Recent progress in protein 3D structure comparison

Quantitation of protein 3-D structure similarity is crucial in such fields as evolutionary studies, structural modeling and prediction of biological function. There are various approaches, many of which are tailored to specific problems. This review summarizes the recent developments in this field with particular interest in two main areas: i) improvements to and statistical interpretation of the root-man-square distance between equivalent atoms, rmsd; and ii) methods of protein structural classification based on geometrical features. Special attention is given to fast methods capable of analyzing large structural databases.     

Determination of radiostrontium in soil samples using a crown ether

A simple and rapid method has been developed for the separation and determination of total radiostrontium in soil. The method consists of three basic steps: oxalate precipitation to remove bulk potassium, chromatographic separation of strontium from most inactive and radioactive interferences utilizing a crown ether (Sr. Spec, EIChroM Industries, Il. USA) and oxalate precipitation of strontium to evaluate the chemical yield. Radiostrontium is then determined by liquid scintillation counting of the dissolved precipitate. When 10 g samples of soil are used, the sensitivity of the method is about 10 Bq/kg. The chemical yield is about 80%. The separation and determination of radiostrontium can be carried out in about 8 hours.     

Anomalous grazing incidence small-angle x-ray scattering studies of platinum nanoparticles formed by cluster deposition

The size evolution of platinum nanoparticles formed on a SiO2/Si(111) substrate as a function of the level of surface coverage with deposited clusters has been investigated. The anisotropic shapes of sub-nanometer-size nanoparticles are changed to isotropic on the amorphous substrate as their sizes increased. Using anomalous grazing incidence small-angle x-ray scattering (AGISAXS), the scattering from nanoparticles on the surface of a substrate is well separated from that of surface roughness and fluorescence. We show that AGISAXS is a very effective method to subtract the background and can provide unbiased information about particle sizes of less than 1 nm.     

Electron diffraction studies of the molecular structures of iron(II) chloride and iron(II) bromide. Evidence on the structure of dimeric species Fe2Br4

An expression for the extreme values of mean-square amplitudes of vibrations in polyatomic molecules has been derived which permits estimation of the mean-square amplitude without solving the vibrational problem. This expression can be improved for the stretching and scissoring modes when the assignment of frequencies is known. In turn, the corresponding vibrational frequency may be estimated from the experimental value of the mean-square amplitude. The mean-square amplitudes of the butadiene-1,3 molecule are considered as an example.     

Thermal analysis and X-ray studies of chiral ferroelectric liquid crystalline materials and their binary mixtures

Summary Thermal properties of a homologous series of ferroelectric liquid crystals S-(-)-[4-(2-n-alkoxy-propionyloxy)]biphenyl-4'-[n-alkoxy-(3,5-dimethyl)]benzoate have been investigated by polarizing optical microscopy and differential scanning calorimetry. The mesophases were identified and confirmed by X-ray too. Three binary mixtures were prepared from the individual homologues. In one of the mixtures (Mix1), the ferroelectric SmC* phase has broadened and became enantiotropic. This mesophase remained monotropic in the other two mixtures (Mix2, Mix3). The chiral nematic N* phase did not appear in Mix1, but remained monotropic for the other two mixtures. Two molecular parameters, the layer spacing and the average intermolecular distance have been calculated from the X-ray results for the homologues and their mixtures. An intercalated tail-to-tail packing of molecules was found both in the single compounds and their mixtures resulting in the layer spacing about half of the molecular length of the single compounds.     

Improved sample preparation method for environmental plutonium analysis by ICP-SFMS and alpha-spectrometry

A rapid and simple sample preparation method for plutonium determination in environmental samples by inductively coupled plasma sector field mass spectrometry (ICP-SFMS) and alpha-spectrometry is described. The developed procedure involves a selective CaF₂ co-precipitation for preconcentration followed by extraction chromatographic separation. The proposed method effectively eliminates the possible interferences in mass spectrometric analysis and also removes interfering radionuclides that may disturb alpha-spectrometric measurement. For ²³⁹Pu, ²⁴⁰Pu and ²⁴¹Pu limits of detection of 9.0 fg·g⁻¹ (0.021 mBq), 1.7 fg·g⁻¹ (0.014 mBq) and 3.1 fg·g⁻¹ (11.9 mBq) were achieved by ICP-SFMS, respectively, and 0.02 mBq by alpha-spectrometry. Results of certified reference materials agreed well with the recommended values.     

The photoelectron spectrum of tetramethyldiazetine: The elucidation of ring size effects on azo group ionization potentials

The photoelectron spectrum of 3,3,4,4-tetramethyldiazetine (4-Me₄) has been measured. By comparison with the previously reported photoelectron spectra of 3,3-dimethyldiazirine and 3,3,5,5-tetramethylpyrazoline, 4-Me₄ has three resolved low energy ionization (8.87, 10.36, and 11.65 eV) with an anomalously low second ionization potential. MINDO/3-and ab initio STO-3G calculations on 3-, 4-, and 5-membered ring azo compounds (diazenes) have been carried out, and these allow definite conclusions about the order of n_?, n₊, and π ionization potentials to be made for the diazetine (n_? < N₊ < π) and for 3,3-dimethyldiazirine and 3,3,5,5-tetramethylpyrazoline(n_? < π n₊), in agreement with the predictions of Heilbronner. Ab initio STO-3G calculations on the nitrogen and alkyl fragments of the cyclic diazenes reveal the origin of ionization energy shifts with changes in ring size.     

Line absorption of matrix elements as a background correction error in atomic absorption spectrometry

Accurate measurement of weak atomic absorption signals is only possible after exact background correction. If the accompanying elements in excess have their own resonance lines in the immediate vicinity of the resonance line of the element to be determined,and these fall within the spectral band transmitted by the monochromator, then the value the measured apparent background absorbance is higher than the true one. The error may usually be diminished by choosing an appropriate spectral bandwidth. Tables of such bandwidths for a large number of pairs of elements are given.