Angular auto-correlation functions in molecular crystals and liquids: application to incoherent neutron scattering law

The effect of the local hindered molecular motion in the incoherent neutron scattering spectra in crystals and liquids is studied theoretically on the basis of the angular auto-correlation functions symmetrized on the dynamical point groups. The extended angular jump model simulates the motion. The microscopic properties of the matter, the time scale and the point symmetry of the molecule motion as well as the site symmetry of the molecule, are taken into account with the help of the dynamical variables of the model. The incoherent neutron scattering function is anisotropic in a monocrystalline sample. The scattering function consists of elastic plus quasi-elastic components. The shape of the quasi-elastic scattering spectrum is expressed by the sum of the weighted Lorentzian curves symmetrized with respect to the non-identical irreducible representations of the molecule motion point symmetry group. The elastic part of the intensity is increased by the contribution arising from the molecule motion of the identity representation symmetry. The scattering expression related to the molecule motion symmetry of a perfect cubic group is similar to the well-known expression derived for the scattering from the spherical top molecules exhibiting rotation diffusion.     

Density functional theory investigation of the structure of SO2 and SO3 on Cu(1 1 1) and Ni(1 1 1)

Density functional theory (DFT) slab calculations, mainly using the generalised gradient approximation, have been used to investigate the minimum energy structures of molecular SO₂ and SO₃ on Cu(1 1 1) and Ni(1 1 1) surfaces. On Ni(1 1 1) the optimal local adsorption structures are in close agreement with experimental results for both molecular species obtained using the X-ray standing wavefield technique, although for adsorbed SO₂ the energetic difference between two alternative lateral positions of the lying-down molecule on the surface is marginally significant. On Cu(1 1 1) the results for adsorbed SO₂, in particular, were sensitive to the DFT functional used in the calculations, but in all cases failed to reproduce the experimentally-established preference for adsorption with the molecular plane perpendicular to the surface. This result is discussed in the context of previously published DFT results for these species adsorbed on Cu(1 0 0). The optimal geometry found for SO₃ on Cu(1 1 1) is similar to that on Ni(1 1 1), providing agreement with experiment regarding the molecular orientation but not the adsorption site.     

Dipole polarizability,structure, and stability of [2+2]-linked fullerene nanostructures (C60)n (n≤7)

In the present work, structural features, dipole polarizability, and stability of two most promising oligomeric series (C₆₀)_n with zigzag and linear arrangement of the fullerene cages have been studied by the PBE/3ζ density functional theory method. Their mean polarizabilities and polarizability exaltations are linearly correlated with the molecular size (maximal intercage distance). Linear (C₆₀)_n have higher polarizability than zigzag oligomers with the same n. Based on the example of hexamers (C₆₀)₆, we have shown that connectivity (number of connections) has no effect on the resulting polarizability but maximal remoteness does, i.e. the geometric factor is more decisive for mean polarizability of such fullerene nanostructures. Stability of (C₆₀)_n decreases with growing molecular size for linear structures and slowly increases in the case of zigzag (C₆₀)_n. The found dependences of polarizability and stability on the molecular size may be used for assessing these parameters of larger fullerene nanostructures, hardly computable with quantum chemical methods.     

Ab initio simulation of the BaZrO3 (0 0 1) surface structure

Electronic and atomic structures of different terminations of the (0 0 1) non-polar orientation of BaZrO₃ surfaces have been studied using first-principles calculations. We found that surface energies at both possible surface terminations, BaO and ZrO₂, were very close. The (0 0 1)-BaO and (0 0 1)-ZrO₂ terminated surfaces have bandgap values smaller than that of a bulk BaZrO₃ crystal. In addition, the relative surface stability has been analyzed as a function of chemical environment.     

Physical consequences of the mitochondrial targeting of single-walled carbon nanotubes probed computationally

Experiments by F. Zhou and coworkers (2010) [16] showed that mitochondria are the main target of the cellular accumulation of single-walled carbon nanotubes (SWCNTs). Our in silico experiments, based on geometrical optimization of the system consisting of SWCNT+proton within Density Functional Theory, revealed that protons can bind to the outer side of SWCNT so generating a positive charge. Calculation results allow one to propose the following mechanism of SWCNTs mitochondrial targeting. SWCNTs enter the space between inner and outer membranes of mitochondria, where the excess of protons has been formed by diffusion. In this compartment SWCNTs are loaded with protons and acquire positive charges distributed over their surface. Protonation of hydrophobic SWCNTs can also be carried out within the mitochondrial membrane through interaction with the protonated ubiquinone. Such “charge loaded” particles can be transferred as “Sculachev ions” through the inner membrane of the mitochondria due to the potential difference generated by the inner membrane. Physiological consequences of the described mechanism are discussed.     

