Jesus Rodriguez

MEPSIM: A computational package for analysis and comparison of molecular electrostatic potentials

SummaryMEPSIM is a computational system which allows an integrated computation, analysis, and comparison of molecular electrostatic potential (MEP) distributions. It includes several modules. Module MEPPLA supplies MEP values for the points of a grid defined on a plane which is specified by a set of three points. The results of this program can easily be converted into MEP maps using third-parties graphical software. Module MEPMIN allows to find automatically the MEP minima of a molecular system. It supplies the cartesian coordinates of these minima, their values, and all the geometrical relationships between them (distances, angles, and dihedral angles). Module MEPCOMP computes a similarity coefficient between the MEP distributions of two molecules and finds their relative position that maximizes the similarity. Module MEPCONF performs the same process as MEPCOMP, considering not only the relative position of both molecules but also a conformational degree of freedom of one of them. The most recently developed module, MEPPAR, is another modification of MEPCOMP in order to compute the MEP similarity between two molecules, but only taking into account a particular plane. The latter module is particularly useful to compare MEP distributions generated by π systems of aromatic rings. MEPSIM can use several wavefunction computation approaches to obtain MEP distributions. MEPSIM has a menu type interface to simplify the following tasks: creation of input files from output files of external programs (GAUSSIAN and AMPAC/MOPAC), setting the parameters for the current computation, and submitting jobs to the batch queues of the computer. MEPSIM has been coded in FORTRAN and its current version runs on VMS/VAX computers.

Exploring the Structure–Solubility Relationship of Asphaltene Models in Toluene, Heptane, and Amphiphiles Using a Molecular Dynamic Atomistic Methodology

The solubility parameters, δ, of several asphaltene models were calculated by mean of an atomistic NPT ensemble. Continental and archipelago models were explored. A relationship between the solubility parameter and the molecule structure was determined. In general, increase of the fused-rings number forming the aromatic core and the numbers of heteroatoms such as oxygen, nitrogen, and sulfur produces an increase of the solubility parameter, while increases of the numbers and length of the aliphatic chains yield a systematic decrease of this parameter. Molecules with large total carbon atom number at the tails, n(c), and small aromatic ring number, n(r), exhibit the biggest values of δ, while molecules with small n(c) and large n(r) show the smallest δ values. A good polynomial correlation δ = 5.967(n(r)/n(c)) - 3.062(n(r)/n(c))(2) + 0.507(n(r)/n(c))(3) + 16.593 with R(2) = 0.965 was found. The solubilities of the asphaltene models in toluene, heptane, and amphiphiles were studied using the Scatchard-Hildebrand and the Hansen sphere methodologies. Generally, there is a large affinity between the archipelago model and amphiphiles containing large aliphatic tails and no aromatic rings, while continental models show high affinity for amphiphiles containing an aromatic ring and small aliphatic chains.

Semiempirical study of compounds with intramolecular O—H---O hydrogen bonds. II: further verification of a modified MNDO method

In the forerunner of this article, we described a MNDO modification designed for studies of compounds with intramolecular OH…︁O hydrogen bonds. Here, we report the further verification of the modification by means of its application to 14 compounds not considered in its development. Comparison of the calculated structural parameters and proton transfer characteristics with available experimental or ab initio results, and with those obtained using MNDO, AM1, MNDO/H, MNDO/M, and PM3, supports the validity of the new modification for prediction of hydrogen bond characteristics.

First Principles Study of Low Miller Index RuS2 Surfaces in Hydrotreating Conditions

Density functional theory (DFT) calculations combined with surface thermodynamic arguments and the Gibbs-Curie-Wulff equilibrium morphology formalism have been employed to explore the effect of the reaction conditions, temperature (T), and gas-phase partial pressures (p h2 and p h2s ) on the stability of low Miller index ruthenium sulfide (RuS 2 ) surfaces. The calculated thermodynamic surface stabilities and the resulting equilibrium morphology models suggest that unsupported RuS 2 nanoparticles in HDS conditions are like to a polyhedron with six, eight, and twelve (100), (111), and (102) faces, respectively. The area of these faces covers about 40%, 37%, and 23% of the total particle, respectively. The atomic basins of the outermost individual atoms of the exposed surfaces were determined using the quantum theory of atoms in molecules methodology. Direct visualization of these basins has shown that a hole just at the middle of the outermost sulfur basins provides access to uncovered metal sites. Analysis of the electrostatic potential mapped onto a selected electron density isocontour (0.001 au) on the exposed surface reveals a very high potential reactivity of these holes toward electrodonating reagents. Consequently, the high attraction between these uncovered sites and S atoms coming from reagent polluting molecules makes these kinds of particles quite active for HDS catalysis.

