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Search Results: 1 - 10 of 20092 matches for " Quantum Chemical Methods "
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Application of Hartree-Fock Method for Modeling of Bioactive Molecules Using SAR and QSPR  [PDF]
Cleydson B. R. Santos, Cleison C. Lobato, Francinaldo S. Braga, Sílvia S. S. Morais, Cesar F. Santos, Caio P. Fernandes, Davi S. B. Brasil, Lorane I. S. Hage-Melim, Williams J. C. Macêdo, José C. T. Carvalho
Computational Molecular Bioscience (CMB) , 2014, DOI: 10.4236/cmb.2014.41001
Abstract:
The central importance of quantum chemistry is to obtain solutions of the Schr?dinger equation for the accurate determination of the properties of atomic and molecular systems that occurred from the calculation of wave functions accurate for many diatomic and polyatomic molecules, using Self Consistent Field method (SCF). The application of quantum chemical methods in the study and planning of bioactive compounds has become a common practice nowadays. From the point of view of planning it is important to note, when it comes to the use of molecular modeling, a collective term that refers to methods and theoretical modeling and computational techniques to mimic the behavior of molecules, not intend to reach a bioactive molecule simply through the use of computer programs. The choice of method for energy minimization depends on factors related to the size of the molecule, parameters of availability, stored data and computational resources. Molecular models generated by the computer are the result of mathematical equations that estimate the positions and properties of the electrons and nuclei, the calculations exploit experimentally, the characteristics of a structure, providing a new perspective on the molecule. In this work we show that studies of Highest Occupied Molecular Orbital Energy (HOMO), Low Unoccupied Molecular Orbital Energy (LUMO) and Map of molecular electrostatic potential (MEP) using Hatree-Fock method with different basis sets (HF/3-21G*, HF/3-21G**, HF/6-31G, HF/6-31G*, HF/6-31G** and HF/6-311G), that are of great importance in modern chemistry, biochemistry, molecular biology, and other fields of knowledge of health sciences. In order to obtain a significant correlation, it is essential that the descriptors are used appropriately. Thus, the quantum chemical calculations are an attractive source of new molecular descriptors that can, in principle, express all the geometrical and electronic properties of molecules and their interactions with biological receptor.
Evaluation of Quantum Chemical Methods and Basis Sets Applied in the Molecular Modeling of Artemisinin  [PDF]
Cleydson B. R. dos Santos, Cleison C. Lobato, Josinete B. Vieira, Davi S. B. Brasil, Alaan U. Brito, Williams J. C. Macêdo, José Carlos T. Carvalho, José C. Pinheiro
Computational Molecular Bioscience (CMB) , 2013, DOI: 10.4236/cmb.2013.33009
Abstract: In this paper, we evaluate semiempirical methods (AM1, PM3, and ZINDO), HF and DFT (B3LYP) in different basis sets to determine which method best describes the sign and magnitude of the geometrical parameters of artemisinin in the region of the endoperoxide ring compared to crystallographic data. We also classify these methods using statistical analysis. The results of PCA were based on three main components, explaining 98.0539% of the total variance, for the geometrical parameters C3O13, O1O2C3, O13C12C12a, and O2C3O13C12. The DFT method (B3LYP) corresponded well with the experimental data in the hierarchical cluster analysis (HCA). The experimental and theoretical angles were analyzed by simple linear regression, and statistical parameters (correlation coefficients, significance, and predictability) were evaluated to determine the accuracy of the calculations. The statistical analysis exhibited a good correlation and high predictive power for the DFT (B3LYP) method in the 6-31G** basis set.
