Surface pressure-area isotherms for Langmuir monolayers and a docking molecular orientation of perylene tetracarboxylic derivatives on a water surface

The surface pressure-molecular area (pi-A) isotherms for Langmuir monolayers of four perylenetetracarboxylic (PTCD) derivatives, measured with varying subphase temperatures and compression speeds, are reported. The behavior of these PTCD derivatives at the water-air interface is modeled using the rigid docking method. This approach is the first attempt to model the molecular orientation of PTCD on the water surface to be compared with experimental Langmuir isotherms. Through this methodology, it would be possible to anticipate aggregation and determine if favorable spatial orientations of perylenes are generated on the water surface. The pi-A isotherm experiments show that these molecules can support high surface pressures, indicating strong packing on the water surface and that the isotherms are compression speed independent but temperature dependent. The molecular orientation and stacking was further examined in Langmuir-Blodgett (LB) monolayers deposited onto glass and glass coated with Ag island films using UV-visible absorption and surface-enhanced fluorescence (SEF) measurements.

Distribution of Cr, Ni, Cu, Cd and Pb in different molecular size of humic fractions extracted from water and sediment samples collected at Anhumas reservoir - Araraquara/SP

In this work was studied the distribution of Cr, Ni, Cu, Cd and Pb in humic fractions with different molecular size. The HS were extracted from waters (AHS), surface sediments (HESS), interface water sediment (HSIS) and bottom sediment (HSBS) collected in the Anhumas surface water collection reservoir, located in the district of Araraquara - São Paulo State Brazil. The humic substances were extracted by procedures recommended by International Humic Substances Society (IHSS). After purification by dialysis, the humic substances were fractionated using a multistage tangential flow ultrafiltration system. The fractionation patterns of HS characterized a mass distribution relatively uniform among the fractions with different molecular sizes, with larger values in the fractions F-2 (20.8%) and F-4 (23.8%), Except for the ions Pb(II) and Cu(II), which presented relatively higher concentrations in the fractions F-2 and F-4, respectively. In general, chromium, nickel, cadmium and lead have similar distributions in the five fractions with larger and medium molecular sizes (F-1 to F-5). With relation to the mass distributions in the different humic substances fractions extracted from sediment samples collected at three depth, they presented 42-48% of HS in the fractions with larger molecular sizes (F-1 and F-2), 29-31% in the middle fractions (F-3 and F-4) and 13-20% in the fractions with smaller molecular sizes (F-5 and F-6). In general, the metallic ions presented distributions similar among the respective fractions F-1 to F-6, Exceptions for Pb(II) and M(II) in surface sediment with concentrations relatively smaller in the fractions F-2 and F-4, respectively,

Application of a new reverse Monte Carlo algorithm to polyatomic molecular systems. I. Liquid water

Using a new reverse Monte Carlo algorithm, we present simulations that reproduce very well several structural and thermodynamic properties of liquid water. Both Monte Carlo, molecular dynamics simulations and experimental radial distribution functions used as input are accurately reproduced using a small number of molecules and no external constraints. Ad hoc energy and hydrogen bond analysis show the physical consistency and limitations of the generated RMC configurations. (C) 2001 American Institute of Physics.

Clinical and molecular study of a new form of hereditary myotonia in Murrah water buffalo

Hereditary myotonia caused by mutations in CLCN1 has been previously described in humans, goats, dogs, mice and horses. The goal of this study was to characterize the clinical, morphological and genetic features of hereditary myotonia in Murrah buffalo. Clinical and laboratory evaluations were performed on affected and normal animals. CLCN1 cDNA and the relevant genomic region from normal and affected animals were sequenced. The affected animals exhibited muscle hypertrophy and stiffness. Myotonic discharges were observed during EMG, and dystrophic changes were not present in skeletal muscle biopsies; the last 43 nucleotides of exon-3 of the CLCN1 mRNA were deleted. Cloning of the genomic fragment revealed that the exclusion of this exonic sequence was caused by aberrant splicing, which was associated with the presence of a synonymous SNP in exon-3 (c.396C>T). The mutant allele triggered the efficient use of an ectopic 5' splice donor site located at nucleotides 90-91 of exon-3. The predicted impact of this aberrant splicing event is the alteration of the CLCN1 translational reading frame, which results in the incorporation of 24 unrelated amino acids followed by a premature stop codon. Copyright © 2012 Elsevier B.V. All rights reserved.

