International Journal of Molecular Sciences

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13 pages, 531 KiB

Open AccessArticle

Density Functional Theory (DFT) Study of Edaravone Derivatives as Antioxidants

by Rosivaldo S. Borges, Auriekson N. Queiroz, Anna P. S. Mendes, Sanderson C. Araújo, Luiz C. S. França, Edna C. S. Franco, Walace G. Leal and Albérico B. F. Da Silva

Int. J. Mol. Sci. 2012, 13(6), 7594-7606; https://doi.org/10.3390/ijms13067594 - 20 Jun 2012

Cited by 26 | Viewed by 8935

Abstract

Quantum chemical calculations at the B3LYP/6–31G* level of theory were employed for the structure-activity relationship and prediction of the antioxidant activity of edaravone and structurally related derivatives using energy (E), ionization potential (IP), bond dissociation energy (BDE), and stabilization energies (∆ [...] Read more.

Quantum chemical calculations at the B3LYP/6–31G* level of theory were employed for the structure-activity relationship and prediction of the antioxidant activity of edaravone and structurally related derivatives using energy (E), ionization potential (IP), bond dissociation energy (BDE), and stabilization energies (∆E_iso). Spin density calculations were also performed for the proposed antioxidant activity mechanism. The electron abstraction is related to electron-donating groups (EDG) at position 3, decreasing the IP when compared to substitution at position 4. The hydrogen abstraction is related to electron-withdrawing groups (EDG) at position 4, decreasing the BDE_CH when compared to other substitutions, resulting in a better antioxidant activity. The unpaired electron formed by the hydrogen abstraction from the C–H group of the pyrazole ring is localized at 2, 4, and 6 positions. The highest scavenging activity prediction is related to the lowest contribution at the carbon atom. The likely mechanism is related to hydrogen transfer. It was found that antioxidant activity depends on the presence of EDG at the C₂ and C₄ positions and there is a correlation between IP and BDE. Our results identified three different classes of new derivatives more potent than edaravone. Full article

(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)

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14 pages, 276 KiB

Open AccessArticle

Spectroscopic Parameter and Molecular Constant Investigations on Low-Lying States of BeF Radical

by Zun Lue Zhu, Qing Peng Song, Su Hua Kou, Jian Hua Lang and Jin Feng Sun

Int. J. Mol. Sci. 2012, 13(2), 2501-2514; https://doi.org/10.3390/ijms13022501 - 22 Feb 2012

Cited by 6 | Viewed by 6332

Abstract

The potential energy curves (PECs) of X²Σ⁺, A²Π_r and B²Σ⁺ states of BeF radical have been investigated using the complete active space self-consistent-field (CASSCF) method, followed by the highly accurate valence internally contracted [...] Read more.

The potential energy curves (PECs) of X²Σ⁺, A²Π_r and B²Σ⁺ states of BeF radical have been investigated using the complete active space self-consistent-field (CASSCF) method, followed by the highly accurate valence internally contracted multireference configuration interaction (MRCI) approach at the correlation-consistent basis sets, cc-pV5Z for Be and aug-cc-pV6Z for F. Based on the PECs of X²Σ⁺, A²Π_r and B²Σ⁺ states, the spectroscopic parameters (D_e, R_e, ω_e, ω_eχ_e, α_e and B_e) have also been determined in the present work. With the PECs determined at the present level of theory, vibrational states have been predicted for each state when the rotational quantum number J equals zero (J = 0). The vibrational levels, inertial rotation and centrifugal distortion constants are determined for the three states, and the classical turning points are also calculated for the X²Σ⁺ state. Compared with the available experiments and other theories, it can be seen that the present spectroscopic parameter and molecular constant results are more fully in agreement with the experimental findings. Full article

(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)

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37 pages, 602 KiB

Open AccessArticle

Introducing Catastrophe-QSAR. Application on Modeling Molecular Mechanisms of Pyridinone Derivative-Type HIV Non-Nucleoside Reverse Transcriptase Inhibitors

by Mihai V. Putz, Marius Lazea, Ana-Maria Putz and Corina Duda-Seiman

Int. J. Mol. Sci. 2011, 12(12), 9533-9569; https://doi.org/10.3390/ijms12129533 - 20 Dec 2011

Cited by 13 | Viewed by 8541

Abstract

The classical method of quantitative structure-activity relationships (QSAR) is enriched using non-linear models, as Thom’s polynomials allow either uni- or bi-variate structural parameters. In this context, catastrophe QSAR algorithms are applied to the anti-HIV-1 activity of pyridinone derivatives. This requires calculation of the [...] Read more.

