HTMoL: full-stack solution for remote access,visualization, and analysis of molecular dynamics trajectory data

Research on biology has seen significant advances with the use of molecular dynamics (MD) simulations. The MD methodology enables explanation and discovery of molecular mechanisms in a wide range of natural processes and biological systems. The need to readily share the ever-increasing amount of MD data has been hindered by the lack of specialized bioinformatic tools. The difficulty lies in the efficient management of the data, i.e., in sending and processing 3D information for its visualization. In this work, we present HTMoL, a plug-in-free, secure GPU-accelerated web application specifically designed to stream and visualize MD trajectory data on a web browser. Now, individual research labs can publish MD data on the Internet, or use HTMoL to profoundly improve scientific reports by including supplemental MD data in a journal publication. HTMoL can also be used as a visualization interface to access MD trajectories generated on a high-performance computer center directly. Furthermore, the HTMoL architecture can be leveraged with educational efforts to improve learning in the fields of biology, chemistry, and physics.     

On the transition moment of the CO2 40°1II-00°0 band near 7740 cm-1

Using intensity measurements on the CO₂ 40°1_II-00°0 band obtained by Valero and Boese, we have expanded the F(m)-factor for the parallel band by using the Herman-Wallis formula. We have calculated the transition moment and determined the coefficients in the expansion of F(m).     

Comparative energies of Zn(II) cation localization as a function of the distance between two forming cation position aluminium ions in high-silica zeolites

Periodical calculations of Zn(II) metal cation stabilization in cationic positions with distantly placed aluminium ions has been performed for high-silica ferrierite. It was found that decrease of the stabilization energy at large distances between Al ions (more than 10 Å) is about of 2 eV in comparison with nearest possible position of two Al ions in the zeolite lattice and weekly depended on following increase of the Al-Al distance. Main changes in stabilization energy occured within a 3-Å interval of these distances. Only for the localizations of both Al ions in one zeolite ring zinc cationic form is more stable than hydrogen form.     

Theoretical and experimental consideration of the reactions between VxOy+ and ethylene

We present joint theoretical and experimental results which provide evidence for the selectivity of V(x)O(y)(+) clusters in reactions toward ethylene due to the charge and different oxidation states of vanadium for different cluster sizes. Density functional calculations were performed on the reactions between V(x)O(y)(+) and ethylene, allowing us to identify the structure-reactivity relationship and to corroborate the experimental results obtained by Castleman and co-workers (Zemski, K. A.; Justes, D. R.; Castleman, A. W., Jr. J. Phys. Chem. A 2001, 105, 10237). The lowest-energy structures for the V(2)O(2)(-)(6)(+) and V(4)O(8)(-)(10)(+) clusters and the V(2)O(3)(-)(6)(+)-C(2)H(4) and V(4)O(10)(+)-C(2)H(4) complexes, as well as the energetics for reactions between ethylene and V(2)O(4)(-)(6)(+) and V(4)O(10)(+) are presented here. The oxygen transfer reaction pathway was determined to be the most energetically favorable one available to V(2)O(5)(+) and V(4)O(10)(+) via a radical-cation mechanism.The association and replacement reaction pathways were found to be the optimal channels for V(2)O(4)(+) and V(2)O(6)(+), respectively. These results are in agreement with the experimental results reported previously. Experiments were also conducted for the reactions between V(2)O(5)(+) and ethylene to include an energetic analysis at increasing pressures. It was found that the addition of energy depleted the production of V(2)O(4)(+), confirming that a more involved reaction rather than a collisional process is responsible for the observed phenomenon. In this contribution we show that investigation of reactions involving gas-phase cationic vanadium oxide clusters with small hydrocarbons is suitable for the identification of reactive centers responsible for selectivity in heterogeneous catalysis.     

Synthesis of 2-(N-Benzylpyrrolyl)-benzimidazoles Using Polyphosphoric Acid Prompted Cyclocondensation

Synthesis of a series of 2-substituted benzimidazoles was carried out for screening anti-inflammatory activities. 2-(N-benzylpyrrolyl)-benzimidazoles 9a-k were synthesized from N-benzyl-2-pyrrole carboxylic acids 8a-d and 4-substituted-1,2-phenylenediamines by cyclocondensation utilizing polyphosphoric acid (PPA) as condensing agent. The N-benzyl-2-pyrrole carboxylic acids were prepared by standard method of N-benzylation of 2-pyrrole carboxylate using NaH/DMF and appropriately substituted benzyl halides followed by alkaline hydrolysis.     

