Refining details of the structural and electronic properties of the CuB site in pMMO enzyme through sequential molecular dynamics/CPKS-EPR calculations.

This work investigated the structural and electronic properties of the copper mononuclear site of the PmoB part of the pMMO enzyme at the molecular level. We propose that the CuB catalytic site in the soluble portion of pMMO at room temperature and under physiological conditions is a mononuclear copper complex in a distorted octahedral arrangement with the residues His33, His137, and His139 on the equatorial base and two water molecules on the axial axis. Our view was based on the molecular dynamics results and DFT calculations of the electronic paramagnetic resonance parameters and comparisons with experimental EPR data. This new proposed model for the CuB site brings additional support concerning the recent experimental evidence, which pointed out that a saturated coordination sphere of the copper ion in the CuB center is an essential factor that makes it less efficient than the CuC site in the methane oxidation. Therefore, according to the CuB site model proposed here, an additional step involving a displacement of at least one water molecule of the copper coordination sphere by the O2 molecule prior to its activation must be necessary. This scenario is less likely to occur in the CuC center once this one is buried in the alpha-helices, which are part of the pMMO structure bound to the membrane wall, and consequently located in a less solvent-exposed region. In addition, we also present a simple and efficient sequential S-MD/CPKS protocol to compute EPR parameters that can, in principle, be expanded for the study of other copper-containing proteins.

A "turn-off" fluorescent sensor based on electrospun polycaprolactone nanofibers and fluorene(bisthiophene) derivative for nitroaromatic explosive detection.

The preparation of fluorene(bisthiophene)-based fluorescent nanofibers for nitroaromatic explosive detection provides a convenient rapid and low-cost strategy aiming at forensic applications. Polycaprolactone (PCL) and fluorene(bisthiophene) derivative (FBT) nanofibers were obtained by electrospinning technique as a free-standing mat and characterized by SEM, FTIR, thermal analysis and fluorescence spectroscopy. The PCL/FBT nanofibers presented high sensitivity towards 2,4,6-trinitrotoluene (TNT) and picric acid (PA), with fluorescence quenching (turn-off mechanism), and selectivity to another kind of explosives. The free-standing mats were used as a cloth strip that was swiped on surfaces contaminated with TNT traces allowing its visual detection under UV light source. These findings are particularly important for the development of a facile and promising strategy to assembly portable optical devices for nitroaromatic explosive detection.

Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi.

Four chemotypes of the rough lipopolysaccharides (LPS) membrane from Pseudomonas aeruginosa were investigated by a combined approach of explicit water molecular dynamics (MD) simulations and Poisson-Boltzmann continuum electrostatics with the goal to deliver the distribution of the electrostatic potential across the membrane. For the purpose of this investigation, a new tool for modeling the electrostatic potential profile along the axis normal to the membrane, MEMbrane POTential (MEMPOT), was developed and implemented in DelPhi. Applying MEMPOT on the snapshots obtained by MD simulations, two observations were made: (a) the average electrostatic potential has a complex profile but is mostly positive inside the membrane due to the presence of Ca(2+) ions, which overcompensate for the negative potential created by lipid phosphate groups; and (b) correct modeling of the electrostatic potential profile across the membrane requires taking into account the water phase, while neglecting it (vacuum calculations) results in dramatic changes including a reversal of the sign of the potential inside the membrane. Furthermore, using DelPhi to assign different dielectric constants for different regions of the LPS membranes, it was investigated whether a single frame structure before MD simulations with appropriate dielectric constants for the lipid tails, inner, and the external leaflet regions, can deliver the same average electrostatic potential distribution as obtained from the MD-generated ensemble of structures. Indeed, this can be attained by using smaller dielectric constant for the tail and inner leaflet regions (mostly hydrophobic) than for the external leaflet region (hydrophilic) and the optimal dielectric constant values are chemotype-specific.

Outer Membrane Remodeling: The Structural Dynamics and Electrostatics of Rough Lipopolysaccharide Chemotypes.

