Origins of the activity of PAL and LAP enzyme inhibitors: toward ab initio binding affinity prediction

Interaction energies of phenylalanine ammonia-lyase (PAL) active site residues with a series of PAL inhibitors have been partitioned into electrostatic, exchange, delocalization, and correlation components and compared with analogous results obtained previously for leucine aminopeptidase (LAP). In the latter metalloenzyme, either of the two charged residues controls entirely relative inhibitor binding energies, while at least four residues are required to determine ligand relative stabilization in neutral PAL. Significant correlation with experimental inhibitory activity was found between the stabilization energy at gradually decreasing levels of theory (MP2, SCF) down to the first-order Heitler-London term. Contrary to the LAP case, where the electrostatic term was sufficient to reproduce experimentally observed trends, in the case of PAL, exchange repulsion effects also have to be considered. Computational protocol presented herein constitutes a promising way to incorporate the first principle calculation's accuracy into the process of rational binding affinity prediction, revealing the physical nature of the interactions, where successive approximations can be introduced in a systematic and justifiable manner.     

Nickel foam-based composite electrodes for electrooxidation of methanol

Nickel foam and five nickel foam-based composite electrodes were prepared for being used as anode materials for the electrooxidation of methanol in KOH solution containing 0.1 and 1.0 M of methanol. The layered electrodes composed of nickel foam, platinum nanoparticles, polyaniline (PANI) and/or porous carbon (C) prepared in various assemblies. As shown by SEM analysis, depending on the preparation conditions, the electrodes of different morphologies were obtained. Using the cyclic voltammetry method, the oxidation of methanol on nickel foam electrode was observed in the potential range 0.4 V ↔ 0.7 V, where the Ni(OH)₂/NiOOH transformation occurred. The presence of Pt particles in electrode gave rise to the increase in electrocatalytic activity in this potential range. For electrodes containing dispersed platinum catalyst (Ni/Pt, Ni/PANI/Pt and Ni/C/Pt), the oxidation of methanol was noted also in the potential range −0.5 V ↔ 0.1 V. The electrocatalytic activities of the examined electrodes toward methanol oxidation at low potentials were in order Ni/Pt > Ni/C/Pt > Ni/PANI/Pt, whereas at high potentials in order Ni/PANI/Pt > Ni/Pt> Ni/C/Pt > Ni. Among the examined electrodes, the most resistant to cyclic poisoning appeared to be the Ni/C/Pt electrode. Presented at the 4Th Baltic Conference on Electrochemistry, Greifswald, March 13–16, 2005     

Compact multipolar representation of the electrostatic potential for flexible molecules

A new method for generating a compact multipolar representation of the electrostatic potential (EP) for flexible molecules is presented. The method is based on a constrained minimization of the difference between the quantum mechanical and the classical EP. The fitting procedure used adopts the least absolute shrinkage and selection operator technique [R. Tibshirani, J. Roy. Stat. Soc. B 58, 267 (1996)] which can be seen as penalized ordinary least squares. The penalty function optimized for the particular molecule of interest effectively removes redundant multipoles. It is shown that the use of multiple conformations is crucial for the predictive ability of the EP model for flexible molecules. The multipole local coordinate systems are chosen in a way that best reflects the key conformational changes. It was demonstrated that such an approach improves the predictive ability of EP models. It also allows to exploit equivalence of atoms in the calculation of multipoles components. In the case of polar flexible molecules, the augmentation of the EP model based on charges by higher multipoles decreases the relative root mean square error by a factor of 1.5-5. The corresponding effect of enlargement of the set of multipoles was significantly reduced.     

Primary and secondary relaxations in bis-5-hydroxypentylphthalate revisited

The molecular structure of bis-5-hydroxypentylphthalate (BHPP) is like dihexyl phthalate but having appended to it two hydroxyl end groups, which contribute additional dipole moments and capacity for hydrogen-bond formation. In a previously published dielectric study of the primary and secondary relaxations of BHPP, it was found that all the dynamic properties are normal except for the anomalously large width of the primary relaxation loss peak. There are two secondary relaxations, the relaxation time of the slower one increases with increasing pressure, whereas that of the faster one is practically insensitive to pressure. Hence, the slower secondary relaxation is the "universal" Johari-Goldstein (JG) [J. Chem. Phys. 53, 2372 (1970); 55, 4245 (1971)] relaxation in BHPP. All is well except if the observed large width of the primary relaxation were an indication of a corresponding large coupling parameter n=0.45 in the coupling model. Then the predicted relations between the primary relaxation time tau(alpha) and the JG relaxation time tau(JG) found previously to hold in many glass formers would be violated. It was recognized that this singular behavior of BHPP is likely due to broadening of the primary loss peak by the overlapping contributions of two independent dipole moments present in BHPP, and the actual coupling parameter is smaller. However, at the time of publication of the previous work there were not enough data to support this explanation. By making broadband dielectric measurements of dibutyl phthalate (DBP) and dioctyl phthalate (DOP) that have chemical structures closely related to BHPP but with only one dipole moment, we show that all their dynamic properties are almost the same as BHPP but the widths of their primary relaxation loss peaks are significantly narrower corresponding to a smaller coupling parameter n=0.34. The new data presented here indicate that the coupling parameter of BHPP is about the same as DBP and DOP, and the predicted relations between tau(alpha) and tau(JG) of BHPP are brought back in agreement with the experimental data.     

