Monte Carlo thermodynamic and structural properties of the TIP4P water model: dependence on the computational conditions

Classical Monte Carlo simulations were carried out on the NPT ensemble at 25°C and 1 atm, aiming to investigate the ability of the TIP4P water model [Jorgensen, Chandrasekhar, Madura, Impey and Klein; J. Chem. Phys., 79 (1983) 926] to reproduce the newest structural picture of liquid water. The results were compared with recent neutron diffraction data [Soper; Bruni and Ricci; J. Chem. Phys., 106 (1997) 247]. The influence of the computational conditions on the thermodynamic and structural results obtained with this model was also analyzed. The findings were compared with the original ones from Jorgensen et al [above-cited reference plus Mol. Phys., 56 (1985) 1381]. It is notice that the thermodynamic results are dependent on the boundary conditions used, whereas the usual radial distribution functions g(O/O(r)) and g(O/H(r)) do not depend on them.

Descrições estruturais cristalinas de zeólitos

Crystalline structures of zeolites can be studied using different representations: the internal symmetry obtained by X-Ray or neutron diffraction crystallography techniques or a systematic analysis of the basic structural units which can be arranged to build the geometries of each kind of zeolite. In this work the basic concepts of three building units, SBU (Secondary Building Units), SSU (Structural SubUnits) and PBU (Periodic Building Units) are presented. The properties of the resulting crystalline structures are discussed (pores, cavities, channels), describing the influence of each one of these properties in processes of physical-chemical interest. Representative case studies of known zeolite crystalline structures are also discussed in terms of their space group classification.

UDP-N-acetilglicosamina enolpiruvil transferase: determinação dos estados de protonação de resíduos de aminoácidos do sítio ativo pelo método PM6

UDP-N-acetylglucosamine-enolpyruvyl transferase (MurA) catalyzes the reaction between phosphoenol pyruvate and UDP-N-acetylglucosamine. We present a theoretical approach using the semiempirical PM6 method for defining protonation state of three active site residues, K22, H125, and K160. Prior comparison with neutron diffraction data showed that PM6 accurately predicted protonation states of active site residues of b-trypsin and D-xylose isomerase. Using the same methodology with MurA crystallographic data, we conclude that when reaction intermediate is located at the active site, H125 and K22 are in protonated form and K160 in neutral form.

Aggregation of subtropical soil under liming: a study using laser diffraction

Laser diffraction (LD) provides detailed analysis of particle size distribution. Its application to testing the stability of soil aggregates can assist studies on the aggregation of soils with contrasting electrochemical properties. The objectives of the present work were: (a) to propose a protocol for using LD to study soil aggregation, (b) to study the aggregation of an Acrisol under the influence of different doses and forms of lime. Samples were collected in 2005 from a Brazilian Acrisol that in 1994 had received 0.0; 2.0; 8.5 and 17.0 Mg ha-1 of lime, left on the soil surface or incorporated. Aggregates from 4.76 to 8.00 mm diameters were studied using the traditional method proposed by Kemper & Chepil (1965), with wet sieving, while aggregates from 1.00 to 2.00 mm were studied using a CILAS® laser diffractometer that distinguishes particles ranging from 0.04 to 2,500.00 μm. LD readings were made after six consecutive pre-treatments, using agitation times, a chemical dispersion agent and ultrasound. Mean Weighted Diameter (MWD) and the Aggregate Stability Index (ASI) calculated, using the traditional method does not discriminate the treatments. However, LD is able to produce detailed data on soil aggregation, resulting in indexes of stability of aggregates that are linearly related to the doses of lime applied (MWD: R² = 0.986 and ASI: R² = 0.876). It may be concluded that electrochemical changes in the Brazilian Acrisol resulting from incorporated lime affect the stability of aggregates, increasing stability with increased doses of lime.

Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single-crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer.

Nanoporous materials: pillared clays and regular silicas as an example of synthesis and their porosity characterization by X-ray diffraction

Because of their practical applications, porous materials attract the attention of undergraduate students in a way that can be used to teach techniques and concepts in various chemistry disciplines. Porous materials are studied in various chemistry disciplines, including inorganic, organic, and physical chemistry. In this work, the syntheses of a microporous material and a mesoporous material are presented. The porosity of the synthesized materials is characterized by X-ray diffraction analysis. We show that this technique can be used to determine the pore dimensions of the synthesized materials.

Neutron tomography using projection data obtained by Monte Carlo simulation for nondestructive evaluation

This work present the application of a computer package for generating of projection data for neutron computerized tomography, and in second part, discusses an application of neutron tomography, using the projection data obtained by Monte Carlo technique, for the detection and localization of light materials such as those containing hydrogen, concealed by heavy materials such as iron and lead. For tomographic reconstructions of the samples simulated use was made of only six equal projection angles distributed between 0º and 180º, with reconstruction making use of an algorithm (ARIEM), based on the principle of maximum entropy. With the neutron tomography it was possible to detect and locate polyethylene and water hidden by lead and iron (with 1cm-thick). Thus, it is demonstrated that thermal neutrons tomography is a viable test method which can provide important interior information about test components, so, extremely useful in routine industrial applications.