Journal of Computational Methods in Sciences and Engineering

Quantum chemistry calculations were carried out, using density functional theory, in order to investigate the thermodynamic properties, enthalpy (ΔH), Gibbs free energy (ΔG) and equilibrium constant (K_eq), for the dissociation of a series of methylmercury series compounds. Two kind of pseudopotentials were studied, the relativistic compact effective potentials and the Stuttgart pseudopotential. The B3LYP, BLYP, BP86 and BMK functionals were employed. The calculations were performed in gas phase and in presence of solvent. The results reveal that, none of the studied functionals was able to reproduce the experimental C-Hg and Hg-X, X=Cl, Br and I bond distances. The presence of solvent, water, acetonitrile and dimethylsulfoxide, has a strong influence on the ΔH and ΔG values. On the other hand, the results show that there is a lineal correlation between the logarithm of the experimental K_eq(exp) and the calculated K_eq(theo). This type of correlation could be useful in the resolution of problems related with the contamination by methylmercury compounds.

The present study deals with a multiple reaction system in both gas and liquid phases considering the effect of gas-liquid mass transfer limitations in a trickle-bed reactor where the catalytic hydrotreating of gas oil reaction is being carried out. The hydrodesulfurization (HDS) and hydrogenation (HYD) of aromatics reactions over NiMo and CoMo catalysts are taken into account in the model. The reactor model was codified as a user-added unit operation in PROvision process simulator (V 5,0), in FORTRAN language. This model is used to predict reactant conversion and product distribution as a function of inlet condition. The differential equations are solved by the LSODE program. The PROvision process simulator provides the database for physical and thermodynamics properties of the components through appropriate liquid-vapor equilibrium models.

One of the major issues in the kinetic modeling of refining processes, such as hydro treatment (HDT) of gas oil, consists in that oil by-products contain a large number of individual components which are difficult to handle. In this sense, the concept of continuity in order to describe the elements of such mixtures through a continuous distribution function sheds some light to manage the problem. From this approach, a kinetic model is proposed in this paper for the hydrogenation (HYD) of gas oil, whose composition is described by a gamma distribution function regarding the carbon number. Besides, as the first approach, a pseudo-homogeneous model of the reagent system made of the reactions of hydrodesulphurization (HDS) and HYD with a kinetic of pseudo-first order regarding the hydrocarbon was considered. This model allows evaluating the composition of the product for kinetic constants reported in the literature by obtaining outputs with acceptable errors for all the families except for those related to the reaction of HYD of mono aromatics, whose kinetic constant needs to be better adjusted to the experimental data. Additionally, the model allows predicting in details la composition of the families present in the result of the reaction in terms of distribution functions regarding the number of the carbon atoms. This yields to a molecular detail level good enough to estimate properties of interest, such as density and distillation, for the characterization of the hydro treated gas oil.

In this work, a QSAR analysis of antimalarial activities of a set of 21 ester and ether derivatives of dihydroartemisinin is performed by employing molecular quantum similarity indexes as descriptors. The QSAR model deals with the IC₅₀ biological response of the parasite P. falciparum, and is constructed employing a partial least square method from the quantum similarity results used as molecular descriptors, finding that a satisfactory quantitative model is obtained. A statistical analysis is performed to elucidate the relevant structural features in the biological activity, revealing the importance of the lactol oxygen conformation in dihydroartemisin.

In this work we present an algorithm for finding the global minimum of the energy in atomic clusters. The proposed algorithm combines the Monte-Carlo Wang-Landau random walk, local minimizations and heuristic moves of the energetic surface atoms. We test the algorithm with the optimizations of Lennard-Jones clusters. The algorithm is able to obtain each one of the global energy minima that are reported for Lennard-Jones clusters between 2 and 150 atoms.

A general and numerical algorithm using Mathematica v. 2.0 is presented for calculating the stability ratios and interaction potential energy between two spherical colloidal particles according to the DLVO theory. The algorithm is applicable to electrolytes with any number of ionic species having any valence state and superficial potentials on the particles. The algorithm is versatile to allow change the values of the parameters that characterizes the colloidal system and is suitable to plot the stability curves for a given set of radii, Hamaker constant, superficial potential, electrolyte concentration range, and electrolyte valence. The algorithm was implemented on two models of DLVO interaction potential and is appropriate for analysis of coagulation tendencies of spherical colloidal particles.