Lipopolysaccharides (LPS) are the primary constituent of the outer membrane of Gram-negative bacteria such as Pseudomonas aeruginosa. Gram-negative bacteria can synthesize modified forms of LPS in response to environmental stimuli or due to genetic mutations, a process known as outer membrane remodeling. Chemical modifications of the LPS modulate the integrity and antibiotic susceptibility of bacterial outer membranes. It also governs microbial adhesion to tissues and artificial material surfaces. We have extended a previous model of the rough LPS to include four novel chemotypes rmlC, galU, LPS Re, and Lipid-A. Atomistic molecular dynamics (MD) simulations were performed for outer membrane models constituted of each LPS chemotypes and 1,2-dipalmitoyl-3-phosphatidylethanolamine. It is shown that the decrease in the LPS polysaccharide chain length leads to a significant increase in the diffusion coefficients for the Ca(2+) counterions, increase in acyl chain packing (decrease in membrane fluidity), and attenuation of the negative potential across the LPS surface as positive counterions becomes more exposed to the solvent. The electrostatic potential on the LPS surfaces reflects heterogeneous charge distributions with increasingly larger patches of positive and negative potentials as the polysaccharide chain length decreases. Such a pattern originates from the spatial arrangement of charged phosphate-Ca(2+) clusters in the LPS inner-core that becomes exposed in the membrane surface as monosaccharide units are lost in the shortest chemotypes LPS Re and Lipid-A. These MD-derived conformational ensembles reproduce experimental trends and provide atom-level structural information on the rough LPS chemotypes that can help to rationalize antibiotic resistance and bacterial adhesion processes.

Pyridine-derived thiosemicarbazones and their tin(IV) complexes with antifungal activity against Candida spp.

[(n-Bu)Sn(2Ac4oClPh)Cl2] (1), [(n-Bu)Sn(2Ac4oFPh)Cl2] (2), [(n-Bu)Sn(2Ac4oNO2Ph)Cl2] (3), [(n-Bu)Sn(2Bz4oClPh)Cl2] (4), [(n-Bu)Sn(2Bz4oFPh)Cl2] (5) and [(n-Bu)Sn(2Bz4oNO2Ph)Cl2] (6) were obtained by reacting [(n-Bu)SnCl3] with 2-acetylpyridine-N4-orthochlorophenyl thiosemicarbazone (H2Ac4oClPh), 2-acetylpyridine-N4-orthofluorphenyl thiosemicarbazone (H2Ac4oFPh), 2-acetylpyridine-N4-orthonitrophenyl thiosemicarbazone (H2Ac4oNO2Ph), and with the corresponding 2-benzoylpyridine-derived thiosemicarbazones (H2Bz4oClPh, H2ABz4oFPh and H2Bz4oNO2Ph). The antifungal activity of the studied compounds was evaluated against several Candida species. Upon coordination of H2Bz4oNO2Ph to tin in complex (6) the antifungal activity increased three times against Candida albicans and Candida krusei and six times against Candida glabrata and Candida parapsilosis. The minimum inhibitory concentration (MIC) values of H2Ac4oNO2Ph and its complex (3) against C. albicans, C. parapsilosis and C. glabrata are similar to that of fluconazole. All studied compounds were more active than fluconazole against C. krusei.

DFT study of the full catalytic cycle for the propene hydroformylation catalyzed by a heterobimetallic HPt(SnCl3)(PH3)2 model catalyst.

DFT calculations were carried out to study the full catalytic cycle for the hydroformylation of propene, catalyzed by the heterobimetallic model catalyst trans-Pt(H)(PH(3))(2)(SnCl(3)). Before the study of the full catalytic cycle, the performance of six pure GGA, one GGA with inclusion of dispersion corrections, four hybrid-GGA, and three meta-GGA exchange correlation functional to describe a model reaction promoted by Pt-Sn catalyst were assessed. It is shown that the BP86 and GPW91 functionals, using extended basis set, provides reliable energetic results when compared with the CCSD(T) calculations. All intermediates and transition states along the elementary steps of the entire catalytic cycle were located and the energies involved in the catalytic cycle calculated using BP86 functional. The solvent effects along the entire catalytic cycle were evaluated using the polarizable continuum model. In contrast with the rhodium catalysts, the regioselectivity of the hydroformylation is set at the carbonylation step. The hydrogenolysis is the rate determining step of the entire cycle, with the activation energy of approximately 21 kcal mol(-1) in agreement with the experimental value of approximately 25 kcal mol(-1). The trans effect of the SnCl(3)(-) ligand seems to be pronounced only in the first step of the catalytic cycle, facilitating the insertion of the olefin into the Pt-H bond trans to it. The analysis of the stationary points obtained along each elementary step of the catalytic cycle is carried out separately and discussed. The BP86/cc-pVTZ/SBKJC results shows that the pathway leading to the linear aldehyde is preferred, being in agreement with the experimental findings.