Brownian dynamics simulations on CPU and GPU with BD_BOX

There has been growing interest in simulating biological processes under in vivo conditions due to recent advances in experimental techniques dedicated to study single particle behavior in crowded environments. We have developed a software package, BD_BOX, for multiscale Brownian dynamics simulations. BD_BOX can simulate either single molecules or multicomponent systems of diverse, interacting molecular species using flexible, coarse-grained bead models. BD_BOX is written in C and employs modern computer architectures and technologies; these include MPI for distributed-memory architectures, OpenMP for shared-memory platforms, NVIDIA CUDA framework for GPGPU, and SSE vectorization for CPU.     

Application of micro-thin-layer chromatography as a simple fractionation tool for fast screening of raw extracts derived from complex biological, pharmaceutical and environmental samples

The main goal of present paper is to demonstrate the separation and detection capability of micro-TLC technique involving simple one step liquid extraction protocols of complex materials without multi-steps sample pre-purification. In the present studies target components (cyanobacteria pigments, lipids and fullerenes) were isolated from heavy loading complex matrices including spirulina dried cells, birds’ feathers and fatty oils as well as soot samples derived from biomass fuel and fossils-fired home heating systems. In each case isocratic separation protocol involving less that 1 mL of one component or binary mixture mobile phases can be completed within time of 5–8 min. Sensitive detection of components of interest was performed via fluorescence or staining techniques using iodine or phosphomolybdic acid. Described methodology can be applied for fast fractionation or screening of whole range of target substances as well as chemo-taxonomic studies and fingerprinting of complex mixtures, which are present in raw biological or environmental samples.     

Vibrational characterization of L-leucine phosphonate analogues: FT-IR, FT-Raman, and SERS spectroscopy studies and DFT calculations

This study reports the Raman (FT-Raman) and absorption infrared (FT-IR) spectra, based on calculated wavenumbers and normal modes of vibrations, of the following compounds: L-Leu-D-NH-CH(Me)-PO(3)H(2) (LI), L-Leu-NH-C(Me)(2)-PO(3)H(2) (LII), L-Leu-D-NH-CH(Et)-PO(3)H(2) (LIII), L-Leu-L-NH-CH(Et)-PO(3)H(2) (LIV), L-Leu-L-NH-CH(EtOH)-PO(3)H(2) (LV), L-Leu-NH-C(Me)(Et)-PO(3)H(2) (LVI), L-Leu-L-NH-CH(PrA)-PO(3)H(2) (LVII), L-Leu-L-NH-CH(c-Pr)-PO(3)H(2) (LVIII), L-Leu-L-NH-CH(t-Bu)-PO(3)H(2) (LIX), L-Leu-L-NH-CH(BuA)-PO(3)H(2) (LX), L-Leu-L-NH-CH(c-Bu)-PO(3)H(2) (LXI), and L-Leu-L-NH-C(Adm)-PO(3)H(2) (LXII). The equilibrium geometries and vibrational wavenumbers were calculated using density functional theory (DFT) at the B3LYP, 6-311++G** level using Gaussian 03, Raint, GaussSum 0.8, and Gar2ped software. We briefly compare and analyze the experimental and calculated vibrational wavenumbers in the range 4000-400 cm(-1). In addition, the Raman wavenumbers are compared to those from the surface-enhanced Raman scattering (SERS) spectra for the phosphono analogues of l-leucine (l-Leu) adsorbed on a colloidal silver surface in an aqueous solution. The geometries of these molecules etched on the silver surface were deduced from observed changes in both the intensity and broadness of Raman bands in the spectra of the bound versus free species. For example, LVI appears to adsorb onto the colloidal silver particles mainly through the amine group and amide bond, which assists in the adsorption process, whereas LII shows strongly enhanced SERS bands due to the rocking, twisting, and stretching vibrations of the N(amid)C(sg)(Me)(2)P fragment, suggesting that this peptide's interaction with the silver surface occurs mainly via this fragment. On the other hand, the most dominant SERS bands of LIII and LIV due to the P═O bond stretches reflect P═O···Ag complex formation.     

