Molecular caps for full quantum mechanical computation of peptide-water interaction energy

We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented.     

On Mercury(I) Oxo Compounds — Quasi‐Relativistic Computational and Experimental Studies

About 60 molecular species composed of up to 10 mercury atoms and of oxygen atoms and/or of some other elements or groups (such as halogen, OH₂, OH, H, alkali, NO₃) have been investigated quantum chemically. Different density functional approaches and the ab initio SCF‐MP2 method were applied, comparing different basis sets and different atomic core sizes. It is important not to treat the Hg 5s, p, d as inactive core shells, and to use sufficiently many polarization functions. The shape of the 〉O‐Hg‐Hg‐O〈 units is not favorable concerning the formation of lattices composed of Hg^I, O and OH only. Despite its bulkiness, the OHgHgO units can easily come into contact with each other and then disproportionate. This is prevented in the so‐called ternary M‐Hg^I oxides by the embedded oxometallate (oxoacidic) anions. Furthermore, the Hg^I and Hg^II oxide bond energies are less favorable towards the stability of Hg^I oxo compounds, as compared to Hg halidic or oxoacidic compounds. Both points are not promising concerning the search for Hg^I oxides/hydroxides, although the preparation of such compounds, including spacer groups, by topochemical reactions can still not be excluded. So far, experimental efforts towards the synthesis of such a new class of compounds have only demonstrated that Hg^II is strictly preferred over Hg^I in the formation of solids of binary Hg‐O or ternary A‐Hg‐O composition (A = electropositive metal such as alkali, in contrast to M = transition or semi‐metal). This is so even if compounds containing ‘electron rich Hg^δ— atoms’ (i.e. A‐Hg amalgams) are oxidized under mild conditions.     

Chaotic micromixers using two-layer crossing channels to exhibit fast mixing at low Reynolds numbers

We report two chaotic micromixers that exhibit fast mixing at low Reynolds numbers in this paper. Passive mixers usually use the channel geometry to stir the fluids, and many previously reported designs rely on inertial effects which are only available at moderate Re. In this paper, we propose two chaotic micromixers using two-layer crossing channels. Both numerical and experimental studies show that the mixers are very efficient for fluid manipulation at low Reynolds numbers, such as stretching and splitting, folding and recombination, through which chaotic advection can be generated and the mixing is significantly promoted. More importantly, the generation of chaotic advection does not rely on the fluid inertial forces, so the mixers work well at very low Re. The mixers are benchmarked against a three-dimensional serpentine mixer. Results show that the latter is inefficient at Re = 0.2, while the new design exhibits rapid mixing at Re = 0.2 and at Re of O(10(-2)). The new mixer design will benefit various microfluidic systems.     

Determination of129I and127I in environmental samples by neutron activation analysis (NAA) and inductively coupled plasma mass spectrometry (ICP-MS)

In order to assess the levels and behavior of¹²⁹I (half-life: 1.6×10⁷ y) and¹²⁷I (stable) in the environment, we have developed analytical procedures involving neutron activation analysis (NAA). Environmental samples collected around Tokaimura, Ibaraki Prefecture, Japan, have been analyzed using this method. Ranges of¹²⁹I and¹²⁷I concentrations in surface soil were 0.9–180 mBq kg^–1 and 1–60 mg kg^–1, respectively. Higher¹²⁹I concentrations were found in soil samples collected from coniferous forests, suggesting a contribution from tree canopies in the deposition of this nuclide. Most of the¹²⁹I in soil, was found to be retained in the first 10 cm. The¹²⁹I/¹²⁷I ratios in wheat fields were lower than those in rice paddy fields.A soil sample collected by IAEA from an area contaminated by the Chemobyl accident was also determined. The¹²⁹I concentration and the¹²⁹I/¹²⁷I ratio were 1.6 mBq kg^–1 and 1.7×10^–7, respectively. The¹²⁹I level in this sample was higher than the values obtained in areas far from nuclear facilities in Japan. It was suggested that the analysis of¹²⁹I in soils in the Chernobyl area may be useful in evaluating the¹³¹I levels at the time of the accident.Analyses of¹²⁹I and¹²⁷I by ICP-MS in water samples were also made. The analytical speed of this method was very high, i.e., 3 minutes for a sample. However, there is a sensitivity limitation for¹²⁹I detection due to interference from¹²⁹Xe with the¹²⁹I peak. The detection limits for¹²⁹I and¹²⁷I in water samples were about 0.5 mBq ml^–1 and 0.1 ng ml^–1, respectively.     

Measurements of short-lived cosmogenic nuclides in rain samples

Summary Extremely low activity levels of cosmic ray induced nuclides have been measured in freshly precipitated rainwater by quick chemical separation coupled with ultra low background gamma-spectrometry. The nuclides detected were ³⁸S (T_1/2 = 2.83 h)-³⁸Cl (37.2 m), ³⁹Cl (55.6 m), ²⁴Na (14.96 h), ²⁸Mg (20.9 h), ⁷Be (53.3 d) and ²²Na (2.602 y). The number of atoms in rain water were evaluated to be ranging from 400-1900 l^-1 for ³⁹Cl (n = 6, mean: 1200), 30-1500 l^-1 for ²⁴Na (n = 16, mean: 520), 80-600 l^-1 for ²⁸Mg (n = 13, mean: 260), 1 ^. 10⁶-4 ^. 10⁷ l^-1 for 7Be (n = 16, mean: 7 ^. 10⁶) and 2 ^. 10³-1 ^. 10⁵ l^-1 for ²²Na (n = 9, mean: 2 ^. 10⁴). Measurements of activity levels and activity ratios of short-lived cosmic-ray induced short-lived nuclides will open new method to understand atmospheric processes occurred at the altitude of rain cloud.     

