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.     

Can triorganoboroxins exist in a “monomeric” R---B=O form? MNDO calculations and ebulliometric molecular weight determination

MNDO calculations were made for triethylboroxin (EtBO)₃ and triphenylboroxin (PhBO)₃ using both X-ray determined and optimized geometry of these molecules. The results were compared with hypothetical “monomeric” molecules R---B=O. Calculated energies of trimerization are about −200 kJ mol⁻¹ for both compounds and confirm the much higher stability of the “trimer”. Ebulliometric determination of molecular weight of triphenylboroxin in 2-pentanone confirms its trimeric character.     

Dispersive solid-phase extraction for the determination of sulfonamides in chicken muscle by liquid chromatography

A new, fast and low-cost sample preparation for the determination of sulfonamide (SA) residues in chicken muscle by LC technique has been developed. The procedure involves single extraction of sample with acetonitrile, followed by a rapid clean-up and was called "dispersive solid-phase extraction" (dispersive SPE). Using dispersive SPE 25 mg of octadecyl sorbent was added to 1 ml of acetonitrile extract, mixed and centrifuged. The acetonitrile layer was evaporated and residue was dissolved in acetate buffer (pH 3.5). Analysed compounds were detected by fluorescence detector after pre-column derivatization with fluorescamine. The separation of analytes was performed with gradient elution with mobile phase methanol: 2% acetic acid and RP-LC analytical column. The whole procedure was evaluated for six sulfonamides (sulfadiazine, sulfamerazine, sulfamethazine, sulfametoxypirydazine, sulfametoxazole and sulfadimetoxine) according to the European Commission Decision 2002/657/EC. Specificity, decision limit (CCalpha), detection capacity (CCbeta), trueness and precision were determined during validation process. The dispersive SPE with octadecyl sorbent was found suitable for sample preparation before sulfonamide determination in chicken muscle. As it was found the most of endogenous matrix components were removed and the analytes were isolated from spiked samples with recoveries above 90%. The used analytical conditions allow to successively separate all the tested sulfonamides with the limit of detection at the level of 1-5 microg/kg. The method is simple, rapid and more effective than conventional methods.     

Discrete dynamical equations in Minkowski space

Discrete difference equations in Minkowski space are obtained and the discrete Minkowski force is shown to be a four-vector. A transformation from a discrete dynamical equation in Minkowski space to a Lorentz-invariant difference equation in one-dimensional space is given.     

Photophysics of eumelanin: ab initio studies on the electronic spectroscopy and photochemistry of 5,6-dihydroxyindole.

Excited-state reaction paths and energy profiles of 5,6-dihydroxyindole (DHI), one of the elementary building blocks of eumelanin, have been determined with the approximated singles-and-doubles coupled-cluster (CC2) method. 6-Hydroxy-4-dihydro-indol-5-one (HHI) is identified as a photochromic species, which is formed via nonadiabatic hydrogen migration from the dangling OH group of DHI to the neighboring carbon atom of the six-membered ring. It is shown that HHI is a typical excited-state hydrogen-transfer (ESIHT) system. HHI absorbs strongly in the visible range of the spectrum. A barrierless hydrogen transfer in the (1)pipi* excited state, followed by barrierless torsion of the hydroxyl group, lead to a low-lying S(1)-S(0) conical intersection and thus to ultrafast internal conversion. This very efficient mechanism of excited-state deactivation provides HHI with a high degree of intrinsic photostability. It is suggested that the metastable photochemical product HHI plays an essential role for the photoprotective biological function of eumelanin.     

Time-dependent quantum wave-packet description of the 1pi sigma* photochemistry of phenol

The photoinduced hydrogen elimination reaction in phenol via the conical intersections of the dissociative 1pi sigma* state with the 1pi pi* state and the electronic ground state has been investigated by time-dependent quantum wave-packet calculations. A model including three intersecting electronic potential-energy surfaces (S0, 1pi sigma*, and 1pi pi*) and two nuclear degrees of freedom (OH stretching and OH torsion) has been constructed on the basis of accurate ab initio multireference electronic-structure data. The electronic population transfer processes at the conical intersections, the branching ratio between the two dissociation channels, and their dependence on the initial vibrational levels have been investigated by photoexciting phenol from different vibrational levels of its ground electronic state. The nonadiabatic transitions between the excited states and the ground state occur on a time scale of a few tens of femtoseconds if the 1pi pi*-1pi sigma* conical intersection is directly accessible, which requires the excitation of at least one quantum of the OH stretching mode in the 1pi pi* state. It is shown that the node structure, which is imposed on the nuclear wave packet by the initial preparation as well as by the transition through the first conical intersection (1pi pi*-1pi sigma*), has a profound effect on the nonadiabatic dynamics at the second conical intersection (1pi sigma*-S0). These findings suggest that laser control of the photodissociation of phenol via IR mode-specific excitation of vibrational levels in the electronic ground state should be possible.     

Some remarks on equilibrium state in dynamic condition

For dehydration of CaC₂O₄·H₂O and thermal dissociation of CaCO₃ carried out in Mettler Toledo TGA/SDTA-851^e/STAR^e thermobalance similar experimental conditions was applied: 9–10 heating rates, q = 0.2, 0.5, 1, 2, 3, 6, 12, 24, 30, and 36 K min⁻¹, for sample mass 10 mg, in nitrogen atmosphere (100 ml min⁻¹) and in Al₂O₃ crucibles (70 μl). There were analyzed changes of typical TGA quantities, i.e., T, TG and DTG in the form of the relative rate of reaction/process intended to be analyzed on-line by formula (10). For comparative purposes, the relationship between experimental and equilibrium conversion degrees was used (for P = P^\ominus P = P^{{\ominus}} ). It was found that the solid phase decomposition proceeds in quasi-equilibrium state and enthalpy of reaction is easily “obscured” by activation energy. For small stoichiometric coefficients on gas phase side (here: ν = 1) discussed decomposition processes have typical features of phenomena analyzable by known thermokinetic methods.     

The combi-CLEA approach: enzymatic cascade synthesis of enantiomerically pure (S)-mandelic acid

Enantiomerically pure (S)-mandelic acid was synthesised from benzaldehyde by sequential hydrocyanation and hydrolysis in a bienzymatic cascade at starting concentrations up to 0.25 M. A cross-linked enzyme aggregate (CLEA) composed of the (S)-selective oxynitrilase from Manihot esculenta and the non-selective nitrilase from Pseudomonas fluorescens EBC 191 was employed as the biocatalyst. The nitrilase produces approx. equal amounts of (S)-mandelic acid and (S)-mandelic amide from (S)-mandelonitrile under standard conditions, but we surprisingly found that high (up to 0.5 M) concentrations of HCN induced a marked drift towards amide production. By including the amidase from Rhodococcus erythopolis in the CLEA we obtained (S)-mandelic acid as the sole product in 90% yield and >99% enantiomeric purity.