The classical method of quantitative structure-activity relationships (QSAR) is enriched using non-linear models, as Thom’s polynomials allow either uni- or bi-variate structural parameters. In this context, catastrophe QSAR algorithms are applied to the anti-HIV-1 activity of pyridinone derivatives. This requires calculation of the so-called relative statistical power and of its minimum principle in various QSAR models. A new index, known as a statistical relative power, is constructed as an Euclidian measure for the combined ratio of the Pearson correlation to algebraic correlation, with normalized t-Student and the Fisher tests. First and second order inter-model paths are considered for mono-variate catastrophes, whereas for bi-variate catastrophes the direct minimum path is provided, allowing the QSAR models to be tested for predictive purposes. At this stage, the max-to-min hierarchies of the tested models allow the interaction mechanism to be identified using structural parameter succession and the typical catastrophes involved. Minimized differences between these catastrophe models in the common structurally influential domains that span both the trial and tested compounds identify the “optimal molecular structural domains” and the molecules with the best output with respect to the modeled activity, which in this case is human immunodeficiency virus type 1 HIV-1 inhibition. The best molecules are characterized by hydrophobic interactions with the HIV-1 p66 subunit protein, and they concur with those identified in other 3D-QSAR analyses. Moreover, the importance of aromatic ring stacking interactions for increasing the binding affinity of the inhibitor-reverse transcriptase ligand-substrate complex is highlighted. Full article

(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)

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18 pages, 764 KiB

Open AccessArticle

Spectroscopic Study of Solvent Effects on the Electronic Absorption Spectra of Flavone and 7-Hydroxyflavone in Neat and Binary Solvent Mixtures

by Matias I. Sancho, Maria C. Almandoz, Sonia E. Blanco and Eduardo A. Castro

Int. J. Mol. Sci. 2011, 12(12), 8895-8912; https://doi.org/10.3390/ijms12128895 - 5 Dec 2011

Cited by 62 | Viewed by 12679

Abstract

The solvatochromic characteristics of flavone and 7-hydroxyflavone were investigated in neat and binary solvent mixtures. The spectral shifts of these solutes were correlated with the Kamlet and Taft parameters (α, β and π*) using linear solvation energy relationships. The multiparametric analysis indicates that [...] Read more.

The solvatochromic characteristics of flavone and 7-hydroxyflavone were investigated in neat and binary solvent mixtures. The spectral shifts of these solutes were correlated with the Kamlet and Taft parameters (α, β and π*) using linear solvation energy relationships. The multiparametric analysis indicates that both specific hydrogen bond donor ability and non-specific dipolar interactions of the solvents play an important role in absorption maxima of flavone in pure solvents. The hydrogen bond acceptor ability of the solvent was the main parameter affecting the absorption maxima of 7-hydroxyflavone. The simulated absorption spectra using a TD-DFT method were in good agreement with the experimental ones for both flavones. Index of preferential solvation was calculated as a function of solvent composition. Preferential solvation by ethanol was detected in cyclohexane-ethanol and acetonitrile-ethanol mixtures for flavone and in acetonitrile-ethanol mixtures for 7-hydroxyflavone. These results indicate that intermolecular hydrogen bonds between solute and solvent are responsible for the non-linear variation of the solvatochromic shifts on the mole fraction of ethanol in the analyzed binary mixtures. Full article

(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)

