Modeling solvent effects on electron-spin-resonance hyperfine couplings by frozen-density embedding

In this study, we investigate the performance of the frozen-density embedding scheme within density-functional theory [J. Phys. Chem. 97, 8050 (1993)] to model the solvent effects on the electron-spin-resonance hyperfine coupling constants (hfcc's) of the H2NO molecule. The hfcc's for this molecule depend critically on the out-of-plane bending angle of the NO bond from the molecular plane. Therefore, solvent effects can have an influence on both the electronic structure for a given configuration of solute and solvent molecules and on the probability for different solute (plus solvent) structures compared to the gas phase. For an accurate modeling of dynamic effects in solution, we employ the Car-Parrinello molecular-dynamics (CPMD) approach. A first-principles-based Monte Carlo scheme is used for the gas-phase simulation, in order to avoid problems in the thermal equilibration for this small molecule. Calculations of small H2NO-water clusters show that microsolvation effects of water molecules due to hydrogen bonding can be reproduced by frozen-density embedding calculations. Even simple sum-of-molecular-densities approaches for the frozen density lead to good results. This allows us to include also bulk solvent effects by performing frozen-density calculations with many explicit water molecules for snapshots from the CPMD simulation. The electronic effect of the solvent at a given structure is reproduced by the frozen-density embedding. Dynamic structural effects in solution are found to be similar to the gas phase. But the small differences in the average structures still induce significant changes in the computed shifts due to the strong dependence of the hyperfine coupling constants on the out-of-plane bending angle.     

The intermediacy of metathiophosphonate PhPSO in the reaction of N-tert-butyl-P-phenylphosphonamidothioic acid with alcohols

Kinetic studies of the reaction of N-tert-butyl-P-phenylphosphonamidothioic acid (1) with alcohols were carried out in CH2Cl2 by means of 31P NMR spectrometry. The reaction is of the first order with respect to thio acid 1. The first-order rate constant at 30 degrees C increases with increasing methanol concentration below 0.25 M, but otherwise the rate constants are either independent of alcohol concentration (MeOH above 0.25 M, BuOH) or decrease with increasing alcohol concentration (i-PrOH, t-BuOH). The effect of alcohols on the order of the reaction and parameters of activation, as well as results of competition experiments, lead us to the conclusion that reaction of 1 with alcohols occurs by an elimination-addition mechanism involving the association of the thio acid 1 and the alcohol and then formation in the rate-determining step of an encounter complex 2' ' involving metathiophosphonate 4, amine, and alcohol. Metathiophosphonate 4 reacts preferentially with the alcohol as the encounter complex (primary alcohols) or after diffusion apart as a "free" intermediate (hindered alcohols).     

Thermal decomposition of HO2NO2 (peroxynitric acid, PNA): rate coefficient and determination of the enthalpy of formation

Rate coefficients for the gas-phase thermal decomposition of HO(2)NO(2) (peroxynitric acid, PNA) are reported at temperatures between 331 and 350 K at total pressures of 25 and 50 Torr of N(2). Rate coefficients were determined by measuring the steady-state OH concentration in a mixture of known concentrations of HO(2)NO(2) and NO. The measured thermal decomposition rate coefficients k(-)(1)(T,P) are used in combination with previously published rate coefficient data for the HO(2)NO(2) formation reaction to yield a standard enthalpy for reaction 1 of Delta(r)H degrees (298K) = -24.0 +/- 0.5 kcal mol(-1) (uncertainties are 2sigma values and include estimated systematic errors). A HO(2)NO(2) standard heat of formation, Delta(f)H degrees (298K)(HO(2)NO(2)), of -12.6 +/- 1.0 kcal mol(-1) was calculated from this value. Some of the previously reported data on the thermal decomposition of HO(2)NO(2) have been reanalyzed and shown to be in good agreement with our reported value.     

Isotachophoretic determination of carboxylic acids in biodegradation samples

In the current study a method of isotachophoretic separation of selected carboxylic acids was developed. The method was used for the determination of carboxylated oligo(ethylene glycol)s and their degradation products in biodegradation tests of PEG 250 DA [a mixture of dicarboxylated oligo(ethylene glycol)s]. Two tests were performed in the studies: the Organization for Economic Cooperation and Development (OECD) screening test and the river water die-away test. Both the biodegradation tests proved relatively fast biodegradation of the studied compounds. In the OECD screening test the biodegradation was faster than in the river water die-away test which can be ascribed to a higher concentration of bacteria in the biodegradation liquor. The minimal sample pretreatment and relatively low cost of analysis by the isotachophoretic method used here make it a good alternative to existing methods of carboxylic acids analysis.     

Suppression of deleterious effects of free silanols in liquid chromatography by imidazolium tetrafluoroborate ionic liquids

Silica-based stationary phases are commonly used in liquid chromatography, but their surface acidity causes known problems, especially when separating basic compounds. Deleterious effects of free silanols are not fully removed by standard prevention procedures consisting in adding alkylamines or other amino quenchers to the eluents. We found that ionic liquids of the imidazolium tetrafluoroborate class, added to mobile phases at concentrations of 0.5-1.5% (v/v), blocked silanols and provided excellent thin-layer chromatographic separations of strongly basic drugs which were otherwise not eluted, even with neat acetonitrile as the mobile phase. The silanol suppressing potency of imidazolium tetrafluoroborates was demonstrated to markedly exceed that of the standard mobile phase additives, like triethylamine, dimethyloctylamine and ammonia. The proposed new mobile phase additives were also demonstrated to provide reliable lipophilicity parameters of base drug analytes as determined by gradient mode of high-performance liquid chromatography. By applying the readily available and environmentally friendly imidazolium tetrafluoroborate ionic liquids, simple and efficient means of improvement of liquid chromatographic analysis of organic bases were elaborated.     

