Expanding dialogues: from natural autoinducers to non-natural analogues that modulate quorum sensing in Gram-negative bacteria

Bacteria are capable of "communicating" their local population densities via a process termed quorum sensing (QS). Gram-negative bacteria use N-acylated l-homoserine lactones (AHLs), in conjunction with their cognate LuxR-type receptors, as their primary signalling circuit for QS. In this critical review, we examine AHL signalling in Gram-negative bacteria with a primary focus on the design of non-natural AHLs, their structure-activity relationships, and their application in chemical biological approaches to study QS (72 references).     

A lattice model of vitrification and gelation

In this work we introduce a simple lattice model with T-shaped molecules in two dimensions that exhibits a rich range of morphological behaviors. Depending on the volume fraction and quench path, this system can adopt uniform liquid, solution, and phase-separated states, as well as inhomogeneous glass or gel-like states, as revealed by dynamic mean-field simulations. An important characteristic of this system is the existence of a large number of degenerate low-energy states with small barriers that leads to a broad, kinetically explored landscape. The mean-field stability and phase diagram of this model is constructed and provides a useful guide for understanding the complex behaviors of the system. One striking feature is that there is a cascade of instabilities that converge to mark the onset of what we identify as the glass transition. Both dynamic mean-field and Monte Carlo simulations reveal glass-like relaxation dynamics. Our results lead to a picture of gelation as a continuation of the glass transition into the two-phase region, or equivalently, as an incomplete phase separation arrested by the onset of the glass transition.     

Tight binding inhibitors of N-acyl amino sugar and N-acyl amino acid deacetylases

Very potent inhibitors were synthesized for the enzymatic deacetylation of N-acetyl-d-glucosamine-6-phosphate (NagA) and N-acetyl-d-glutamate (DGD). The methyl phosphonamidate derivative of d-glucosamine-6-phosphate bound to N-acetyl-d-glucosamine-6-phosphate deacetylase with an equilibrium dissociation constant of 34 +/- 5 nM at pH 7.5 and an association rate constant of 6.1 x 103 M-1 s-1. The inhibition constant is 4000-fold lower than the Michaelis constant for the substrate N-acetyl-d-glucosamine-6-phosphate. N-Acetyl-d-glutamate deacetylase was inhibited by the methyl phosphonamidate derivative of d-glutamate with an inhibition constant of 460 +/- 70 pM at pH 7.6. The inhibitor bound to the enzyme 500 000-fold tighter than the Michaelis constant for N-formyl-d-glutamate. These compounds mimic the putative tetrahedral intermediate formed upon nucleophilic attack of an activated water molecule on the amide bond of the target substrate. These inhibitors should prove useful in the elucidation of the enzyme-substrate interactions for enzymes within the amidohydrolase superfamily.     

Growth mechanism of textured MgO thin films via SSCVD

Magnesium oxide thin films have been deposited with use of single source chemical vapor deposition (SSCVD). The resultant films were examined by using transmission electron microscopy, X-ray texture analysis, and pole figure analysis. Due to the nature of the chemical reactions occurring at the surface during SSCVD growth, which result in a high growth rate/low flux environment, films of (111) orientation have been achieved without an amorphous underlayer, an unusual result for films of this orientation. Moreover the films have a strong degree of biaxial texturing in the x-y plane as found with X-ray texture analysis. These findings have important implications for buffer layers in perovskite thin film devices. The mechanism producing these structures has been revealed by using TEM and is discussed here.     

Divergent reactivity of allene-containing α-diazoesters using Cu and Rh catalysis

A versatile intramolecular reaction of allene-containing diazomalonates that exhibits excellent chemoselectivity for either allenic C–H insertion or cyclopropanation is demonstrated. The identity of the product depends on the transition metal catalyst that is employed for the reaction. Rh catalysts promote exclusive C–H insertion with good diastereoselectivity for the trans product, while Cu catalysis enables intramolecular cyclopropanation to yield methylenecyclopropanes with moderate to good E:Z ratios.     

Surfactant control of gas uptake: effect of butanol films on HCl and HBr entry into supercooled sulfuric acid

The entry of HCl into 60-68 wt % D(2)SO(4) and HBr into 68 wt % acid containing 0-0.18 M 1-butanol was monitored by measuring the fractions of impinging HCl and HBr molecules that desorb as DCl and DBr after undergoing H --> D exchange within the deuterated acid. The addition of 0.18 M butanol to the acid creates butyl films that reach approximately 80% surface coverage at 213 K. Surprisingly, this butyl film does not impede exchange but instead enhances it: the HCl --> DCl exchange fractions increase from 0.52 to 0.74 for 60 wt % D(2)SO(4) and from 0.14 to 0.27 for 68 wt % D(2)SO(4). HBr --> DBr exchange increases even more sharply, rising from 0.22 to 0.65 for 68 wt % D(2)SO(4). We demonstrate that this enhanced exchange corresponds to enhanced uptake into the butyl-coated acid for HBr and infer this equivalence for HCl. In contrast, the entry probability of the basic molecule CF(3)CH(2)OH exceeds 0.85 at all acid concentrations and is only slightly diminished by the butyl film. The OD groups of surface butanol molecules may assist entry by providing extra interfacial protonation sites for HCl and HBr dissociation. The experiments suggest that short-chain surfactants in sulfuric acid aerosols do not hinder heterogeneous reactions of HCl or HBr with other solute species.     

