Hélio F. Dos Santos

The hydrolysis process of the cis-dichloro(ethylenediamine)platinum(II): A theoretical study

The hydrolysis process of the cisplatin analog cis-dichloro(ethylenediamine)platinum(II) (cis-DEP) was theoretically investigated at the Hartree–Fock, density functional theory and the second order Moller–Plesset perturbation theory levels of calculation. The stationary points on the gas phase potential energy surface for the first and second hydrolysis steps were fully optimized and characterized. For the first aquation process the gas phase results are in satisfactory agreement with the experimental data. However in order to reproduce the observed rate constant for the second hydrolysis step it is essential to include the solvent effect. The structures and energetic properties are similar to the values found for the parent compound cisplatin, showing that the cis-DEP analog should be considered as a potential drug concerning its hydrolysis process.

Supramolecular complex of fluoxetine with β-cyclodextrin: An experimental and theoretical study

In this work the complex formed between beta-cyclodextrin (betaCD) and fluoxetine (FLU) was investigated by experimental and computational methods. From Horizontal Attenuated Total Reflectance (HATR) was possible to verify a strong modification in the vibrational modes of betaCD and FLU, indicating interactions between them. The Nuclear Magnetic Resonance (NMR) experiments confirm these interactions through the change in chemical shifts in (1)H spectra, reduction in longitudinal relaxation times values, and the Nuclear Ouverhauser Effect confirm the inclusion of aromatic rings of FLU into the betaCD. The structures of the proposed inclusion compounds were optimized at PM3 semiempirical level of theory. In addition, single point calculations at the Density Functional Theory (DFT) level, using the Becke, Lee, Yang, and Parr functional and 6-31G(d,p) basis set, were used to determine the interaction energy for these structures. The DFT calculations identified the aromatic ring, which contains the CF(3) group as the most stable into the betaCD by an amount of, 11.7 kcal mol(-1), in the gas phase. Polarized continuum model, at the DFT level mentioned, was used to investigate the solvent effect, and the results corroborated the gas phase analysis. A high equilibrium constant (K approximately 6921+/-316) and the stoichiometry, 1:1, were obtained by Isothermal Titration Calorimetry (ITC) experiments.

Improved quantum mechanical study of the potential energy surface for the bithiophene molecule

The potential energy surface (PES) for the 2,2′-bithiophene molecule was investigated using Hartree–Fock, correlated MP2, MP4(SDQ), CCSD, and density functional theory levels. Distinct basis sets ranging from double-zeta to triple-zeta quality, with polarization functions added on all atoms, were employed as well as the Dunning correlated consistent polarized valence double-zeta (cc-pVDZ) basis set. Single point configuration interaction CISD calculations were also performed using the cc-pVDZ basis set. Harmonic frequency calculations were performed for the unambiguous characterization of the stationary points located on the PES and also to calculate thermal Gibbs free energy corrections. Regarding the structural predictions we found that the B3LYP/6-311G** and MP2/cc-pVDZ fully optimized geometries exhibit the best agreement with the gas phase electron diffraction data. The calculated B3LYP/6-311G**, MP2/cc-pVDZ and experimental torsional angle for the syn-gauche structure are, respectively, 37.4° (B3LYP...

Spectroscopic and theoretical study of the "azo"-dye E124 in condensate phase: evidence of a dominant hydrazo form.

Spectroscopic techniques, including Raman, IR, UV/vis, and NMR were used to characterize the samples of the azo dye Ponceau 4R (also known as E124, New Coccine; Cochineal Red; C.I. no. 16255; Food Red No. 102), which is 1,3-naphthalenedisulfonic acid, 7-hydroxy-8-[(4-sulfo-1-naphthalenyl) azo] trisodium salt in aqueous solution and solid state. In addition, first principle calculations were carried out for the azo (OH) and hydrazo (NH) tautomers in order to assist in the assignment of the experimental data. The two intense bands observed in the UV/vis spectrum, centered at 332 and 507 nm, can be compared to the calculated values at 296 and 474 nm for azo and 315 and 500 nm for hydrazo isomer, with the latter in closer agreement to the experiment. The Raman spectrum is quite sensitive to tautomeric equilibrium; in solid state and aqueous solution, three bands were observed around 1574, 1515, and 1364 cm(-1), assigned to mixed modes including deltaNH + betaCH + nuCC, deltaNH + nuC horizontal lineO + nuC horizontal lineN + betaCH and nuCC vibrations, respectively. These assignments are predicted only for the NH species centered at 1606, 1554, and 1375 cm(-1). The calculated Raman spectrum for the azo (OH) tautomer showed two strong bands at 1468 (nuN = N + deltaOH) and 1324 cm(-1) (nuCC + nuC-N), which were not obtained experimentally. The (13)C NMR spectrum showed a very characteristic peak at 192 ppm assigned to the carbon bound to oxygen in the naphthol ring; the predicted values were 165 ppm for OH and 187 for NH isomer, supporting once again the predominance of NH species in solution. Therefore, all of the experimental and theoretical results strongly suggest the food dye Ponceau 4R or E124 has a major contribution of the hydrazo structure instead of the azo form as the most abundant in condensate phase.