X-ray and Thermal Analysis of Selected Drugs Containing Acetaminophen

Studies carried out by X-ray and thermal analysis confirmed that acetaminophen (paracetamol), declared by the manufacturers as an Active Pharmaceutical Ingredient (API), was present in all studied medicinal drugs. Positions of diffraction lines (2θ angles) of the studied drugs were consistent with standards for acetaminophen, available in the ICDD PDF database Release 2008. |Δ2θ| values were lower than 0.2°, confirming the authenticity of the studied drugs. Also, the values of interplanar distances d_hkl for the examined samples were consistent with those present in the ICDD. Presence of acetaminophen crystalising in the monoclinic system (form I) was confirmed. Various line intensities for API were observed in the obtained diffraction patterns, indicating presence of the preferred orientation of the crystallites in the examined samples. Thermal analysis of the studied substances confirmed the results obtained by X-ray analysis. Drugs containing only acetaminophen as an API have melting point close to that of pure acetaminophen. It was found that presence of other active and auxiliary substances affected the shapes and positions of endothermal peaks significantly. A broadening of endothermal peaks and their shift towards lower temperatures were observed accompanying an increase in the contents of additional substances being “impurities” in relation to the API. The results obtained by a combination of the two methods, X-ray powder diffraction (XRPD) and differential scanning calorimetry/thermogravimetry (DSC/TGA), may be useful in determination of abnormalities which can occur in pharmaceutical preparations, e.g., for distinguishing original drugs and forged products, detection of the presence of a proper polymorphic form or too low content of the active substance in the investigated drug.     

Structural studies of new chiral nickel (II) complexes of cyclams: The influence of a systematically varied number of amide groups

The synthesis and structures of nickel (II) complexes of chiral cyclams originating from l-proline are presented. Upon addition of nickel acteate, oxocyclams having amide groups underwent deprotonation forming distorted square-planar complexes. In the case of the all-amine analogue a six-coordinate octahedral complex is formed.     

Complexes of heteroscorpionate trispyrazolylborate ligands. Part VI. Carboxylate induced conversion of mono-ligand Tp′M(L) into bis-ligand Tp′2M complexes (M=Co(II) and Cu(II))

A series of homoleptic complexes of hexacoordinate cobalt(II) and copper(II) complexes with 3,5-disubstituted homo- and heteroscorpionate tris(pyrazolyl)borate anionic ligands (Tp′) were synthesized, i.e. bis[hydrotris(3-phenyl,5-methylpyrazol-1-yl)borato]cobalt(II), bis[hydrobis(3-phenyl,5-methylpyrazol-1-yl)(3-methyl,5-phenylpyrazol-1-yl)borato]cobalt(II) and bis[hydrobis(3-phenyl,5-methylpyrazol-1-yl)(3-methyl,5-phenylpyrazol-1-yl)borato]copper(II) and their structures were elucidated crystallographically. The complexes were also formed spontaneously during attempted metathesis of the corresponding Tp′M(NCS) complexes into Tp′M(OOCCH(OH)CH₃) complexes. In the case of the analogous conversion applied for the thiocyanato [hydrobis(3-phenyl,5-methylpyrazol-1-yl)(3,5-dimethylpyrazol-1-yl)boratocobalt(II) complex with sodium carboxylates (lactate, pyruvate and 2-hydroxybutyrate), the cross-transfer of pyrazolyl residues between starting anionic ligands was observed resulting in formation of bis-ligand homo- and heteroleptic Tp′CoTp″ complexes, where Tp′, Tp″ were tris(pyrazolyl)borates composed of n 3(5)-phenyl,5(3)-methylpyrazolyl and (3−n) 3,5-dimethylpyrazolyl residues (n=0–3) identified by mass spectrometry. Metathesis of thiocyanate in thiocyanato hydrotris(3-phenyl,5-methylpyrazol-1-yl)boratocobalt(II) into pyruvate led to the isolation of stable the pyruvato hydrotris(3-phenyl,5-methylpyrazol-1-yl)boratocobalt(II) complex, the structure of which was determined crystallographically. The Tp′ ligands are η³ coordinated to metal ions in every case, whereas the pyruvate anion is coordinated through carboxylate and carbonyl oxygen atoms to the cobalt center. Two rotational isomers distinguishable by ¹H NMR spectroscopy for the hexacoordinate bis[hydrobis(3-phenyl,5-methylpyrazol-1-yl)(3-methyl,5-phenylpyrazol-1-yl)borato]cobalt(II) complex were detected in solution.     

Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA

The oxazole yellow dye, YOYO-1 (a symmetric homodimer), is a commonly used molecule for staining DNA. We applied the brightness analysis to study the intercalation of YOYO-1 into the DNA. We distinguished two binding modes of the dye to dsDNA: mono-intercalation and bis-intercalation. Bis-intercalation consists of two consecutive mono-intercalation steps, characterised by two distinct equilibrium constants (with the average number of base pair per binding site equals 3.5): K1=3.36±0.43×107M−1 and K2=1.90±0.61×105M−1, respectively. Mono-intercalation dominates at high concentrations of YOYO-1. Bis-intercalation occurs at low concentrations.