Chemisorption of O and O2 on Ag(110): An LCGTO-LSD cluster study

As part of a study aimed at better understanding of molecular and dissociative chemisorption of oxygen on Ag(110), linear combinations of Gaussian type orbitals-local spin density (LCGTO -LSD ) calculations have been performed for O, O^?, O₂, O^?₂, O^2?₂ and a variety of silver clusters interacting with O or O₂. For atomic O adsorption a very small cluster, Ag₄, chosen to model the long-bridge site already affords very good agreement with both recent EXAFS experiments and recent ab initio calculations. We calculate O to be 0.25 Å above the surface (exp. 0.2 Å). The Ag₄? O vibrational frequency is estimated to be 400 cm^?1, in reasonable accord with the experimental EELS value of 325 cm^?1. Determination of the geometry for O₂ (ads.) and, ultimately, of the dissociation path are far more difficult tasks. An extensive search for local minima in the vicinity of the LB site is being carried out. Results to date for small, Ag₂ and Ag₄, clusters have furnished insight into the factors influencing the structure. Overlap between the π* orbital of the O₂ moiety and Ag s functions is a key factor; that is, there is an important covalent component of the binding. For geometries with O₂ parallel to the surface, this is achieved by twisting the O₂ fragment with respect to the [11¯0] grooves (geometries either parallel or perpendicular to the grooves yield zero π‖*?s overlap by symmetry). The structure with O₂ perpendicular to the surface also achieves reasonable overlap and lies close in energy to the most stable ‘parallel’ geometry.     

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high-level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated-B-LYP, B3-LYP, PBE, TPSS, TPSSh, and BH-LYP-and even surpass the MP2/cc-pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, s(R), scaling globally the vdW radii. For good results, a basis set of at least triple-zeta quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen-bonded and stacked complexes considered, respectively.     

Density functional theory-based conformational analysis of a phospholipid molecule (dimyristoyl phosphatidylcholine)

The conformational space of the dimyristoyl phosphatidylcholine (DMPC) molecule has been studied using density functional theory (DFT), augmented with a damped empirical dispersion energy term (DFT-D). Fourteen ground-state isomers have been found with total energies within less than 1 kcal/mol. Despite differences in combinations of their torsion angles, all these conformers share a common geometric profile, which includes a balance of attractive, repulsive, and constraint forces between and within specific groups of atoms. The definition of this profile fits with most of the structural characteristics deduced from measured NMR properties of DMPC solutions. The calculated vibrational spectrum of the molecule is in good agreement with experimental data obtained for DMPC bilayers. These results support the idea that DMPC molecules preserve their individual molecular structures in the various assemblies.     

Development of the cyclic cluster model formalism for Kohn-Sham auxiliary density functional theory methods

The development of the cyclic cluster model (CCM) formalism for Kohn-Sham auxiliary density functional theory (KS-ADFT) methods is presented. The CCM is a direct space approach for the calculation of perfect and defective systems under periodic boundary conditions. Translational symmetry is introduced in the CCM by integral weighting. A consistent weighting scheme for all two-center and three-center interactions appearing in the KS-ADFT method is presented. For the first time, an approach for the numerical integration of the exchange-correlation potential within the cyclic cluster formalism is derived. The presented KS-ADFT CCM implementation was applied to covalent periodic systems. The results of cyclic and molecular cluster model (MCM) calculations for trans-polyacetylene, graphene, and diamond are discussed as examples for systems periodic in one, two, and three dimensions, respectively. All structures were optimized. It is shown that the CCM results represent the results of MCM calculations in the limit of infinite molecular clusters. By analyzing the electronic structure, we demonstrate that the symmetry of the corresponding periodic systems is retained in CCM calculations. The obtained geometric and electronic structures are compared with available data from the literature.     

