Publications by authors named "João Bosco P da Silva"

9 Publications

  • Page 1 of 1

Modeling zigzag CNT: dependence of structural and electronic properties on length, and application to encapsulation of HCN and CH.

J Mol Model 2017 Apr 31;23(4):144. Epub 2017 Mar 31.

Departamento de Química Fundamental, Universidade Federal de Pernambuco (UFPE), 50740-540, Recife, PE, Brazil.

Density functional theory (B3LYP, B3LYP-D2 and wB97XD functionals) was used in finite models of zigzag carbon nanotubes (CNT), (n,0)×k with n = 6-9 and k = 2-4, to systematically investigate the effects of size on their structural and electronic properties. We found that the ratio between the length (L ) and the diameter (d ) of the pristine CNT has to be larger than 2, i.e., L /d  > 2, in order to provide the observed experimental trends of C=C bond distances, as well as to maintain the atomic charges nearly constant and zero around the center of the tube. Therefore, the concepts of useful length and volume were developed and tested for the encapsulation process of HCN and CH into CNTs. The energies involved in these processes, as well as the changes in molecular structure and electronic properties of the dopants and the CNTs are discussed and rationalized by the amount of charge transferred between dopant and CNT. Graphical Abstract Illustration of zigzag CNT length and diameter ratio in order to represent C=C bond experimental trend.
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http://dx.doi.org/10.1007/s00894-017-3319-7DOI Listing
April 2017

Thiosemicarbazones as Aedes aegypti larvicidal.

Eur J Med Chem 2015 Jul 28;100:162-75. Epub 2015 May 28.

Quantum Theory Project, University of Florida, 2234 New Physics Building, Gainesville, PO Box 118435, Florida, USA.

A set of aryl- and phenoxymethyl-(thio)semicarbazones were synthetized, characterized and biologically evaluated against the larvae of Aedes aegypti (A. aegypti), the vector responsible for diseases like Dengue and Yellow Fever. (Q)SAR studies were useful for predicting the activities of the compounds not included to create the QSAR model as well as to predict the features of a new compound with improved activity. Docking studies corroborated experimental evidence of AeSCP-2 as a potential target able to explain the larvicidal properties of its compounds. The trend observed between the in silico Docking scores and the in vitro pLC50 (equals -log LC50, at molar concentration) data indicated that the highest larvicidal compounds, or the compounds with the highest values for pLC50, are usually those with the higher docking scores (i.e., greater in silico affinity for the AeSCP-2 target). Determination of cytotoxicity for these compounds in mammal cells demonstrated that the top larvicide compounds are non-toxic.
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http://dx.doi.org/10.1016/j.ejmech.2015.04.061DOI Listing
July 2015

Adenine formation without HCN.

J Phys Chem A 2014 May 12;118(20):3637-44. Epub 2014 May 12.

Quantum Theory Project, University of Florida , 2234 New Physics Building, Gainesville, 32611 Florida, United States.

From a historic point of view adenine was always presumed to be the product of HCN pentamerization. In this work a new mechanism for adenine synthesis in the gas phase without HCN is proposed. The concept of retrosynthetic analysis was employed to create a tautomer of adenine, which can be reached from previously observed interstellar molecules C3NH and HNCNH and its isomer H2NCN. MP2/6-311++G(2d,2p) calculations were performed to calculate the Gibbs free energy of the minimum and the transition state (TS) structures involved in the six step mechanism. This new mechanism requires a smaller number of steps, the reaction energy is twice as exergonic, and the rate determining TS is lower in energy than the corresponding ones proposed elsewhere in the literature.
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http://dx.doi.org/10.1021/jp5018778DOI Listing
May 2014

Anionic form of usnic acid promotes lamellar to nonlamellar transition in DPPC and DOPC membranes.

J Phys Chem B 2014 Apr 28;118(14):3881-6. Epub 2014 Mar 28.

Fundamental Chemistry Department, Federal University of Pernambuco , Recife PE 50.740-540, Brazil.

