Molecular Cluster Model Research Articles

Influence of N−H···O and C−H···O Hydrogen Bonds on the 17O NMR Tensors in Crystalline Uracil: Computational Study

We report a computational study for the 17O NMR tensors (electric field gradient and chemical shielding tensors) in crystalline uracil. We found that N-H...O and C-H...O hydrogen bonds around the uracil molecule in the crystal lattice have quite different influences on the 17O NMR tensors for the two C=O groups. The computed 17O NMR tensors on O4, which is involved in two strong N-H...O hydrogen bonds, show remarkable sensitivity toward the choice of cluster model, whereas the 17O NMR tensors on O2, which is involved in two weak C-H...O hydrogen bonds, show much smaller improvement when the cluster model includes the C-H...O hydrogen bonds. Our results demonstrate that it is important to have accurate hydrogen atom positions in the molecular models used for 17O NMR tensor calculations. In the absence of low-temperature neutron diffraction data, an effective way to generate reliable hydrogen atom positions in the molecular cluster model is to employ partial geometry optimization for hydrogen atom positions using a cluster model that includes all neighboring hydrogen-bonded molecules. Using an optimized seven-molecule model (a total of 84 atoms), we were able to reproduce the experimental 17O NMR tensors to a reasonably good degree of accuracy. However, we also found that the accuracy for the calculated 17O NMR tensors at O2 is not as good as that found for the corresponding tensors at O4. In particular, at the B3LYP/6-311++G(d,p) level of theory, the individual 17O chemical shielding tensor components differ by less than 10 and 30 ppm from the experimental values for O4 and O2, respectively. For the 17O quadrupole coupling constant, the calculated values differ by 0.30 and 0.87 MHz from the experimental values for O4 and O2, respectively.

Molecular dynamics simulation of self- and mutual diffusion coefficients for confined mixtures

The self- and mutual diffusion coefficients for binary mixtures of Ar-Kr both in the bulk and in the nanopores were studied by molecular dynamics simulations. The composition dependences and the relationships between the self- and the mutual diffusion coefficients both in the bulk and in the nanopores were further discussed. It was found that the simulation results (D(c.m.)) are close to the calculated ones (D(s)) for the Ar-Kr system. Both self- and mutual diffusion coefficients in nanopores are much lower than that of the bulk, and they ever decrease as the pore width decreases. Nevertheless, the self- and mutual diffusion coefficients increase as the mole fraction of Ar increases, and as expected, increase as the temperature increases. The self-diffusion coefficients of mixtures both in the bulk and in the nanopores are predicted by the Carman model and by the molecular cluster model.

Theoretical study on the microstructures of hydrotalcite lamellae with Mg/Al ratio of two

The microstructures of lamellae of hydrotalcites with Mg/Al ratio of two are studied using quantum chemical method. A series of molecular cluster models of lamellae are established. The geometries of lamellae are computed by semiempirical molecular orbital methods (MNDO/d and PM3). The optimized cluster models show a hexagonal morphology. The Mg/Al ratio of lamella is found to be an alterable number and its limit is two when the lamella diameter becomes large. The molecular orbital calculations show that the edge and the center of lamellae are respectively easy to attract cations and accept anions, to form intercalated structure.

Hiral Effects of Single Wall Carbon Nanotube Fluorination and Hydrogenation

In the paper the results of calculations of the electronic and energy characteristics of atomic hydrogen and fluorine adsorption processes on an external surface of single wall hiral carbon nanotubes (n, m) are represented. Molecular cluster model within a framework of quantum chemical semi‐empirical schemes MNDO and PM3 has been used. Sorption properties of (4, 1), (4, 2), (4, 3), (5, 1), (5, 3), (5, 4), (6, 1), (6, 2), (6, 3), (6, 4), and (6, 5) tubes have been considered. Periodical behavior of the chemical bond and activation energies as nanotube diameter functions has been found. It appeared that (4, 2), (4, 3), (5, 1) nanotubes show more effective adsorption processes and (5, 3), (5, 4), (6, 2), (6, 3) tubes are not advantage for the chemisorptions.

