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Functional Methods (functional + methods)
Kinds of Functional Methods Selected AbstractsChemInform Abstract: A Structural and Vibrational Study of Uranium(III) Molecules by Density Functional Methods.CHEMINFORM, Issue 49 2001Laurent Joubert Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] A Series of Lithium Rare Earth Polyphosphates [LiLn(PO3)4] (Ln = La, Eu, Gd) and Their Structural, Optical, and Electronic PropertiesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 2 2007Jing Zhu Abstract The structural, optical, and electronic properties of a series of lithium rare earth polyphosphates [LiLn(PO3)4] [Ln = La (1), Eu (2), Gd (3)] have been investigated by means of single-crystal X-ray diffraction, elemental analyses, and spectroscopic measurements, as well as calculations of energy-band structures, density of states, and optical response functions by density functional methods. These LiLn(PO3)4 systems are monoclinic with space group C2/c and Z = 4. Their unit-cell parameters decrease as the ionic radius of Ln3+ decreases (La3+ > Eu3+ > Gd3+). Both (PO4)3, zig-zag chains and infinite chains formed by the alternate connection of LnO8 polyhedra and LiO4 tetrahedra run parallel to the b -axis in the structure. The energy-band structures, density of states, the chemical bonds, and optical properties have been investigated by density functional methods for some of the title compounds. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] 2,5-Disubstituted Pyrrolidines as Chiral Auxiliaries in Radical Reactions: A Theoretical ApproachEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 25 2010Miglena K. Georgieva Abstract The radical addition to amides derived from chiral 2,5-disubstituted pyrrolidines has been theoretically studied by the use of density functional methods and the results compared with known experimental data. The results agree quite well with those obtained experimentally and allow the full rationalization of the factors influencing the diastereoselectivity. Steric effects are the main factors determining the selectivity, but electronic interactions can also be very important when the attacking alkene is ,,,-conjugated, as in acrylic esters or acrylamides. Additions at the ,- and ,-positions of the amide chain in the auxiliary are subject to different rules, with the former usually yielding high diastereoselectivities both experimentally and theoretically, whereas the latter is theoretically predicted to occur with low selectivity. We fully rationalize these two opposite behaviours and suggest several ways to circumvent this limitation, thus strongly increasing the interest of this type of structure as chiral auxiliaries in radical reactions. [source] The Tautomerism of 5-Amino-3-oxo-1,2,4-thiadiazole: An Experimental and Theoretical StudyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 33 2007Arantxa Encinas Abstract The 1,2,4-thiadiazole system was the subject of our research as a consequence of the pharmacological activity of some derivatives as GSK3 inhibitors. Therefore, in order to explore the active form responsible for receptor interaction, a systematic study of the tautomerism in the 5-amino-3-oxo-1,2,4-thiadiazole system was performed by using experimental and theoretical methods. Thus, the relative stability of the possible tautomers was studied in the gas phase by density functional theory and local density functional methods. The theoretical study in solution was carried out by using severalcontinuum solvation models. Finally, experimental studies were carried out to unambiguously establish the tautomeric form.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Understanding selenocysteine through conformational analysis, proton affinities, acidities and bond dissociation energiesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2008Damanjit Kaur Abstract Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energy surface using density functional B3LYP/6-31+G* method. The conformers are analyzed in terms of intramolecular hydrogen bonding interactions. The proton affinity, gas phase acidities, and bond dissociation energies have also been evaluated for different reactive sites of selenocysteine for the five lowest energy conformers at B3LYP/6-311++G*//B3LYP/6-31+G* level. Evaluation of these intrinsic properties reflects the antioxidant activity of selenium in selenocysteine. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Benzonitriles: Survey of their importance and scaling of their vibrational frequenciesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2003M. Alcolea Palafox Abstract This work provides a short survey of the studies carried out on benzonitrile and its derivatives, with special attention on a spectroscopic point of view. The importance and main applications of these molecules are also briefly indicated. For an accurate assignment of their vibrational spectra, the scaling procedures for the wave numbers are described. For this purpose, the performance of semiempirical, ab initio, and density functional methods, with different basis sets, is determined. A "resume" of the main scaling factors to be used in the calculated wave numbers is shown. The results obtained for several benzene derivatives, and in particular for four benzonitriles, are analyzed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 189,204, 2003 [source] Molecular relaxation and metalloenzyme active site modelingINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2002James W. Whittaker Abstract Metalloenzymes represent a broad class of important biomolecules containing an essential metal ion cofactor in their catalytic active sites, forming