Usnic acid is a secondary metabolite found in several species of lichens, organisms resulting from the symbiosis between fungi and algae. This compound has been extensively studied because of its pharmacological properties. Despite its potential medicinal importance, it exhibits a high degree of toxicity. The confinement of the usnic acid within liposomes has been investigated as a possibility to reduce its toxicity. In this work, we characterize the interaction of usnic acid in its neutral and anionic states (usniate) with DPPC and DOPC by means of molecular dynamics simulations. A lamellar to nonlamellar transition is observed for both membranes upon contact with usniate within 100 ns time scale. The transition suggests the formation of a liposome-like structure encapsulating the metabolyte. Furthermore, such process occurs at a significantly shorter time frame for DOPC.
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http://dx.doi.org/10.1021/jp412176fDOI Listing
April 2014

PICVib: an accurate, fast, and simple procedure to investigate selected vibrational modes at high theoretical levels.

J Comput Chem 2013 Mar 23;34(8):611-21. Epub 2012 Nov 23.

Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Cidade Universitária, Recife-PE, Brazil.

A new approach Procedure for Investigating Categories of Vibrations (PICVib) for estimating vibrational frequencies of selected modes using only the structure and energy calculations at a more demanding computational level is presented and explored. The PICVib has an excellent performance at only a small fraction of the computational demand required for a complete analytical calculation. The errors are smaller than ca. 0.5% when DFT functionals are combined with high level ab initio methods. The approach is general because it can use any quantum chemical program and electronic structure method. It is very robust because it was validated for a wide range of frequency values (ca. 20-4800 cm(-1)) and systems: XH(3) (D(3h) ) with X = B, Al, Ga, N, P, As, O, S, and Se, YH(4) (D(4h) ) with Y = C, Si, and Ge, conformers of RDX, S(N) 2 and E2 reactions, [W(dppe)(2)(NNC(5)H(10))] complex, carbon nanotubes, and hydrogen-bonded complexes including guanine-cytosine pair.
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http://dx.doi.org/10.1002/jcc.23166DOI Listing
March 2013

Theoretical calculations of the molecular properties of maleimide and its dimer.

Spectrochim Acta A Mol Biomol Spectrosc 2008 Nov 17;71(1):5-9. Epub 2007 Nov 17.

Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50740-540 Recife PE, Brazil.

B3LYP theoretical calculations with 6-31++G(d,p) basis set have been performed to study the infrared spectrum of maleimide and its dimer. Our calculations have shown that the dimer formation leads to a binding energy of 44.0 kJ mol(-1) involving two intermolecular hydrogen bonds between the amide hydrogen and a carbonyl group of two neighboring maleimides. This value is essentially due to the electrostatic interaction term. Our calculations have also revealed the vibrational changes, in terms of frequencies and IR intensities, after dimer formation. The most affected modes are associated with the N-H stretching and in-plane bending bands. This behavior can be adequately interpreted by the hydrogen atomic charge and N-H charge-flux based on the modified charge-charge flux-overlap model for infrared intensities. The B3LYP frequency shifts are in very good agreement with the experimental ones.
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http://dx.doi.org/10.1016/j.saa.2007.11.002DOI Listing
November 2008

A theoretical study of hydrogen complexes of the XH-pi type between propyne and HF, HCL or HCN.

Spectrochim Acta A Mol Biomol Spectrosc 2006 May 5;64(2):412-7. Epub 2005 Dec 5.

Departamento de Química, Universidade Federal da Paraíba, Rua José Simões Araújo 352 apto 501, Bessa, 58036-300 João Pessoa, PB, Brazil.

