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Special Issue "Advances in Molecular Electronic Structure Calculations"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (31 May 2012)

Special Issue Editor

Guest Editor
Prof. Dr. Eduardo A. Castro

INIFTA, Suc.4, C.C. 16, La Plata 1900, Buenos Aires, Argentinia
E-Mail
Fax: +54 221 4254642
Interests: QSAR/QSPR theory; molecular electronic structure; scientific education; scientific and technological research management and organization; scientific communication; the relationship between science and humanities; mathematical and physics and mathematics

Special Issue Information

Dear Colleagues,

One of the most important and difficult problems in science is the accurate calculation of material properties from first priniciples. This can be viewed as the central challenge for theorists from a wide range of fields, including chemistry, condensed matter physics, materials science, biophysics, biochemistry, pharmacology and closely related disciplines.
The challenge of first-principles calculations arises because the computational resources required to obtain exact solutions of the stationary Schrodinger equation on a standard computer generally increase exponentially with the number of atoms involved. This renders such calculations within ranges of chemical accuracy really intractable for all but the smallest systems even resorting the latest supercomputers.
In chemistry, the most important task is to calculate the energy of molecules to within chemical accuracy of 1kJ/mol, which is required to predict reaction rates. The real difficulty of solving this problem exactly has led to the development of several approximate methods for first-principles quantum chemistry. The present issue is devoted to present the methodological progress and the growth of the power of classical computers that have allowed for outstanding computational successes and impressive practical predictions within the field of calculation of material properties.

Prof. Dr. Eduardo A. Castro
Guest Editor

Keywords

  • electronic molecular structure
  • theoretical chemistry calculations
  • post Hartree-Fock methods
  • quantum computers
  • first-principles
  • quantum chemistry
  • chemical accuracy
  • theoretical predictions and correlations

Published Papers (9 papers)

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Research

Open AccessArticle Density Functional Theory (DFT) Study of Edaravone Derivatives as Antioxidants
Int. J. Mol. Sci. 2012, 13(6), 7594-7606; doi:10.3390/ijms13067594
Received: 18 May 2012 / Revised: 9 June 2012 / Accepted: 11 June 2012 / Published: 20 June 2012
Cited by 8 | PDF Full-text (531 KB) | HTML Full-text | XML Full-text
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 (∆Eiso). 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 BDECH 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)
Open AccessArticle Spectroscopic Parameter and Molecular Constant Investigations on Low-Lying States of BeF Radical
Int. J. Mol. Sci. 2012, 13(2), 2501-2514; doi:10.3390/ijms13022501
Received: 12 December 2011 / Revised: 3 February 2012 / Accepted: 9 February 2012 / Published: 22 February 2012
Cited by 2 | PDF Full-text (276 KB) | HTML Full-text | XML Full-text
Abstract
The potential energy curves (PECs) of X2Σ+, A2Πr 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+, A2Πr 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+, A2Πr and B2Σ+ states, the spectroscopic parameters (De, Re, ωe, ωeχe, αe and Be) 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)
Open AccessArticle Introducing Catastrophe-QSAR. Application on Modeling Molecular Mechanisms of Pyridinone Derivative-Type HIV Non-Nucleoside Reverse Transcriptase Inhibitors
Int. J. Mol. Sci. 2011, 12(12), 9533-9569; doi:10.3390/ijms12129533
Received: 27 October 2011 / Revised: 28 November 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
Cited by 10 | PDF Full-text (602 KB) | HTML Full-text | XML Full-text
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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Open AccessArticle Spectroscopic Study of Solvent Effects on the Electronic Absorption Spectra of Flavone and 7-Hydroxyflavone in Neat and Binary Solvent Mixtures
Int. J. Mol. Sci. 2011, 12(12), 8895-8912; doi:10.3390/ijms12128895
Received: 6 September 2011 / Revised: 5 November 2011 / Accepted: 14 November 2011 / Published: 5 December 2011
Cited by 15 | PDF Full-text (764 KB) | HTML Full-text | XML Full-text | Supplementary Files
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)
Open AccessArticle Estimating the Octanol/Water Partition Coefficient for Aliphatic Organic Compounds Using Semi-Empirical Electrotopological Index
Int. J. Mol. Sci. 2011, 12(10), 7250-7264; doi:10.3390/ijms12107250
Received: 8 September 2011 / Revised: 8 October 2011 / Accepted: 14 October 2011 / Published: 24 October 2011
Cited by 12 | PDF Full-text (174 KB) | HTML Full-text | XML Full-text
Abstract
A new possibility for estimating the octanol/water coefficient (log P) was investigated using only one descriptor, the semi-empirical electrotopological index (ISET). The predictability of four octanol/water partition coefficient (log P) calculation models was compared using a set of
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A new possibility for estimating the octanol/water coefficient (log P) was investigated using only one descriptor, the semi-empirical electrotopological index (ISET). 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 ISET 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)
Open AccessArticle Nitrogen Substituted Phenothiazine Derivatives: Modelling of Molecular Self-Assembling
Int. J. Mol. Sci. 2011, 12(5), 3102-3116; doi:10.3390/ijms12053102
Received: 4 March 2011 / Revised: 27 April 2011 / Accepted: 5 May 2011 / Published: 12 May 2011
Cited by 3 | PDF Full-text (893 KB) | HTML Full-text | XML Full-text
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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Open AccessArticle First-Principles Investigation of Ag-Doped Gold Nanoclusters
Int. J. Mol. Sci. 2011, 12(5), 2972-2981; doi:10.3390/ijms12052972
Received: 18 February 2011 / Revised: 28 April 2011 / Accepted: 6 May 2011 / Published: 9 May 2011
Cited by 20 | PDF Full-text (743 KB) | HTML Full-text | XML Full-text
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 Au20−nAgn 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)
Open AccessArticle Highly Unsaturated Binuclear Butadiene Iron Carbonyls: Quintet Spin States, Perpendicular Structures, Agostic Hydrogen Atoms, and Iron-Iron Multiple Bonds
Int. J. Mol. Sci. 2011, 12(4), 2216-2231; doi:10.3390/ijms12042216
Received: 22 February 2011 / Revised: 8 March 2011 / Accepted: 14 March 2011 / Published: 30 March 2011
Cited by 5 | PDF Full-text (689 KB) | HTML Full-text | XML Full-text | Supplementary Files
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)
Open AccessArticle On Heisenberg Uncertainty Relationship, Its Extension, and the Quantum Issue of Wave-Particle Duality
Int. J. Mol. Sci. 2010, 11(10), 4124-4139; doi:10.3390/ijms11104124
Received: 11 August 2010 / Revised: 27 September 2010 / Accepted: 17 October 2010 / Published: 22 October 2010
Cited by 5 | PDF Full-text (294 KB) | HTML Full-text | XML Full-text
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
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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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