Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem

Herein, we present results from MD simulations of the Michaelis complex formed between the dizinc beta-lactamase from B. fragilis and imipenem. We considered two catalytically important configurations, which differ in the presence or absence of a hydroxide bridge connecting the two zinc ions in the active site. The structural and dynamical effects induced by substrate binding, the specific roles of the conserved residues and the zinc-bound water molecules, the near attack conformers of the Michaelis complex, and so forth, are discussed in detail. The relative stability of the two configurations was estimated from QM linear scaling calculations on the enzyme-substrate complex combined with Poisson-Boltzmann electrostatic calculations and normal mode calculations. Importantly, we find that the two configurations have similar energies, indicating that these two structures could readily be interchanged, thereby facilitating catalysis. The configuration with the hydroxide bound to the two zinc ions is predicted to be the resting form of the enzyme, while the configuration without the bridge is the reactive form that was found to place the hydroxide in position to attack the carbonyl of the beta-lactam ring. Thus, we propose that the enzyme initiates catalysis by converting from the hydroxide bridge form into the configuration that lacks the hydroxide bridge. This interconversion increases the nucleophilicity of the hydroxide ion and exposes it to the beta-lactam carbonyl, which ultimately facilitates nucleophilic attack. The implications of the observed modes of binding, the possible influence of mutating the Lys184 and Asn193 residues on substrate binding, and the reaction mechanism are also discussed in detail.     

Can TMS and DSS be used as NMR references for cyclodextrin species in aqueous solution?

Tetramethylsilane (TMS) can be included by -cyclodextrin (-CD), and sodium 2,2-dimethylsilapentane-5-sulphonate (DSS) can form inclusion complexes with - and -CD. The NMR chemical shifts are changed considerably as a result of the strong interaction between CD and the guest compound in the inclusion complexes. A downfield shift of as much as 0.63 ppm shift downfield has been observed for the protons of external TMS in CD aqueous solution. In view of this, the question arises of whether TMS and DSS can be used as internal references. DSS in D₂O is suggested as an external reference for aqueous cyclodextrin solution in NMR measurements.     

Solvent-modulated chemoselective deprotections of trialkylsilyl esters and chemoselective esterifications

A series of trialkylsilyl esters were deprotected or transesterificated into their corresponding carboxylic acids or methyl esters under a catalytic amount of CBr₄ in alcohol reaction system. This method enables to desilylate secondary sp³-carbon, sp²-carbon, sp-carbon and aryl tethered trialkylsilyl esters to carboxylic acids, whereas primary sp³-carbon tethered trialkylsilyl esters were further converted into their methyl esters under CBr₄/MeOH reaction conditions. The highly chemoselective deprotections can be modulated and achieved by the introduced protecting trialkylsilyl groups and the used alcohols such as MeOH and EtOH under this photochemically-induced reaction conditions.     

Aging of poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene)/toluene solutions and subsequent effects on luminescence behavior of cast films

Morphological effects in luminescence properties of a representative semiconducting polymer, poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV), has recently attracted much attention. Previous studies indicated that short-term heat treatment of solution-cast MEH-PPV films may result in the formation of mesomorphic order that is responsible for the "red" emission around 640 nm, in contrast to the single-chromophore "yellow" emission near 590 nm from the disordered matrix. On the basis of microscopic and spectroscopic evidence for films cast from freshly prepared and aged solutions, here we show that prolonged storage of MEHyellowPPV solutions at room temperature or lower may result in retardation of the thermally induced mesophase formation in the subsequently cast films. According to small-angle neutron scattering and differential scanning calorimetric observations over aged MEH-PPV/toluene solutions, we propose that the suppressed transformation into mesomorphic order is due to further development of nanocrystalline aggregates that serve as physical cross-links among MEH-PPV chains in the solution state upon long-term storage. These solvent-induced nanocrystalline aggregates, however, do not exhibit new spectroscopic features beyond the suppression of "red" emission at 640 nm from the mesomorphic phase.     