Molecular and serological prevalence of Babesia bovis and Babesia bigemina in water buffaloes in the north region of Brazil

Bovine babesiosis is a tick-borne disease caused mainly by Babesia bovis and Babesia bigemina, which are associated to considerable economic losses in cattle herds worldwide. Approximately 60% of buffalo herds in South America are located in Northern Brazil. Little is known about the impact of babesiosis on buffalo herds in Brazil. The present work aimed to verify the occurrence of B. bovis and B. bigemina in 542 water buffaloes in the state of Pará, Northern Brazil, using molecular and serological techniques. The percentage of seropositive animals for B. bovis and B. bigemina was 41.2% and 19.0%, respectively, by ELISA. B. bovis and B. bigemina DNA were detected in 15 and 16% of sampled buffaloes, respectively. A high correlation (Kappa index of 0.9) between serological and molecular tests suggests that the combination of the utilized techniques in the present study is suitable for babesiosis diagnosis in an endemic unstable area. Significantly difference of positivity for serological and molecular assays was verified to localities and reproductive status of sampled animals, but not between buffalo breeds. The immune status of sampled buffaloes associated to the circulation of babesiosis agents in sampled population suggests that the studied area is at risk to clinical babesiosis outbreaks. Furthermore, this study demonstrated that this region can be classified as endemically unstable. © 2013 Elsevier B.V.

Molecular and serological prevalence of Anaplasma marginale in water buffaloes in northern Brazil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

MOLECULAR DYNAMICS STUDIES OF SIMPLE MODEL FLUIDS AND WATER CONFINED IN CARBON NANOTUBE

Molecular Dynamics (MD) simulation is one of the most important computational techniques with broad applications in physics, chemistry, chemical engineering, materials design and biological science. Traditional computational chemistry refers to quantum calculations based on solving Schrodinger equations. Later developed Density Functional Theory (DFT) based on solving Kohn-Sham equations became the more popular ab initio calculation technique which could deal with ~1000 atoms by explicitly considering electron interactions. In contrast, MD simulation based on solving classical mechanics equations of motion is a totally different technique in the field of computational chemistry. Electron interactions were implicitly included in the empirical atom-based potential functions and the system size to be investigated can be extended to ~106 atoms. The thermodynamic properties of model fluids are mainly determined by macroscopic quantities, like temperature, pressure, density. The quantum effects on thermodynamic properties like melting point, surface tension are not dominant. In this work, we mainly investigated the melting point, surface tension (liquid-vapor and liquid-solid) of model fluids including Lennard-Jones model, Stockmayer model and a couple of water models (TIP4P/Ew, TIP5P/Ew) by means of MD simulation. In addition, some new structures of water confined in carbon nanotube were discovered and transport behaviors of water and ions through nano-channels were also revealed.

Morphological and molecular studies of Sphaerospermopsis torques-reginae (Cyanobacteria, Nostocales) from South American water blooms

Sphaerospermopsis torques-reginae (Komarek) Werner, Laughinghouse IV, Fiore & Sant'Anna comb. nov. was originally described as Anabaena torques-reginae Komarek from planktonic populations of Cuban eutrophic environments, characterized by twisted trichomes with spherical akinetes adjacent to the heterocytes. Recently, using molecular analyses, all planktonic Anabaena Bory ex Bornet & Flahault morphospecies were transferred into the genus Dolichospermum (Ralfs ex Bornet & Flahault) Wacklin el al., including Dolichospermum torques-reginae (Komarek) Wacklin et al. However, by a polyphasic characterization of strains of Anabaena reniformis Lemmermann and Aphanizomenon aphanizomenoides (Forti) Horecka & Komarek (=Anabaena aphanizomenoides Forti), these planktonic species were reclassified into Sphaerospermopsis Zapomelova et al. Our study's main objective was to characterize morphologically and molecularly cyanobacterial populations identified as Dolichospermum torques-reginae, observed in different aquatic ecosystems in South America. The 16S rRNA gene of two Dolichospermum torques-reginae strains (ITEP-024 and ITEP-026) was sequenced and phylogenetically analyzed for the first time. The morphological and phylogenetic analyses demonstrated the affiliation of the studied populations with the genus Sphaerospermopsis and, consequently, were denominated as Sphaerospermopsis torques-reginae. Furthermore, geographic distribution, ecology, and toxicity of the species are discussed. It was observed in different aquatic environments, natural and artificial, tropical and subtropical in Brazil, temperate in Argentina, and tropical in Colombia, suggesting a wide distribution in South America. It normally occurred in dense freshwater blooms, although it was also found in water with low salinity. Sphaerospermopsis torques-reginae toxic blooms have been reported in tropical water bodies in northeastern Brazil.