Bubble nucleation and growth in polymer solutions

AbstractThe molecular cluster model for homogeneous bubble nucleation was extended to predict the bubble nucleation events in elastomers, polymers and polymer solutions. For nucleation in elastomers and polymers, the strain energy overcome by a critical bubble during growth period was also considered. The calculation results for the number of bubbles nucleated are in good agreement with observed results. Further, the growing of the critical bubble by the diffusion process in a viscoelastic medium was treated by an integral method for the concentration boundary layer. The calculated cell sizes depending on the initial saturation pressure are in close agreement with the observed sizes. The governing equations developed in this study may be used in polymer processing of microcellular foams. Polym. Eng. Sci. 44:1890–1899, 2004. © 2004 Society of Plastics Engineers.

The hole trappers related to lead vacancy in PbWO4 crystal

Abstract Several lattice structures around a lead vacancy VPb2− in PbWO4 (PWO) are optimized using a plane-wave pseudo-potential formulation within the framework of density function theory, with generalized gradient correction in the form of Perdew–Wang-91. The electronic structures around VPb2− in the PWO crystal are studied using the molecular-cluster model within the framework of the fully relativistic self-consistent Dirac-Slater theory by using a numerically discrete variational (DV-Xα) method. By analyzing the lattice relaxation and electronic structures around VPb2− we can reasonably believe that once VPb2− is formed in PWO crystal, O2− turns to be prior to trap holes to compensate the electrical negativity of VPb2− Pb2+ may never be the hole-trap compensating VPb2− and Pb3+ and Pb4+ in PWO crystal may not actually exist. The possible defect micro-model caused by VPb2− in the as-grown PWO crystal is that each VPb2− creates a VK+−VF− aggregate color center.

Vapor Bubble Nucleation: A Microscopic Phenomenon

In this article, vapor bubble nucleation in liquid and the evaporation process of a liquid droplet at its superheat limit were discussed from the viewpoint of molecular clustering (molecular cluster model for bubble nucleation). For the vapor bubble formation, the energy barrier against bubble nucleation was estimated by the molecular interaction due to the London dispersion force. Bubble nucleation by quantum tunneling in liquid helium under negative pressure near the absolute zero temperature and bubble nucleation on cavity free micro heaters were also presented as the homogenous nucleation processes.

Reactivity and stability of Au in and on TS-1 for epoxidation of propylene with H 2 and O 2

The direct vapor-phase epoxidation of propylene using hydrogen and oxygen over gold particles prepared by the deposition-precipitation (DP) method on various modified titanium silicalite-1 (TS-1) supports was studied over a reaction time of 24–36 h at a space velocity of 7000 ml g −1 cat h −1 and temperatures of 413, 443, and 473 K. Gold deposition at pH 9–10 allowed for a consistent amount of 1–3 wt% of the gold available in solution to be deposited, while still maintaining gold particle diameters in the 2–5 nm range, as observed by TEM. These Au/TS-1 catalysts achieved propylene conversions of 2.5–6.5% and PO selectivities of 60–85% at 443 K, with dilute Au and Ti catalysts exhibiting good stability. A key result of the work is that PO rates were not highly influenced by the TS-1 particle size and are thus not proportional to the specific external surface area of the support. The conclusion that activity may reside in the channels of the TS-1 is supported by the finding that the observable gold particles decorating the TS-1 particles only account for ca 30% of the total gold content of the catalyst. Increasing the gold loading up to 0.74 wt% did not increase the PO rates proportionally, suggesting that the active Au–Ti PO-forming centers are limited. In contrast to the prevailing interpretation of this catalyst that a critical Au particle diameter of 2–5 nm is essential for PO activity, our results are consistent with a molecular cluster model where extremely small gold clusters located near Ti sites inside the TS-1 pores or on the external surface are active for propylene epoxidation.

