Journal of Computational Methods in Sciences and Engineering

The gas-phase elimination kinetic of 4-bromobutyric acid to give butyrolactone, and hydrogen bromide was studied using Density Functional Theory (DFT) and Moller-Plesset Perturbation Theory of Second Order (MP2) to investigate the more reasonable reaction mechanism. Good agreement of calculated activation parameters with the experimental values was obtained when using PBEPBE/6-31++G(d,p) level of theory. Analysis of the calculated thermodynamic and kinetic parameters suggested the reaction mechanism is unimolecular, with involvement of the hydroxyl oxygen of the carboxylic moiety of the substrate assisting the exit of bromide in nucleophilic substitution. The alternate mechanism with the participation of the carbonyl oxygen in a slow step to give an intimate ion-pair intermediate was disregarded due to the high energy of activation. Bond order analysis shows the process is dominated by the breaking of the C-Br bond. The reaction can be described as unimolecular and moderately non-synchronous process.

The mechanisms of the gas-phase elimination kinetics of 1-chloro-3-methylbut-2-ene and 3-chloro-3-methylbut-1-ene and their interconversion have been examined at MP2 and DFT levels of theory. These halide substrates yield isoprene and hydrogen chloride. The results MPW1PW91 calculations agree with the experimental kinetic parameters showing the elimination reaction occurs at greater rate for 1-chloro-3-methylbut-2-ene than that for the 3-chloro-3-methylbut-1-ene isomer. The mechanism for the molecular elimination of 1-chloro-3-methylbut-2-ene suggests proceeding through an uncommon six-membered cyclic transition state for alkyl halides in the gas phase, while 3-chloro-3-methylbut-1-ene eliminates through the usual four-membered cyclic transition state. The elongation and subsequent polarization of the C-Cl bond, in the direction of C^δ+…Cl^δ-, is rate determining step of these reactions. The isomerization of 1-chloro-3-methylbut-2-ene and 3-chloro-3-methylbut-1-ene was additionally studied. The 1-chloro-3-methylbut-2-ene converts to 3-chloro-3-methylbut-1-ene easier than the reverse reaction. This means that 1-chloro-3-methylbut-2-ene was found thermodynamically more stable than 3-chloro-3-methylbut-1-ene.

We study by kinetic Monte Carlo simulations the dynamic behavior of a Ziff-Gulari-Barshad (ZGB) model for the catalytic oxidation of CO on a surface. It is well known that the ZGB model presents a continuous transition between an oxygen poisoned state and a reactive state that it is not observed in nature. Based on some experimental results that indicate that the oxygen atoms move away from each other upon dissociation at the surface, we modify the standard ZGB model by changing the entrance mechanism of the oxygen molecule. We study three different ways in which the oxygen atoms can be adsorbed at the surface such that the nonphysical continuous phase transition disappears. We calculate the phase diagram for the three cases and study the effects of including a CO desorption mechanism.

The hydrodynamics of a dispersed air-water system within a spouted column with a concentric draft tube and a conical base is simulated using CFD based on a two-fluid Euler-Euler (E-E) modeling framework and k-𝜀 two-equation turbulence closure. The interaction between the dispersed gas phase and the continuous liquid phase is characterized by bubble-liquid interphase forces (drag, turbulent dispersion and lift forces). The Ishii-Zuber drag model [1] and Grace adjusted drag model [2], the latter represented by: C D Grace , dense = υ g p C D Grace , are compared for their capability to match experimental gas hold-up. Numerical results of Reynolds-averaged Navier-Stokes equations with k-𝜀 two-equation turbulence closure model when compared with Pironti experimental data [3] indicated that both drag models, predicted the air hold-up within experimental errors. Furthermore, Ishii-Zuber liquid-gas drag model consistently provided better agreement with experimental results; it correctly determines the hold-up within 0.14%. Numerical agreement with adjusted Grace liquid-gas drag model, is exponent dependent ( 4 ⩽ p ⩽ − 0.5 ), turning down that the best computed hold-up is within 0.44% for p = 0.5 .

