The use of spreadsheets in chemistry is common, mainly in analytical and physical chemistry, where they are used to calculate systems of linear equations, nonlinear equations using the iterative NewtonRaphson method, linear least squares regressions, etc. All these applications are well described in articles (15) and books (6, 7). Besides calculational facilities, commercial spreadsheets also have advanced numerical tools packages that allow sophisticated calculations in multivariate statistics, as well as linear and nonlinear optimizations, Fourier transforms, and much more. These packages often contain graphical facilities that allow 2D and 3D graphics of functions and discrete point sets. However, finding these tools is not easy, because they are usually not readily apparent from the documentation accompanying the programs. The goal of this article is to emphasize the capabilities of spreadsheets in solving specific problems common in chemistry, such as nonlinear curve fitting. Nonlinear least squares fitting is used, for example, in deconvolutions of overlapping bands in vibrational or electronic spectra and in analysis of chemical kinetics. Frequently, fits of nonlinear equations are done using the GaussNewton or Marquardt methods (810). However in this work we use the quasi-Newton method (11).
Purple acid phosphatases (PAPs) constitute a new class of metalloenzymes that catalyze the hydrolysis of certain phosphate esters, including nucleoside di- and triphosphates and aryl phosphates, under acidic conditions. To provide some insight into these metalloenzymes we have performed quantum chemical and molecular mechanics calculations based on the mixed-valence [FeIIFeIII(BPBPMP)(OAc)2]+ model complex (1) (H2BPBPMP = 2-bis[{(2-pyridylmethyl)-aminomethyl}-6-{(2-hydroxybenzyl)-(2-pyridylmethyl)}-aminomethyl]-4-methylphenol). The geometric and the vibrational parameters calculated by molecular mechanics show that the force fields established in this work reproduce the binuclear iron core with µ-phenoxo or µ-alkoxo and di-µ-acetate bridges presented in the PAPs model complexes. The atomic orbital analysis of the SOMO contributions indicated that the FeIII atom and the terminal phenolate are involved in the phenolate to FeIII charge transfer electronic transition in 1 as argued from electronic spectroscopic data in the PAPs. Key words: mixed-valence FeIIFeIII complex, purple acid phosphatases, molecular modeling.
The equilibrium geometries, vibrational frequencies, heat capacity, and heat of formation for compounds of general formula HBrOx were calculated by DFT (BP and pBP methods) with DN* and DN** numerical basis sets. The comparison of our HOBr calculated results with the HOBr experimental values points out that the BP and pBP methods are as good as other ab initio and DFT methods related in the literature employing extended basis sets. The calculated HBrOx total energy and heat of formation values, at 0 and 298.15 K, present the following order: HOBr < HBrO; HOOBr < HOBrO < HBrO2; HOOOBr < HOBrO2 < HOOBrO < HBrO3. The HBrOx heat of formation was calculated using isodesmic and homodesmic reactions and the results show that, in general, the use of these reactions gives similar results.Key words: HOBr, HBrO2, HBrO3, DFT, numerical basis.
Recebido em 3/9/01; aceito em 27/2/02 METHODOLOGY TO OBTAIN MOLECULAR MECHANICS PARAMETERS APPLIED TO COORDINATION COMPOUNDS. A methodology is presented to obtain force field parameters to be used in molecular mechanics. The case of Ru(II) is investigated and the parameters obtained, specially its covalent radii, are employed to model Ru(II) coordination compound. The combined use of molecular mechanics with ab initio methods allowed us to predict the metal-ligand stretching force constant for Ru(II) coordination compounds.
The geometrical structures and the vibrational spectra of the HOBr·(H2O)n clusters (n = 14) have been calculated at the DFT level of theory, using the pBP method and the DN* and DN** numerical basis sets. The results showed that the interaction involving the H of the HOBr and the O of the water molecule represent the preferred arrangements for these hydrated compounds. Both HOBr·H2O and HOBr·(H2O)2 clusters presented stable structures with syn and anti conformations, the syn being the most stable. The HOBr·(H2O)3 and the HOBr·(H2O)4 clusters have presented stable cyclic structures. In the HOBr·H2O and HOBr·(H2O)2 clusters, low-frequency stretching values could be assigned to hydrogen bonds, but the same could not be done so clearly for the HOBr·(H2O)3 and the HOBr·(H2O)4 cyclic clusters. The binding energies were also determinated for these HOBr hydrated clusters, showing that the addition of a water molecule to the HOBr·H2O and HOBr·(H2O)2 clusters increases the binding energy by approximately 4 kcal mol1, while the addition of a water molecule to the HOBr·(H2O)3 cluster decreases this value by 4 kcal mol1.Key words: DFT, numerical basis, HOBr·(H2O)n, clusters.
Recebido em 1/11/10; aceito em 28/4/11; publicado na web em 14/6/11 INTERACTION OF SMALL ATOMS WITH TRANSITION METAL CLUSTERS. Density Functional Theory (DFT) calculations on the interactions of small atoms (H, C, O, and S) on first-row transition metal clusters were performed. The results show that the adsorption site may vary between the metal surface and the edge of the cluster. The adsorption energies, adatom-nearest neighbor and adatom-metal plane distances were also determined. Finally, the authors present a discussion about the performance of these metals as anodes on solid oxide fuel cells. The results obtained agree with empirical data, indicating that the theoretical model used is adequate.Keywords: density functional theory; solid oxide fuel cells; transition metal. INTRODUÇÃOA posição dos átomos adsorvidos em uma superfície metálica é uma característica importante na descrição dos processos que dependem da adsorção. Além disso, a interação de átomos com superfícies metálicas tem um papel preponderante em vários processos catalíticos e eletroquímicos. Por isso, espera-se que tais parâmetros fundamentais sejam rigorosamente descritos em termos de energia. O nível atual de desenvolvimento da Química Computacional permite uma abordagem mais próxima do real nestes tópicos.1,2 Os sítios de adsorção em superfícies metálicas diferem principalmente no número de primeiros vizinhos (número de coordenação) e simetria bidimensional. Como a interação adsorvente-adsorbato é atrativa, espera-se que um átomo adsorvido interaja com o maior número de átomos metálicos, a fim de reduzir a energia de interação.Cálculos usando a teoria do funcional de densidade (DFT) foram usados a fim de se estimar a energia de adsorção de pequenos átomos sobre superfícies metálicas. Espera-se que tais cálculos complementem o conhecimento adquirido com dados experimentais. Diversas reações de interesse industrial, bem como alguns processos de conversão de energia, como o desenvolvimento de células a combustível, podem se beneficiar destes esforços combinados. Neste assunto específico, o papel de átomos como H, C, O e S é importante, pois estas espécies estão presentes em combustíveis (seja na forma de constituintes ou de contaminantes) usados em células a combustível. [3][4][5] Ao se considerar o mecanismo mais apropriado para descrever os fenômenos que ocorrem em anodos do tipo cermet, é preciso considerar diferentes rotas reacionais que possam ocorrer nas superfícies anódicas, formadas pelas interfaces entre metais, eletrólitos e gás combustível (ponto triplo, TPB). O transporte de gás e íons ocorre em várias etapas: difusão das espécies reativas pela fase gasosa; adsorção dissociativa de gases na superfície do metal ou eletrólito (formação de H ad e O ad ); difusão das espécies adsorvidas na superfície e, transferência de carga na superfície metálica, seguindo a equação geral:(1) onde, [] metal refere-se a um sítio ativo na superfície metálica e os demais símbolos seguem a notação de Kroger-Vink.De acordo com alguns resultados empírico...
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