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15 pages, 174 KiB

Open AccessArticle

Estimating the Octanol/Water Partition Coefficient for Aliphatic Organic Compounds Using Semi-Empirical Electrotopological Index

by Erica Silva Souza, Laize Zaramello, Carlos Alberto Kuhnen, Berenice da Silva Junkes, Rosendo Augusto Yunes and Vilma Edite Fonseca Heinzen

Int. J. Mol. Sci. 2011, 12(10), 7250-7264; https://doi.org/10.3390/ijms12107250 - 24 Oct 2011

Cited by 46 | Viewed by 8439

Abstract

A new possibility for estimating the octanol/water coefficient (log P) was investigated using only one descriptor, the semi-empirical electrotopological index (I_SET). The predictability of four octanol/water partition coefficient (log P) calculation models was compared using a set of [...] Read more.

A new possibility for estimating the octanol/water coefficient (log P) was investigated using only one descriptor, the semi-empirical electrotopological index (I_SET). The predictability of four octanol/water partition coefficient (log P) calculation models was compared using a set of 131 aliphatic organic compounds from five different classes. Log P values were calculated employing atomic-contribution methods, as in the Ghose/Crippen approach and its later refinement, AlogP; using fragmental methods through the ClogP method; and employing an approach considering the whole molecule using topological indices with the MlogP method. The efficiency and the applicability of the I_SET in terms of calculating log P were demonstrated through good statistical quality (r > 0.99; s < 0.18), high internal stability and good predictive ability for an external group of compounds in the same order as the widely used models based on the fragmental method, ClogP, and the atomic contribution method, AlogP, which are among the most used methods of predicting log P. Full article

(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)

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15 pages, 893 KiB

Open AccessArticle

Nitrogen Substituted Phenothiazine Derivatives: Modelling of Molecular Self-Assembling

by Attila Bende and Ioan Turcu

Int. J. Mol. Sci. 2011, 12(5), 3102-3116; https://doi.org/10.3390/ijms12053102 - 12 May 2011

Cited by 6 | Viewed by 8495

Abstract

The study aims to present a detailed theoretical investigation of noncovalent intermolecular interactions between different π–π stacking nitrogen substituted phenothiazine derivatives by applying second-order Møller-Plesset perturbation (MP2), density functional (DFT) and semiempirical theories. The conformational stability of these molecular systems is mainly given [...] Read more.

The study aims to present a detailed theoretical investigation of noncovalent intermolecular interactions between different π–π stacking nitrogen substituted phenothiazine derivatives by applying second-order Møller-Plesset perturbation (MP2), density functional (DFT) and semiempirical theories. The conformational stability of these molecular systems is mainly given by the dispersion-type electron correlation effects. The density functional tight-binding (DFTB) method applied for dimer structures are compared with the results obtained by the higher level theoretical methods. Additionally, the optimal configuration of the investigated supramolecular systems and their self-assembling properties are discussed. Full article

(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)

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10 pages, 743 KiB

Open AccessArticle

First-Principles Investigation of Ag-Doped Gold Nanoclusters

by Xiao-Dong Zhang, Mei-Li Guo, Di Wu, Pei-Xun Liu, Yuan-Ming Sun, Liang-An Zhang, Yi She, Qing-Fen Liu and Fei-Yue Fan

Int. J. Mol. Sci. 2011, 12(5), 2972-2981; https://doi.org/10.3390/ijms12052972 - 9 May 2011

Cited by 32 | Viewed by 11577

Abstract

Gold nanoclusters have the tunable optical absorption property, and are promising for cancer cell imaging, photothermal therapy and radiotherapy. First-principle is a very powerful tool for design of novel materials. In the present work, structural properties, band gap engineering and tunable optical properties [...] Read more.

