Hideo Orita

Efficiency of numerical basis sets for predicting the binding energies of hydrogen bonded complexes: Evidence of small basis set superposition error compared to Gaussian basis sets

Binding energies of selected hydrogen bonded complexes have been calculated within the framework of density functional theory (DFT) method to discuss the efficiency of numerical basis sets implemented in the DFT code DMol3 in comparison with Gaussian basis sets. The corrections of basis set superposition error (BSSE) are evaluated by means of counterpoise method. Two kinds of different numerical basis sets in size are examined; the size of the one is comparable to Gaussian double zeta plus polarization function basis set (DNP), and that of the other is comparable to triple zeta plus double polarization functions basis set (TNDP). We have confirmed that the magnitudes of BSSE in these numerical basis sets are comparative to or smaller than those in Gaussian basis sets whose sizes are much larger than the corresponding numerical basis sets; the BSSE corrections in DNP are less than those in the Gaussian 6‐311+G(3df,2pd) basis set, and those in TNDP are comparable to those in the substantially large scale Gaussian basis set aug‐cc‐pVTZ. The differences in counterpoise corrected binding energies between calculated using DNP and calculated using aug‐cc‐pVTZ are less than 9 kJ/mol for all of the complexes studied in the present work. The present results have shown that the cost effectiveness in the numerical basis sets in DMol3 is superior to that in Gaussian basis sets in terms of accuracy per computational cost.

TiO2 Band Shift by Nitrogen-Containing Heterocycles in Dye-Sensitized Solar Cells: a Periodic Density Functional Theory Study

A density functional theory (DFT) method (periodic DMol3) with full geometry optimization was used to study the adsorption of nitrogen-containing heterocycles such as pyrazole, imidazole, 1,2,4-triazole, pyridine, pyrimidine, pyrazine, and 4-t-butylpyridine (TBP) on TiO2 anatase (101), (100), and (001) surfaces. All structures displayed a negative shift in the TiO2 Fermi level upon adsorption of N-containing heterocycles. Additionally, the heterocycles were examined as an additive in an I-/I3- redox electrolyte solution of dye-sensitized TiO2 solar cell. The DFT results indicated that the negative shift of TiO2 Fermi level was due to the adsorbate dipole moment component normal to the TiO2 surface plane, and corresponded to the enhanced open-circuit photovoltage (Voc) and the reduced short-circuit photocurrent density (Jsc) in a dye-sensitized solar cell.

Adsorption of thiophene on an MoS2 cluster model catalyst: ab initio density functional study

Abstract Adsorption of thiophene on the coordinately unsaturated Mo atom on the ( 3 0 3 0 ) plane of an Mo16S32 cluster has been investigated to develop fundamental understanding of the adsorption sites of MoS2 catalysts in the hydrotreatment process. By using the density functional theory (DFT) method, full geometry optimization and vibrational analysis of the thiophene/cluster complex have been carried out. Adsorption energies and vibrational frequencies for different adsorption configurations have been computed. The thiophene molecule remains almost flat in the upright configuration, but becomes bent in the parallel configurations. The CS distances become longer for all the adsorption configurations, indicating that activation of the CS bond occurs. The CC and CC distances become shorter and longer for the upright configuration, respectively. For the parallel configurations, the change of distances is in the opposite direction. The most stable configuration is the bridged and rotated parallel geometry. It is easy to distinguish whether thiophene is adsorbed in the upright or parallel coordination on sulfided Mo catalysts by means of the vibrational frequencies of adsorbed thiophene. With respect to the calculated vibrational frequencies of free thiophene, the ν(CC)asym and ν(CC)sym bands shift to higher frequencies for the upright configuration, whereas they shift to lower for the parallel configurations.

First-principles lattice energy calculation of urea and hexamine crystals by a combination of periodic DFT and MP2 two-body interaction energy calculations.

This article proposes a new method for the accurate evaluation of the lattice energies (stabilization energies associated with the formation of crystals from isolated molecules) of molecular crystals by a combination of DFT and MP2 calculations. The interactions of well-separated molecules were evaluated by periodic DFT calculations. The interactions with neighboring molecules were evaluated by MP2-level two-body interaction energy calculations with the neighboring molecules. The sublimation energies calculated for crystals of urea and hexamine using the proposed method (21.2 and 20.0 kcal/mol, respectively) were close to the experimental values (20.9-23.6 and 17.7-18.8 kcal/mol, respectively). The lattice energies calculated for the two crystals by the proposed method are significantly different from those obtained by DFT calculations, suggesting that the dispersion contribution to the lattice energy is significant even in the crystal, where molecules are bound by hydrogen bonds. Lattice energies calculated by changing the range of the neighboring molecules show that the nearest-neighboring molecules are mainly responsible for the dispersion interactions in the crystals.

