Intermolecular interactions of oligothienoacenes: Do S⋯S interactions positively contribute to crystal structures of sulfur-containing aromatic molecules?

Intermolecular interactions in the crystals of tetra- and penta-thienoacene were studied using ab initio molecular orbital calculations for evaluating the magnitude of characteristic S⋯S interactions with great attention paid to their origin. The interactions between the π-stacked neighboring molecules are significantly greater than those between the neighboring molecules exhibiting the S⋯S contact, although it has sometimes been claimed that the S⋯S interactions play important roles in adjusting the molecular arrangement of sulfur-containing polycyclic aromatic molecules in the crystals owing to short S⋯S contacts. The coupled cluster calculations with single and double substitutions with noniterative triple excitation interaction energies at the basis set limit estimated for the π-stacked and S⋯S contacted neighboring molecules in the tetrathienoacene crystal are -11.17 and -4.27 kcal/mol, respectively. Those for π-stacked molecules in the pentathienoacene crystal is -14.38 kcal/mol, while those for S⋯S contacted molecules are -7.02 and -6.74 kcal/mol. The dispersion interaction is the major source of the attraction between the π-stacked and S⋯S contacted molecules, while the orbital-orbital interactions are repulsive: The orbital-orbital interactions, which are significant for charge carrier transport properties, are not much more than the results of the short S⋯S contact caused by the strong dispersion interactions. Besides, the intermolecular interaction energy calculated for a trithienoacene dimer has strong orientation dependence.

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.

Highly ordered cobalt-phthalocyanine chains on fractional atomic steps: one-dimensionality and electron hybridization.

Precisely controlled fabrication of low-dimensional molecular structures with tailored morphologies and electronic properties is at the heart of the nanotechnology research. Especially, the formation of one-dimensional (1D) structures has been strongly desired due to their expected high performance for information processing in electronic/magnetic devices. So far, however, they have been obtained by tough and slow methods such as manipulation of individual molecules, which are totally unsuited for mass production. Here we show that highly ordered cobalt-phthalocyanine chains can be self-assembled on a metal surface using fractional atomic steps as a template. We also demonstrate that the substrate surface electrons, which can be confined by cobalt-phthalocyanine molecules, can propagate along the step arrays and can hybridize with the molecular orbitals. These findings provide a significant step toward readily realization of 1D charge/spin transport, which can be mediated either directly by the molecules or by the surface electrons.

Crystal structure of quinine: the effects of vinyl and methoxy groups on molecular assemblies of Cinchona alkaloids cannot be ignored.

Quinine, one of Cinchona alkaloids, has been of great interest from medical, synthetic, and supramolecular viewpoints. However, unaccountably, the guest-free (GF) crystal of quinine containing no solvent or other molecules has not been reported for nearly three decades, although GF crystals of other Cinchona alkaloids, such as quinidine, cinchonidine, and cinchonine, are already known. In this study, we successfully revealed the crystal structure of quinine, which belongs to the P2(1) space group with the cell parameters of a=6.0587(1), b=19.2492(5), c=22.2824(7) Å, ß=92.1646(11)°, and V=2596.83(12) Å(3). Interestingly, the crystal has three crystallographically independent molecules in the cell (Z'=3) that are connected through a N(quinoline)⋅⋅⋅H-O hydrogen bond to form a pseudo three-two-fold (3(2)) double-helical motif. The helical motif is completely different from those observed in GF crystals of other Cinchona alkaloids. Hierarchical comparison on the crystal structures of a series of Cinchona alkaloids including quinine clearly demonstrated that only small structural differences of a molecule, particularly the position of the vinyl group, cause a significant variety of assembly manner in the crystalline state. There have been no reports systematically demonstrating such steric effect in crystals of Cinchona alkaloids, and, therefore, the present system contributes to the design of desired functional crystal structures.

Atomic structures of the defective SrTiO3 (001) surface.

