International Journal of Quantum Chemistry

Cover image for Vol. 112 Issue 20

Special Issue: The Brazilian Symposium on Theoretical Chemistry

15 October 2012

Volume 112, Issue 20

Pages i–iv, 3277–3438

Issue edited by: Sylvio Canuto, Hélio Anderson Duarte

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      Cover Image, Volume 112, Issue 20 (pages i–ii)

      Article first published online: 11 SEP 2012 | DOI: 10.1002/qua.24322

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      The Brazilian Symposium of Theoretical Chemistry is a traditional event covering all aspects of molecular physics and theoretical chemistry. This includes quantum chemistry as well as computer simulation and modeling. In some recent years, following a world tendency, there has been an increase in the study of biomolecular systems with emphasis on biomolecular properties, reactivity, structure and function in aqueous environment, the natural solvent. In this special issue some interesting investigations on biomolecules (such as amino-acids, lipids and membranes) are reported using quantum chemical calculations, classical simulations and also a combination of the two methods.

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      Inside Cover, Volume 112, Issue 20 (pages iii–iv)

      Article first published online: 11 SEP 2012 | DOI: 10.1002/qua.24323

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      This special issue features peer-reviewed conference proceedings from the Brazilian Symposium of Theoretical Chemistry, of which the work by Wenli Zou, Michael Filatov, and Dieter Cremer on page 3277 is an excellent example. The cover image is a stylized contourline diagram of a bond pseudorotation energy surface of the cyclopentadienyl cation. In their work, they find that the pseudo Jahn-Teller effect turns out to be much more important than the Jahn-Teller effect in this cation, contrary to commonly held assumptions.

  2. Full Papers

    1. Top of page
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    3. Full Papers
    1. Bondpseudorotation, Jahn-Teller, and pseudo-Jahn-Teller effects in the cyclopentadienyl cation and its pentahalogeno derivatives (pages 3277–3288)

      Wenli Zou, Michael Filatov and Dieter Cremer

      Article first published online: 27 APR 2012 | DOI: 10.1002/qua.24116

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      Bondpseudorotation has been investigated so far only for a few small molecules. This work presents for the first time, the complete bondpseudorotation surface of cyclopentadienyl cations as spanned by newly developed deformation coordinates, which provide a quantitative assessment of Jahn-Teller and pseudo Jahn-Teller effects leading to bondpseudorotation. The pseudo Jahn-Teller effect turns out to be much more important than the Jahn-Teller effect despite of commonly spread assumptions.

    2. Nicotinamide and picolinamide in phospholipid monolayers (pages 3289–3295)

      María Florencia Martini, Edgardo Aníbal Disalvo and Mónica Pickholz

      Article first published online: 24 MAY 2012 | DOI: 10.1002/qua.24124

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      Molecular dynamics simulations have been performed to investigate the interactions between nicotinamide and picolinamide with monolayers of dimyristoylphosphatidylcholine and dimyristoylphosphatidylethanolamine. The analysis captures important features of these interactions. Different properties as electron density profiles, order parameters, lipid head orientation, and electrostatic surface potential were computed and compared against experimental results when available. For instance, calculated electrostatic surface potentials are in good agreement with experimental results.

    3. Benzothiadiazoles as DNA intercalators: Docking and simulation (pages 3296–3302)

      Paulo Augusto Netz

      Article first published online: 29 MAY 2012 | DOI: 10.1002/qua.24174

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      Derivatives of 4-(arylethynyl)-7-(4-methoxyphenyl)-2,1,3-benzothiadiazoles are very sensitive DNA probes, exhibiting an extended planar structure. In light of experimental reports that have suggested that they may intercalate with DNA, this article studies this problem using docking with an oligonucleotide bearing an artificial gap as receptor and molecular dynamics simulations. Starting from several independent but energetically favorable docking poses, it was found that the intercalation is indeed the preferential binding mode and that the presence of the ethynyl spacer in the molecule is needed for the intercalation.