Quantitative comparison of molecular electrostatic potential distributions from several semiempirical and ab initio wave functions

A quantitative comparative analysis of molecular electrostatic potential (MEP) distributions generated from different wave functions was carried out. Wave functions were computed by using MNDO, AMl, STO‐3G, 3‐21G, 4‐31G, 6‐31G, 4‐31G*, 6‐31G*, and 6‐31G** methods. Ten different compounds, which include usual atoms and groups of biomolecules, such as hydroxyl, carbonyl, amine, amide, imine, double and triple bonds, and heteroaromatic rings, were studied. For each compound, MEP values in the points of a common 3‐D grid were computed; thereafter, the similarity between each pair of MEP distributions generated by different methods was assessed. Similarities were measured using the Spearman rank correlation coefficient. A similarity matrix was obtained for each compound. Similarity matrices were averaged and a hierarchical cluster analysis was carried out to classify the different quantum chemical methods. In the compounds studied, the main conclusion is the negligible difference between the pattern of MEP distributions generated from all split valence basis sets (with and without polarization functions).

Impacto del recuento plaquetario preoperatorio en la evolución perioperatoria tras la esplenectomía laparoscópica por púrpura trombocitopénica idiopática

INTRODUCTION Laparoscopic splenectomy (LS) is the preferred treatment of idiopathic thrombocytopenic purpura (ITP) when medical treatment fails. The objective was to evaluate the feasibility and safety of LS according to the preoperative platelet count. METHODS This study is a retrospective analysis of a series of 199 patients who underwent LS for ITP from 1993 to 2015. The patients were divided into 3 groups according to platelet count: group i (<10×10(9)/L), group ii (10-50×10(9)/L) and group iii (> 50×10(9)/L). RESULTS Operative time was significantly lower in Group III compared to Group I and II (100±53 and 105±61min, P<.025)). Intraoperative blood loss was statistically higher in group i (263±551ml) with respect to the other 2: group ii (128±352ml) and group iii (24±62ml) (P<.003). Hospital stay was 6.4±5.8 days in group i, significantly higher compared to groups ii and iii (3.8±2.3 and 3.2±1.8 days, respectively (P<.003)). CONCLUSION Conducting a LS in ITP patients with low platelet counts is effective and safe.

Effects of UV-C Radiation on Viability, Outer Membrane Proteins and Lipopolysaccharides of Shigella

The annual incidence of shigellosis throughout the world is estimated at 164.7 million cases and 1.1 million of those infected die with 69% of all deaths involving children less than 5 years old.

DFT study of the sulfidation pretreatment of molybdenum carbides in the hydrodechlorination reaction of chlorobenzene

The effect of the pre-adsorption of sulfur on the hexagonal-Mo_{2}C-001 surface in the hydrodechlorination HDC reaction of chlorobenzene was studied using density functional theory DFT calculations. The results related with the coordination modes and the adsorption energies of the aromatic molecule suggest that the main effect of the sulfur incorporation into the surface is to lead towards a weaker chlorobenzene adsorption that will benefit the continuity of the catalytic cycle and therefore to avoid the carbonization and chlorination of the catalyst. The study of the HDC mechanism was also performed and two different reaction paths were considered. The calculated energy barriers indicate that both mechanisms may occur at the normal reaction temperature 350°C. These latter approaches involve new roles of the superficial sulfur as atomic or radical hydrogen scavenger for the S-Hformation and as a precursor of the σ chlorobenzene coordination, necessary for effective hydrogenation in the proposed mechanisms.