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Structure Calculations (structure + calculation)
Kinds of Structure Calculations Selected AbstractsChemInform Abstract: Structure and Heats of Formation of Iodine Fluorides and the Respective Closed-Shell Ions from CCSD(T) Electronic Structure Calculations and Reliable Prediction of the Steric Activity of the Free-Valence Electron Pair in ClF6 - , BrF6 - , and IF6 -CHEMINFORM, Issue 37 2008David A. Dixon Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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] ChemInform Abstract: Analysis of the Spin Lattice Model for the Spin-Gapped Layered Compounds Na3Cu2SbO6 and Na2Cu2TeO6 on the Basis of Electronic Structure Calculations.CHEMINFORM, Issue 14 2008Hyun-Joo Koo Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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] ChemInform Abstract: Heats of Formation of Krypton Fluorides and Stability Predictions for KrF4 and KrF6 from High Level Electronic Structure Calculations.CHEMINFORM, Issue 7 2008David A. Dixon Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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] Unpaired Spin Populations and Spin-Pairing Tendencies of the Nonequivalent Vanadium Sites of the Magnetic Metal NaV6O11 Investigated by Electronic Band Structure Calculations and Spin Dimer Analysis.CHEMINFORM, Issue 43 2005A. Villesuzanne No abstract is available for this article. [source] X-Ray Crystal Structures of [XF6][Sb2F11] (X: Cl, Br, I); 35,37Cl, 79,81Br, and 127I NMR Studies and Electronic Structure Calculations of the XF6+ Cations.CHEMINFORM, Issue 1 2005John F. Lehmann Abstract For Abstract see ChemInform Abstract in Full Text. [source] Electronic Structure Calculations for LaNi5 and LaNi5H7: Energetics and Elastic Properties.CHEMINFORM, Issue 24 2003L. G. Jr. Hector Abstract For Abstract see ChemInform Abstract in Full Text. [source] ChemInform Abstract: First-Principles Electronic Structure Calculations of BaSi7N10 with Both Corner- and Edge-Sharing SiN4 Tetrahedra.CHEMINFORM, Issue 24 2002C. M. Fang 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] ChemInform Abstract: First-Principles Electronic Structure Calculations of Ba5Si2N6 with Anomalous Si2N6 Dimeric Units.CHEMINFORM, Issue 34 2001C. M. Fang 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] ChemInform Abstract: Electronic Structure Calculations for the Ternary Intermetallic Compounds A2MX and AMX2 (A: Li; M: Rh, Pd, Ir, Pt; X: Al, Ga, In) Using Density-Functional Theory.CHEMINFORM, Issue 23 2001Lydia Drews-Nicolai 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] Semiempirical electronic structure calculation on Ca and Pb apatitesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2009Maria Matos Abstract A systematic study is made on the electronic structure of stoichiometric calcium and lead apatites, using the tight binding extended Hückel method (eHT). The aim is to investigate the applicability of the semiempirical theory to study this family of compounds. A10(BO4)6X2 (A = Ca, Pb) apatites, differing by substitutions in the BO4 tetrahedral unit (B = P, As, and V) and X-channel ion (X = OH, Cl), are considered. The calculations show that eHT is suitable to describe basic properties especially concerning trends with atomic substitution and geometry changes. Band structure, Mulliken charge distribution, and bond orders are in good agreement with results of ab initio density functional theory (DFT) found in the literature. Large variations in the optical gap due to vanadium and lead substitutions are newly found. Changes in the anion X-channel affect the optical gap, which is in close agreement with DFT results. Analysis involving subnets are performed to determine the role of halogenic orbitals in the electronic structure of chloroapatites, showing evidence of covalent Cl bonding. It was also found that PbOH bonding in hydroxy-vanadinite Pb10(VO4)6(OH)2, recently synthesized, is weaker than that of CaOH in vanadate Ca10(VO4)6(OH)2. Arsenium is found to be more weakely bound to the O-tetrahedron than phosphorous, although CaO bond is increased with the substitution. We investigate, in addition, the electronic structure of a model system Ca10(AsO4)6(OH)2, obtained from direct As substitution in the vanadate Ca10(VO4)6(OH)2. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Spin-adapted states: A basis for quantum dot structure calculationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2006R. D. Muhandiramge Abstract The exact diagonalization method using a spin-adapted basis is employed to calculate the electronic structure of a multi-electron quantum dot. By isolating spin and orbital angular momentum eigenstates, we have significantly reduced the size of the matrices required in comparison with the standard configuration interaction method. A novel approach to the simplification of the interaction integrals that arise in the calculation is also presented, which allows exact evaluation of the Hamiltonian matrix required in the calculations. This Mathematica package permits accurate calculation of energy levels and wave functions for both ground and excited states of multiple electrons confined in a circular quantum dot. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Electronic structure calculation by monte carlo diagonalization methodINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2001Y. Shigeta We propose an electronic structure calculation scheme for ground and low-lying excited states of molecular systems by using the generalized coherent state for fermion, where the coefficients of the coherent states are determined by a stochastic approach. This method has both the advantage of the ordinary quantum Monte Carlo and that of the direct diagonalization methods and does not suffer from the negative sign problem. We demonstrate a performance of the present method. © 2001 John Wiley & Sons, Inc. Int J Quant Chem, 2001 [source] Interesting properties of Thomas,Fermi kinetic and Parr electron,electron-repulsion DFT energy functional generated compact one-electron density approximation for ground-state electronic energy of molecular systemsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2009Sandor Kristyan Abstract The reduction of the electronic Schrodinger equation or its calculating algorithm from 4N -dimensions to a (nonlinear, approximate) density functional of three spatial dimension one-electron density for an N -electron system, which is tractable in the practice, is a long desired goal in electronic structure calculation. If the Thomas-Fermi kinetic energy (,,,5/3dr1) and Parr electron,electron repulsion energy (,,,4/3dr1) main-term functionals are accepted, and they should, the later described, compact one-electron density approximation for calculating ground state electronic energy from the 2nd Hohenberg,Kohn theorem is also noticeable, because it is a certain consequence of the aforementioned two basic functionals. Its two parameters have been fitted to neutral and ionic atoms, which are transferable to molecules when one uses it for estimating ground-state electronic energy. The convergence is proportional to the number of nuclei (M) needing low disc space usage and numerical integration. Its properties are discussed and compared with known ab initio methods, and for energy differences (here atomic ionization potentials) it is comparable or sometimes gives better result than those. It does not reach the chemical accuracy for total electronic energy, but beside its amusing simplicity, it is interesting in theoretical point of view, and can serve as generator function for more accurate one-electron density models. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Equivalent potential of water molecules for electronic structure of glutamic acidJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2007Tian Zhang Abstract The fundamental importance of the electronic structure of molecules is widely recognized. To get reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. Here, the first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of glutamic acid, which is a hydrophilic amino acid and is negatively charged (Glu,) in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Glu, and water molecules is calculated by free cluster calculation. Then, based on the geometric structure, the electronic structure of Glu, with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Glu, with the potential of dipoles is calculated. Our calculations show that the major effect of water molecules on Glu,'s electronic structure is lowering the occupied electronic states by about 0.017 Ry, and broadening energy gap by 12%. The effect of water molecules on the electronic structure of Glu, can be well simulated by dipoles potential. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Combined structure-factor phase measurement and theoretical calculations for mapping of chemical bonds in GaNACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2010B. Jiang For non-centrosymmetric crystals, the refinement of charge-density maps requires highly accurate measurements of structure-factor phase, which can now be obtained using the extinction-free convergent-beam electron microdiffraction method. We report here accurate low-order structure-factor phases and amplitudes for gallium nitride (GaN) in the wurtzite structure. The measurement accuracy is up to 0.1% for amplitude and 0.2° for phases. By combining these with high-order structure factors from electronic structure calculation, charge-density maps were obtained. Fine bonding features suggest that the Ga,N bonds are polar and covalent, with