    4. Positive molecular ions and ion-neutral complexes in the gas phase: Structure and stability of C2H4O2 and C2H4O22+ isomers (pages 3303–3311)

      F. Fantuzzi, L. Baptista, A. B. Rocha and H. M. Boechat-Roberty

      Article first published online: 5 JUL 2012 | DOI: 10.1002/qua.24181

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      The structure and stability of several conformations of methyl formate ions were investigated. Ninety minimum structures—38 related to the C2H4O2ion, 33 to the C2H4O22+· ion, and 19 to ion-neutral complexes were found. This work stressed the importance of a systematic conformational search to obtain the minimum energy structure. The dissociative recombination process was also investigated and it importance to interstellar medium discussed.

    5. First-principles study of oxidized BC2N nanotubes (pages 3312–3319)

      Caroline Jaskulski Rupp, Jussane Rossato and Rogério José Baierle

      Article first published online: 14 JUN 2012 | DOI: 10.1002/qua.24190

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      BC2N is one of the most stable forms of ternary BCN nanotubes. The adsorption of atomic and molecular oxygen as well as oxygen substitutions in the nanotube are studied by means of spin-polarized density functional theory. It is found that the O2 molecule can be adsorbed in the inner or outer surface, depending on the spin state, and that the electronic properties of the nanotubes are affected by the adsorption and incorporation of oxygen.

    6. Calculations of structures and reaction energy profiles of As2O3 and As4O6 species by quantum chemical methods (pages 3320–3324)

      Gabriel Costa A. da Hora, Ricardo L. Longo and João Bosco P. da Silva

      Article first published online: 26 JUN 2012 | DOI: 10.1002/qua.24196

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      Arsenic oxide has been used as tumor growth inhibition in medical treatments. The stable structures of both As4O6 and As2O3 forms are identified in this work by quantum chemical calculations, and the mechanism connecting the two species is also proposed.

    7. Probability current in protein electron transfer: Löwdin population analysis (pages 3325–3332)

      Paulo Cesar Peres de Andrade

      Article first published online: 15 JUN 2012 | DOI: 10.1002/qua.24197

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      A careful analysis of local probability currents in macromolecules is presented in this article. A generalization of Stuchebrukhov analysis of Mulliken population of the interatomic tunneling currents in the protein electron transfer problem is more rigorously formulated, based on Liouville equation and Löwdin projector decomposition. Within this framework, overlapping atomic population analysis is obtained with nonorthogonal projectors, in contrast with previous results.

    8. Inverse virtual screening studies of selected natural compounds from cerrado (pages 3333–3340)

      Ana Paula Carregal, Moacyr Comar Jr., Stênio Nunes Alves, João Máximo de Siqueira, Luciana A. Lima and Alex Gutterres Taranto

      Article first published online: 5 JUN 2012 | DOI: 10.1002/qua.24205

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      Several medicinal plants have been studied in recent years in Brazil. However, the pharmacological mechanisms of many natural products are still unknown. In this study, inverse virtual screening (IVS), molecular dynamics simulation, and quantum mechanical/molecular mechanical, suggested pharmacological receptors for selected natural products. The identification and evaluation of these targets can be useful for predication the activity and toxicity of compounds. Thus, IVS can be considered as a new tool for structure-based drug design.

    9. Molecular dynamics study of uncharged bupivacaine enantiomers in phospholipid bilayers (pages 3341–3345)

      M. Florencia Martini and Mónica Pickholz

      Article first published online: 5 JUN 2012 | DOI: 10.1002/qua.24208

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      Bupivacaine is a popular anesthetic drug, normally delivered to patients as racemic mixture. Its enantiomers present different activity and R-(+) shows higher toxicity than S-(−). The understanding of the interaction of each enantiomer with biological membranes is fundamental to increase their efficacy and minimize their side effects. This is achieved in this study using molecular dynamics simulations.

    10. Metal organic frameworks for drug delivery and environmental remediation: A molecular docking approach (pages 3346–3355)

      Marcelo O. Rodrigues, Marcos V. de Paula, Kaline A. Wanderley, Iane B. Vasconcelos, Severino Alves Jr. and Thereza A. Soares

      Article first published online: 8 JUN 2012 | DOI: 10.1002/qua.24211

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      The efficient delivery of drugs via nanocarriers is a challenge in medicine. Hybrid materials composed of metal ions and organic bridging ligands have great potential to act as platform for drug delivery. In this report, the molecular docking technique is used to predict the binding of a set of medically relevant drugs to the [Zn(BDC)(H2O)2]n framework. The computational results are compared against experimental measurements in order to validate the procedure.

