Combining reactive and configurational-bias Monte Carlo: confinement influence on the propene metathesis reaction system in various zeolites

In order to efficiently calculate chemical equilibria of large molecules in a confined environment the reactive Monte Carlo technique is combined with the configurational-bias Monte Carlo approach. To prove that detailed balance is fulfilled the acceptance rule for this combination of particular Monte Carlo techniques is derived in detail. Notably, by using this derivation all other acceptance rules of any Monte Carlo trial moves usually carried out in combination with the configurational-bias Monte Carlo approach can be deduced from it. As an application of the combination of reactive and configurational-bias Monte Carlo the influence of different zeolitic confinements (MFI, TON, LTL, and FER) on the reaction equilibrium and the selectivity of the propene metathesis reaction system was investigated. Compared to the bulk phase the conversion is increased significantly. The authors study this reaction system in the temperature range between 300 and 600 K, and the pressure range from 1 to 7 bars. In contrast to the bulk phase, pressure and temperature have a strong influence on the composition of the reaction mixture in confinement. At low pressures and temperatures both conversion and selectivity are highest. Furthermore, the equilibrium composition is strongly dependent on the type of zeolite. This demonstrates the important role of the host structure in catalytic systems.     

Synthesis of 5,6-dihydro-4H-thiopyran-4-ones

The anions of 1,4-diaryl-3-buten-2-ones 1 reacts with arylisothiocyanates, yielding intermediates 4 which can ring close to 5,6-dihydro-4H-thiopyran-4-ones 5 . Under similar reaction conditions ethyl 3-oxo-4-pentenoates 7 gives the 6-spiropyrans 9 . Methylation of 3 gives the S-methylated open form 6 .     

Discovery of a new phosphotyrosine mimetic for PTP1B using breakaway tethering

Protein tyrosine phosphatases play important roles in many signaling cascades involved in human disease. The identification of druglike inhibitors for these targets is a major challenge, and the discovery of suitable phosphotyrosine (pY) mimetics remains one of the key difficulties. Here we describe an extension of tethering technology, "breakaway tethering", which is ideally suited for discovering such new chemical entities. The approach involves first irreversibly modifying a protein with an extender that contains both a masked thiol and a known pY mimetic. The extender is then cleaved to release the pY mimetic, unmasking the thiol. The resulting protein is screened against a library of disulfide-containing small molecule fragments; any molecules with inherent affinity for the pY binding site will preferentially form disulfides with the extender, allowing for their identification by mass spectrometry. The ability to start from a known substrate mimimizes perturbation of protein structure and increases the opportunity to probe the active site using tethering. We applied this approach to the anti-diabetic protein PTP1B to discover a pY mimetic which belongs to a new molecular class and which binds in a novel fashion.     

Comparison of microbial receptor assay and liquid chromatography for determination of penicillin G and amoxicillin in milk powder

A microbial receptor assay (Charm II Tablet Beta-Lactam Test) and liquid chromatography (LC) were compared for determination of penicillin G (PG) and amoxicillin (AMOX) in reconstituted milk powder. Nonfat dry milk and whole dry milk were reconstituted (10%, w/v) to concentrations of 0, 2.5, 5, 7.5, and 10 ppb PG; nonfat dry milk was reconstituted (10%, w/v) to 0, 7.5, 10, and 15 ppb AMOX. Reconstituted samples were analyzed blindly by each method. Concentrations determined by both methods demonstrated good agreement. A significant difference between methods (p < or = 0.05) was observed only for 7.5 ppb PG in defatted dry milk. Significant differences were not observed between known concentrations and concentrations determined by the Charm II assay for PG or AMOX in defatted dry milk and PG in whole dry milk. Results by LC showed significant differences (p < 0.05) between known and measured concentrations at 10 ppb PG in both milks and 0 ppb AMOX in defatted dry milk. These results suggest that both the microbial receptor assay and LC may be useful for determination of PG and AMOX near safe level and tolerance, respectively, in reconstituted milk powder.     

Wetting transitions of ionic solutions

Cahn's phenomenological theory of wetting of a solid substrate by a saturated vapor is generalized to the case where the substrate is charged and the wetting film contains counterions, with or without added salt. The electrostatic contribution to the grand potential associated with these ions is calculated within a nonlinear Poisson-Boltzmann theory. In the salt-free case, when the wetting film includes only counterions released by the substrate, the wetting transition is always first order, regardless of its nature in a neutral system. When salt is present, other wetting scenarios may arise, depending on the salt concentration and substrate surface charge. Over a restricted range of salt concentrations, a wetting scenario similar to that of prewetting, is predicted to occur along the liquid-vapor coexistence line. This scenario includes a discontinuous wetting transition between microscopic and mesoscopic film thicknesses, followed by a continuous divergence of the film thickness at higher temperatures.     