charge transfer from Ga to N; however, the polarity effect is extremely small. [source] A helix-turn motif in the C-terminal domain of histone H1PROTEIN SCIENCE, Issue 4 2000Roger Vila Abstract The structural study of peptides belonging to the terminal domains of histone H1 can be considered as a step toward the understanding of the function of H1 in chromatin. The conformational properties of the peptide Ac-EPKRSVAFKKT KKEVKKVATPKK (CH-1), which belongs to the C-terminal domain of histone Hl° (residues 99,121) and is adjacent to the central globular domain of the protein, were examined by means of 1H-NMR and circular dichroism. In aqueous solution, CH-1 behaved as a mainly unstructured peptide, although turn-like conformations in rapid equilibrium with the unfolded state could be present. Addition of trifluoroethanol resulted in a substantial increase of the helical content. The helical limits, as indicated by (i, i + 3) nuclear Overhauser effect (NOE) cross correlations and significant up-field conformational shifts of the C, protons, span from Pro100 to Val 116, with Glu99 and Ala117 as N- and C-caps. A structure calculation performed on the basis of distance constraints derived from NOE cross peaks in 90% trifluoroethanol confirmed the helical structure of this region. The helical region has a marked amphipathic character, due to the location of all positively charged residues on one face of the helix and all the hydrophobic residues on the opposite face. The peptide has a TPKK motif at the C-terminus, following the ,-helical region. The observed NOE connectivities suggest that the TPKK sequence adopts a type (I) ,-turn conformation, a ,-turn conformation or a combination of both, in fast equilibrium with unfolded states. Sequences of the kind (S/T)P(K/R)(K/R) have been proposed as DNA binding motifs. The CH-1 peptide, thus, combines a positively charged amphipathic helix and a turn as potential DNA-binding motifs. [source] Quantitative Use of Paramagnetic Relaxation Enhancements for Determining Orientations and Insertion Depths of Peptides in MicellesCHEMBIOCHEM, Issue 14 2009Magnus Franzmann Abstract We describe the background and implementation of a method to determine, at atomic resolution, the insertion depths and orientations of peptides embedded in micelles. A nonperturbing paramagnetic agent,Gd(DTPA,BMA),was used to induce paramagnetic relaxation enhancements (PREs) of peptide atoms inside the micelle. By calibrating these PREs it was possible to translate them into distance restraints that could be used for structure calculation. We demonstrate this here on the antimicrobial peptides novicidin and novispirin. Characterization of the interactions between antimicrobial peptides and membranes is important for understanding of their biological activities and functions, and a further development of tools to study these interactions is described. [source] Performance of computationally intensive parameter sweep applications on Internet-based Grids of computers: the mapping of molecular potential energy hypersurfacesCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 4 2007S. Reyes Abstract This work focuses on the use of computational Grids for processing the large set of jobs arising in parameter sweep applications. In particular, we tackle the mapping of molecular potential energy hypersurfaces. For computationally intensive parameter sweep problems, performance models are developed to compare the parallel computation in a multiprocessor system with the computation on an Internet-based Grid of computers. We find that the relative performance of the Grid approach increases with the number of processors, being independent of the number of jobs. The experimental data, obtained using electronic structure calculations, fit the proposed performance expressions accurately. To automate the mapping of potential energy hypersurfaces, an application based on GRID superscalar is developed. It is tested on the prototypical case of the internal dynamics of acetone. Copyright © 2006 John Wiley & Sons, Ltd. [source] Eight-Coordinate Endohedral Rhenium, Osmium and Iridium Atoms in Rare-Earth Halide Cluster ComplexesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 18 2010Sina Zimmermann Abstract Endohedral (interstitial) atoms are essential for almost all of the rare-earth halide cluster complexes. Most of these contain octahedral clusters, some are isolated, but the majority exhibits condensation by common edges to structures of higher dimensionality. Higher coordination numbers of the endohedral atoms are rare. Four examples of extended cluster complexes with eight-coordinate endohedral atoms of sixth-period elements (Re, Os, Ir) are presented. In the quasi-isostructural, non-isotypic halides {ReGd4}Br4 and {OsSc4}Cl4, square antiprisms of gadolinium and scandium atoms, respectively, are