Molecular Structure of Bis(trimethylsilyl) Hypophosphite HP(OSiMe3)2 by Gas-Phase Electron Diffraction and Quantum Chemistry

Geometric parameters and conformation of the bis(trimethylsilyl)hypophosphite molecule were determined by gas-phase electron diffraction and quantum-chemical calculations. The molecule has an asymmetric structure, including an asymmetric P(OSiMe₃)₂ group. The principal geometric parameters are as follows: (r _a; in parentheses are standard deviations): bond lengths: P-O 1.616 and 1.633(1), Si-O 1.670(1), Si-C 1.892(1), C-H 1.097(3) Å; bond angles: OPO 100.8(8), POSi 133.3, and 138.4(3)°; torsion angles about P-O bonds 120(2) and 41.(3)°; and torsion angles about Si-O bonds are 145 and −178(4)°.__________Translated from Zhurnal Obshchei Khimii, Vol. 75, No. 6, 2005, pp. 897–902.Original Russian Text Copyright © 2005 by Naumov, Oberhammer, Tafipol’skii.     

A Highly Sensitive and Selective Assay for Cysteine Using the Chemiluminescence Reaction of Luminol and Hydrogen Peroxide

A very simple, highly sensitive and selective chemiluminescence (CL) method was established for the determination of cysteine. This method is based on the fact that the CL reaction of luminol and hydrogen peroxide can be greatly enhanced by cysteine. The CL intensities at maximum light emission were linearly correlated with the concentration of cysteine over the range of 2.0×10^–8–6.0×10^–6molL^–1 with a detection limit of 7.5×10^–9molL^–1. The relative standard deviation was 1.7% for the determination of 1.0×10^–7molL^–1 cysteine (n=9). The feasibility of utilizing the proposed method for the determination of total concentration of cysteine in human serum was examined.     

Liquid chromatographic isolation of coplanar PCB congeners on an activated carbon stationary phase

A rapid and uncomplicated method for the fractionation of PCBs leading to an isolation of the highly toxic non-ortho substituted PCBs is described. The liquid chromatographic separation was achieved on a stationary phase consisting of activated carbon and Celite 545. Using eluents with different polarity, isolation of the non-ortho substituted PCBs in a single fraction was achieved. The fractions were analysed by GC/MS. The method was tested by the determination of non-ortho substituted PCBs in technical mixtures (Aroclor 1254 and Aroclor 1242). The results were compared with those obtained by using an HPLC fractionation on a porous graphitic carbon column. Finally, the micro-column fractionation was used for the determination of non-ortho substituted PCBs in native soil samples. Received: 5 March 1997 / Revised: 4 June 1997 / Accepted: 6 June 1997     

Interaction of zinc finger ZNF191(243—368) and its I323 W and R327W mutants with oligonucleotides by florescence spectrum

Two mutants of the zinc finger protein, ZNF191 (243–368) I323W and R327W, are successfully obtained by site-directed mutagenesis. The fluorescence spectrum is used to study the interaction between these two mutants and the oligonucleotides. The influence of the mutation on the interaction has been studied using ethidium bromide (EB) as the fluorescence probe. The binding constants of the I323W-DNA and R327W-DNA have been calculated and the possible binding models have been discussed.     

Theoretical prediction on vibrational spectra of [Ar...Ar-H]<Superscript>+</Superscript>

Centrosymmetric linear [Ar-H-Ar]⁺ and asymmetric linear [Ar---Ar-H]⁺ are two stable configurations of [Ar₂H]⁺. Based on the global potential energy surface of [Ar₂H]⁺ provided by our group recently, we calculated the vibrational spectra of [Ar---Ar-H]⁺ with total angular momentum J = 0 by time-dependent quantum mechanical method, and the influence of quantum tunneling effect on vibrational spectra was found. With the help of the observation on the eigenstate functions and the modified potential energy surface, assignments were made to the spectra. The strong coupling between the excited bending mode of [Ar-H-Ar]⁺ and the vibrational states of [Ar---Ar-H]⁺ was discussed.     

Determination of S-carboxymethyl-L-cysteine and some of its metabolites in urine and serum by high-performance liquid chromatography using fluorescent pre-column labelling.