A Watersoluble Sulfonatomethylated Calix[4]resorcinarene as Artificial Receptor of Metal Complexes

The binding of different sized and shaped metal complexes [Co(His)₂]ClO₄(1), [Co(en)₂C₂O₄]Cl (2) and [K18-crown-6]SCN (3)(en-ethylendiamine, His-L-histidynate-anion) with a new tetrasulfonatomethylcalix[4]resorcinarene([H₈X]Na4) was investigated in neutral and alkaline aqueous media by NMR and pH-metrictitration methods and compared with those of recently studied NMe₄Br (4). The resultsobtained indicate that the outer-sphere coordination of complexes 1–3 by[H₈X]^4- proceeds via the interaction of hydrophobic fragments of the guestswith both the negatively charged rim and the hydrophobic cavity as a -base. Thenature of binding does not change for cations 1, 2 and 4 on going from[H₈X]^4- in neutral to [H₄X]^8- in alkaline media, while the inclusionof 3 decreases on going from [H₈X]^4- to [H₄X]^8-.     

Capillary electrophoresis of Cr(VI) reducer Arthrobacter oxydans

Rapid and effective separation of bacteria Arthrobacter oxydans was performed using capillary electrophoresis. For optimal separation of bacteria the influence of buffer concentration, pH and applied voltage were studied. It was found that the most appropriate conditions for electrophoretic mobility measurements are as follows: applied voltage 6-14 kV; buffer concentration 5-10 mM pH 6-8. At the stationary phase of growth there are always two main heterogeneous peaks. They are connected with the morphology of bacteria as well as with cell aggregation. The heterogeneity of samples may be explained by surface modifications of bacterial cells.     

Kinetics and Mechanism of Mineral Respiration: How Iron Hemes Synchronize Electron Transfer Rates

Anaerobic microorganisms of the Geobacter genus are effective electron sources for the synthesis of nanoparticles, for bioremediation of polluted water, and for the production of electricity in fuel cells. In multistep reactions, electrons are transferred via iron/heme cofactors of c‐type cytochromes from the inner cell membrane to extracellular metal ions, which are bound to outer membrane cytochromes. We measured electron production and electron flux rates to 5×10⁵ e s^?1 per G. sulfurreducens. Remarkably, these rates are independent of the oxidants, and follow zero order kinetics. It turned out that the microorganisms regulate electron flux rates by increasing their Fe²⁺/Fe³⁺ ratios in the multiheme cytochromes whenever the activity of the extracellular metal oxidants is diminished. By this mechanism the respiration remains constant even when oxidizing conditions are changing. This homeostasis is a vital condition for living systems, and makes G. sulfurreducens a versatile electron source.     

Improved method for isotopic and quantitative analysis of dissolved inorganic carbon in natural water samples

We present here an improved and reliable method for measuring the concentration of dissolved inorganic carbon (DIC) and its isotope composition (delta(13)C(DIC)) in natural water samples. Our apparatus, a gas chromatograph coupled to an isotope ratio mass spectrometer (GCIRMS), runs in a quasi-automated mode and is able to analyze about 50 water samples per day. The whole procedure (sample preparation, CO(2(g))-CO(2(aq)) equilibration time and GCIRMS analysis) requires 2 days. It consists of injecting an aliquot of water into a H(3)PO(4)-loaded and He-flushed 12 mL glass tube. The H(3)PO(4) reacts with the water and converts the DIC into aqueous and gaseous CO(2). After a CO(2(g))-CO(2(aq)) equilibration time of between 15 and 24 h, a portion of the headspace gas (mainly CO(2)+He) is introduced into the GCIRMS, to measure the carbon isotope ratio of the released CO(2(g)), from which the delta(13)C(DIC) is determined via a calibration procedure. For standard solutions with DIC concentrations ranging from 1 to 25 mmol . L(-1) and solution volume of 1 mL (high DIC concentration samples) or 5 mL (low DIC concentration samples), delta(13)C(DIC) values are determined with a precision (1sigma) better than 0.1 per thousand. Compared with previously published headspace equilibration methods, the major improvement presented here is the development of a calibration procedure which takes the carbon isotope fractionation associated with the CO(2(g))-CO(2(aq)) partition into account: the set of standard solutions and samples has to be prepared and analyzed with the same 'gas/liquid' and 'H(3)PO(4)/water' volume ratios. A set of natural water samples (lake, river and hydrothermal springs) was analyzed to demonstrate the utility of this new method.