Quantum-mechanical study of the interaction of α-cyclodextrin with methyl mercury chloride

Abstract The inclusion process involving α-cyclodextrin (α-CD) and methyl mercury chloride (CH 3 HgCl) was investigated using the PM3 quantum-mechanical semi-empirical method. Fully unconstrained geometry optimizations were carried out for the free α-CD and the complexed forms with CH 3 HgCl. The inclusion orientation with the methyl mercury chloride passing perpendicular to the center of the cyclodextrin ring was found to be favored over the experimentally hinted parallel structure. It was also observed that the inclusion takes place in a more favored way when solvation water molecules are explicitly included, therefore stabilizing the complex in relation to the free species. The experimentally observed Raman shift for the Hg–Cl stretching mode after the complexation was used in conjunction with the respective PM3 calculated vibrational frequencies for the determination of the preferred structure for the inclusion complex.

Tetraciclinas e glicilciclinas: uma visão geral

Tetracyclines exhibits activity to a broad range of Gram-negative and Gram-positive bacteria and this fact allied to the low toxicity, low cost, and the advantage of administration by oral route led to their indiscriminate use, which caused the appearance of bacterial resistance to these agents, wich has restricted its clinical utility, though new applications have emerged. On the other hand, the glycylcyclines, semi-synthetic products are similar to tetracyclines, which are active against many bacteria resistant to tetracycline and other classes of antibiotics. The purpose of this paper is to give an overview of this important class of antibiotics focusing on its coordination chemistry and possible applications.

The role of the basis set and the level of quantum mechanical theory in the prediction of the structure and reactivity of cisplatin.

In this article, we conducted an extensive ab initio study on the importance of the level of theory and the basis set for theoretical predictions of the structure and reactivity of cisplatin [cis‐diamminedichloroplatinum(II) (cDDP)]. Initially, the role of the basis set for the Pt atom was assessed using 24 different basis sets, including three all‐electron basis sets (ABS). In addition, a modified all‐electron double zeta polarized basis set (mDZP) was proposed by adding a set of diffuse d functions onto the existing DZP basis set. The energy barrier and the rate constant for the first chloride/water exchange ligand process, namely, the aquation reaction, were taken as benchmarks for which reliable experimental data are available. At the B3LYP/mDZP/6‐31+G(d) level (the first basis set is for Pt and the last set is for all of the light atoms), the energy barrier was 22.8 kcal mol−1, which is in agreement with the average experimental value, 22.9 ± 0.4 kcal mol−1. For the other accessible ABS (DZP and ADZP), the corresponding values were 15.4 and 24.5 kcal mol−1, respectively. The ADZP and mDZP are notably similar, raising the importance of diffuse d functions for the prediction of the kinetic properties of cDDP. In this article, we also analyze the ligand basis set and the level of theory effects by considering 36 basis sets at distinct levels of theory, namely, Hartree‐Fock, MP2, and several DFT functionals. From a survey of the data, we recommend the mPW1PW91/mDZP/6‐31+G(d) or B3PW91/mDZP/6‐31+G(d) levels to describe the structure and reactivity of cDDP and its small derivatives. Conversely, for large molecules containing a cisplatin motif (for example, the cDDP‐DNA complex), the lower levels B3LYP/LANL2DZ/6‐31+G(d) and B3LYP/SBKJC‐VDZ/6‐31+G(d) are suggested. At these levels of theory, the predicted energy barrier was 26.0 and 25.9 kcal mol−1, respectively, which is only 13% higher than the actual value.