Ab initio density functional study of the structural and electronic properties of an MoS2 catalyst model: a real size Mo27S54 cluster

Abstract Ab initio investigation of the structural and electronic properties of a real size Mo27S54 cluster has been performed to develop a fundamental understanding of the active sites of MoS2 catalysts in the hydrotreatment process. The cluster is a stoichiometric and regular hexagonal one with ( 1 0 1 0 ) plane (S edge) and ( 3 0 3 0 ) plane (Mo edge) only, and does not need any saturating H atom and charge compensation. By using density functional theory (DFT) method, a full geometry optimization of the cluster has been carried out. The structure of the cluster is more relaxed towards the edges, and two types of the Mo–Mo distances, which are shorter or longer than that in the MoS2 crystal, are observed at the periphery. These results agree well with the EXAFS data of dispersed unsupported MoS2 particle. The electronic properties of the atoms at various sites (i.e. corner, edge, outer, and inner positions) have been distinguished clearly by means of charge distribution and molecular orbital (MO) calculations. The corner Mo atom is expected to be the most active site for the hydrotreatment reactions.

Peculiar decomposition behavior of N2O on Ni(755)

The adsorption and decomposition behavior of N 2 O on Ni(755) has been investigated by TPD and XPS. Decomposition of N 2 O (into N 2 and atomic oxygen) is observed between 96 and 200 K. There are two desorption peaks of N 2 at 170 and 120 K. The saturated amount of N 2 produced from N 2 O is quite close to the step density of Ni(755). The molecular desorption of N 2 O occurs only for large exposures of N 2 O where the desorption peak of N 2 is saturated. The desorption peak at 170 K is due to desorption of adsorbed N 2 which is formed at bare step sites from initial dissociation of N 2 O below 105 K. On the other hand, the peak at 120 K comes from spontaneous desorption of N 2 by decomposition of molecular N 2 O at oxygen-modified step sites.

Oxidative CC bond cleavage of vic-diols with H2O2 catalyzed by heteropolyacids

Abstract vic-Diols were oxidized with aqueous hydrogen peroxide in the presence of heteropolyacids to yield carboxylic acids as main products in good yields. Although the oxidation proceeded via α-ketol or α-diketone intermediates, another oxidation path such as direct CC bond cleavage is suggested in the case of tetra-substituted vic-diols as substrates.

Promoting effect of coadsorbed CO on the decomposition of saturated hydrocarbons on Ni(755)

Abstract Coadsorption of saturated hydrocarbons and CO has been investigated by temperature-programmed desorption (TPD). Coadsorbed CO promotes the decomposition of low reactive hydrocarbons during TPD. The coverage and decomposition fraction (ratio of decomposed molecules to adsorbed ones) are determined from TPD by using the effect of coadsorbed CO.

Synthesis, Ion Recognition Ability, and Metal-Assisted Aggregation Behavior of Dinuclear Metallohosts Having a Bis(Saloph) Macrocyclic Ligand

Macrocyclic molecule 1 that has two saloph coordination sites was designed and synthesized. The macrocycle 1 was easily converted into the corresponding metallohosts 2 and 3 by the reaction with nickel(II) and palladium(II), respectively. As expected from the molecular structure of these metallohosts having an 18-crown-6-like cavity, the nickel(II) metallohost 2 showed excellent binding affinity toward Na(+), Ca(2+), and Sr(2+) to give 1:1 host-guest complexes. Preorganization effect due to the extremely rigid metal-containing macrocycle was suggested to be a major factor for the strong binding. Larger cations such as K(+), Rb(+), Cs(+), and Ba(2+) gave higher aggregated host-guest complexes such as 22M, 23M2, and 24M3. Density functional theory calculations revealed that smaller metal ions do not occupy the center of each macrocycle in the sandwich structures 22M, while larger Cs(+) simultaneously interacts with all the 12 oxygen donor atoms. On the basis of the interaction energy calculations, the preference for 2·Na over 22Na can be explained by destabilization of 22Na due to the elongated Na-O bonds and repulsive three-body interactions. When the ionic radius of the guest ion increases (K(+), Rb(+), Cs(+)), this destabilization becomes less significant and the formation of sandwich complexes 22M is favored. Such aggregation would significantly affect the physical and chemical properties of the metal complexes due to the interplane interactions between the metal centers.

A density functional study of NO adsorption and decomposition on Ni(211) and Pd(211) surfaces

The adsorption and decomposition of NO have been investigated by using density functional theory method at the generalized gradient approximation level. We have performed calculations on adsorption energies and structures of NO on Ni(211) and Pd(211) surfaces with full-geometry optimization and compared them with the experimental data. The most favorite adsorption on both surfaces occurs at the bridge site parallel to step edge (sb), while the energy difference from the second favorite site of a threefold hollow site near step edge is less than 0.1 eV. Decomposition pathways have been investigated with transition state search. The decomposition pathway, where NO leans toward the step, is most probable for both surfaces. The overall activation energy for decomposition is 0.39 and 1.26 eV for Ni(211) and Pd(211), respectively. The present results clearly show that the NO molecules on Pd(211) are less activated than those on Ni(211). We have studied also reorganization of NO on Pd(211) at higher coverages up to 1/3 ML (monolayer) [three NO molecules in a (3 x 1) unit cell]. The site occupation is not in a sequential manner as the NO coverage is increased, and a reorganization of NO adsorbates occurs (the NO molecule at sb becomes tilting up at higher coverage), which can interpret the experimental data of Yates and co-workers very well.