Ruthenium half-sandwich complexes as protein kinase inhibitors: derivatization of the pyridocarbazole pharmacophore ligand

A general route to ruthenium pyridocarbazole half-sandwich complexes is presented and applied to the synthesis of sixteen new compounds, many of which have modulated protein kinase inhibition properties. For example, the incorporation of a fluorine into the pyridine moiety increases the binding affinity for glycogen synthase kinase 3 by almost one order of magnitude. These data are supplemented with cyclic voltammetry experiments and a protein co-crystallographic study.     

Analysis of oversulfation in a chondroitin sulfate oligosaccharide fraction from bovine aorta by nanoelectrospray ionization quadrupole time-of-flight and fourier-transform ion cyclotron resonance mass spectrometry

A combination of negative ion nano-electrospray ionization Fourier-transform ion cyclotron resonance and quadrupole time-of-flight mass spectrometry was applied to analysis of oversulfation in glycosaminoglycan oligosaccharides of the chondroitin sulfate type from bovine aorta. Taking advantage of the high-resolution and high mass accuracy provided by the FT-ICR instrument, a direct compositional assignment of all species present in the mixture can be obtained. An oligosaccharide fraction containing mainly hexasaccharides exhibited different levels of sulfation, indicated by the presence of species with regular sulfation pattern as well as oversulfated oligosaccharides with one additional sulfate group. Oversulfation can be directly identified from the high-resolution/high mass accuracy FT-ICR mass spectra according to their specific isotopic fine structure. Location of sulfate groups was analyzed by Q-TOF MS and low-energy CID MS/MS. Tetrasulfated hexasaccharides were analyzed by use of collision-induced dissociation at variable collision energy for an unambiguous assignment of the attachment site of the sulfate groups by minimizing unspecific neutral losses. Cleavage of glycosidic bonds gave rise to B- and C-type ions and their respective complementary Y- and Z-type fragment ions.     

Extension of the PS-GVB electronic structure code to transition metal complexes

We have developed a parameterization enabling ab initio electronic structure calculation via the PS-GVB program on transition-metal-containing systems using two standard effective core potential basis sets. Results are compared with Gaussian-92 for a wide range of complexes, and superior performance is demonstrated with regard to computational efficiency for single-point energies and geometry optimization. Additionally, the initial guess strategy in PS-GVB is shown to provide considerably more reliable convergence to the ground state. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1863–1874, 1997     

Effect of mixing on the crystal size distribution of borax decahydrate in a batch cooling crystallizer

The effect of the impeller speed upon the metastable zone width, supersaturation level, crystal growth and the crystal size distribution of borax decahydrate have been investigated to find operating conditions of a batch cooling crystallizer. The importance of impeller speed was studied in baffled stirred crystallizer with a volume of about 2 dm³, equipped with four straight blade turbine (4-SBT) cooling at a constant cooling rate. The metastable zone width was determined by visual method, while concentration changes during the process were monitored in line using ion-selective electrode. The crystal size distribution was determined by optical microscope and sieve analysis respectively. The power consumption measurements were performed for all impeller speeds examined as well. On the basis of the experimental results and observations it is evident that in an agitated batch crystallizer the above mentioned parameters are significantly influenced by hydrodynamic regime in the system determined by impeller used and its revolution speed.     

A new approach to the analysis of nicarbazin and ionophores in eggs by HPLC/MS/MS

An HPLC/MS/MS method has been developed and validated for the quantification and confirmation of nicarbazin and ionophores (lasalocid, monensin, salinomycin, and narasin) in eggs. Nicarbazin is determined in the negative electrospray mode with a basic mobile phase that supports creation of negative ions. Consequently, our ability to maintain instrument sensitivity over time has significantly improved. The analysis of the ionophores is done in the positive electrospray mode using ammonium buffer for HPLC separation. Monitoring ammonium adduct parent ions resulted in enhanced sensitivity and better reproducibility of the ionophore analysis. The validation of this improved HPLC/MS/MS method for the detection of nicarbazin and the ionophores demonstrated excellent precision of below 10% RSD and lower LOD values (microg/kg) for nicarbazin (0.018), lasalocid (0.015), monensin (0.015), salinomycin (0.033), and narasin (0.039).     

Reconstructing Free Energy Profiles from Nonequilibrium Relaxation Trajectories

Reconstructing free energy profiles is an important problem in bimolecular reactions, protein folding or allosteric conformational changes. Nonequilibrium trajectories are readily measured experimentally, but their statistical significance and relation to equilibrium system properties still call for rigorous methods of assessment and interpretation. Here we introduce methods to compute the equilibrium free energy profile of a given variable from a set of short nonequilibrium trajectories, obtained by externally driving a system out of equilibrium and subsequently observing its relaxation. This protocol is not suitable for the Jarzynski equality since the irreversible work on the system is instantaneous. Assuming that the variable of interest satisfies an overdamped Langevin equation, which is frequently used for modeling biomolecular processes, we show that the trajectories sample a nonequilibrium stationary distribution that can be calculated in closed form. This allows for the estimation of the free energy via an inversion procedure that is analogous to that used in equilibrium and bypasses more complicated path integral methods, which we derive for comparison. We generalize the inversion procedure to systems with a diffusion constant that depends on the reaction coordinate, as is the case in protein folding, as well as to protocols in which the trajectories are initiated at random points. Using only a statistical pool of tens of synthetic trajectories, we demonstrate the versatility of these methods by reconstructing double and multi-well potentials, as well as a proposed profile for the hydrophobic collapse of a protein.