connected by two common faces to chains, surrounded and loosely connected by halogenido ligands. The Re and Os atoms build a slightly bent chain with only little bonding interactions. Chemical bonding is dominated by endohedral atom,cluster atom and cluster atom,halide interactions. The same is true for the two scandium bromides {Ir3Sc12}Br16 and {Os3Sc12}Br16Sc, which contain chains of face-sharing square antiprisms and cubes in a ratio of 2:1. Metal,metal bonding is attested by short distances between those endohedral Ir and Os atoms, respectively, which center the square antiprisms (283 pm and 290 pm, respectively). Magnetic and conductivity measurements on {Ir3Sc12}Br16 reveal paramagnetism and a small-band-gap semiconductor. This is in accord with electronic structure calculations. [source] Use of Molecular Scaffolding for the Stabilization of an Intramolecular Dative PIII -PV SystemEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 2 2003Petr Kilian Abstract The reaction of NapP2S4 (1; Nap = naphthalene-1,8-diyl) with chlorine gas gave [Nap(PCl2)(PCl4)] (2), displaying a rare ,4P-,6P bonding interaction. An X-ray structure analysis confirmed the PCl5 -like, P,P bond containing phosphonium-phosphoride structure of 2 in the crystal, which was also found in solution at low temperature. At ambient and higher temperatures, dynamic behaviour on the NMR time-scale was observed, which was assigned to interchange of the ionic phosphonium-phosphoride form 2 and the molecular bis(phosphorane) Nap(PCl3)2 form 3, rather than to the ionic phosphonium salt-phosphorane form [Nap(PCl3)(PCl2)][Cl] 4. Electronic structure calculations were performed at the B3LYP/6,31G(d,p) level of theory on structures 2 and 3; structure 3 was located as a local minimum on the potential energy surface, 15 kcal·mol,1 higher in energy than structure 2. The crystal structure and calculated P,P distances are 2.34 and 2.31 Ĺ for 2 and 3, respectively. An activation energy of 19.7 kcal·mol,1 was found for the transition state structure by coordinate driving calculations; the line-shape analysis of variable temperature 31P{1H} NMR spectra gave an activation energy of 14.4 kcal·mol,1. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Thickness Dependent Loss Function of Si with 0.14 eV Energy ResolutionADVANCED ENGINEERING MATERIALS, Issue 10 2004M. Stöger-Pollach Si band gap spectra were recorded by using electron energy loss spectrometry with very high energy resolution of 0.14 eV using a transmission electron microscope with a monochromated electron source. The shape of the spectra change with thickness, becoming indistinct at very thin regions. But even for higher thicknesses structureal evolution of the spectra can be observed. A comparison with band structure calculations is given, too. [source] Solution structure of the functional domain of Paracoccus denitrificans cytochrome c552 in the reduced stateFEBS JOURNAL, Issue 13 2000Primo, Pristov In order to determine the solution structure of Paracoccus denitrificans cytochrome c552 by NMR, we cloned and isotopically labeled a 10.5-kDa soluble fragment (100 residues) containing the functional domain of the 18.2-kDa membrane-bound protein. Using uniformly 15N-enriched samples of cytochrome c552 in the reduced state, a variety of two-dimensional and three-dimensional heteronuclear double-resonance NMR experiments was employed to achieve complete 1H and 15N assignments. A total of 1893 distance restraints was derived from homonuclear 2D-NOESY and heteronuclear 3D-NOESY spectra; 1486 meaningful restraints were used in the structure calculations. After restrained energy minimization a family of 20 structures was obtained with rmsd values of 0.56 ± 0.10 Ĺ and 1.09 ± 0.09 Ĺ for the backbone and heavy atoms, respectively. The overall topology is similar to that seen in previously reported models of this class of proteins. The global fold consists of two long helices at the N-terminus and C-terminus and three shorter helices surrounding the heme moiety; the helices are connected by well-defined loops. Comparison with the X-ray structure shows some minor differences in the positions of the Trp57 and Phe65 side-chain rings as well as the heme propionate groups. [source] Tuning Crystalline Solid-State Order and Charge Transport via Building-Block Modification of OligothiophenesADVANCED MATERIALS, Issue 36 2009Colin Reese The packing structure of a series of oligothiophenes is tuned via terminal substitution (see figure). The structural changes dramatically alter intermolecular interactions and charge-transport properties, as measured by elastomeric single-crystal field-effect transistors. Electronic structure calculations reveal the sensitivity of the transport efficiency to orbital nodal alignment, as correlated to the observed trend in field-effect