The present manuscript reports a systematic investigation of the basis set dependence of some properties of hydrogen-bonded (pi type) complexes formed by propyne and a HX molecule, where X=F, Cl and CN. The calculations have been performed at Hartree-Fock, MP2 and B3LYP levels. Geometries, H-bond energies and vibrational have been considered. The more pronounced effects on the structural parameters of the isolated molecules, as a result of complexation, are verified on RCtriple bondC and HX bond lengths. As compared to double-zeta (6-31G**), triple-zeta (6-311G**) basis set leads to an increase of RCtriple bondC bond distance, at all three computational levels. In the case where diffuse functions are added to both hydrogen and 'heavy' atoms, the effect is more pronounced. The propyne-HX structural parameters are quite similar to the corresponding parameters of acetylene-HX complexes, at all levels. The largest difference is obtained for hydrogen bond distance, RH, with a smaller value for propyne-HX complex, indicating a stronger bond. Concerning the electronic properties, the results yield the following ordering for H-bond energies, DeltaE: propynecdots, three dots, centeredHF>propynecdots, three dots, centeredHCl>propynecdots, three dots, centeredHCN. It is also important to point out that the inclusion of BSSE and zero-point energies (ZPE) corrections cause significant changes on DeltaE. The smaller effect of ZPE is obtained for propynecdots, three dots, centeredHCN at HF/6-311++G** level, while the greatest difference is obtained at MP2/6-31G** level for propynecdots, three dots, centeredHF system. Concerning the IR vibrational it was obtained that larger shift can be associated with stronger hydrogen bonds. The more pronounced effect on the normal modes of the isolated molecule after the complexation is obtained for HX stretching frequency, which is shifted downward.
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http://dx.doi.org/10.1016/j.saa.2005.07.038DOI Listing
May 2006

Chemometric study of liquid water simulations. I. The parameters of the TIP4P model potential.

J Comput Chem 2003 Jun;24(8):973-81

Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50740-540 Recife (PE), Brazil.

The multivariate chemometric techniques two level factorial design (TLFD) and principal component analysis (PCA) were used to investigate the TIP4P model potential behavior with respect to perturbations on all intermolecular interaction parameters. The effects of these perturbations were calculated for the enthalpy of vaporization, the density, the first maximum of the radial distribution functions of the O-H and O-O pairs, and the second maximum of the radial distribution function of the O-H pair obtained from Monte Carlo simulations of liquid water at 25 degrees C. The principal effects were quantified and rationalized in terms of the pair-wise interaction potential of the TIP4P model. They also corroborate previously published sensitivity analysis results using molecular dynamics and other model potentials. In addition, significant interaction effects between some parameters of the TIP4P model potential were observed and quantified, which hardly could be obtained without such a statistic approach. These interaction effects are very regular and systematic, and their behavior has not been encountered in other chemometric studies and cannot be rationalized in terms of the functional form of the pair-wise potential.
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http://dx.doi.org/10.1002/jcc.10273DOI Listing
June 2003

Conformational studies on 1,2-di- and 1,2,3-trisubstituted heterocycles. A spectroscopic and theoretical study of 3-acylaminopicolinic Acid derivatives and their N-oxides.

J Org Chem 2002 Jan;67(2):370-82

Departamento de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, 50.670-901 Recife-PE, Brazil.

Theoretical studies involving minimization of model 3-propanoylaminopicolinic acids (10d-trans, 10d-cis), methyl ester (10a), and corresponding -N-oxide derivatives (10b, 10c-trans, 10c-cis) using AM1 gave conformations contrary to both sound chemical intuition and experimental data. RHF ab initio calculations using the 6-31G and 6-31G basis sets on the other hand corroborated spectroscopic data. 3-Amidopicolinic acid derivatives (7a-9a, 7b-9b, 7c-9c, 9d) were prepared and studied by NMR and IR spectroscopy. The results show that a strong intramolecular hydrogen bond between amide-H and the 2-carboxyl substituent results in a planar molecular conformation. This is particularly profound in the 3-acylaminopicolinic acid N-oxides (c-series). When the 2-substituent is a methyl ester on the other hand, repulsion between N-oxide and ester functions induces twisting of the carbomethoxy group out of the plane of the aromatic ring. The type of method used in molecular modeling can have profound impact on the final theoretical result in the case of the above-mentioned class of compounds. Our results indicate, that it is advisable to employ ab initio methods for modeling these types of compounds, and further, that the choice of basis set used for such calculations should depend on the type of information required. Thus, for most purposes pertaining to molecular conformation the 6-31G basis set provides sufficiently sound data in relatively short CPU time. For data related to electronic properties such as involvement of the N-oxide function or spectroscopic information such as IR frequencies or (1)H or (15)N NMR chemical shifts, the use of polarization functions as contained in the 6-31G basis set seems to be a must.
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http://dx.doi.org/10.1021/jo000993jDOI Listing
January 2002
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