Surface structures of defective SrTiO(3) (001) have been studied by using scanning probe microscopy and density functional theory calculations. We observed several defective surface structures with true atomic resolution under reducing ultrahigh vacuum conditions. It is found that all the defects are terminated by (001), (100) and (010) microfacets of the TiO(2) plane. We propose microfaceting TiO(2) termination with Sr adatom models. The formation of various types of defects is driven by the changes of the surface stoichiometry depending on surface preparations.

High-yielding synthesis of the anti-influenza neuraminidase inhibitor (-)-oseltamivir by two "one-pot" sequences.

The efficient asymmetric total synthesis of (-)-oseltamivir, an antiviral reagent, has been accomplished by using two "one-pot" reaction sequences, with excellent overall yield (60 %) and only one required purification by column chromatography. The first one-pot reaction sequence consists of a diphenylprolinol silyl ether mediated asymmetric Michael reaction, a domino Michael reaction/Horner-Wadsworth-Emmons reaction combined with retro-aldol/Horner-Wadsworth-Emmons reaction and retro Michael reactions, a thiol Michael reaction, and a base-catalyzed isomerization. Six reactions can be successfully conducted in the second one-pot reaction sequence; these are deprotection of a tert-butyl ester and its conversion into an acyl chloride then an acyl azide, Curtius rearrangement, amide formation, reduction of a nitro group into an amine, and a retro Michael reaction of a thiol moiety. A column-free synthesis of (-)-oseltamivir has also been established.

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.

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.

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.

Surface structures of rutile TiO2 (011).

Surface structures of rutile TiO(2) (011) are determined by a combination of noncontact atomic force microscopy (NC-AFM), scanning tunneling microscopy (STM), and density functional calculations. The surface exhibits rowlike (n x 1) structures running along the [01] direction. Microfaceting missing-row structural models can explain the experimental results very well. Calculated images for NC-AFM and STM are in good agreement with the experimental results. A decrease of the density of dangling bonds stabilizes the surface energy, which results in the microfaceting missing-row reconstructions.

N+NO reaction on Rh(111) surfaces studied with fast near-edge X-ray absorption fine structure spectroscopy: role of NO dimer as an extrinsic precursor.

We studied the mechanism of the N+NO reaction on Rh(111) surfaces by means of fast near-edge X-ray absorption fine structure spectroscopy. This reaction is important as a basis of NOx reduction reactions on platinum-group metal surfaces. Atomic nitrogen layers on Rh(111) were titrated with NO at various temperatures. N2O is exclusively formed and desorbs into the gas phase below 350 K. The consumption rate of atomic nitrogen exhibits strange temperature dependence between 100 and 350 K; the reaction proceeds slower with increasing temperature. Reaction kinetics analyses and isotope-controlled experiments have revealed that the surface N atoms do not react with chemisorbed NO molecules but with NO dimers weakly bound on top of the chemisorbed layer, which play a role as an extrinsic precursor. The present results may support the possibility that NO dimers participate in various NO-related synthetic, biochemical, and surface reactions as an intermediate.

Structural study of NO adsorbed on the reconstructed Pt(110)-(1 x 2) surface with X-ray photoelectron diffraction and near-edge X-ray absorption fine structure spectroscopy.

The adsorption structure of NO on the reconstructed Pt(110)-(1 x 2) surface was studied with X-ray photoelectron spectroscopy (XPS), X-ray photoelectron diffraction (XPD), low-energy scanned-angle photoelectron diffraction (LESA-PD), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The experiments were performed at 180 K, where no surface lifting from (1 x 2) to (1 x 1) takes place after NO adsorption. XPS indicates that the (1 x 2) unit cell of the Pt(110) surface contains 1.5 NO molecules at the saturated coverage. XPD and LESA-PD analyses allow us to propose a structural model for the NO adlayer, where two-thirds of the NO molecules in the (1 x 2) unit cell are adsorbed on the atop site of the close-packed Pt rows (ridges) along the [10] direction with an inclined geometry and one-third of the NO molecules adsorb on the bridge site between the Pt ridges with an upright configuration. This model is supported by the N K-edge NEXAFS experiments and is consistent with the recently reported model based on the density functional theory (Orita, H.; Nakamura, I.; Fujitani, T. J. Phys. Chem. B 2005, 109, 10312).