Rational design of an “all-in-one” phototheranostic

We report here porphodilactol derivatives and their corresponding metal complexes. These systems show promise as “all-in-one” phototheranostics and are predicated on a design strategy that involves controlling the relationship between intersystem crossing (ISC) and photothermal conversion efficiency following photoexcitation. The requisite balance was achieved by tuning the aromaticity of these porphyrinoid derivatives and forming complexes with one of two lanthanide cations, namely Gd³⁺ and Lu³⁺. The net result led to a metalloporphodilactol system, Gd-trans-2, with seemingly optimal ISC efficiency, photothermal conversion efficiency and fluorescence properties, as well as good chemical stability. Encapsulation of Gd-trans-2 within mesoporous silica nanoparticles (MSN) allowed its evaluation for tumour diagnosis and therapy. It was found to be effective as an “all-in-one” phototheranostic that allowed for NIR fluorescence/photoacoustic dual-modal imaging while providing an excellent combined PTT/PDT therapeutic efficacy in vitro and in vivo in 4T1-tumour-bearing mice.

We report here porphodilactol derivatives and their corresponding metal complexes as “all-in-one” phototheranostics by controlling the relationship between intersystem crossing (ISC) and photothermal conversion efficiency following photoexcitation.     

Screening the origin and weathering of oil slicks by attenuated total reflectance mid-IR spectrometry

The combination of attenuated total reflectance-fourier transform mid-infrared spectrometry (ATR-FTMIR) and multivariate pattern recognition is presented as a fast and convenient methodology to ascertain the source product an oil slick comes from and to evaluate the extent of its weathering. Different types of hydrocarbons (including crude oils, several heavy distillates and the Prestige's heavy fuel oil) were spilled on metallic containers designed ad hoc and their fate monitored by ATR-FTMIR. Not only environmental conditions were considered for weathering but artificial IR- and UV-irradiation. Pattern-recognition studies revealed that the different hydrocarbons clustered at different locations on the score plots and that the samples corresponding to each oil became ordered according to the extent of their weathering. Among them, fuel oil samples coming from the recent disaster of the Prestige tanker off the Galician shoreline showed a distinctive behaviour. Comparison of natural-, IR- and UV-weathering of a crude oil showed that IR solar radiation can be important in oil-weathering, in addition to broadly-reported UV degradation.     

A study of the electrospray ionisation and ion-trap fragmentation of [M - H](-) ions of new 3,5-disubstituted tetrahydro-2H-1,3,5-thiadiazin-2-thiones

The electrospray ionisation (ESI) in negative mode of the pharmacologically significant 3,5-disubstituted tetrahydro-2H-1,3,5-thiadiazin-2-thiones, and their subsequent fragmentations using an ion-trap mass spectrometer, have been investigated. Experiments on sequential product ion fragmentations (MS(n)) were performed in order to elucidate the degradation pathways for these compounds. The data presented show that the fragmentation of the even-electron [M - H](-) ions could proceed through an internal nucleophilic substitution displacement. Decarboxylation and extrusion of carbon disulfide are other fragmentations observed.     

Direct titrations of antibiotics with iodate solutions: Part 2. Some selected cephalosporins

A previous method for the determination of penicillins by direct titration with potassium iodate under strongly acidic conditions has been extended to the assay of some selected cephalosporins. Results are presented, including error and precision analyses, for the determination of cephaloridine, cephalothin and cephalexin. The appropriate stoichiometries are 1 mol cephalosporin to 3 mol iodate for cephalothin and cephaloridine; 1 mol to 2 mol iodate for cephalexin. An irreversible aqueous end-point technique has been compared with the chloroform layer method; the latter gives more precise results for the determination of cephaloridine and cephalothin (0.8% and 1.3% r.s.d. respectively). Comparable precision was obtained by either technique for the determination of cephalexin (1.39% r.s.d.).     

Retention behavior and solvent optimization of organochlorine pesticides in solid-phase extraction

Summary Plots of capacity factor and retention time vs. elution solvent composition were proved to be useful to interpret the retention behavior of Kepone and its metabolites in a reversed-phase solid-phase extraction and to optimize the elution solvent. The percent recovery of Kepone was largely improved when the solvent was optimized. The standard deviations of the results of extractions were also improved upon the optimization of the solvent.