A cellular automata model of polyelectrolytes is studied using NetLogo, a multi-agent modelling environment based on the Java virtual machine. NetLogo allows easy construction of cellular automata models, is free to use and has a detailed documentation and examples library. In order to illustrate the working principles of NetLogo, we study polyelectrolyte conformations in a liquid salt solution using the so called cluster entropy ( S C ) as an order parameter. Our results predict the correct evolution of polyelectrolyte conformations, from collapsed clustered structures, at low charge/high salt concentration conditions, to elongated chains, at high charge/low salt concentration, as had been reported in the literature. In both of these situations the cluster entropy is approximately zero ( S C ≈ 0 ). In intermediate charge and salt concentration conditions the well-known pearl necklace structure is observed, in this case the values of S C reach a maximum. The use of NetLogo modelling environment along the cluster entropy concept, permits quick and objective descriptions of the spatial properties of polyelectrolytes.

In this work, a study of the optical properties of Dibenzylideneacetones (a-c) and 3-Benzylidenethiochroman-4-ones (d-e) is presented. Optical measurements and theoretical approaches are used to establish the contribution of electron donor-acceptor groups in the apparition of fluorescence emission.

Recently, multi component crystals composed of two or more molecules that form a unique crystalline structure having unique phase and properties, where its components are bond together via hydrogen bonds, have been the subject of great deal of attention, in particular those where aminoacids participate in their structure. In this work we have studied a system formed by the acids 1,1-cyclobutanedicarboxilic and isonipecotic. We have analyzed the HB-network present in the crystallographic system and compared it with that found computationally. Next, we have studied the energetic of the system and the factors that lead to its stabilization. Finally a comparison between the geometry of the crystallographic packing and that obtained from the computational calculations has been carried out, looking for an understanding of the elements that lead to the observed relative distribution and orientations of the participant molecules, i.e. to the special arrangement of the reported crystallographic structure.

In this paper we study the manifestations of cooperative effects in the formation of clusters4-methyloxycarbonyl-2-azetidinone. Structural properties of the clusters were obtained at the DFT/B3LYP/6-311G(d) level of calculation, while the energetic ones were calculated at the B3LYP/6-311G(d), B3LYP/6-31++G(d,p) and HCTH407/6-31++G(d,p) DFT levels. The calculated structural parameters were compared with those corresponding to crystal structures reported for similar compounds in the Cambridge Structural Database. It is obtained that the theoretically optimized clusters form hydrogen bond patterns resembling those patterns reported for the crystal structure of azetidinone derivatives. We find that, due to the formation of consecutives hydrogen bonds of the type N-H…O between the 2-azetodinone rings, the addition of monomers gradually increases the stabilization energy per monomer of the system. It is also observed that after the hexamer formation, the value of this stabilization energy tends to reach an asymptotic limit, behavior typical of the existence of cooperative effects. Additionally, manifestations of these effects were observed in the variations with the size of the clusters of the calculated charges and of the structural parameters.

A reaction network for acid-catalyzed hydrocarbon hydroprocessing in the C2 to C12 range has been generated, as part of a larger work to model a naphtha hydrocraking unit at the elementary step level. The structure of the feedstock molecules is stored as Boolean matrixes, facilitating their mathematical manipulation according to the rules of each elementary reaction step during the reaction network generation. Detailed algorithms and examples are shown for every elementary reaction step. Acyclic and cyclic species are considered, up to two fused aromatic, olefinic or naphthenic rings. Besides conventional elementary reactions, algorithms for aromatic isomerization (methyl and ethyl migration) and dealkylation were developed. It must be highlighted that the complexity of the reaction network should be weighed against the available chromatographic data resolution. Therefore, mathematical restrictions might be added to the generated structures, such as maximum number of ramifications or maximum molecule size within a group of isomers. A sensitivity analysis of these restrictions was carried out, to determine their impact on the dimension of the generated reaction network.