mobilities. [source] Electron Energy Loss SpectroscopyIMAGING & MICROSCOPY (ELECTRONIC), Issue 2 2007Chemical Information at the Nanometer Scale Abstract The combination of high resolution imaging with energy loss spectroscopy allows to resolve questions about the morphology, structure, composition and electronic structure of a material in a single instrument. By the assistance of band structure calculations and simulated EELS spectra, the experimental data can be analyzed in detail. Following this approach it is possible to study the relation between the geometric and electronic structure of materials at the nanometer scale. [source] Shock tube study of 1,3,5-triazine dissociation and relaxation and relaxation of pyrazineINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 4 2010Hui Xu The three-body dissociation of 1,3,5-triazine (s-triazine, s-C3H3N3 , 3HCN) has been observed in incident shock waves with the laser-schlieren technique. The experiments use 5% triazine/Kr and cover 1630,2350 K for 100,600 Torr. These experiments show dissociation rates with strong falloff and a slight but fully expected pressure dependence. The dissociation is without secondary reaction save for a possible, but rather unlikely, contribution from the isomerization HCN , HNC. Electronic structure calculations of the transition-state properties (G3B3, HL1, Eo = 84.6 kcal/mol) are used to construct a Rice,Ramsperger,Kassel,Marcus (RRKM) model whose fit to the rate measurements suggests a ,,E,down of 1200 cm,1. However, a seemingly better fit is achieved using the barrier of 81 kcal/mol proposed by Dyakov et al. (J. Phys. Chem. A 2007, 111, 9591,9599). With this barrier k, (s,1) = 5.3 × 1016 exp(,86.6(kcal/mol)/RT), and the fit now accepts the more routine ,,E,down = 126(T/298)0.9. It seems the dissociation most likely occurs by a direct, one-step, "triple" dissociation to 3HCN, although the present experiments cannot rule out a multistep process. Vibrational relaxation of the triazine was also examined in 5% and 20% mixtures with Kr over 770,1500 K for pressures between 6 and 14 Torr. Relaxation is very fast, with a slight inverse temperature dependence, P, rising from 100 to 200 ns-atm over the full temperature range. Integrated gradients are in good accord with calculated total changes in density, indicating a single exponential relaxation. A separate investigation of relaxation in the related molecule pyrazine (500,1300 K, in 1% and 5% in Kr, between 13 and 66 Torr) is included. Again relaxation is rapid, but here the temperature dependence seems more normal, the relaxation times decreasing slightly with temperature. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 211,220, 2010 [source] The S and G transformations for computing three-center nuclear attraction integralsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2009Richard Mikael Slevinsky Abstract It is now well established that nonlinear transformations can be extremely useful in the case of oscillatory integrals. In previous work, we could show that the G transformation, which is not so well known among those interested in the numerical evaluation of highly oscillatory integrals, works very well for the extremely challenging integral called Twisted Tail. In this work, we demonstrate that these techniques also apply to three-center nuclear attraction integrals over exponential type functions. The accurate and rapid evaluation of these integrals is required in ab initio molecular structure calculations and density functional theory. Using a basis set of B functions and profiting from their relatively simple Fourier representation, these integrals are formulated as analytical expressions involving highly oscillatory spherical Bessel integral functions. In the present work, we implement two highly accurate algorithms for three-center nuclear attraction integrals. The first algorithm is based on the G transformation and the second is based on a combination of the S and G transformations. The application of these transformations is largely due to the properties of special functions that allow the computation of higher order derivatives of the integrands with exceptional simplicity. The numerical results illustrate the accuracy of these algorithms applied to three-center nuclear attraction integrals over exponential type functions with a miscellany of different parameters. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Extrapolation methods for improving convergence of spherical Bessel integrals for the two-center Coulomb integralsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 11 2006Hassan Safouhi Abstract Multi-center two-electron Coulomb integrals over Slater-type functions are required for any accurate molecular electronic structure calculations. These integrals, which are numerous, are to be evaluated rapidly and accurately. Slater-type functions are expressed in terms of the so-called B functions, which are best suited to apply the Fourier transform method. The Fourier transform method allowed analytic expressions for these integrals to be developed. Unfortunately, the analytic expressions obtained turned out to be extremely difficult to evaluate accurately due to the presence of highly oscillatory spherical Bessel integrals. In this work, we used techniques based on nonlinear transformation and extrapolation methods for improving convergence of these oscillatory spherical Bessel integrals. These techniques, which led to highly efficient and rapid algorithms for the numerical evaluation of three- and four-center two-electron Coulomb and exchange integrals, are now shown to be applicable to the two-center two-electron Coulomb integrals. The numerical results obtained for the molecular integrals under consideration illustrate the efficiency of the algorithm described in the present work compared with algorithms using the epsilon (,) algorithm of Wynn and Levin's u transform. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Theoretical study of the reactions BF3 + BX, where X = H or NINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Patrícia R. P. Barreto Abstract This work presents the rate constant for the gas-phase reaction BF3 + BX, where X = H or N, over the temperature range of 200,4,000 K. Conventional transition state theory (TST) is used to study these reactions. Geometries, frequencies, and the potential energy for reactant, products, and saddle point are obtained from accurate electronic structure calculations performed with the GAUSSIAN 98 program. The reaction rate for these reactions are determined using a simple code developed for this task. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Computational linear dependence in molecular electronic structure calculations using universal basis setsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2005D. Moncrieff Abstract Distributed universal even-tempered basis sets have been developed over recent years that are capable of supporting Hartree,Fock energies to an accuracy approaching the sub-,Hartree level. These basis sets have also been exploited in correlation studies, in applications to polyatomic molecules, and in the calculation of electric properties, such as multipole moments, polarizabilities, and hyperpolarizabilities. Jorge and coworkers have also developed universal basis sets and have recently reported applications to diatomic molecular systems. In this article, we compare the molecular calculations reported by Jorge and coworkers with our previous studies. Particular attention is given to the degree of computational linear dependence associated with the various basis sets employed and the consequential effects of the accuracy of the calculated energies. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] 27 ps DFT molecular dynamics simulation of ,-maltose: A reduced basis set study,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2010Udo Schnupf Abstract DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as ,-maltose. In a recent publication (Momany et al., J. Mol. Struct. THEOCHEM, submitted) forces for dynamics were generated from B3LYP/6-31+G* electronic structure calculations. The implicit solvent method COSMO was applied to simulate the solution environment. Here we present a modification of the DFT method that keeps the critical aspects of the larger basis set (B3LYP/6-31+G*) while allowing the less-essential atom interactions to be calculated using a smaller basis set, thus allowing for faster completion without sacrificing the interactions dictating the hydrogen bonding networks in ,-maltose. In previous studies, the gg,-gg-c solvated form quickly converged to the "r" form during a 5 ps dynamics run. This important conformational transition is tested by carrying out a long 27 ps simulation. The trend for the "r" conformer to be most stable during dynamics when fully solvated, is confirmed, resulting in ,20/80% c/r population. Further, the study shows that considerable molecular end effects are important, the reducing end being fairly stable, the O6H pointing at the O5, while the nonreducing end moves freely to take on different conformations. Some "kink" and transition state forms are populated during the simulation. The average H1,···H4 distance of 2.28 Ĺ confirms that the syn form is the primary glycosidic conformation, while the average C1,O1,C4 bond angle was 118.8°, in excellent agreement with experimental values. The length of this simulation allowed the evaluation of vibrational frequencies by Fourier transform of the velocity correlation function, taken from different time segments along the simulation path. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] | |||||||||||||||||||||||||||||||