Thiol-functionalized anthraquinones: mass spectrometry and electrochemical studies

Abstract  

In this work, the synthesis of various thiol-functionalized anthraquinone compounds is presented. The studied compounds were characterized by mass spectrometry and the main fragmentation pathways are discussed. The compounds studied formed stable self-assembled monolayers (SAMs) in the gold surface. The parameters for the reduction processes in the gold surface of the studied new anthraquinones were determined by cyclic voltamperometry tests.     

Promoted ternary CuO-ZrO2-Al2O3 catalysts for methanol synthesis

Ternary CuO-ZrO₂-Al₂O₃ catalysts promoted by palladium or gold were prepared and tested in CO hydrogenation reaction at 260°C under elevated pressure (4.8 MPa). The promotion effect of palladium or gold addition on the physicochemical and catalytical properties of CuO-ZrO₂-Al₂O₃ catalysts in methanol synthesis (MS) was studied. The catalysts were characterized by BET, XRD, TPR-H₂, TPD-NH₃ methods. The BET results showed that the ternary system CuO-ZrO₂-Al₂O₃ had the largest specific surface area, cumulative pore volume and average pore size in comparison with the promoted catalysts. The yield of methanol can be given through the following sequence: 5%Pd/CuO-ZrO₂-Al₂O₃ > CuO-ZrO₂-Al₂O₃ > 2%Au/CuO-ZrO₂-Al₂O₃. We also found that the presence of gold or palladium on catalyst surface has strong influence on the reaction selectivity. The high selectivity of gold doped ternary catalyst is explained by the gold-oxide interface sites created on the catalyst surface and the acidity of those systems. The higher selectivity to methanol in the case of the palladium catalyst is explained by the spillover effect between Pd and CuO.      

Thermal properties of pressure sintered alumina–graphene composites

Journal of Thermal Analysis and Calorimetry - The work concerns the alumina–graphene materials sintered by two different pressure methods. The different particle sizes of graphene were used....     

Quinazoline Antifolate Thymidylate Synthase Inhibitors: Replacement of Glutamic Acid by Aminophosphonic Acids

The synthesis of six analogues of the potent thymidylate synthase (TS) inhibitor N -[4-[ N -[(3,4-dihydro-2-methyl-4-oxo-6-quinazolinoyl)-methyl]- N -prop-2-ynylamino]benzoyl]- L -glutamic acid 2 is described in which the glutamic acid residue has been replaced by DL -aminophosphonic acids. New antifolates were tested as inhibitors of TS isolated from mouse L1210 leukemic cells as well as inhibitors of growth mouse leukemic L5178Y cells. In general these modifications result in compounds that are considerably less potent than 2 as TS inhibitors with K i 's 0.17-1.10 w M. Very poor solubility in water limited their proper assay of growth cells inhibition.     

Synthesis of Some Aminophosphonates Bearing N‐(Fluorophenyl)‐piperazynyl Moiety and Their Activity toward Serotonin Receptors

Syntheses of a series of compounds bearing a 1‐(fluorophenyl)piperazin‐4‐ylmethyl moiety, namely dialkyl 1‐(fluorophenyl)piperazin‐4‐ylmethyl phosphonates 3a–f , diethyl 2‐[1‐(fluorophenyl)piperazin‐4‐yl]‐ethyl phosphonates 4a,b , diethyl 3‐[1‐(4‐fluorophenyl)‐piperazin‐4‐yl]‐propyl phosphonate 5 , and di[1‐(fluorophenyl)piperazin‐4‐yl]methanes 6a,b were performed, and some of them were screened for their affinity for serotonin 5‐HT_1A, 5‐HT₆, and 5‐HT₇ receptors. Moderate interactions with these receptors were demonstrated.