Dissociation, solvation, and dynamics of HBr in small water clusters

The dissociation of hydrogen bromide in a small water cluster (H₂O)_n (n=3–5) has been studied with quantum chemical methods. The dynamics of dissociation was followed by classical molecular dynamics, and stationary points were studied in order to compute the free energy change associated with the ionization process. The nudged elastic band method was used to map out the energy profile of the reaction paths. The results show that HBr can dissociate in the presence of just four water molecules if they are in the correct configuration.The relation of our results to recent experiments is discussed.     

CNDO,INDO and RCNDO-CI calculations on the electronic spectra of saturated hydrocarbons

CNDO, INDO and RCNDO (CNDO including higher (Rydberg) atomic orbitals in the basis) calculations completed by first order configuration interaction were performed on straight chain and branched chain paraffins.The results interpret reasonably the main characteristics of the observed electronic spectra. The importance of outer atomic orbitals is stressed and it is found that the first singlet-singlet transition of highly branched paraffins leads to an excited state with considerable Rydberg character.

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Zusammenfassung Rechnungen vom Typ CNDO, INDO und RCNDO (CNDO mit höheren (Rydberg) Atomorbitalen in der Basis) unter Einschluß von Konfigurationswechselwirkung 1. Ordnung wurden für unverzweigte und verzweigte gesättigte Kohlenwasserstoffe durchgeführt.Die Resultate lassen eine Deutung der Hauptcharakteristika der beobachteten Elektronen-spektren zu. Die Wichtigkeit der äußeren Atomorbitale ist zu betonen. Die ersten Singulett-Singulett-Übergänge der stark verzweigten Paraffine führen zu angeregten Zuständen mit beträchtlichem Rydbergcharakter.

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Résumé Des calculs CNDO, INDO et RCNDO (ayant des orbitales atomiques supérieures dans la base) ont été effectués sur les paraffines normales et ramifiées tenant compte de l'intéraction de configuration de premier ordre jusqu'à 30 configurations.Les résultats interprêtent d'une manière raisonnable les spectres électroniques mesurés. L'importance des orbitales atomiques supérieures apparaît clairement. La première bande observée des hydrocarbures hautement ramifiés comme le néopentane ou l'isobutane est attribuée à une transition dont l'état excité possède un fort caractère Rydberg.

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The research for this paper was supported in part by the Defense Research Board of Canada; Grant Number 9530-63.     

A density functional study of the glycine molecule: Comparison with post-Hartree–Fock calculations and experiment

The potential energy surface of un-ionized glycine has been explored with density functional theory. The performance of several nonlocal functionals has been evaluated and the results are presented in the context of available experimental information and post-Hartree–Fock quantum chemical results. The zero-point and thermal vibrational energies along with vibrational entropies play a very important role in determining the relative stability of glycine conformers; the realization of this has led to some revision and reinterpretation of the experimental results. Uncertainties in the vibrational contributions to the energy differences of several tenths of a kilocalorie/mole remain. The uncertainty in the vibrational free energy is even larger, about 1 kcal/mol. In the final analysis, we suggest that the best estimate of the electronic energy difference between the two lowest glycine conformers should be revised downward from 1.4 to 1.0 kcal/mol. Thirteen stationary points on the potential energy surface have been localized. For the majority of these, there is close agreement among various nonlocal density functionals and the post-Hartree–Fock methods. However, the second conformer (IIn), which has a strong hydrogen bond between the hydroxyl hydrogen and the nitrogen of the amine group, presents a distinct challenge. The relative energy of this conformer is extremely sensitive to the basis set, the level of correlation, or the functional used. The widely used BP86, PP86, and BP91 nonlocal functionals overestimate the strength of the hydrogen bond and predict that this conformer is the lowest energy structure. This contradicts both experiment and high-level post-Hartree–Fock studies. The adiabatic connection method (ACM) and the BLYP functional yield the correct order. The ACM method, in particular, gives energies which are in reasonable agreement with MP2, although these are somewhat low as compared with experiment. Based on this study, ACM should perform well for this type of bioorganic application, with typical errors of a few tenths of a kilocalorie/mole and only rarely exceeding 0.5 kcal/mol. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1609–1631, 1997