Gold nanoclusters have the tunable optical absorption property, and are promising for cancer cell imaging, photothermal therapy and radiotherapy. First-principle is a very powerful tool for design of novel materials. In the present work, structural properties, band gap engineering and tunable optical properties of Ag-doped gold clusters have been calculated using density functional theory. The electronic structure of a stable Au₂₀ cluster can be modulated by incorporating Ag, and the HOMO–LUMO gap of Au_20−nAg_n clusters is modulated due to the incorporation of Ag electronic states in the HOMO and LUMO. Furthermore, the results of the imaginary part of the dielectric function indicate that the optical transition of gold clusters is concentration-dependent and the optical transition between HOMO and LUMO shifts to the low energy range as the Ag atom increases. These calculated results are helpful for the design of gold cluster-based biomaterials, and will be of interest in the fields of radiation medicine, biophysics and nanoscience. Full article

(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)

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16 pages, 689 KiB

Open AccessArticle

Highly Unsaturated Binuclear Butadiene Iron Carbonyls: Quintet Spin States, Perpendicular Structures, Agostic Hydrogen Atoms, and Iron-Iron Multiple Bonds

by Yi Zeng, Shijian Wang, Hao Feng, Yaoming Xie and R. Bruce King

Int. J. Mol. Sci. 2011, 12(4), 2216-2231; https://doi.org/10.3390/ijms12042216 - 30 Mar 2011

Cited by 6 | Viewed by 8442

Abstract

The highly unsaturated binuclear butadiene iron carbonyls (C₄H₆)₂Fe₂(CO)_n (n = 2, 1) have been examined using density functional theory. For (C₄H₆)₂Fe₂(CO)_n (n = [...] Read more.

The highly unsaturated binuclear butadiene iron carbonyls (C₄H₆)₂Fe₂(CO)_n (n = 2, 1) have been examined using density functional theory. For (C₄H₆)₂Fe₂(CO)_n (n = 2, 1), both coaxial and perpendicular structures are found. The global minima of (C₄H₆)₂Fe₂(CO)_n (n = 2, 1) are the perpendicular structures 2Q-1 and 1Q-1, respectively, with 17- and 15-electron configurations for the iron atoms leading to quintet spin states. The Fe=Fe distance of 2.361 Å (M06-L) in the (C₄H₆)₂Fe₂(CO)₂ structure 2Q-1 suggests a formal double bond. The Fe≡Fe bond distance in the (C₄H₆)₂Fe₂(CO) structure 1Q-1 is even shorter at 2.273 Å (M06-L), suggesting a triple bond. Higher energy (C₄H₆)₂Fe₂(CO)_n (n = 2, 1) structures include structures in which a bridging butadiene ligand is bonded to one of the iron atoms as a tetrahapto ligand and to the other iron atom through two agostic hydrogen atoms from the end CH₂ groups. Singlet (C₄H₆)₂Fe₂(CO) structures with formal Fe–Fe quadruple bonds of lengths ~2.05 Å were also found but at very high energies (~47 kcal/mol) relative to the global minimum. Full article

(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)

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16 pages, 294 KiB

Open AccessArticle

On Heisenberg Uncertainty Relationship, Its Extension, and the Quantum Issue of Wave-Particle Duality

by Mihai V. Putz

Int. J. Mol. Sci. 2010, 11(10), 4124-4139; https://doi.org/10.3390/ijms11104124 - 22 Oct 2010

Cited by 13 | Viewed by 8131

Abstract

Within the path integral Feynman formulation of quantum mechanics, the fundamental Heisenberg Uncertainty Relationship (HUR) is analyzed in terms of the quantum fluctuation influence on coordinate and momentum estimations. While introducing specific particle and wave representations, as well as their ratio, in quantifying [...] Read more.

Within the path integral Feynman formulation of quantum mechanics, the fundamental Heisenberg Uncertainty Relationship (HUR) is analyzed in terms of the quantum fluctuation influence on coordinate and momentum estimations. While introducing specific particle and wave representations, as well as their ratio, in quantifying the wave-to-particle quantum information, the basic HUR is recovered in a close analytical manner for a large range of observable particle-wave Copenhagen duality, although with the dominant wave manifestation, while registering its progressive modification with the factor √1-n², in terms of magnitude n ε [0,1] of the quantum fluctuation, for the free quantum evolution around the exact wave-particle equivalence. The practical implications of the present particle-to-wave ratio as well as of the free-evolution quantum picture are discussed for experimental implementation, broken symmetry and the electronic localization function. Full article

(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)

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