[Azo-Hyd] Tautomerism and Structure of Selected Metal Complex Dyes AM1 and ZINDO/1 Methods  [PDF]
Krzysztof Wojciechowski, Lucjan Szuster
Computational Chemistry (CC) , 2016, DOI: 10.4236/cc.2016.44010
Abstract: Quantum-chemical calculation methods have been used to examine an influence of tautomeric equilibrium [Azo \"\"\"\"?Hydrazo] on a structure of 1:2 chromium metal complex dyes called Gryfalan Navy Blue RL (CI 15 707, Acid Blue 193) and Gryfalan Black RL (Acid Black 194). Chromatographic analysis indicates that synthesis yields a mixture of several dyes with different shades. Studies conducted to date have suggested that such dye complexes can constitute Drew-Pfitzner or Pfeiffer-Schetty structural isomers [1]. It is a know fact, that o-hydroxy-azo dyes exist in equilibrium of tautomeric azo and hydrazone forms. We decided to examine, whether color properties of examined metal-complex dyes can be influenced also by an azo-hydrazone equilibrium and what kind of influence on it has sulphonic groups present in molecules. Calculation and optimization of the geometrical structure were performed using the AM1 methods for monoazoo-hydroxy-azo dyesand ZINDO/1 for 1:2 chromium metal complex dyes. It was stated that monoazo dyes can create complexes in both forms: azo and hydrazone, because energy differences between each form of the metal complex dye are so small, that the monoazo dye can, in practice, create complexes in both the azo and the hydrazone form, with energy differences not exceeding about 4 - 11 kcal/mol. It is calculated that spatial structure changes with an angle of about 90° between two molecules of the dye, and angles of 10° - 20° between the naphthalene moieties. Similar electron density on the hydroxyl and ketone groups suggests that the mixture contains a dominant share of the azo form. The presence of an ionised sulphonic group was also found to affect on the tautomer equilibrium.
Gold complexes with
DA Pichugina,NE Kuz'menko,AF Shestakov
Gold Bulletin , 2007, DOI: 10.1007/BF03215567
Abstract: The reactions of methane with the gold complexes [Au(OH)] , [Au(OCH3)4] , [Au(O(CO)2O2] and [Au(O2CH)2]+, [AuI(acac)], [AuIII(acac)2]+ (acac-acetylacetonato) were studied using the DFT/PBE method with the SBK basis set. High activation barriers were obtained for the electrophilic substitution in [Au(OH)] , [Au(OCH3)4] , [Au(O(CO)2O)2]-and [AuIII(acac)2]+ complexes, which excludes the possibility that these reactions might proceed under mild conditions. The reactions of the [Au(HCO2)2]+ and [AuI(acac)] complexes with methane have rather low energy barriers and proceed through the formation of an intermediate complex. The alternative mechanism of methane oxidation with a gold complex in the presence of oxygen is simulated.
Compactness Aromaticity of Atoms in Molecules
Mihai V. Putz
International Journal of Molecular Sciences , 2010, DOI: 10.3390/ijms11041269
Abstract: A new aromaticity definition is advanced as the compactness formulation through the ratio between atoms-in-molecule and orbital molecular facets of the same chemical reactivity property around the pre- and post-bonding stabilization limit, respectively. Geometrical reactivity index of polarizability was assumed as providing the benchmark aromaticity scale, since due to its observable character; with this occasion new Hydrogenic polarizability quantum formula that recovers the exact value of 4.5 a 0 3 for Hydrogen is provided, where a 0 is the Bohr radius; a polarizability based–aromaticity scale enables the introduction of five referential aromatic rules (Aroma 1 to 5 Rules). With the help of these aromatic rules, the aromaticity scales based on energetic reactivity indices of electronegativity and chemical hardness were computed and analyzed within the major semi-empirical and ab initio quantum chemical methods. Results show that chemical hardness based-aromaticity is in better agreement with polarizability based-aromaticity than the electronegativity-based aromaticity scale, while the most favorable computational environment appears to be the quantum semi-empirical for the first and quantum ab initio for the last of them, respectively.