Combining sedimentological, trace metal (Mn, Mo) and molecular evidence for reconstructing past water-column redox conditions: The example of meromictic Lake Cadagno (Swiss Alps)

Here, we present sedimentological, trace metal, and molecular evidence for tracking bottom water redox-state conditions during the past 12,500 years in nowadays sulfidic and meromictic Lake Cadagno (Switzerland). A 10.5 m long sediment core from the lake covering the Holocene period was investigated for concentration variations of the trace metals Mn and Mo (XRF core scanning and ICP-MS measurements), and for the presence of anoxygenic phototrophic sulfur bacteria (carotenoid pigment analysis and 16S rDNA real time PCR). Our trace metal analysis documents an oxic-intermediate-sulfidic redox-transition period beginning shortly after the lake formation similar to 12.5 kyr ago. The oxic period is characterized by low sedimentary Mn and Mo concentrations, as well as by the absence of any remnants of anoxygenic phototrophic sulfur bacteria. Enhanced accumulation/preservation of Mn (up to 5.6 wt%) in the sediments indicates an intermediate, Mn-enriched oxygenation state with fluctuating redox conditions during a similar to 2300-year long transition interval between similar to 12.1 and 9.8 kyr BP. We propose that the high Mn concentrations are the result of enhanced Mn2+ leaching from the sediments during reducing conditions and subsequent rapid precipitation of Mn-(oxyhydr) oxide minerals during episodic and short-term water-column mixing events mainly due to flood-induced underflows. At 9800 +/- 130 cal yr BP, a rapid transition to fully sulfidic conditions is indicated by the marked enrichment of Mo in the sediments (up to 490 ppm), accompanied by an abrupt drop in Mn concentrations and the increase of molecular biomarkers that indicate the presence of anoxygenic photosynthetic bacteria in the water column. Persistently high Mo concentrations >80 ppm provide evidence that sulfidic conditions prevailed thereafter until modern times, without any lasting hypolimnetic ventilation and reoxygenation. Hence, Lake Cadagno with its persistently stable chemocline offers a framework to study in great temporal detail over similar to 12 kyr the development of phototrophic sulfur bacteria communities and redox processes in a sulfidic environment, possibly depicting analogous conditions in an ancient ocean. Our study underscores the value of combining sedimentological, geochemical, and microbiological approaches to characterize paleo-environmental and -redox conditions in lacustrine and marine settings.

Seasonal variation of high-molecular-weight compounds in the water-soluble fraction of organic urban aerosols

Aerosol samples were collected in Zurich, Switzerland, at an urban background site and were analyzed with size exclusion chromatography (SEC) and laser/desorption ionization mass spectrometry (LDI-MS) for water-soluble organic compounds with high molecular weight. Daily samples were collected during two campaigns in winter and summer, for 1 month each. The concentration of high-molecular-weight compounds (humic-like substances (HULIS)) was between 0.4 and 4 μg/m3 in winter and summer. The most intense signals in the LDI-MS mass spectra were measured between m/z150 and 500, comparing well with the mode of the two main high mass peaks determined with SEC corresponding to masses between 200 and 600 Da. For the maximum molecular weight, however, different results were obtained by the two techniques: whereas a maximum molecular weight between 1300 and 3300 Da was found with SEC, hardly any peaks above m/z700 were measured with LDI-MS. During summer the maximum molecular weight of HULIS (determined with SEC) correlates positively with several parameters such as ozone and increased temperature indicative of enhanced atmospheric photo-oxidation. The HULIS concentration also correlates positively with the oxalic acid concentration in the particles. This suggests that HULIS are generated by secondary processes in summer. The lack of such correlations during winter suggests that other sources and processes might be important during colder seasons.

Molecular Machanics of Water Monomer-Maple Code

This is the Maple code to support the molecular dynamics of a water monomer molecule, allowing investigation of the classical vibrations of this molecule.

Molecular Mechanics of Water Monomer

Simulation of the classical molecular dynamics of a water molecule can be useful in explaining normal modes of motion, Fourier Transforms, and fundamental frequencies of vibration, as illustrated herein.