pH effect on the photochemistry of 4-methylcoumarin phosphate esters: caged-phosphate case study

There are numerous reports of coumarin ester derivatives, in particular phosphate esters, as photocleavable cages in biological systems. Despite the comprehensive analysis of the photocleavage mechanism, studies of 4-methylcoumarin caged phosphates and/or nucleotides were always performed at constant pH. In this work, we present the study of the pH effect on the photochemistry of (7-diethylaminocoumarin-4-yl)methyl phosphate (DEACM-P). Fluorescence and photocleavage quantum yields, as well as the fluorescence decay times were measured as a function of the pH. It was found that the pH produces significant changes in the overall photochemical quantum yield of DEACM-P, and the observed changes are complementary to those obtained from the fluorescence quantum yield. Deprotonation of DEACM-HPO(4)(-) to yield DEACM-PO(4)(2-), produces a decrease in the photochemical quantum yield (from 0.0045 to 0.0003) and an increase in the fluorescence quantum yield (from 0.072 to 0.092). Moreover, from the analysis of the decay times, we have also found that hydroxyl ion is not only relevant, but it is mechanistically involved in the photoreaction of DEACM-HPO(4)(-).     

Poly{guanidinium} salts: application in the preparation of a coordinatively saturated aluminium cation

Protonation of the linked bis(guanidine), H(2)C{hpp}(2), affords isolated guanidinium salts that have been used to prepare a coordinatively saturated aluminium cation.     

A universal temperature controlled membrane interface for the analysis of volatile and semi-volatile organic compounds

A universal temperature controlled membrane interface (TCMI) has been constructed for hollow-fibre membranes. The membrane temperature is controllable in the range -70 to 250 degrees C using an electric heater and a flow of cooled nitrogen or helium gas. Volatile and semi-volatile organic compounds may be detected either by continuous diffusion across the membrane or by in-membrane pre-concentration followed by thermal desorption into the detector. The TCMI interface is demonstrated in combination with mass spectrometry and GC-MS, for the determination of VOCs and SVOCs in aqueous and air samples and for the on-line monitoring of a bioreactor.     

Surface tensions of imidazolium based ionic liquids: anion, cation, temperature and water effect

This work addresses the experimental measurements of the surface tension of eight imidazolium based ionic liquids (ILs) and their dependence with the temperature (288-353 K) and water content. The set of selected ionic liquids was chosen to provide a comprehensive study of the influence of the cation alkyl chain length, the number of cation substitutions and the anion on the properties under study. The influence of water content in the surface tension was studied for several ILs as a function of the temperature as well as a function of water mole fraction, for the most hydrophobic IL investigated, [omim][PF(6)], and one of the more hygroscopic IL, [bmim][PF(6)]. The surface thermodynamic functions such as surface entropy and enthalpy were derived from the temperature dependence of the surface tension values.     

A new approach for separating low-molecular-weight RNA molecules by staircase electrophoresis in non-sequencing gels

Low-molecular-weight (LMW) RNA profiles, which include ribosomal and transfer RNA molecules with similar small sizes, are molecular signatures of microorganisms with a great potential in microbial identification. The greatest resolution of these profiles was achieved by staircase electrophoresis in sequencing gels. Nevertheless, this technique is difficult to use because it takes 7 h, the gels have large sizes and it is necessary to heat the system and to recycle the buffer to maintain the denaturing conditions and avoid smile effects. Most available sequencing slabs have no internal temperature control or homogenizing devices, which by contrast are present in some newly designed non-sequencing slabs. Nevertheless, these slabs present two important problems for separating LMW RNA molecules, the size of gels is only 20 cm (instead of 40 cm) and the maximum voltage that can be reached is only 840 V (instead 2400 V). Staircase electrophoresis follows a model in which the external polarization is incrementally modified with a constant time step value. In the present work, we experimentally confirmed that by reducing the time step and increasing the total number of steps a suitable resolution is achieved. Under these conditions, despite the smaller size of the gels and the lower values of the electric field, the intensity reaches higher values than in sequencing gels and the LMW RNA profiles are correctly separated in 5 h. The resolution of these profiles obtained in non-sequencing gels is similar to that obtained in sequencing ones facilitating the analysis of large populations of microorganisms in any laboratory.     

Development of an empirical force field for silica. Application to the quartz-water interface

Interactions of pulverized crystalline silica with biological systems, including the lungs, cause cell damage, inflammation, and apoptosis. To allow computational atomistic modeling of these pathogenic processes, including interactions between silica surfaces and biological molecules, new parameters for quartz, compatible with the CHARMM empirical force field were developed. Parameters were optimized to reproduce the experimental geometry of alpha-quartz, ab initio vibrational spectra, and interactions between model compounds and water. The newly developed force field was used to study interactions of water with two singular surfaces of alpha-quartz, (011) and (100). Properties monitored and analyzed include the variation of the density of water molecules in the plane perpendicular to the surface, disruption of the water H-bond network upon adsorption, and space-time correlations of water oxygen atoms in terms of Van Hove self-correlation functions. The vibrational density of states spectra of water in confined compartments were also computed and compared with experimental neutron-scattering results. Both the attenuation and shifting to higher frequencies of the hindered translational peaks upon confinement are clearly reproduced by the model. However, an upshift of librational peaks under the conditions of model confinement still remains underrepresented at the current empirical level.     