First-principles study of thiophene on β-SiC (0 0 1)-(2×1) surface

In this work, we performed density functional calculations to examine the molecular adsorption states of thiophene on β-SiC(0 0 1)-2×1 surface. A number of possible adsorption geometries are considered into two groups as the polymeric thiophene chain and the individual molecules covalently bonded onto the surface. The results show that the polymeric chain on the surface is the less stable adsorption case and individual arch like adsorption case structure is more stable than others. In all adsorption cases, the adsorbed SiC surfaces are characterized as different semiconductors.     

The surface science of enzymes

One of the largest challenges to science in the coming years is to find the relation between enzyme structure and function. Can we predict which reactions an enzyme catalyzes from knowledge of its structure—or from its amino acid sequence? Can we use that knowledge to modify enzyme function? To solve these problems we must understand in some detail how enzymes interact with reactants from its surroundings. These interactions take place at the surface of the enzyme and the question of enzyme function can be viewed as the surface science of enzymes. In this article we discuss how to describe catalysis by enzymes, and in particular the analogies between enzyme catalyzed reactions and surface catalyzed reactions. We do this by discussing two concrete examples of reactions catalyzed both in nature (by enzymes) and in industrial reactors (by inorganic materials), and show that although analogies exist and the two kinds of catalyst can be described by similar tools, nature and human effort have come up with different solutions. This on the other hand implies that new and improved catalysts may be made by learning from nature.     

Evolution of geometrical structures,stabilities and electronic properties of neutral and anionic Li n Cu λ (n = 1–9, λ = 0, −1) clusters: compare with pure lithium clusters

The structural evolution, stabilities, and electronic properties of copper-doped lithium Li _n Cu^λ (n?=?1–9, λ?=?0, ?1) clusters have been systematically investigated using a density functional method at PW91PW91 level. Extensive searches for ground-state structures were carried out, and the results showed the copper tends to occupy the most highly coordinated position and form the largest probable number of bonds with lithium atoms. By calculating the binding energies per atom, fragmentation energies and the HOMO-LOMO gaps, we found LiCu, Li₇Cu, LiCu^?, Li₂Cu^? and Li₈Cu^? clusters have the stronger relative stability and enhanced chemical stability. The content and pattern of frontier MOs for the most stable doped isomers were analysed to investigate the bond nature of interaction among Li and Cu atoms. The results show some σ-type and π-type bonds are formed among them, and with small admixture of the Cu d characters. To achieve a deep insight into the electron localization and reliable electronic structure information, the natural population analysis and electron localization function were performed and discussed.     

Structural, electronic, and optical properties of ZnOl_xSex alloys using first-principles calculations

The structural, electronic, and optical properties of binary ZnO, ZnSe compounds, and their ternary ZnOl_xSex alloys are computed using the accurate full potential linearized augmented plane wave plus local orbital （FP-LAPW ＋ lo） method in the rocksalt （B 1） and zincblende （B3） crystallographic phases. The electronic band structures, fundamental energy band gaps, and densities of states for ZnO1_xSex are evaluated in the range 0 〈 x 〈 1 using Wu-Cohen （WC） generalized gradient approximation （GGA） for the exchange-correlation potential. Our calculated results of lattice parameters and bulk modulus reveal a nonlinear variation for pseudo-binary and their ternary alloys in both phases and show a considerable deviation from Vegard＇s law. It is observed that the predicted lattice parameter and bulk modulus are in good agreement with the available experimental and theoretical data. We establish that the composition dependence of band gap is semi-metallic in B1 phase, while a direct band gap is observed in B3 phase. The calculated density of states is described by taking into account the contribution of Zn 3d, O 2p, and Se 4s, and the optical properties are studied in terms of dielectric functions, refractive index, reflectivity, and energy loss function for the B3 phase and are compared with the available experimental data.