Interactions of porphyrin covalently attached to poly(methacrylic acid) with liposomal membranes

The interactions between the 5-(4-acryloyloxyphenyl)-10,15,20-tritolylporphyrin covalently attached to poly(methacrylic acid) chain (PMA-Po) and phosphatidylcholine liposomes in aqueous solution at different pH values were studied. The binding constants (K(b)) for the liposome- PMA-Po in solutions in the pH range from 6.5 to 9.2 were determined using fluorescence spectroscopy. The binding was found to be efficient. The acid-base properties of the porphyrin chromophores were also studied. Both pK values associated with imine-N protonation of the porphyrin core were found to be 6.4. The quantum yield (Phi(Delta)) of singlet oxygen production by Po in the lipid-PMA-Po system was found to be high (0.88 +/- 0.05).     

Spectrophotometric determination of dopamine in microliter scale using microfluidic system based on polymeric technology

In this paper we report two simple and sensitive spectrophotometric procedures for the determination of dopamine in microfluidic system based on poly(dimethylsiloxane) (PDMS) technology and comparison of their interference-susceptibility. The analytical reactions and measurements were carried out at ambient temperature in a microreactor of total volume 6 μl coupled with a spectrophotometric flow-through cuvette.     

Application of a retention database to the identification of individual polychlorinated biphenyl congeners in Aroclors mixture using selected polychlorinated biphenyls as a reference series

The database of the relative retention times (RRTs) of polychlorinated biphenyls (PCBs) reported in literature was used to calculate the retention indices (RIs) of all 209 PCB congeners on temperature programmed capillary column Rtx-5. Calculation of retention indices was based on reference series of seven congeners (PCB IUPAC Nos. 18, 52, 101, 143, 185, 203 and 206) that exhibit linear relative retention time behaviour as a function of chlorine number. The calculated indices were compared to those determined in our laboratory as well as to those obtained by other authors. The proposed indices system was applied for identification individual congeners in mixture of Aroclors 1242:1254:1260, using only reference series of PCBs.     

Cadmium speciation in Arabidopsis thaliana as a strategy to study metal accumulation system in plants

The strategy to identify cadmium deactivation mechanism in Arabidopsis thaliana has been developed using selective and sensitive hyphenated techniques. Cadmium concentrations, in main parts of the plant, were determined by ICP-MS and total amount was found as 0.43-0.44 μg g⁻¹ in leaves and 3.3-3.4 μg g⁻¹ in roots. Speciation of the metal complexes in cells was investigated by SEC-ICP-MS in order to estimate the accumulation process. Phytochelatins, desglycyl-phytochelatins and phytochelatins homologues lacking the N-terminal γ-linked glutamic acid were extracted from plant and were identified by RPLC-ESI-MS. Two-dimensional chromatography allowed to link the metal complexes separated by SEC with isoforms of phytochelatins analyzed by high resolution RPLC and confirm their significant responsibility for metal accumulation. The potential of the cadmium complexes speciation indicates that obtained results could be reliable source of knowledge to confirm the information coming from the well-known genomic sequence of Arabidopsis and to estimate the role of γ-glutamyl transpeptidase in metabolism of glutathione.     

Rhodium(I) complexes with 1′-(diphenylphosphino)ferrocenecarboxylic acid as active and recyclable catalysts for 1-hexene hydroformylation

The rhodium complex trans-[Rh(CO)(Hdpf-κP)(dpf-κ²O,P)] (1), (Hdpf = 1′-(diphenylphosphino)ferrocenecarboxylic acid) was used as an efficient and recyclable catalyst for 1-hexene hydroformylation producing ca. 80% of aldehydes at 10 atm CO/H₂ and 80 °C. After the reaction, unchanged complex 1 was separated from the reaction mixture and used again three times with the same catalytic activity. The effect of modifying ligands, phosphines and phosphites, on the reactivity of 1 was investigated. The active catalytic systems containing 1 or trans-[Rh(CO)(L)(dpf-κ²O,P)] (2) were formed in situ from acetylacetonato rhodium(I) precursors [Rh(CO)₂(acac)] (3) or [RhL(CO)(acac)] (4) and Hdpf or Medpf (L = phosphine, Medpf = methyl ester of Hdpf).     

Hidden minima of the gibbs free energy revealed in a phase separation in polymer/surfactant/water mixture

We observed a very unusual kinetic pathway in a separating C(12)E(6)/PEG/H(2)O ternary mixture. We let the mixture separate above the spinodal temperature (cloud point temperature) for some time and next cool it into a metastable region of a phase diagram, characterized by two minima of the Gibbs potential, one corresponding to the homogeneous mixture and one to the fully separated PEG-rich and C(12)E(6)-rich phases. Despite the fact that in the metastable region the thermodynamic equilibrium corresponds to the separated phases (global minimum of the Gibbs free energy), we observe perfect mixing of the initially separated phase. The homogeneous state, obtained in this way, does not separate, if left undisturbed. However, many cooling-heating cycles or full separation with visible meniscus above the cloud point temperature induce the phase separation in the metastable region. The metastable region can exist tens of degrees below the cloud point temperature. This effect is not observed in the binary mixture of C(12)E(6)/H(2)O.