A Comparison of Modeling Approaches for Dispersion Homopolymerization of MMA and Styrene in Supercritical CO2

A comparison of kinetic models for dispersion polymerization of MMA and styrene in supercritical CO₂ is presented. The limiting case of solution polymerization, as a simplified case, was also addressed. Calculation of the partition of components between the continuous and dispersed phases was emphasized. Experimental data for the solution and dispersion polymerizations of styrene and MMA, using different types of stabilizers, were used to guide the study. Although all the models analyzed can be considered as “adequate” in representing the behavior of the system, some of their strengths and drawbacks have been highlighted.

     

Reaction mechanism of the vitamin K-dependent glutamate carboxylase: a computational study

In the reaction cycle of glutamate carboxylase, vitamin K epoxidation by O2 has been proposed to generate a very strong base able to remove a proton from the gamma carbon of a Glu residue, thus yielding a Glu-based carbanion that readily reacts with CO2. We have used hybrid density functional theory to study this appealing mechanism. Our calculations show a very exergonic four-step mechanism with the reaction of (triplet) O2 with the singlet vitamin K anion as the rate-limiting step, with a rate similar to the experimental value. Our study also establishes the need to apply continuum models when performing the optimization of minimum-energy crossing points between potential energy surfaces of different multiplicities for enzyme model systems.     

Removal of envelope protein-free retroviral vectors by anion-exchange chromatography to improve product quality

We have investigated the role of the retroviral lipid bilayer and envelope proteins in the adsorption of retroviral vectors (RVs) to a Fractogel DEAE matrix. Intact RVs and their degradation components (envelope protein-free vectors and solubilized vector components) were adsorbed to this matrix and eluted using a linear gradient. Envelope protein-free RVs (Env(-)) and soluble envelope proteins (gp70) eluted in a significantly lower range of conductivities than intact RVs (Env(+)) (13.7-30 mS/cm for Env(-) and gp70 proteins vs. 47-80 mS/cm for Env(+)). The zeta (zeta)-potential of Env(+) and Env(-) vectors was evaluated showing that envelope proteins define the pI of the viral particles (pI (Env(+)) < 2 versus 3 < pI (Env(-)) < 4) and that Env(+) and Env(-) vectors have similar zeta-potentials within pH 5 and 8. The results presented herein indicate that the adsorption of retroviral particles occurs through multi-point interaction of the envelope proteins with the cationic groups on the chromatographic matrix. The strength of this adsorption is thus dependent on the amount of envelope protein present in the viral lipid bilayer. In conclusion, AEXc enables the separation of gp70 proteins as well as envelope protein-free vectors constituting a significant improvement to the quality of retroviral preparations for gene therapy applications.     

Methoxycarbonylation of olefins catalyzed by palladium complexes bearing P,N-donor ligands

The methoxycarbonylation of alkenes catalyzed by palladium(II) complexes with P,N-donor ligands, 2-(diphenylphosphinoamino)pyridine (Ph2PNHpy), 2-[(diphenylphosphino)methyl]pyridine (Ph2PCH2py), and 2-(diphenylphosphino)quinoline (Ph2Pqn) has been investigated. The results show that the complex [PdCl(PPh3)(Ph2PNHpy)]Cl or an equimolar mixture of [PdCl2(Ph2PNHpy)] and PPh3, in the presence of p-toluensulfonic acid (TsOH), is an efficient catalyst for this reaction. This catalytic system promotes the conversion of styrene into methyl 2-phenylpropanoate and methyl 3-phenylpropanoate with nearly complete chemoselectivity, 98% regioselectivity in the branched isomer, and high turnover frequency, even at alkene/Pd molar ratios of 1000. Best results were obtained in toluene-MeOH (3 : 1) solvent. The Pd/Ph2PNHpy catalyst is also efficient in the methoxycarbonylation of cyclohexene and 1-hexene, although with lower rates than with styrene. Related palladium complexes [PdCl(PPh3)L]Cl (L = Ph2PCH2py and Ph2Pqn) show lower activity in the methoxycarbonylation of styrene than that of the 2-(diphenylphosphinoamino)pyridine ligand. Replacement of the last ligand by (diphenylphosphino)phenylamine (Ph2PNHPh) or 2-(diphenylphosphinoaminomethyl)pyridine (Ph2PNMepy) also reduces significantly the activity of the catalyst, indicating that both the presence of the pyridine fragment as well as the NH group, are required to achieve a high performing catalyst. Isotopic labeling experiments using MeOD are consistent with a hydride mechanism for the [PdCl(PPh3)(Ph2PNHpy)]Cl catalyst.