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.

Studies of CO adsorption on Pt(100), Pt(410), and Pt(110) surfaces using density functional theory.

Adsorption of CO on Pt(100), Pt(410), and Pt(110) surfaces has been investigated by density functional theory (DFT) method (periodic DMol(3)) with full geometry optimization and without symmetry restriction. Adsorption energies, structures, and vibrational frequencies of CO on these surfaces are studied by considering multiple possible adsorption sites and comparing them with the experimental data. The same site preference as inferred experiments is obtained for all the surfaces. For Pt(100), CO adsorbs at the bridge site at low coverage, but the atop site becomes most favorable for the c(2 x 2) structure at 1/2 monolayer. For Pt(410) (stepped surface with (100) terrace and (110) step), CO adsorbs preferentially at the atop site on the step edge at 1/4 monolayer, but CO populates also at other atop and bridge sites on the (100) terrace at 1/2 monolayer. The multiple possible adsorption sites probably correspond to the multiple states in the temperature-programmed desorption spectra for CO desorption. For Pt(110), CO adsorbs preferentially at the atop site on the edge for both the reconstructed (1 x 2) and the un-reconstructed (1 x 1) surfaces. When adjacent sites along the edge row begin to be occupied, the CO molecules tilt alternately by ca. 20 degrees from the surface normal in opposite directions for both the (1 x 2) and (1 x 1) surfaces.

Studies of NO adsorption on Pt(110)-(1 x 2) and (1 x 1) surfaces using density functional theory.

Adsorption of NO on Pt(110)-(1 x 2) and (1 x 1) surfaces has been investigated by density functional theory (DFT) method (periodic DMol(3)) with full geometry optimization and without symmetry restriction. Adsorption energies, structures, and N-O stretching vibrational frequencies of NO are studied by considering multiple possible adsorption sites and comparing with the experimental data. Adsorption is strongly dependent on both coverage and surface phase. The assignment of adsorption sites has been carried out with precise calculation of vibrational frequencies for NO on various sites. We clearly show the NO site switching on both of the surfaces as found in the experiments: at low coverages, bridge species is formed on the surface, and at high coverages, NO switches to atop sites.

DFT investigation of CO adsorption on Pt(211) and Pt(311) surfaces from low to high coverage.

Adsorption of CO on Pt(211) and Pt(311) surfaces has been investigated by the density functional theory (DFT) method (periodic DMol3) with full geometry optimization. Adsorption energies, structures, and C-O stretching vibrational frequencies are studied by considering multiple possible adsorption sites and comparing them with the experimental data. The calculated C-O stretching frequencies agree well with the experimental ones, and precise determination of adsorption sites can be carried out. For Pt(211), CO adsorbs at the atop site on the step edge at low coverage, but CO adsorbs at the atop and bridge sites simultaneously on both the step edge and the terrace with further increasing CO coverage. The present results interpret the reflection adsorption infrared (RAIR) spectra of Brown and co-workers very well from low to high coverage. For Pt(311), CO adsorbs also at the atop site on the step edge at low coverage. The lifting of reconstruction by CO adsorption occurs also for Pt(311), whereas the energy gain for lifting the reconstruction of the Pt(311) surface is smaller than that for Pt(110). The largest difference between the stepped Pt(211)/Pt(311) and Pt(110) surfaces is the occupation on the edge sites at higher coverage. For the stepped surfaces, the bridge site begins to be occupied at higher coverage, whereas the atop site is always occupied for the Pt(110) surface.