Pre-column labelling techniques are described for the determination of S-carboxymethyl-L-cysteine (CMC) and its metabolites in urine and plasma samples by high-performance liquid chromatography (HPLC) without prior extraction. All substances containing an amino group were converted into fluorescent fluorenylmethyl derivatives with 9-fluorenylmethyloxycarbonyl chloride (FMOC). Deaminated or N-acetylated carbocysteine metabolites were coupled with 1-pyrenyldiazomethane (PDAM) to give fluorescent PDAM esters. Similar results were obtained with the two commercially available and stable diazomethane derivatives PDAM and 9-anthryldiazomethane (ADAM). Following double derivatization with PDAM and FMOC, in a single chromatographic run with two fluorescence detectors connected in series, amines and amino(carboxylic) acids could be detected by their FMOC residues and, simultaneously, carboxylic acids were detected as fluorescent PDAM esters. The (R) and (S) enantiomers of the sulphoxides of CMC, of methylcysteine and of N-acetyl CMC were separated, although the reversed-phase HPLC system did not contain a chiral additive or stationary phase designed for the separation of enantiomers. The methods do not include liquid extraction steps and can therefore be performed either manually or automatically using an HPLC autosampler. These methods were used for the investigation of a disputed pharmacogenetic polymorphism of S-oxidation of CMC in humans, which until now has most often been studied using paper chromatography. The described techniques were applied to the determination of CMC and its metabolites in human urine and plasma samples.     

Construction of 4D-QSAR Models for Use in the Design of Novel p38-MAPK Inhibitors

The p38-mitogen-activated protein kinase (p38-MAPK) plays a key role in lipopolysaccharide-induced tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1) release during the inflammatory process, emerging as an attractive target for new anti-inflammatory agents. Four-dimensional quantitative structure-activity relationship (4D-QSAR) analysis [Hopfinger et al., J. Am. Chem. Soc., 119 (1997) 10509] was applied to a series of 33 (a training set of 28 and a test set of 5) pyridinyl-imidazole and pyrimidinyl-imidazole inhibitors of p38-MAPK, with IC50 ranging from 0.11 to 2100 nM [Liverton et al., J. Med. Chem., 42 (1999) 2180]. Five thousand conformations of each analogue were sampled from a molecular dynamics simulation (MDS) during 50 ps at a constant temperature of 303 K. Each conformation was placed in a 2 angstroms grid cell lattice for each of three trial alignments. 4D-QSAR models were constructed by genetic algorithm (GA) optimization and partial least squares (PLS) fitting, and evaluated by leave-one-out cross-validation technique. In the best models, with three to six terms, the adjusted cross-validated squared correlation coefficients, Q2adj, ranged from 0.67 to 0.85. Model D (Q2adj = 0.84) was identified as the most robust model from alignment 1, and it is representative of the other best models. This model encompasses new molecular regions as containing pharmacophore sites, such as the amino-benzyl moiety of pyrimidine analogs and the N1-substituent in the imidazole ring. These regions of the ligands should be further explored to identify better anti-inflammatory inhibitors of p38-MAPK.     

Synchrotron radiation circular dichroism spectroscopy of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides.

Synchrotron radiation circular dichroism (SRCD) spectra of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides and cyclic derivatives were measured in the vacuum ultraviolet region (down to 168 nm for sugars and 175 nm for adenine derivatives) and at different pH values (3, 6-7, 9-10) and temperatures (between 5 and 45 degrees C). The information content in the VUV region is important since the CD bands strongly depend on the chemical structure of the sugar, the presence and orientation of a phosphate group and the protonation state of adenine. On the other hand, single or double deprotonation of the phosphoric acid group has no influence on the spectra. We assign the vacuum ultraviolet (VUV) CD bands of the nucleoside and nucleotides to be due mainly to n-->pi* transitions in the adenine nucleobase based on a comparison with the absorption spectra. The CD bands of the sugars are due to n(O -->sigma*) transitions and are much smaller than the CD signal from the nucleotides in the VUV region. Bands are assigned to both pyranose and open-chain forms.     

A kinetic stability study of <Emphasis Type="Italic">M</Emphasis>N<Subscript>5</Subscript> (<Emphasis Type="Italic">M</Emphasis>=Li,Na, K,and Rb)

A structure and kinetic stability study on some complexes with the general formula MN₅, where M are the alkali-metal atoms, Li, Na, K, and Rb, has been carried by using hybrid density functional methods. Complex B (C_2v) with two points of attachment to the N₅ ring is the most energetically favored for all metals considered here. Pyramidal structures A (C_5v) are kinetically unstable and they rapidly rearrange to the most stable planar structures B. At the QCISD(T)/6-311 + G*//B3LYP/6-311 + G* + ZPE (B3LYP/6-311 + G*) level, the decomposition barrier heights of LiN₅-B, NaN₅–B, KN₅-B, and RbN₅-B are predicted to be 19.9, 22.0, 22.5, and 23.0 kcal/mol, respectively. In addition, the rate constants of the decomposition reaction MN₅-B MN₃ + N₂ (M + Li, Na, K, and Rb) are also predicted using conventional transition state theory and canonical variational transition state theory, respectively.