A Quantum Chemical Study on Polythiophenes Derivatives as Donor Materials in Bulk-heterojunction Polymer Solar Cell
Bushra Mohamed Omer,Ahmed Khogali
Research Journal of Applied Sciences, Engineering and Technology , 2012,
Abstract: For the optimum design of the donor and acceptor materials in polymer solar cells, it is very important to do a theoretical calculation for the energy levels and energy gaps. In this work we used the semiempirical method Austin Model1 (AM1) to investigate the Higher Occupied Molecular Orbital (HOMO) and Lower Unoccupied Molecular Orbital (LUMO) of polythiophenes derivatives/fullerenes combination (bulk heterojunction polymer solar cells). The overestimation on the HOMO and LUMO values was corrected by using experimental data from literature as criteria of correctness. Using our correction method, a reasonable linear relationship between the computed energy band gaps of polythiophenes derivatives and the experimental band gaps were found. The corrected HOMO and LUMO energies of polythiophenes derivatives match well with the experimental one. This method can serve as a road map inorder to design and synthesis appropriate combination of polythiophenes derivatives/fullerenes for bulk heterojunction solar cells.
From Molecular Phylogenetics to Quantum Chemistry: Discovering Enzyme Design Principles through Computation
Troy Wymore,Charles L. Brooks III
Computational and Structural Biotechnology Journal , 2012,
Abstract:
Modeling Metal Binding Sites in Proteins by Quantum Chemical Calculations  [PDF]
Todor Dudev
Computational Chemistry (CC) , 2014, DOI: 10.4236/cc.2014.22003
Abstract: Modeling Metal Binding Sites in Proteins by Quantum Chemical Calculations
A multidisciplinary study on magnesium
Rankovi? Radomir,Stojadinovi? Stevan,Sarvan Mirjana,Kasalica Be?ko
Journal of the Serbian Chemical Society , 2012, DOI: 10.2298/jsc120912105r
Abstract: During plasma electrolytic oxidation of a magnesium alloy (96% Mg, 3% Al, 1% Zn) we obtained a luminescence spectrum in the wave number range between 19 950 and 20 400 cm-1. The broad peak with clearly pronounced structure was assigned to the v’-v” = 0 sequence of the B 1Σ+ → X 1Σ+ electronic transition of MgO. Quantum-mechanical perturbative approach was applied to extract the form of the potential energy curves for the electronic states involved in the observed spectrum, from the positions of spectral bands. These potential curves, combined with the results of quantum-chemical calculations of the electric transition moment, were employed in subsequent variational calculations to obtain the Franck-Condon factors and transition moments for the vibrational transitions observed. Comparing the results of these calculations with the measured intensity distribution within the spectrum we derived relative population of the upper electronic state vibration levels. This enabled us to estimate the plasma temperature. Additionally, the temperature was determined by analysis of the recorded A 2Σ+ (v’ = 0) - X 2П (v” = 0) emission spectrum of OH. The composition of plasma containing magnesium, oxygen, and hydrogen under assumption of local thermal equilibrium was calculated in the temperature range up to 12 000 K and for pressures of 105, 106, 107, and 108 Pa, in order to explain the appearance of the observed spectral features and to contribute to elucidation of processes taking place during the electrolytic oxidation of Mg. [Projekat Ministarstva nauke Republike Srbije, br. 172040]
Homotopy Approach to Fractional Quantum Hall Effect  [PDF]
Janusz Jacak, Patrycja ?yd?ba, Lucjan Jacak
Applied Mathematics (AM) , 2015, DOI: 10.4236/am.2015.62033
Abstract: The topology-based explanation of the origin of the fractional quantum Hall effect is summarized. The cyclotron braid subgroups crucial for this approach are introduced in order to identify the origin of Laughlin correlations in 2D Hall systems. The so-called composite fermions are explained in terms of the homotopy cyclotron braids. Some new concept for fractional Chern insulator states is formulated in terms of the homotopy condition applied to the Berry field flux quantization.
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