In a previous work (J. Mol. Struct.: THEOCHEM, 769, 165 (2006)) we have addressed a detailed study of the set of parameters that must be used within the scope of DLVO theory for a calculation of stability ratios of colloidal particles through an approximate expression. The approximate form of the equation that defines of the stability ratio W, derived in the mentioned work above, requires as much of the knowledge of the maximum of interaction potential energy between particles, V m a x , and its position H m a x , as well as the absolute value of the second derivative of interaction potential energy with respect to position at H m a x , | V ( H m a x ) | . Since these maximum parameters come determined for a concentration defined of the electrolyte is possible to establish the dependence of those with such concentration by letting the fitting constants depend on superficial potential, Hamaker constant and size of the particles. In this work we presented correlations between the maximum parameters ( V m a x and H m a x ) and the univalente symmetrical electrolyte concentration for a system of two spherical colloidal particles with constant of Hamaker, superficial potential and size well-known. The curves of energy of interaction as a function of the distance of separation of particle surface were obtained for two models of DLVO potentials. For appropriate conditions, the reported correlations give equations that are independent of DLVO potential model and can be used to evaluate the approximated stability ratio for systems of identical particles (homocoagulation) as well as the particle systems with different superficial potentials (heterocoagulation). The approximate stability ratios calculated with these correlations can be determined with an error smaller than 5% compared to obtain from the DLVO potential curves.

MoS₂ bulk packing was studied using the Atoms in Molecules Theory. The network of bond paths describing the atomic connectivity has shown that the crystal graph of this material results from the packing of three types of polyhedra containing cage critical points localized at d, f and a Wyckoff position. Alternatively, the crystal packing can be described by means of the basin of the Mo and S atoms with D 3 h and C 3 v symmetry, respectively. These basins display the full local point-group symmetry at the nuclear sites, and fill the space without overlapping. S-S secondary bonds in the interlayer region of this layered material were also determined. The presence of these bonds is fundamental for the found packing of the MoS₂ bulk.

Calculations with an asphaltene model were carried out by the CATIVIC program using an average asphaltene molecule that reproduces a set of physical–chemical properties of the Tia Juana Venezuelan heavy crude oil 500 + residue. The asphaltene was divided into several fragments to study the interaction of H°, CH₃°, and CH₃CH₂° radicals on the aromatic region of each fragment. Validation respect to DFT was performed. CATIVIC code gives higher adsorption energy values than DFT one. Qualitative results indicate, in both programs, that it is feasible the formation of radical species adsorbed on the asphaltene surface fragments. These adsorptions lead to surface distortions and electronic charge transfers from the adsorbate to the asphaltene surface. The adsorption energy for all fragments follows the order: H°> CH₃°> CH₃CH₂°. It is proposed that the presence of asphaltene in thermal cracking may be to act as an inhibitor of radical chain formation.

In this study, we carried out two-layer ONIOM calculations to determine the energy changes for the gold-exchanged silicoaluminophospate (Au/SAPO-11) catalysts interaction with CO, H₂, and H₂O molecules, and the formation of possible intermediate species, such as HO=C=OH. The results reveal that the [CO(OH)Au(H)]⁺ and [H⁺OHAu]⁺species formation as well as HCOOH and the HO=C=OH intermediate formation are energetically favorable processes. This work shows for the first time the potential ability of the Au/SAPO-11 catalyst to perform water gas shift reaction (WGS).

A study of the ground and the first five electronic excited singlet states properties of urea and thiourea molecules is reported. Our interest lies on structural features (bond distances and angles), electronic behavior (energy, dipole moment, charges), and the linear (polarizability) and nonlinear (first hyperpolarizability) optical properties of these relevant molecules within each excited state and how different they are from the ground state. Ground state properties were evaluated using ab initio and Density Functional Theory methods at HF, MP2, BLYP, and B3LYP levels on the corresponding optimized geometries, while excited states properties were determined through the CIS and CIS(D) procedures. The standard 6-31+G(d,p) and 6-311++G(3d,3p) basis sets were employed for all these calculations. The results of the ground state properties of urea and thiourea excellently agree with most of the available data in the literature. Moreover, excited state properties appear to be strongly affected within each state, and in general, they are quite different from the ground state values. Particularly, the first hyperpolarizability β represents the most affected property, and some interesting trends are proposed and discussed. Finally, based on our results, we suggest that a study of the excited state properties of both urea and thiourea derivatives can be useful as a guide for designing new nonlinear optical materials.

The nature of small nickel sulfide clusters was explored using the atoms in molecules theory and a based-electrostatic potential methodology. It was found that Ni₃S₄, whose structure corresponds to a C_3V {7, 9, 3} pyramid, should be (at 0 K) the most stable of the studied nickel sulfide clusters. Electrostatic potential results suggest that the Lewis acidity of the studied cluster is much larger (and therefore much more HDS reactive) than the respective acidity of the practically inactive Ni₃S₂ (111) surfaces. Atomistic thermodynamic calculations have shown that at typical HDS working conditions very small particles of non supported nickel sulphide should be mainly present as Ni₃S₄ cluster.