    11. Homology modeling studies of beta(1,3)-D-glucan synthase of Moniliophthora perniciosa (pages 3356–3363)

      Antonio Anderson Freitas Pinheiro, Alex Gutterres Taranto, Angelo Amâncio Duarte, Aristóteles Góes Neto, Braz Tavares da Hora Júnior, Gonçalo Amarante Guimarães Pereira, Manoelito Coelho dos Santos Júnior and Sandra Aparecida de Assis

      Article first published online: 8 JUN 2012 | DOI: 10.1002/qua.24212

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      The homology modelling methodology was used to generate a tridimensional model of the beta(1,3)-Dglucan synthase from M. perniciosa. In this enzyme, the binding site is located at amino acids Asp353 and Asp354, and the residues that contribute to this region are consistent with experimental data from the GTenzyme family (Asp345, Asp324, Tyr311).

    12. Theoretical models for the antitrypanosomal activity of thiosemicarbazone derivatives (pages 3364–3370)

      N. B. H. Lozano, K. C. Weber, K. M. Honorio, R. V. C. Guido, A. D. Andricopulo and A. B. F. Da Silva

      Article first published online: 8 JUN 2012 | DOI: 10.1002/qua.24213

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      Cruzain inhibitors (thiosemicarbazones) have been identified as potential antitrypanosomal agents. Theoretical studies revealed some molecular properties that can be considered responsible for the discrimination between high and low activity compounds. The results obtained are in good agreement with previous findings from the literature, suggesting that models presented in this study can be useful on further investigations on the molecular determinants for the antichagasic activity.

    13. Vertical triple ionization with diffusion quantum monte carlo (pages 3371–3373)

      W. F. D. Angelotti, W. R. Batista and A. C. Granato

      Article first published online: 26 JUN 2012 | DOI: 10.1002/qua.24221

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      The study of triply ionized states enables greater understanding of the nature of the chemical bond. However, due tobecause of their computational complexity such calculations are quite rare, in comparison to those of involving single and double ionization. This article introduces diffusion quantum Monte Carlo as an accurate and affordable theoretical approach for the description of triply ionized states.

    14. A novel set of β-N-biaryl ether sulfonamide hydroxamates as potential MMPs inhibitors: Molecular dynamics simulations and molecular properties evaluation (pages 3374–3389)

      Kely Medeiros Turra, Kerly Fernanda Mesquita Pasqualoto and Silvia Berlanga de Moraes Barros

      Article first published online: 19 JUN 2012 | DOI: 10.1002/qua.24222

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      Descriptors that can discriminate the activity of a class of novel matrix metalloproteinases inhibitors are obtained by means of Molecular dynamic simulation and molecular properties calculations. Thermodynamic, electronic, and steric properties are found to be the most effective of these descriptors. The findings are very helpful in the path to the rational design of novel antitumor leads.

    15. Docking between natural peroxides and heme group by parametric method 6 (pages 3390–3397)

      Franco Henrique Andrade Leite, José Walkimar de Mesquita Carneiro, Martha Teixeira de Araujo, Moacyr Comar Jr. and Alex Gutterres Taranto

      Article first published online: 22 JUN 2012 | DOI: 10.1002/qua.24247

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      Semiempirical docking studies between natural peroxide and heme group were evaluated for the identification of new potential antimalarial drugs from natural sources as well as to find possible correlations between in silico parameters and experimental data. The interactions of 51 peroxides with heme were studied by parametric method 6. The result indicated two possible promising compounds, 5 and 24, based on theoretical data.

    16. Insights for design of Trypanosoma cruzi GAPDH inhibitors: A QM/MM MD study of 1,3-bisphospo-D-glyceric acid analogs (pages 3398–3402)

      José Rogério Araújo Silva, Jerônimo Lameira and Cláudio Nahum Alves

      Article first published online: 26 JUN 2012 | DOI: 10.1002/qua.24253

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      The glyceraldehydes-3-phosphate dehydrogenase (GAPDH) is an important target against Chagas disease. This enzyme is responsible for catalyzing the oxidative phosphorylation of glyceraldehydes-3-phosphate to 1,3-bisphospho-D-glyceric acid (1,3-BPGA). In this article, quantum mechanical/molecular mechanical and molecular dynamics simulations are applied to study details of the interactions between GAPDH and 1,3-BPGA inhibitor analogs.