biologic metal complexes that perform a wide range of important functions: activation of small molecules (O2, N2, H2, CO), atom transfer chemistry, and the control of oxidation equivalents. The structures of many metalloenzyme active sites have been defined by X-ray crystallography, revealing transition metal ions in unique low-symmetry environments. These bioinorganic complexes present significant challenges for computational studies aimed at going beyond crystal structures to develop a detailed understanding of the catalytic mechanisms. Considerable progress has been made in the theoretical characterization of these sites in recent years, supported by the availability of efficient computational tools, in particular density functional methods. However, the ultimate success of a theoretical model depends on a number of factors independent of the specific computational method used, including the quality of the initial structural data, the identification of important environmental perturbations and constraints, and experimental validation of theoretical predictions. We explore these issues in detail and illustrate the effects of molecular relaxation in calculations of two metalloenzymes, manganese superoxide dismutase and galactose oxidase. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] An approximate diatomics in molecules formulation of generalized valence bond theoryJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2008John Cullen Abstract The slow computational speed of the generalized valence bond perfect pairing method (GVB-PP) has been an impediment to its routine use. We have addressed this problem by employing a diatomics in molecules Hamiltonian derived from a second quantization perturbation approach. This results in all three- and four-centered two-electron integrals being dropped from the traditional GVB-PP calculation. For moderate sized molecules, as for example C20 computed with a double zeta + polarization basis, there is on average a fifty-fold decrease in computational times. In this article, we present the theory behind our approach and analyze the accuracy and speed of this approximate GVB-PP method for several cases where density functional methods have produced ambivalent results. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Geometry optimization in density functional methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2004J. Ulises Reveles Abstract The geometry optimization in delocalized internal coordinates is discussed within the framework of the density functional theory program deMon. A new algorithm for the selection of primitive coordinates according to their contribution to the nonredundant coordinate space is presented. With this new selection algorithm the excessive increase in computational time and the deterioration of the performance of the geometry optimization for floppy molecules and systems with high average coordination numbers is avoided. A new step selection based on the Cartesian geometry change is introduced. It combines the trust radius and line search method. The structure of the new geometry optimizer is described. The influence of the SCF convergence criteria and the grid accuracy on the geometry optimization are discussed. A performance analysis of the new geometry optimizer using different start Hessian matrices, basis sets and grid accuracies is given. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1109,1116, 2004 [source] Molecules for materials: Germanium hydride neutrals and anions.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2002Ge2Hn/Ge2H (n = 0, Molecular structures, electron affinities, thermochemistry of GeHn/GeH (n = 0 Abstract The GeHn (n = 0,4) and Ge2Hn (n = 0,6) systems have been studied systematically by five different density functional methods. The basis sets employed are of double-, plus polarization quality with additional s- and p-type diffuse functions, labeled DZP++. For each compound plausible energetically low-lying structures were optimized. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chemical Reviews 102, 231, 2002). The geometries predicted in this work include yet unknown anionic species, such as Ge2H,, Ge2H, Ge2H, Ge2H, and Ge2H. In general, the BHLYP method predicts the geometries closest to the few available experimental structures. A number of structures rather different from the analogous well-characterized hydrocarbon radicals and anions are predicted. For example, a vinylidene-like GeGeH structure is the global minimum of Ge2H. For neutral Ge2H4, a methylcarbene-like HGë-GeH3 is neally degenerate with the trans -bent H2GeGeH2 structure. For the Ge2H anion, the methylcarbene-like system is the global minimum. The three different neutral-anion energy differences reported in this research are: the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). For this family of molecules the B3LYP method appears to predict the most reliable electron affinities. The adiabatic electron affinities after the ZPVE correction are predicted to be 2.02 (Ge2), 2.05 (Ge2H), 1.25 (Ge2H2), 2.09 (Ge2H3), 1.71 (Ge2H4), 2.17 (Ge2H5), and ,0.02 (Ge2H6) eV. We also reported the dissociation energies for the GeHn (n = 1,4) and Ge2Hn (n = 1,6) systems, as well as those for their anionic counterparts. Our theoretical predictions provide strong motivation for the further experimental study of these important germanium hydrides. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1642,1655, 2002 [source] Ab initio study on N,N,,N, -triaminoguanidineJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 12 2007Pansy Iqbal Abstract Electronic structure calculations and second-order delocalizations in N,N,,N,,-triaminoguanidine (TAG) have been studied by employing ab initio MO and density functional methods. There are total 10 rotational isomers on the potential energy (PE) surface of TAG. The effect of three amino groups substitution on guanidine (Gu) has been studied in terms of the primary and the secondary electron delocalizations in TAG by employing Natural Population Analysis (NPA). An increased electron delocalization is observed in protonated triaminoguanidine (TAGP) due to the three strong intramolecular hydrogen bonds and hence accounts for its extra stability. The increase in the electron delocalization upon protonation in TAG can be compared to that in guanidine. The absolute proton affinity (APA) of TAG is less than that of Gu. HOMA and NICS studies have been carried out to understand electron delocalization in TAGP. Copyright © 2007 John Wiley & Sons, Ltd. [source] Prediction of experimentally unknown re distances of organic molecules from Dunning basis set extrapolations for ab initio post-HF calculationsJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 3 2006Alexander Neugebauer Abstract An approach to estimate equilibrium re bond lengths of organic molecules which contain standard bonding situations for CC, CH, CO and CN distances from only one equation is presented. For this, optimizations of molecular geometries using correlated post-Hartree,Fock and density functional methods have been performed. A selection scheme was developed to determine the most reliable methodology for prediction of equilibrium re distances of covalent bonds from a set of investigated theoretical methods. Consequently, distances computed in the CCSD(T) procedure via exponential extrapolation from a consecutive set of Dunning cc-pVXZ basis sets by use of Eqn (2) are accurate up to ±,0.0005,Å in comparison to experimentally available re distances. Applications for predictions of the experimentally unknown re distances of methanol, methylamine and methylenimine are presented. Additionally the estimation of re distances of larger, chemically more interesting molecules is possible by lower order calculations (e.g. DFT B3LYP/cc-pVDZ) via linear correlation statistics using the results from our re reference model system via Eqn (3). Copyright © 2006 John Wiley & Sons, Ltd. [source] Computational study of stereoelectronic effects in fluorinated alkylamines,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 11 2005Joseph J. Urban Abstract A systematic evaluation of the stereoelectronic effects in a series of fluorinated amine compounds has been carried out. A variety of computational methods have been employed, including molecular mechanics, semi-empirical, density functional and ab initio methods. An analysis of the natural bond orbital populations has been carried out and the effect of solvent was considered via the polarized continuum model (PCM). The results indicate a preference for conformations that result in an anti-periplanar arrangement between the nitrogen lone pair and the CX bond (XF or CF3). There are variations in geometry and natural bond orbital population, with conformation that are consistent with a stereoelectronic effect whereby electron density from the nitrogen lone pair is delocalized into the CX ,* orbital. Similar results are obtained for trifluoromethyl methylamines, although the magnitude of the stereoelectronic effect is attenuated resulting in greater expected conformational diversity for these compounds. The PCM results suggest that these preferences should persist in solution. Comparison among the computational methods used reveals that there is good agreement among the ab initio and density functional methods (at the HF/6-31,+,G(d), MP2/6-31,+,G(d), MP2/6-311,+,G(2d,p) and B3LYP/6-31,+,G(d) levels) and these methods agree well with the available experimental data for ethylmethylamine. Published in 2005 by John Wiley & Sons, Ltd. [source] Theoretical studies on the S,N interaction in sulfinamidesJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 4 2002Prasad V. Bharatam Abstract The potential energy surface of sulfinamide H(O)S,NH2 (1) was searched, using ab initio and density functional methods, to study the conformational preferences. High-accuracy G2MP2 calculations showed that the S,N rotational barrier in 1 is 7.0,kcal,mol,1. The inversion around N in 1 goes through a very low energy barrier. Charge analysis using the NPA method was performed to elucidate the electronic factors responsible for the observed trends in the S,N interactions. The strength of negative hyperconjugation in 1 was estimated using NBO analysis and by studying the substituent effect. The repulsions between the lone pairs on oxygen and nitrogen and the nN , ,*S,O negative hyperconjugation play an important role in the conformations. Copyright © 2002 John Wiley & Sons, Ltd. [source] Keto,enol tautomerism in ,-ketoesters: CH3C(O)CHXC(O)OY (X = H, Cl; Y = CH3, C2H5).JOURNAL OF RAMAN SPECTROSCOPY, Issue 5 2001NMR spectra, Vibrational analyses, quantum chemical calculations The tautomeric equilibria of the ,-ketoesters [CH3C(O)CH2C(O)OCH3 (I), CH3C(O)CHClC(O)OCH3 (II), CH3C(O)CH2C(O)OCH2CH3 (III) and CH3C(O)CHClC(O)OCH2CH3 (IV)] were studied by NMR spectroscopy and, in the case of I and II, by quantum chemical calculations (ab initio and density functional methods). In addition, liquid-state Fourier transform infrared and Raman spectra were analysed for all four compounds. They revealed the existence of two tautomers, diketo and enol forms. In the NMR spectra only signals for the diketo form could be observed for I and III. However, the calculations for I and II predicted the enol structures to be the most stable species. Copyright © 2001 John Wiley & Sons, Ltd. [source] Comparison