Electric field-controlled water permeation coupled to ion transport through a nanopore

We report molecular dynamics simulations of a generic hydrophobic nanopore connecting two reservoirs which are initially at different Na(+) concentrations, as in a biological cell. The nanopore is impermeable to water under equilibrium conditions, but the strong electric field caused by the ionic concentration gradient drives water molecules in. The density and structure of water in the pore are highly field dependent. In a typical simulation run, we observe a succession of cation passages through the pore, characterized by approximately bulk mobility. These ion passages reduce the electric field, until the pore empties of water and closes to further ion transport, thus providing a possible mechanism for biological ion channel gating.     

Comparison of chromatographic ion-exchange resins. III. Strong cation-exchange resins

A comparative study was performed on strong cation-exchangers to investigate the pH dependence, efficiency, binding strength, particle size distribution, static and dynamic capacity, and SEM pictures of chromatographic resins. The resins tested included: SP Sepharose XL, Poros 50 HS, Toyopearl SP 550c, SP Sepharose BB, Source 30S, TSKGel SP-5PW-HR20, and Toyopearl SP 650c. Testing was performed with four different proteins: anti-FVII Mab (IgG), aprotinin, lysozyme, and myoglobin. Dependence of pH on retention was generally very low for proteins with high pI. An unexpected binding at pH 7.5 of anti-FVII Mab with pI < 7.5 was observed on several resins. Efficiency results show the expected trend of higher dependence of the plate height with increasing flow rate of soft resins compared to resins for medium and high-pressure operation. Determination of particle size distribution by two independent methods, Coulter counting and SEM, was in very good agreement. The mono-dispersed nature of Source 30S was confirmed. Binding to cation-exchange resins as a function of ionic strength varies depending on the specific protein. Generally, binding and elution at high salt concentration may be performed with Toyopearl SP 550c and Poros 50 HS, while binding and elution at low salt concentration may be performed with Toyopearl SP 650c. A very high binding capacity was obtained with SP Sepharose XL. Comparison of static capacity and dynamic capacity at 10% break-through shows in general approximately 50-80% utilisation of the total available capacity during chromatographic operation. A general good agreement was obtained between this study and data obtained by others. The results of this study may be used for selection of resins for testing in process development. The validity of experiments and results with model proteins were tested using human insulin precursor in pure state and in real feed-stock on Toyopearl SP 550c, SP Sepharose BB, and Toyopearl SP 650c. Results showed good agreement with experiments with model proteins.     

Simultaneous extraction of tetracycline, macrolide and sulfonamide antibiotics from agricultural soils using pressurised liquid extraction, followed by solid-phase extraction and liquid chromatography-tandem mass spectrometry

The veterinary antibacterial agents chlortetracycline (CTC), oxytetracycline (OTC), sulfadiazine (SDZ), erythromycin (ERY) and tylosin (TYL A, B, C and D) were extracted from soil using pressurized liquid extraction (PLE). Citric acid (pH 4.7) and methanol was used as extraction buffer, followed by tandem-solid-phase extraction (SPE) clean-up (SAX + HLB) for all compounds. For quantification two slightly different methods were employed using LC-MS-MS with MRM detection. The soil extraction method was validated using a loamy sand soil and a sandy soil, representing two typical Danish agricultural soils. Recoveries were 50-80% for the tetracyclines (CTC and OTC) and sulfadiazine (SDZ) and 60-100% for the macrolides (TYL and ERY). Limits of detection for the soil extraction method (LOD(soil)) were 0.6-5.6 microg kg(-1) soil for CTC and OTC, 0.9-2.9 microg kg(-1) soil for SDZ and 2.4-5.5 microg kg(-1) soil for TYL A and ERY. Furthermore, the method was applied to field samples taken from two agricultural fields fertilised with liquid manure containing CTC and TYL A. These results showed a decline in the content of antibacterial agents throughout the sampling period of 155 days from 10 to 15 microg CTC kg(-1) soil and 20-55 microg TYL A kg(-1) soil to below or near the LOD(soil) listed above. Finally, the method was applied to barley grains harvested from the fields. None of the antibacterial agents were measured in grain samples, but recoveries for spiked grain samples were similar to soil recoveries.     

Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.