On the evaluation of thermal corrections to gas phase ab initio relative energies: implications to the conformational analysis study of cyclooctane

Abstract In this paper we present an investigation of the influence of the thermal correction on the conformational population for the boat–chair (BC) and CROWN forms of the cyclooctane molecule, calculated using quantum mechanical ab initio Hartree–Fock (HF), MP2, MP4SDQ, CCSD and density functional methods (B3LYP, BLYP, BP86) in conjunction with various basis sets. A previous experimental gas phase electron diffraction study pointed out that the BC is either the exclusive or at least the strongly predominant form in gas phase at room temperature. We therefore analyzed the performance of various levels of calculation for the evaluation of the relative conformational population and also the role played by the thermal correction to gas phase calculated relative energies. It turns out that the thermal correction is very sensitive to the presence of low frequency modes that are indeed internal rotations and need to be treated separately, in what the cyclooctane molecule is concerned. Once internal rotations were considered, it can be seen that the HF level of calculation produces very satisfactory values for thermal correction, compared to MP2. Therefore, it can be used in single-point energy calculations employing a high correlated level of theory (MP4SDQ, CCSD), leading to a quite trustable Gibbs free energy difference data. When thermal energies are not corrected for low frequency internal rotation modes, a range of contrasting results is obtained by varying both the quantum mechanical approach and the basis set.

Role of the Substituent Effect over the Squarate Oxocarbonic Ring: Spectroscopy, Crystal Structure, and Density Functional Theory Calculations of 1,2-Dianilinosquairane

This work presents the crystal structure and the investigation under a supramolecular perspective of a squaric acid derivative obtained from the replacement of the hydroxyl groups by anilines. The squaraine obtained (1,2-dianilinesquaraine) crystallizes in the Pbcn space group, in a unit cell with a = 26.5911(8) Å, b = 6.1445(10) Å, and c = 7.5515(5) Å. The bond lengths in the oxocarbon ring, squarate-N and C−O bonds present the character of double bonds. Also the difference between the longer and shorter C-C bond in the four-membered ring (ΔCC) is 0.0667 Å, showing a good degree of equalization of these bond lengths. The phenyl rings are slightly distorted in relation to the squarate ring, and the angle measured between the best plane fitted in each ring is 37.2(9)°. Each molecule is connected to the other through a hydrogen bond involving the N-H···O moieties, where the donor···acceptor distance is 2.826(1) Å, forming ribbons in a unidimensional arrangement C(5)R22(10) along the b axis. These structures are mutually connected by π-stacking interactions extending the supramolecular structure in a two-dimensional fashion. Besides, an interesting crossed structure can be easily identified in the formed sheets that are built through the C-H/π interactions. DFT calculations at the B3LYP/6-311++G(d,p) level of theory show an approximately planar molecular structure for the isolated molecule. However, when a dimer model built from hydrogen bonds is considered, the optimized structure presents considerable torsion between the phenyl and squarate rings, as observed in the experimental data. The electronic spectrum shows a strong absorption band at 341 nm that is red-shifted compared to the squarate maximum absorption (290 nm), indicating a more effective electronic delocalization. The most characteristic vibrational modes of the oxocarbon species were used as spectroscopic probe to understand how the substituent groups affect the oxocarbon moiety and, consequently, the vibrational spectra. The analysis shows that the modes associated with the C-Cox bonds are the most affected. Also the character of the double bond of squarate-N and the single bond for the phenyl-N are easily identified. In a general form, the calculated vibrational modes of the dimer model were in better accordance with the experimental data, mainly when the mode has a contribution from the acceptor molecule in the intermolecular interaction.

ANÁLISE ESTRUTURAL DE CICLODEXTRINAS: UM ESTUDO COMPARATIVO ENTRE MÉTODOS TEÓRICOS CLÁSSICOS E QUÂNTICOS

In the present work, we analyzed the accuracy of distinct theoretical methods to reproduce the solid state structures of cyclodextrins. The a, b and g-cyclodextrins (CD) were considered and also their hydrates with included water molecules: a-CD.2H2O, b-CD.10H2O and g-CD.12H2O. The geometries were fully optimized using Molecular Mechanics (MM2), semiempirical (AM1 and PM3) and ab initio (HF/3-21G) methods and quantitatively compared with experimental data from X ray diffraction. The results obtained from the classical MM2 method were in best agreement with the experiment. The semiempirical and ab initio structures were also in satisfactory accordance with the experimental data. In general, the PM3 method was found to be more suitable than the AM1 to describe the CD geometries, mainly when the intramolecular hydrogen bonds are considered.