Spectroscopic characterization of Brooker’s merocyanine in Silicalite-1 and ZSM-5 leading to second harmonic generation

The use of porous materials has become increasingly significant in the pursuit of novel composite materials with nonlinear optical properties. The microporous channels in Silicalite-1 and ZSM-5, which have identical crystal frameworks but different chemical composition, were used to study the role of zeolite composition on dye adsorption and organization, leading to second-harmonic generation (SHG). The dye molecule, known as Brooker’s merocyanine (4-[(1-methyl-4(1H)-pyridinylidene)ethylidene]-2,5-cyclohexadien-1-one), exhibits one of the largest known molecular hyperpolarizabilities for small dye molecules, but it crystallizes centrosymmetrically. When Brooker’s merocyanine was adsorbed to Silicalite-1 powder, no SHG was detected, but when adsorbed to ZSM-5, the powder was SHG-active. Spectroscopic characterization of the new materials was used to determine the dye loading in each zeolite. The hydrophilic ZSM-5 channels proved to be essential for dye adsorption and alignment within the channels as compared to the hydrophobic Silicalite-1 which did not appreciably adsorb the dye. The effect of dye protonation and isomerization on adsorption to each zeolite was also studied, with neither having an effect on the amount of dye adsorbed.     

A computational investigation of the nitrogen-boron interaction in o-(N,N-dialkylaminomethyl)arylboronate systems

o-(N,N-Dialkylaminomethyl)arylboronate systems are an important class of compounds in diol-sensor development. We report results from a computational investigation of fourteen o-(N,N-dialkylaminomethyl)arylboronates using second-order M?ller-Plesset (MP2) perturbation theory. Geometry optimizations were performed at the MP2/cc-pVDZ level and followed by single-point calculations at the MP2/aug-cc-pVDZ(cc-pVTZ) levels. These results are compared to those from density functional theory (DFT) at the PBE1PBE(PBE1PBE-D)/6-311++G(d,p)(aug-cc-pVDZ) levels, as well as to experiment. Results from continuum PCM and CPCM solvation models were employed to assess the effects of a bulk aqueous environment. Although the behavior of o-(N,N-dialkylaminomethyl) free acid and ester proved to be complicated, we were able to extract some important trends from our calculations: (1) for the free acids the intramolecular hydrogen-bonded B-O-H···N seven-membered ring conformers 12 and 16 are found to be slightly lower in energy than the dative-bonded N→B five-membered ring conformers 10 and 14 while conformers 13 and 17, with no direct boron-nitrogen interaction, are significantly higher in energy than 12 and 16; (2) for the esters where no intramolecular B-O-H···N bonded form is possible, the N→B conformers 18 and 21 are significantly lower in energy than the no-interaction forms 20 and 23; (3) H(2)O insertion reactions into the N→B structures 10, 14, 18, and 21 leading to the seven-membered intermolecular hydrogen-bonded B···OH(2)···N ring structures 11, 15, 19, and 22 are all energetically favorable.     

Diamagnetic group 6 tetrakis(di-tert-butylketimido)metal(IV) complexes

The addition of 4 equiv of LiN=C-t-Bu(2) to CrCl(3), MoCl(5), and WCl(6) in diethyl ether produced the complexes M(N=C-t-Bu(2))(4) (M = Cr, Mo, W). Single-crystal X-ray diffraction studies revealed that the molecules have flattened tetrahedral geometries with virtual D(2d) symmetry in the solid state. (1)H and (13)C NMR spectra indicated that the complexes are diamagnetic, and a qualitative MO analysis showed that the orthogonal π-donor and -acceptor orbitals of the ketimide ligand cooperatively split the d(xy) and d(z2) orbitals sufficiently to allow spin pairing in the d(xy) orbital. A more sophisticated quantum-mechanical analysis of Cr(N=C-t-Bu(2))(4) using density functional/molecular mechanics methods confirmed the qualitative analysis by showing that the singlet state is 27 kcal/mol more stable than the triplet state.     

Oligoether-strapped calix[4]pyrrole: an ion-pair receptor displaying cation-dependent chloride anion transport

A ditopic ion-pair receptor (1), which has tunable cation- and anion-binding sites, has been synthesized and characterized. Spectroscopic analyses provide support for the conclusion that receptor 1 binds fluoride and chloride anions strongly and forms stable 1:1 complexes ([1·F](-) and [1·Cl](-)) with appropriately chosen salts of these anions in acetonitrile. When the anion complexes of 1 were treated with alkali metal ions (Li(+), Na(+), K(+), Cs(+), as their perchlorate salts), ion-dependent interactions were observed that were found to depend on both the choice of added cation and the initially complexed anion. In the case of [1·F](-), no appreciable interaction with the K(+) ion was seen. On the other hand, when this complex was treated with Li(+) or Na(+) ions, decomplexation of the bound fluoride anion was observed. In contrast to what was seen with Li(+), Na(+), K(+), treating [1·F](-) with Cs(+) ions gave rise to a stable, host-separated ion-pair complex, [F·1·Cs], which contains the Cs(+) ion bound in the cup-like portion of the calix[4]pyrrole. Different complexation behavior was seen in the case of the chloride complex, [1·Cl](-). Here, no appreciable interaction was observed with Na(+) or K(+). In contrast, treating with Li(+) produces a tight ion-pair complex, [1·Li·Cl], in which the cation is bound to the crown moiety. In analogy to what was seen for [1·F](-), treatment of [1·Cl](-) with Cs(+) ions gives rise to a host-separated ion-pair complex, [Cl·1·Cs], in which the cation is bound to the cup of the calix[4]pyrrole. As inferred from liposomal model membrane transport studies, system 1 can act as an effective carrier for several chloride anion salts of Group 1 cations, operating through both symport (chloride+cation co-transport) and antiport (nitrate-for-chloride exchange) mechanisms. This transport behavior stands in contrast to what is seen for simple octamethylcalix[4]pyrrole, which acts as an effective carrier for cesium chloride but does not operates through a nitrate-for-chloride anion exchange mechanism.