The adiabatic interaction energy (IE) of the ground He ( 1 S ) ⋯ BF ( X 1 Σ + ) and excited He ( 1 S ) ⋯ BF ( a 3 Π ) electronic states of the van der Waals (vdW) system He ⋯ BF are studied in the present contribution in the framework of the supermolecule approach at the RHF-CCSD(T) level of theory. Calculations predict a global minimum and a shallow local minimum separated by a saddle point for the ground state; the most stable configuration occurs at βe=180°, equilibrium distance Re=6.63 a_o and equilibrium dissociation energy De=21.87 cm⁻¹. The calculated IE for the excited 3 A ′ state reveals two local minima and a global minimum separated by saddle points; the most stable configuration occurs at βe=121°, R_e=6.15 a_o and De=28.27 cm⁻¹. The resulting IE of the excited 3 A ″ state reveals two minima separated by a saddle point; the most stable configuration occurs at βe=76°, R_e=6.02 a_o and De=38.47 cm⁻¹. The corresponding vertical electronic excitation energies and shifts in the fluorescent spectrum with respect to the isolated BF molecule are calculated as a guideline for future theoretical and experimental work.

A computational study was conducted to determine the most stable configuration geometry, and to evaluate the stabilization energy in the interaction between different test aromatic compounds. Dimers of benzene, naphthalene, anthracene, and, one trimer comprised of two benzene molecules and one molecule of naphthalene, were the subjects of the study. Gaussian 09 quantum chemistry suite ab initio calculations were performed by using MP2 method and the basis set G-311G**. The exponent for the polarized d orbital of carbon α d(C) was given the value 0.8200. Such value was obtained from the benzene dimer optimization with very similar results as those reported from the CCSD(T) method. This methodology was implemented for evaluating the stabilization energy trend with increasing number of aromatic rings in the interacting molecules. Among all the cases studied the energy minimum was obtained for the one having the conformation of displaced parallel molecules. This result seems to indicate that it is also possibly to obtain such stable conformation in the case of more complex aromatic systems of the same sort as the one considered here.

Intermetallics AlTi, Al₃Ti and AlTi₃ have been characterized in terms of the electron density topology. Atomic properties such as atomic charge and atomic volume were determined using the theory of atoms in molecules (AIM). Our calculations indicate a good match between the electron density difference, Δρ, and enthalpy of formation of each intermetallic, as well as the electric work function (EWF). We also found an excellent correlation between the EWF, deduced from the topological charges of the intermetallics, and EWF determined experimentally, demonstrating the predictive scope of our model.

A method based on an image analysis procedure was developed to calculate the shape and surface tension of pendant droplets hanging down in air from the tip of a syringe. In contrast to most existing methods, a numerical solution of the Young-Laplace equation of capillarity for the calculation of the drop contour is not required. Apart from local gravity and densities of liquid and fluid phases, the only input information needed to determine the surface tension is given by the maximum equatorial radius of the drop and its degree of deformation defined by a shape factor. Specifically it is not necessary to determine the radius of curvature at the apex of the experimental drop profile, the drop height, or the contact angles. When the drops are formed from the tip of a capillary tube, the software obtains direct digitization of the drop image, performs edge detection, and reconstructs the three-dimensional drop from its digitized profile to accurately determine its volume. Surface tension measurements have been performed for distilled water drops suspended in air to test the reliability and accuracy of the method. The results show that reliable values of the surface tension can be obtained for drops larger than about 2–3 μl, with relative errors less than 0.08–0.29 mN m^-1, depending on the size of the holder.

The carbon nanotubes have attracted much interest for their electronic properties which go from metallic to semiconducting behavior, depending both on diameter, number of layers and chirality. The value of their band gap is obviously a crucial point to be addressed because it enters in the nanbotube application as microelectronic devices. This work was developed through an estimate of the behavior of the electronic structure of carbon nanotubes of single walled (8,0) and the assessment of electrical conduction through various methodologies such as LSDA, B3PW91, B3LYP and HF ab initio methods and PM3 and AM1semi-empirical methods. The methods showed similarities with the geometrical parameters reported in the literature. The hybrid methods based on density functional generated a good approximation in the energy gap value of single-walled carbon nanotubes (8,0). Results will be presented.