of various density functional methods for distinguishing stereoisomers based on computed 1H or 13C NMR chemical shifts using diastereomeric penam ,-lactams as a test setMAGNETIC RESONANCE IN CHEMISTRY, Issue 10 2007Keith W. Wiitala Abstract Full 1H and 13C NMR chemical shift assignments were made for two sets of penam ,-lactams: namely, the diastereomeric (2S, 5S, 6S)-, (2S, 5R, 6R)-, (2S, 5S, 6R)-, and (2S, 5R, 6S)-methyl 6-(1,3-dioxoisoindolin-2-yl)-3,3-dimethyl-7-oxo-4-thia-1-aza-bicyclo[3.2.0]heptane-2-carboxylates (1,4) and (2S, 5R, 6R)-, (2S, 5S, 6R)-, and (2S, 5R, 6S)-6-(1,3-dioxoisoindolin-2-yl)-3,3-dimethyl-7-oxo-4-thia-1-aza-bicyclo[3.2.0]heptane-2-carboxylic acids (6,8). Each penam was then modeled as a family of conformers obtained from Monte Carlo searches using the AMBER* force field followed by IEFPCM/B3LYP/6-31G(d) geometry optimization of each conformer using chloroform solvation. 1H and 13C chemical shifts for each conformer were computed at the WP04, WC04, B3LYP, and PBE1 density functional levels as Boltzmann averages of IEFPCM/B3LYP/6-311 + G(2d,p) energies over each family. Comparisons between experimental and theoretical chemical shift data were made using the total absolute error (|,, | T) criterion. For the 1H shift data, all methods were sufficiently accurate to identify the proper stereoisomers. Computed 13C shifts were not always successful in identifying the correct stereoisomer, regardless of which DFT method was used. The relative ability of each theoretical approach to discriminate among stereoisomers on the basis of proton shifts was also evaluated. Copyright © 2007 John Wiley & Sons, Ltd. [source] Multi-impurity complexes for n-type diamond: a computational studyPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 9 2007R. J. Eyre Abstract Doping of diamond using multi-component, multi-species structures has been modelled using density functional methods. We find that few combinations of impurities yield donor levels shallower than phosphorus. Complexes involving impurities from the second or lower rows of the periodic table are unbound, and those involving the soluble element nitrogen can often be arranged in passive or even compensating geometries. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Band structure and optical properties of SbSeI: density-functional calculationPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 10 2007Harun Akkus Abstract The electronic structure and linear optical properties of the ferroelectric semiconductor SbSeI are calculated in the nonpolar phase using the density functional methods in the generalized gradient approximation. The obtained electronic band structure shows that SbSeI has an indirect forbidden gap of 1.65 eV. The linear photon-energy-dependent dielectric functions and some optical functions such as absorption and extinction coefficients, refractive index, energy-loss function, reflectivity and optical conductivity are calculated. Moreover, some important optical parameters such as the effective number of valence electrons and the effective optical dielectric constant are calculated. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Early structural effects of oestrogen on pudendal nerve regeneration in the ratBJU INTERNATIONAL, Issue 6 2004D.D. Kane OBJECTIVE To determine the early effects of oestrogen on the ultrastructure of the pudendal nerve and distal nerve fascicles near the external urethra sphincter (EUS) after a pudendal nerve crush injury. The pudendal nerve is one of the pelvic floor tissues injured during vaginal delivery, possibly contributing to the development of stress urinary incontinence (SUI) in women, the symptoms of which often do not appear until menopause, implicating hormonal factors. MATERIALS AND METHODS Twenty-seven virgin female Sprague-Dawley rats were anaesthetized and underwent ovariectomy. Three days later, they had one of four procedures: bilateral pudendal nerve crush plus implant of a subcutaneous oestrogen-containing capsule (NC+E); nerve crush plus implant of a sham saline-containing capsule (NC+S); no nerve crush with an oestrogen capsule; or no nerve crush with a sham capsule. After 2 weeks the pudendal nerves and urethral tissues were prepared for light and electron microscopy. The number of axons, myelin figures and endoneurial nuclei in the pudendal nerve segment distal to the lesion were counted. Nerve fascicles near the EUS were also counted and categorized as normal or showing signs of degeneration and/or regeneration. The location of each nerve fascicle was specified as either ventral or dorsal. RESULTS As there were no significant differences between the two control groups they were combined to form a single control group. In the distal pudendal nerve there were significantly fewer myelinated axons and large myelinated axons in the NC+E and NC+S groups than in the control group. There were three times as many large unmyelinated axons in the NC+E group than in either the NC+S or control groups (P < 0.05). There were only half as many nerve fascicles near the ventral side of the EUS in the NC+S group than in both the control and NC+E groups (P < 0.05). CONCLUSION Oestrogen appears to affect large unmyelinated axons in both the injured pudendal nerve and at the denervated EUS target. After pudendal nerve crush, nerve fascicles with evidence of degeneration or regeneration near the EUS appear to be spared with oestrogen treatment, particularly in the ventral region. These observations may reflect the early stages of a neuroregenerative effect of oestrogen. Additional studies are needed to confirm these results at later periods and with functional methods. [source] | |||||||||||||||||||||||||