    17. Theoretical study of inclusion of a dinuclear platinum(II) complex in α, β, and γ-cyclodextrins (pages 3403–3408)

      Nathália Magalhães Paixão, Lucas Fagundes Esteves, Cleber Paulo Andrada Anconi, Clebio Soares Nascimento Jr., Wagner Batista De Almeida, Hélio Ferreira Dos Santos and Luiz Antônio Sodré Costa

      Article first published online: 12 JUL 2012 | DOI: 10.1002/qua.24271

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      Platinum-containing complexes play a significant role in cancer research and therapy. In this study, inclusion compounds formed by native cyclodextrins (CDs) and dinuclear platinum(II) complex are investigated by density functional theory and hybrid ONIOM approaches. This is the first attempt to provide a theoretical description of the CDs inclusion complexes for a dinuclear platinum(II) compound, expected to be significant for drug carrier design.

    18. Quadrupole moment of the hydrogen fluoride using the multireference Hartree–Fock CI method (pages 3409–3413)

      Luiz A. C. Malbouisson, Micael D. de Andrade and Antonio M. de C. Sobrinho

      Article first published online: 12 JUL 2012 | DOI: 10.1002/qua.24272

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      This work challenges the conventional wisdom to obtain good values of the one-electron properties are required extended or specialized bases sets. It is shown here that, using the Multireference Hartree–Fock Configuration Interaction method, it is possible to extract quantum-mechanical information from the minimal basis to calculate the permanent electric dipole and electric quadrupole moments of the hydrogen fluoride molecule.

    19. Molecular modeling of bioactive neuropeptides: Substrates of angiotensin I-converting enzyme (pages 3414–3420)

      Luísa Silva Nangi dos Santos, Milton Taidi Sonoda, Roseli Aparecida da Silva Gomes and Odonírio Abrahão Jr.

      Article first published online: 12 JUL 2012 | DOI: 10.1002/qua.24276

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      This study investigates structural and electronical similarities between neurotensin, substance P, and Angiotensin-(1-7) (Ang-1-7) that could be responsible for their molecular recognition by Angiotensin-I converting enzyme (ACE), a chloride-dependent zinc metallopeptidase that is important in regulation of cardiovascular functions. Conformational analysis, semiempirical, and density functional theory calculations were performed, looking for a possible recognition pattern for ACE; furthermore, molecular dynamics simulations of Ang-1-7 both in pure water and saline conditions were undertaken.

    20. Photoabsorption spectroscopy of dimethyl sulfoxide at the O1s, C1s, S2s, and S2p Regions: A comparison with acetone (pages 3421–3433)

      Thays C. M. Leite, Ana L. F. de Barros, Glaucio B. Ferreira, Antonio C. O. Guerra and Cássia C. Turci

      Article first published online: 6 AUG 2012 | DOI: 10.1002/qua.24285

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      The core excitation (K and L edges) of Dimethyl Sulfoxide (DMSO) and acetone using ab initio and density functional theory calculations and synchrotron radiation have been studied. The experimental and theoretical results reveal the influence of the replacement of the carbon atom in acetone by the sulfur atom in DMSO, confirmed by the spectra assignments.

    21. A TD-DFT basis set and density functional assessment for the calculation of electronic excitation energies of fluorene (pages 3434–3438)

      Cristina Aparecida Barboza, Pedro Antonio Muniz Vazquez, Desmond Mac-Leod Carey and Ramiro Arratia-Perez

      Article first published online: 24 JUL 2012 | DOI: 10.1002/qua.24300

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      Fluorinated-conjugated organic molecules have been the subject of intensive optoelectronic research due to their advantageous photonic and electronic properties. This study of different density functionals attempts to compare the sequence of excited states obtained with the result of a linear response-coupled cluster singles and doubles method. Although none of the studied functionals accomplishes this, it is found that asymptotically and long-range corrected B3LYP improved the results significantly. Finally, pseudopotentials can provide further computational cost savings.