Quantum chemistry calculations were done, using the ONIOM2 methodology at two different levels of calculation, B3LYP for the high level and UFF for the low level. These calculations were performed on Au₃/SAPO-11, Au₄/SAPO-11, CO-Au₃/SAPO-11 and CO-Au₄/SAPO-11 aggregates to analyze the geometries of small clusters of Au₃ and Au₄ on SAPO-11 support. Au₃ cluster present a triangle structure in Au₃/SAPO-11. Au₄ cluster shows a “Y shaped” structure in Au₄/SAPO-11. Au₄ as a rhombus structure is also studied but it is an unstable intermediate to the “Y shaped” structure. The CO interaction with Au₃ and Au₄/SAPO-11 is studied, this CO adsorption is different from reported in the literature. The formation energy ΔE_F of the aggregates and the CO adsorption energy ΔE_ads on them are presented.

IVIChem is an integrative web environment for computational chemistry that can be accessed globally from any typical computer via the World Wide Web. It assists users all along the research pipeline by facilitating the introduction of molecular geometries, specification of options for a calculation, assembling input files, submission to the calculation queue, monitoring the status of calculations, and graphical analysis of results. IVIChem's graphical user interfaces considerably improve the usability of computational chemistry software in different areas of chemical modeling, and they enhance the performance of researchers by automating the analysis of results and the addition of further calculation packages.

The static dipole (hyper) polarizabilities (α,β and γ) of p-nitrophenylphospine (PNPhP), a hypothetical Push-Pull organic molecule, were calculated using ab initio (HF, MP2, MP4) and density functional theory DFT (B3LYP, CAM-B3LYP, WB97X-D) hybrid approaches, in conjunction with the standard 6-31+G(d,p) and 6-311++G(3d,3p) basis sets. Similar (hyper) polarizability calculations were additionally carried out for p-Nitroaniline PNA molecule for comparison purposes. These response properties were evaluated within the Finite Field methodology based in the Kurtz equations, where the effects of replacing the -NH₂ donor group of PNA by the -PH₂ group originating the p-nitrophenylphospine PNPhP molecule are analyzed. The results of α, β and γ properties evaluated at different levels of theory show that PNPhP molecule is much more (hyper)polarizable than PNA one. Electron correlation effects, evaluated at MP2, MP4, DFT/B3LYP, CAM-B3LYP and WB97X-D levels of theory, show that α_ave increases between 7 to 16% with respect to the HF values. Likewise, the largest responses are obtained with the most extended basis sets such as 6-311++G(3d,3p), where polarizability increase between 4 to 9% with respect to 6-31+G(d,p) one. The tendencies for β and γ NLO values follow the electron density delocalization of the molecular system, that is more extended in PNPhP than PNA one. Electron correlation effects increase β and γ properties in the order of two or three times with respect to the HF values. Finally, the impact of dynamic and solvent effects on the first hyperpolarizability of PNA molecule were also taken into account, which are discussed in terms of recent literature. The analysis of results, allow us to conclude that PNPhP is an interesting hypothetic molecule that can be useful as building block for the design and creation of new materials with enhanced nonlinear optic applications.

Fundamental issues of quantum chemistry related with parametric quantum methods (PQMs), such as, set of elementary functionals (SEF), exact energy functional, and minimax principle (MMP) are discussed in terms of elementary functionals (EF). In this work, it is shown the possibility of PQM development based on two-centers parametric elementary functionals (PEFs) obtained from simulation of analytical EFs, using q-exponential (QE) type functions. All electrons are included and NDO approximations are not considered. Comparison between analytical and PEF for H-H, C-C and C-H pairs of atoms are performed and very reasonable modeling of intraatomic H core (IH), electron-nucleus potential (V), overlap (S), and Coulomb two-center (G) integrals were obtained. Four- and three-center are proposed to be calculated by Mayer’s partition energy (MPE) approximation in terms of one- and two-centers PEFs. Trials for small molecules using PEFs and for MPE approach are presented and a scheme for a new PQM is proposed.