Preparation of ZnO colloids by aggregation of the nanocrystal subunits

Colloidal ZnO particles with narrow size distribution were prepared via a sol-gel process by base-catalyzed hydrolysis of zinc acetate. The morphology of ordered arrays of the particles was recorded by SEM. SEM also reveals that these uniform particles were composed of tiny ZnO subunits (singlets) sized of several nanometers. The size of the singlets, which is confirmed by X-ray diffraction and UV-vis absorption spectra, increases as the aging time is prolonged. The size-selective formation of colloids by aggregation of nanosized subunits is proposed to consist of two-stage growth by nucleation of nanosized crystalline primary particles and their subsequent aggregation into polycrystalline secondary colloids. The aggregates are all spherical because the internal rearrangement processes are fast enough. The ZnO colloids, i.e., the aggregates, tend to self-assemble into well-ordered hexagonal close-packed structures. Room-temperature photoluminescence was characterized for green and aged ZnO.     

Intriguing self-assembly of large granules of F-actin facilitated by gelsolin and alpha-actinin

We report microscopic observations and a structural determination of actin granules self-assembled in concentrated solutions of actin filaments (F-actin). Optical microscopy shows reproducible formation of numerous and stable granules of densely packed F-actin of variable sizes on the order of 10 microm. These granules coexist with a uniform network of F-actin of a lower concentration. The microscopic segregation of F-actin into two distinct states is assisted by an actin cross-linking protein, alpha-actinin. The rapid on and off rates and temperature sensitivity of the alpha-actinin/F-actin interaction facilitate the formation of multi-micrometer-sized granules of well-defined shapes. Additional physical factors such as the excluded volume effect and the minimization of surface energy act in concert with the specific molecular interactions to define the intriguing granular formation. Both the biochemical specificity of alpha-actinin and the thermodynamics of phase transitions are required for understanding such large scale self-assembly.     

Preclinical evaluation of a novel water-soluble chlorin E6 derivative (BLC 1010) as photosensitizer for the closure of the neovessels

In the present study, photodynamic activity of a novel photosensitizer (PS), Chlorin e(6)-2.5 N-methyl-d-glucamine (BLC 1010), was evaluated using the chorioallantoic membrane (CAM) as an in vivo model. After intravenous (i.v.) injection of BLC 1010 into the CAM vasculature, the applicability of this drug for photodynamic therapy (PDT) was assessed in terms of fluorescence pharmacokinetics, i.e. leakage from the CAM vessels, and photothrombic activity. The influence of different PDT parameters including drug and light doses on the photodynamic activity of BLC 1010 has been investigated. It was found that, irrespective of drug dose, an identical continuous decrease in fluorescence contrast between the drug inside and outside the blood vessels was observed. The optimal treatment conditions leading to desired vascular damage were obtained by varying drug and light doses. Indeed, observable damage was achieved when irradiation was performed at light doses up to 5 J/cm(2) 1 min after i.v. injection of drug doses up to 0.5 mg/kg body weight(b.w.). However, when irradiation with light doses of more than 10 J/cm(2) was performed 1 min after injection of drug doses up to 2 mg/kg body weight, this led to occlusion of large blood vessels. It has been demonstrated that it is possible to obtain the desired vascular occlusion and stasis with BLC 1010 for different combinations of drug and/or light doses.     

Comparing ligand interactions with multiple receptors via serial docking

Standard uses of ligand-receptor docking typically focus on the association of candidate ligands with a single targeted receptor, but actual applications increasingly require comparisons across multiple receptors. This study demonstrates that comparative docking to multiple receptors can help to select homology models for virtual compound screening and to discover ligands that bind to one set of receptors but not to another, potentially similar, set. A serial docking algorithm is furthermore described that reduces the computational costs of such calculations by testing compounds against a series of receptor structures and discarding a compound as soon as it fails to satisfy specified bind/no bind criteria for each receptor. The algorithm also realizes substantial efficiencies by taking advantage of the fact that a ligand typically binds in similar conformations to similar receptors. Thus, once detailed docking has been used to fit a ligand into the first of a series of similar receptors, much less extensive calculations can be used for the remaining structures.     

Effect of mobile phase acidic additives on enantioselectivity for phenylalanine analogs

The use of acidic mobile phase additives allows the chiral separation of underivatized phenylalanine analogs on a common amylosic column. In addition to decreasing retention and band-broadening arising from non-ideal interactions, acidic additives may also increase selectivity. This appears to be due to the minimization of non-selective binding in the recognition site. Effects of the additives are related to additive pKa and size. Ethanesulfonic acid was typically the most effective additive with trifluoroacetic acid being one of the least effective.