Thiyl radical interaction with pyrimidine C5-C6 double bond

Addition and elimination interaction of thiyl radicals with the C5-C6 double bond in pyrimidines was studied by the pulse radiolysis technique in aqueous solution with the use of different monitoring systems. For this purpose, p-thiocresol, cysteamine hydrochloride, and mercaptoethanol were used. The rate constants of addition and elimination of thiyl radicals were determined by applying the modified version of ACUCHEM (computer program for modeling complex reaction systems). Aliphatic thiyl radicals add to the pyrimidine C5-C6 double bond with k = 1.0-3.0 x 10(7) dm3 mol(-1) s(-1), whereas elimination takes place with k = 0.7-2.0 x 10(5) s(-1). Quantum chemical calculations at the B3LYP/6-31G(d)/PCM level show that the addition should occur at the C6 position of the pyrimidine ring and that the energy of interaction between thiyl radicals and the pyrimidine double bond C5-C6 is low.     

Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study

A method for performing implicit-solvent molecular dynamics simulations at constant pH was applied to a pentapeptide acetyl-Ala-Asp-Ala-Lys-Ala-amide at pH 4. As a reference, molecular dynamics simulations were done for the same peptide with two variants of its fixed protonation patterns expected to dominate at pH 4, i.e., with a protonated and a deprotonated side chain of the Asp residue and the protonated Lys residue in both cases. The dynamic trajectories of the peptide were used to discuss the problem of the significance of the solute-solvent proton exchange phenomena for the dynamics and structural distributions of the polypeptide chain. The Asp-Lys distance was used as a probe of the overall molecular structure of the investigated pentapeptide. To characterize the dynamics, distributions of the "waiting" times for a transition from a "short" distance conformation to a "long" distance conformation were constructed, based on the generated molecular dynamics trajectories. We show that the relaxation time for the transitions, derived from the constant-pH simulations, is very close to the relaxation time characterizing a permanently protonated molecule, although the average protonation probability of the short-distance conformation is close to zero. However, the distribution of the Asp-Lys distances obtained from constant-pH simulations cannot be reproduced as a linear combination of the distributions resulting from the simulations with fixed protonation states.     

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.     

C-H...N and C-H...S hydrogen bonds--influence of hybridization on their strength

Simple complexes connected through C-H...S and C-H...N interactions are investigated: CH4...NH3, C2H4...NH3, C2H2...NH3, CH4...SH2, C2H4...SH2, and C2H2...SH2. Ab initio and DFT calculations are performed (SCF, MP2, B3LYP) using different basis sets up to the MP2/aug-cc-pVQZ//MP2/aug-cc-pVDZ level of approximation. The Bader theory is applied since MP2/6-311++G(d,p) wave functions are used to find and to characterize bond critical points in terms of electron densities and their Laplacians. The influence of hybridization on the properties of C-H...S and C-H...N systems is also studied showing that the strength of such interactions increases in the following order: C(sp3)-H...Y, C(sp2)-H...Y, C(sp)-H...Y, where Y = S, N--it is in line with the previous findings on C-H...O hydrogen bonds. The results also show that CH4...SH2 and C2H4...SH2 complexes should be rather classified as van der Waals interactions and not as hydrogen bonds. The frequency associated with the C-H stretch of C(sp3)-H...S is blue-shifted.     

Effect of temperature and concentration on the structure of N-methylacetamide-water complexes: Near-infrared spectroscopic study

Generalized two-dimensional (2D) FT-NIR correlation spectroscopy and chemometric methods have been used to study temperature-dependent spectral changes in pure N-methylacetamide (NMA) and NMA-water mixtures. We also examined the effect of varying water content on the structure of the mixture. It has been found that the extent of self-association of NMA in CCl4 is very high; the association occurs even at concentration of 0.001 M. In the pure liquid NMA, the population of the monomers is negligible and the structure is dominated by the linear associates. An increase in temperature reduces the number of hydrogen bonds, but in contrast to alcohols their strength remains nearly the same. This reflects a difference in the mechanism of thermal breaking of the associates of NMA and alcohols. The present results reveal that the interaction between NMA and water in the NMA-rich region (X(H2O) < 0.1) does not have a significant effect on the intrinsic structure of NMA. The structure of NMA is dominant, and the molecules of water do not form separate clusters but are dispersed and incorporated into the structure of NMA. We did not observe the presence of the free OH groups in the mixture. This led to the suggestion that each molecule of water forms two hydrogen bonds to two different molecules of NMA. An analysis of the asynchronous spectra reveals that most of the peaks observed in the asynchronous spectra, constructed from the temperature-dependent data, simply result from the frequency shift. This assumption is supported by the simulation studies.     