A theoretical study on the static linear (α) and nonlinear (β and γ) optical properties in gas phase of Photofrin and Foscan molecules is reported. These compounds are known as porphyrin derivatives which act as photosensibilizers in photo dynamic therapy for cancer treatment. The geometric parameters of Photofrin and Foscan were fully optimized using ab initio and Density Functional Theory levels, at Hartree-Fock and B3LYP hybrid functional approach, respectively. The STO-3G, 3-21G* and the 3-21+G standard basis sets were employed for the calculations. The 3-21+G basis set is augmented with one s and three p diffuse functions for carbon, nitrogen, oxygen and sodium atoms. The bond distances and the bond angles of the two optimized molecules obtained with different method/basis set combinations show only minor variation. The Hartree-Fock and B3LYP methods provide a suitable evaluation of the geometrical and optical properties of Photofrin and Foscan molecules, since the calculated α_ave, β_v and γ_ave results are in good agreement with previous reports for similar porphyrin derivatives. The optical properties of Foscan and Photofrin molecules have the same tendencies: the α_ave results have an almost linear relationship with the conjugated bond number, the β_v results are mainly determined by the nature and symmetry of the susbstituent groups to the porphyrin centre and the γ_ave results are extremely depending on the calculation strategies.

From experimental data of five residues of Venezuelan crudes, standard criteria of molecular characterization, molecular modeling and quantum semi-empirical calculations, a set of average molecular structures are proposed for their corresponding asphaltenes.

The geometries of the proposed molecules were compared with structures of different asphaltene origins reported in the literature, where significant similarities and differences are observed for some cases. However, the molecular weights, H/C ratio, the number of aromatic and aliphatic carbons and the number of-CH3,-CH2-, CH- aliphatic groups of the average structures of the hypothetical asphaltenes, proposed in this work, agree satisfactorily with experimental values of very well know models.

To rationalize the similarities and differences between the proposed asphaltenes and those of the literature, a theoretical study at semi-empiric level of the structures, energetic and thermodynamic properties was performed using the PM3 and PM6 parameterizations as implemented in MOPAC 09 software. As criteria for the stability of the asphaltenes, calculations were carried out for the heats of formation and the associated thermodynamic properties within 200 to 900 K temperature range.

At 298.15 K, the results show that for the extended asphaltene structures the formation heat are underestimated at PM3 level, while the PM6 parametrization lead to values of this property that are consistent with the expected values according to the size, molecular composition and chemical nature of the studied structures.

By other hand, it was determined that there are exist significant linear correlations between calculated thermodynamic parameters and variables that depend on the intrinsic structure of asphaltenes, such as molecular weight, total number of carbon atoms and total number of aromatic rings.

We report a theoretical study of the electron correlation, basis sets and substituent effects on the average of the dipole polarizability and second hyperpolarizability, <α> and <γ>, respectively, of a pair of DAAD quadrupolar isomers. The geometric optimization calculations were carried out at the HF, MP2 and DFT (B3LYP and BHHLYP) levels of theory using different basis sets. The results show that the electron correlation effects for the dipole polarizability <alpha> are consistent between the MP2 and DFT levels, whereas for the second hyperpolarizability <γ> the DFT performance shown significant differences with respect to the corresponding MP2 results. This behavior does not change with the variation of the employed basis sets.

Regarding to the substituent effects, the results show that electron donor groups in conjunction with extended basis sets increase the values of <alpha> and <γ> at all levels of theory. In particular, -N(CH₃)₂ and -OCH₃ groups are the substituents that lead to the highest values for these properties. We have also found that there exists a geometry dependency associated to the type of isomer on the <gamma> values.

One current vaccine candidate against Plasmodium vivax, targeting asexual blood stages, is the major merozoite surface protein-1 of P. vivax (PvMSP-1). Vaccine trials with PvMSP-1₁₉ and PvMSP-1₃₃ have succeeded in protecting monkeys and it has been shown that a large proportion of individuals naturally exposed to P. vivax infection, develop specific antibodies to PvMSP-1₁₉. In the present study, computational protein-protein docking was used to predict the structure of the antigen--antibody complex between PvMSP1₁₉ and the Fab region of the G17.12 monoclonal antibody. This antibody does not inhibit erythrocyte invasion or MSP1 processing, but it recognises a discontinuous epitope on PfMSP1₁₉ that has been mapped to regions recognised by invasion-inhibiting antibodies. The molecular simulations were performed using, as starting structures, the Fab fragment of the P. falciparum MSP1₁₉-mAbG17.12 complex (pdb:1ob1) and the structure of the P. vivax MSP1₁₉ previously determined by homology modeling. The mAb was submitted to a docking procedure with antigen PvMSP1₁₉ using the programs PatchDock and FireDock to obtain an initial structure for the complex. A final optimization was performed with RosettaDock using a Monte Carlo algorithm. The final structure of the PvMP1₁₉-mAb17.12 complex shows that the antibody recognizes a discontinuous epitope that include segments on the first domain and some residues at the end of the second domain. The model provides valuable guidelines for future experimental work devoted to the identification of B-epitopes and synthesis of peptides with antigenic activity.