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Density Functional Theory Methods (density + functional_theory_methods)
Selected AbstractsD5h Cu5H5X: Pentagonal Hydrocopper Cu5H5 Containing Pentacoordinate Planar Nonmetal Centers (X = B, C, N, O)EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 11 2004Si-Dian Li Abstract Pentacoordinate planar nonmetals (PPNs) centered in perfect pentagonal hydrocopper complexes Cu5H5X (X = B, C, N, O), as determined by density functional theory methods, are presented in this communication. The results obtained in this work complete the hypercoordinate planar carbon series with high symmetries (D4h, D5h, and D6h), and may shed new insight in catalyst chemistry. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Kinetics and mechanism for the H-for-X exchange process in the H + C6H5X reactions: A computational studyINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 11 2001I. V. Tokmakov The addition of H atoms to benzene and toluene and subsequent transformations were investigated using high level ab initio and density functional theory methods. Molecular structures and vibrational frequencies calculated at the B3LYP/6-311++G(d,p) level of theory were used in combination with adjusted G2M energetic parameters for RRKM rate constant calculations. Standard heats of formation for cyclohexadienyl and cyclohexadienyl, 6-methyl radicals calculated through isodesmic reactions amounted to 49.5 ± 2 and 42.9 ± 3 kcal/mol, respectively. Rate constants for various elementary reactions involved in the H-for-X exchange (X = D, CH3) were calculated and closely correlated with the available experimental kinetic data. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 633,653, 2001 [source] Principal component analysis of the effects of wavefunction modification on the electrostatic potential of indoleINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2005Maíra A. Carvalho Abstract The molecular electrostatic potential (MEP) of the indole molecule was calculated in a three-dimensional grid in which the molecule was centered at the origin. To evaluate the dependence of MEP on the type of calculation, semiempirical, ab initio, and density functional theory methods with different basis sets were employed. The data matrix generated by these calculations was analyzed by principal component analysis (PCA). The appearance of outliers and the effect of wavefunction modifications such as the introduction of electron correlations and diffuse functions were highlighted by the use of PCA. The spatial localization of such effects around the molecule was possible from the loadings values associated with the graphical analysis of the grid points. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Theoretical versus experimental geometries in S-bridged manganese carbonyl complexesJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2003Juan F. Van der Maelen Uría The experimental geometry obtained from single-crystal X-ray diffraction for a number of binuclear S-bridged manganese complexes is compared with the results of theoretical calculations made at the ab initio level by using Hartree,Fock and density functional theory methods with medium-size and large basis sets. The optimized geometries obtained were somewhat relaxed when compared with the experimental ones, with very similar bond and torsion angles but longer bond lengths. The mean square deviation for bond lengths (angles) was found to be between 0.046,Å (1.1°) and 0.004,Å (0.7°) depending on the theoretical model used. [source] Trends of the bonding effect on the performance of DFT methods in electric properties calculations: A pattern recognition and metric space approach on some XY2 (X = O, S and Y = H, O, F, S, Cl) moleculesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2010Christos Christodouleas Abstract A test set of 10 molecules (open and ring forms of ozone and sulfur dioxide as well as water and hydrogen sulfide and their respective fluoro- and chloro-substituted analogs) of specific atmospheric interest has been formed as to assess the performance of various density functional theory methods in (hyper)polarizability calculations against well-established ab initio methods. The choice of these molecules was further based on (i) the profound change in the physics between isomeric systems, e.g., open (C2v) and ring (D3h) forms of ozone, (ii) the relation between isomeric forms, e.g., open and ring form of sulfur dioxide (both of C2v symmetry), and (iii) the effect of the substitution, e.g., in fluoro- and chloro-substituted water analogs. The analysis is aided by arguments chosen from the information theory, graph theory, and pattern recognition fields of Mathematics: In brief, a multidimensional space is formed by the methods which are playing the role of vectors with the independent components of the electric properties to act as the coordinates of these vectors, hence the relation between different vectors (e.g., methods) can be quantified by a proximity measure. Results are in agreement with previous studies revealing the acceptable and consistent behavior of the mPW1PW91, B3P86, and PBE0 methods. It is worth noting the remarkable good performance of the double hybrid functionals (namely: B2PLYP and mPW2PLYP) which are for the first time used in calculations of electric response properties. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010 [source] Fundamental vibrational frequencies and dominant resonances in methylamine isotopologues by ab initio and density functional theory methods,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2008Chen Levi Abstract Ab initio and density functional theory (DFT) calculations were performed for obtaining fundamental vibrational frequencies of methylamine, CH3NH2, and its deuterated variants CH3ND2, CD3NH2, and CD3ND2. The calculations were carried out using the CCSD(T) coupled cluster approximation with cc-pVTZ and cc-pVQZ basis sets, and by the DFT method with the semiempirical hybrid functional B97-1 with polarization consistent pc-2 and pc-3 basis sets. Reasonable performance of the DFT harmonic and ab initio harmonic calculations was found, which improved considerably upon combination of the harmonic fundamental frequencies with anharmonic corrections from the smaller, pc-2, basis. The computed anharmonic fundamental frequencies of methylamine isotopologues agree very well with the experimental values and represent a useful tool for assignment and analysis of the dominant resonances. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Theoretical studies on nonlinear optical properties of formaldehyde oligomers by ab initio and density functional theory methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2005Hui-Yin Wu Abstract The first and second hyperpolarizability , and , are obtained for formaldehyde oligomers (H2CO)n (n = 1,7) using computational methods. We have used the finite field (FF) approach and hyperpolarizability density analysis (HDA) to predict the microscopic first and second nonlinear hyperpolarizability of the formaldehyde oligomers. The spatial contributions of electrons to the hyperpolarizability by using plots of HDA are presented. It has been found from the numerical stability checking of the hyperpolarizability calculations that the calculated values by FF method are more stable than those by HDA approach. The values of , are zero when n is even as the molecule possesses centrosymmetry, and when n is odd, the differences among , values are not clear. The , values are increased with increase in n. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1543,1564, 2005 [source] Organic cyclic difluoramino-nitramines: infrared and Raman spectroscopy of 3,3,7,7-tetrakis(difluoramino)octahydro 1,5-dinitro-1,5-diazocine (HNFX)JOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2009Philippe F. Weck Abstract We present the first vibrational structure investigation of 3,3,7,7-tetrakis(difluoramino)octahydro-1,5-dinitro- 1,5-diazocine (HNFX),and, more generally, of a member of the new class of gem -bis(difluoramino)-substituted heterocyclic nitramine energetic materials,using combined theoretical and experimental approaches. Optimized molecular structure and vibrational spectra of the Ci, symmetry conformer constituting the HNFX crystal were computed using density functional theory methods. Fourier transform infrared and Raman spectra of HNFX crystalline samples were also collected at ambient temperature and pressure. The average deviation of calculated structural parameters from X-ray diffraction data is ,1% at the B3LYP/6-311 + + G(d,p) level of theory, suggesting the absence of significant molecular distortion induced by the crystal field. Very good agreement was found between simulated and measured spectra, allowing reliable assignment of the fundamental normal modes of vibration of the HNFX crystal. Detailed analysis of the normal modes of the C,(NF2)2 and N,NO2 moieties was performed due to their critical importance in the initial steps of the molecular homolytic fragmentation process. Copyright © 2009 John Wiley & Sons, Ltd. [source] Oxygen Diffusion in Yttria-Stabilized Zirconia: A New Simulation ModelJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 10 2004R. Krishnamurthy We present a multiscale modeling approach to study oxygen diffusion in cubic yttria-stabilized zirconia. In this approach, we employ density functional theory methods to calculate activation energies for oxygen migration in different cation environments. These are used in a kinetic Monte Carlo framework to calculate long-time oxygen diffusivities. Simulation results show that the oxygen diffusivity attains a maximum value at around 0.1 mole fraction yttria. This variation in the oxygen diffusivity with yttria mole fraction and the calculated values for the diffusivity agree well with experiment. The competing effects of increased oxygen vacancy concentration and increasing activation energy and correlation effects for oxygen diffusion with increasing yttria mole fraction are responsible for the observed dopant content dependence of the oxygen diffusivity. We provide a detailed analysis of cation-dopant-induced correlation effects in support of the above explanation. [source] Structural Investigation of a High-Affinity MnII Binding Site in the Hammerhead Ribozyme by EPR Spectroscopy and DFT Calculations.CHEMBIOCHEM, Issue 10 2003Effects of Neomycin B on Metal-Ion Binding Abstract Electron paramagnetic resonance spectroscopy and density functional theory methods were used to study the structure of a single, high-affinity MnIIbinding site in the hammerhead