Preparation and characterization of fused-silica capillary columns coated with <Emphasis Type="Italic">m</Emphasis>-carborane–siloxane copolymers for gas chromatography

The carborane–siloxane copolymers Dexsil 300, a 34.5% bis(dimethylsilyl)-m-carborane–65.5% dimethylsiloxane copolymer, and Dexsil 400, a 24.9% bis(dimethylsilyl)-m-carborane–50.8% dimethyl, 24.3% methylphenylsiloxane copolymer, were coated on fused silica capillary columns and their gas chromatographic properties were evaluated. Their selectivity was evaluated using both Rohrschneider–McReynolds constants and triacylglycerol indices. The bis(dimethylsilyl)-m-carborane unit turned out to be equivalent to two dimethylsiloxy units and one half of a diphenylsiloxy unit. The m-carborane unit was found to cause a 15–25 K shift in the elution temperature between 120 and 360 °C. The working range was from 20 and 0 °C to 380 °C for Dexsil 300 and Dexsil 400, respectively. The column bleeding levels at 380 °C were below 20 and 15 pA for Dexsil 300 and Dexsil 400, respectively.     

Carnitine in Pregnancy

Summary. By the 12^th week of gestation, mean whole blood and plasma carnitine levels are already significantly (p<0.01) lower than those of controls, with a further significant (p<0.01) decrease up to parturition. Diminished carnitine levels may cause a downregulation of carnitine palmitoyltransferase1 (CPT1), both the liver isoform (CPT1A) and muscle isoform (CPT1B), carnitine palmitoyltransferase2 (CPT2), and carnitine acetyltransferase (CRAT) in white blood cells of pregnant women, as determined by real time PCR using the LightCyclerSYBR Green technology.L-Carnitine-L-tartrate supplementation of 2 g/d resulted in an up to 10-fold increase of the relative mRNA abundances of CPT1B, CPT2, and OCTN2 and a 5-fold increase of CPT1A, and CRAT.There is a relationship between the relative mRNA levels of CPT1A and CPT1B and the FFA plasma levels. The substitution of 2 g L-carnitine-L-tartrate/d resulted in significant (p<0.001) lower FFA levels compared to untreated controls and the groups substituted with 0.5 and 1 g L-carnitine/d although plasma carnitine levels were not significantly increased. The most substantial effect was the reduced portion of acylcarnitines on total carnitine in those women receiving 2 g L-carnitine-L-tartrate.Carnitine substitution resulted in an enhanced excretion of both, free carnitine and acylcarnitines, whereas acetylcarnitine accounts for 50–65% of total acylcarnitines.The results of the present study provide evidence that L-carnitine supplementation in pregnancy in sufficient doses avoids a striking increase of plasma FFAs, which are thought to be the main cause of insulin resistance and consequently gestational diabetes mellitus (GDM).     

Retention Behavior of New Oral Antidiabetic Drugs in Reversed-Phase Chromatography

JPC – Journal of Planar Chromatography – Modern TLC - The thin-layer chromatographic behavior of three of the newest oral antidiabetic agents, pioglitazone, rosiglitazone, and...     

Quantification of free and total salicylic acid in plants by solid-phase extraction and isocratic high-performance anion-exchange chromatography

Salicylic acid (SA) is an important signaling compound in plants and is involved in various defense responses. Here we report a new method for quantification of free and total soluble SA in Arabidopsis thaliana with 5-fluorosalicylic acid (5-FSA) as internal standard. The SA was isolated from leaf extracts by solid-phase extraction with phenyl-phase cartridges and selectively eluted as the cationic iron(III)-complex. Recoveries of SA and 5-FSA were equal and exceeded 90%. Free SA was subsequently released from the iron(III)-complex by addition of 2,2-bipyridyl and high-performance anion-exchange chromatography was performed on an NH₂ column. The SA appeared as last peak with a retention time of 15 min, baseline-separated from other substances. On-line detection was performed fluorimetrically for both SA and 5-FSA at an excitation wavelength of 300 nm and an emission wavelength of 410 nm, because both substances give similar fluorescence spectra. The detection limit for SA was 5 ng g^–1 FW for a sample size of 100 mg. Thus the main advantages of the method are highly selective sample preparation, increased sensitivity, reduced analysis time compared with reversed-phase HPLC, and use of a novel internal standard detectable under the same conditions as SA. The techniques described are applicable to other plant materials.     

Novel separation method for highly sensitive speciation of cancerostatic platinum compounds by HPLC–ICP–MS

A high-performance liquid chromatography–inductively coupled plasma mass spectrometry (HPLC–ICP–MS) method is presented for analysis of cisplatin, monoaquacisplatin, diaquacisplatin, carboplatin, and oxaliplatin in biological and environmental samples. Chromatographic separation was achieved on pentafluorophenylpropyl-functionalized silica gel. For cisplatin, carboplatin, and oxaliplatin limits of detection of 0.09, 0.10, and 0.15 g L^–1, respectively, were calculated at m/z 194, using aqueous standard solutions. (3 L injection volume). The method was utilized for model experiments studying the stability of carboplatin and oxaliplatin at different chloride concentrations simulating wastewater and surface water conditions. It was found that a high fraction of carboplatin is stable in ultrapure water and in solutions containing 1.5 mol L^–1 Cl^–, whereas oxaliplatin degradation was increased by increasing the chloride concentration. In order to support the assessment of oxaliplatin eco-toxicology, the method was tested for speciation of patient urine. The urine sample contained more than 17 different reaction products, which demonstrates the extensive biotransformation of the compound. In a second step of the study the method was successfully evaluated for monitoring cancerostatic platinum compounds in hospital waste water.