical properties of nanoparticles in a similar way to salicylic acid. The formation of the inner-sphere charge-transfer (CT) complexes results in a red shift of the semiconductor absorption compared to unmodified nanocrystallites and a reduction in the band gap upon the increase in the electron delocalization when including an additional ring. The investigated ligands have the optimal geometry for binding to surface Ti atoms, resulting in ring coordination complexes of a salicylate-type (binuclear bidentate binding-bridging) thus restoring the six-coordinated octahedral geometry of surface Ti atoms. From both absorption measurements in methanol/water = 90/10 solutions and steady-state quenching measurements of modifier fluorescence upon binding to TiO2 in aqueous solutions, stability constants in the order of 10(3) M(-1) have been determined at pH 2 and pH 3. Fluorescence lifetime measurements, in the presence and absence of colloidal TiO2 nanoparticles, indicated that the fluorescence quenching process is primarily static quenching, thus proving the formation of a nonfluorescent CT complex. The binding structures were investigated by using FTIR spectroscopy. Quantum chemical calculations on model systems using density functional theory (DFT) were performed to obtain the vibrational frequencies of charge transfer complexes, and the calculated values were then compared with the experimental data.