ribozyme. This binding site exhibits a dissociation constant Kdof 4.4 ,M in buffer solutions containing 1,M NaCl, as shown by titrations monitored by continuous wave (cw) EPR. A combination of electron spin echo envelope modulation (ESEEM) and hyperfine sublevel correlation (HYSCORE) experiments revealed that the paramagnetic manganese(II) ion in this binding site is coupled to a single nitrogen atom with a quadrupole coupling constant,of 0.7 MHz, an asymmetry parameter,of 0.4, and an isotropic hyperfine coupling constant of Aiso(14N)=2.3 MHz. All three EPR parameters are sensitive to the arrangement of the MnIIligand sphere and can therefore be used to determine the structure of the binding site. A possible location for this binding site may be at the G10.1, A9 site found to be occupied by MnIIin crystals (MacKay et al., Nature 1994, 372, 68 and Scott et al., Science 1996, 274, 2065). To determine whether the structure of the binding site is the same in frozen solution, we performed DFT calculations for the EPR parameters, based on the structure of the MnIIsite in the crystal. Computations with the BHPW91 density function in combination with a 9s7p4d basis set for the manganese(II) center and the Iglo-II basis set for all other atoms yielded values of,(14N)=+0.80 MHz, ,=0.324, and Aiso(14N)=+2.7 MHz, in excellent agreement with the experimentally obtained EPR parameters, which suggests that the binding site found in the crystal and in frozen solution are the same. In addition, we demonstrated by EPR that MnIIis released from this site upon binding of the aminoglycoside antibiotic neomycin B (Kd=1.2 ,M) to the hammerhead ribozyme. Neomycin B has previously been shown to inhibit the catalytic activity of this ribozyme (Uhlenbeck et al., Biochemistry 1995, 34, 11,186). [source] Aromatic,Carbohydrate Interactions: An NMR and Computational Study of Model SystemsCHEMISTRY - A EUROPEAN JOURNAL, Issue 25 2008Sophie Vandenbussche Ir. Abstract The interactions of simple carbohydrates with aromatic moieties have been investigated experimentally by NMR spectroscopy. The analysis of the changes in the chemical shifts of the sugar proton signals induced upon addition of aromatic entities has been interpreted in terms of interaction geometries. Phenol and aromatic amino acids (phenylalanine, tyrosine, tryptophan) have been used. The observed sugar,aromatic interactions depend on the chemical nature of the sugar, and thus on the stereochemistries of the different carbon atoms, and also on the solvent. A preliminary study of the solvation state of a model monosaccharide (methyl ,-galactopyranoside) in aqueous solution, both alone and in the presence of benzene and phenol, has also been carried out by monitoring of intermolecular homonuclear solvent,sugar and aromatic,sugar NOEs. These experimental results have been compared with those obtained by density functional theory methods and molecular mechanics calculations. [source] Strength of C,H Bonds at Nitrogen , -Position:Implication for Metabolic Stability of Nitrogen-containing Drug MoleculesCHINESE JOURNAL OF CHEMISTRY, Issue 4 2008Xiang-Ming MENG Abstract The available experimental ,C-H BDEs of a variety of amine-containing molecules were examined by using the G3B3 and CBS-Q methods. The verified values were employed to benchmark and calibrate the density functional theory methods. It was found that the (U)BHandH/6-311++G(2df, 2p)//(U)B3LYP/6-31G(d) method was a fast and accurate method for calculating C,H BDEs at nitrogen , -positions. By using the newly benchmarked BHandH method, the ,C,H BDEs in a number of nitrogen-containing drug molecules were calculated, where a dramatic variation of the ,C,H BDEs was discovered. To understand this variation, the effects of mono- and double-substitution at both carbon and nitrogen atoms on the ,C-H BDEs were systematically studied. The origin of the substitution effects was thoroughly discussed in terms of four categories of substituents. [source] Absolute configuration of eremophilane sesquiterpenes from Petasites hybridus: Comparison of experimental and calculated circular dichroism spectraCHIRALITY, Issue 3 2010Antje Bodensieck Abstract In-depth conformational analyses of 10 known eremophilane (= (1S,4aR,7R,8aR)-decahydro-1,8a-dimethyl-7-(1-methylethyl)napththalene) sesquiterpenes, 1,10, from Petasites hybridus were performed with molecular mechanics as well as density functional theory methods. Electronic transition energies and rotational strengths of these eight eremophilane lactones and two petasins were calculated by time-dependent density functional theory (B3PW91/TZVP). The absolute configurations of the constituents could be assigned by comparison of their simulated and experimental circular dichroism (CD) spectra in methanol as (4S,5R,8S,10R) (1, 2), (2R,4S,5R,8S,10R) (3, 4, 5), (2R,4S,5R,8R,9R,10R) (6), (2R,4S,5R,8R,10R) (7, 8), and (3R,4R,5R) (9, 10). Single-crystal X-ray diffraction data of 8,-hydroxyeremophilanolide ((8S)-8-hydroxyeremophil-7(11)-en-12,8-olide) (1) served as starting point for the theoretical conformational calculations of the 8,-epimers of the eremophilane lactones. Experimental CD spectra as well as 1H NMR spectra of compound 1 in methanol were considerably dependent on sample concentration. Chirality, 2010. © 2009 Wiley-Liss, Inc. [source] | ||||||||||