Interstitial O 3 in silica: a molecular cluster density functional study

The electronic and molecular properties of interstitial O 3 in SiO 2 have been theoretically studied by coupling the molecular cluster model to the density functional theory. We find that, on passing from the free species to the interstitial one, electronic and molecular structures of O 3 are only slightly perturbed. Moreover, in agreement with the experimental assignment of Skuja et al., it is confirmed that the ubiquitous absorption band at 4.8 eV characterizing 7.9 eV photon-irradiated SiO 2 samples includes a contribution due to excitations between O 3 based occupied and unoccupied MOs.

Hiral effects of single‐wall carbon nanotube fluorination and hydrogenation

AbstractThe results of calculations of the electronic and energy characteristics of atomic hydrogen and fluorine adsorption processes on an external surface of single‐wall hiral carbon nanotubes (n,m) are represented. Molecular cluster model within a framework of quantum chemical semiempirical schemes modified neglect of diatomic overlap (MNDO) and parametric method 3 (PM3) has been used. Sorption properties of (4,1), (4,2), (4,3), (5,1), (5,3), (5,4), (6,1), (6,2), (6,3), (6,4), and (6,5) tubes have been considered. Periodical behavior of the chemical bond and activation energies as nanotube diameter functions has been found. It appeared that (4,2), (4,3), and (5,1) nanotubes show more effective adsorption processes and (5,3), (5,4), (6,2), and (6,3) tubes are not advantageous for the chemisorptions. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

Defects in titanates

Electronic, structural and optical properties of titanates (BaTiO3, SrTiO3, CaTiO3 and PbTiO3) containing different point defects are reviewed and discussed in the present work. The results are obtained using a quantum-chemical method based on the Hartree-Fock formalism and utilising the Large Unit Cell (LUC) and the Embedded Molecular Cluster (EMC) models. The outcomes of the computations are compared and discussed in the light of the available experimental data. The formation of Jahn-Teller (JT) polarons and bipolarons due to the presence of some point defects in the titanate crystals are found to be very important in order to understand better the behaviour of these materials. In particular, such phenomena as the non-linear photoconductivity in BaTiO3, the drastic increase in the electrical conductivity in CaTiO3 and BaTiO3 crystals, and the superconductivity in SrTiO3 could be completely or partially explained by the presence of JT polarons and different interacting mechanisms between these defects.

Isomorphous cation substitution in dioctahedral phyllosilicates by means of ab initio quantum mechanical calculations on clusters

The geometrical features and electronic structure of molecular cluster models of two edge-sharing octahedrally coordinated cations, with and without a ring of six silica tetrahedra coupled to the two octahedra, were studied by means of ab initio molecular orbital calculations made with Hartree-Fock (at LANL2DZ and 6-311+G* levels) and Density Functional Theory (DFT) methods. These models represent different pairs of Al3+, Fe3+, Fe2+, and Mg2+ cations from the octahedral sheet of clays. The isomorphic substitution reactions of these cations in our molecular clusters were studied by means of isodesmic reactions. A tendency of Mg2+ to mix with Al3+ cations along the octahedral sheet was found, agrees with experimental results. A lower tendency of Fe3+ to mix with Al3+ was found in systems with only Al and Fe octahedral cations. However, the presence of Mg2+ catalyses the clustering of Fe3+ in Al/Fe/Mg samples, giving a cation ordering tendency similar to that found experimentally. The geometry and the hydrogen-bonding interactions of the OH groups were also studied. The ν(OH), δ(OH), and γ(OH) vibration mode frequencies were calculated and show good agreement with experimental values for ν(OH) and δ(OH), which suggests that this technique is a good predictive tool for γ(OH). The octahedral cation substitution effect on the vibrations of OH groups was calculated and reproduced the experimental behavior. The hydrogen-bonding interactions with tetrahedral O atoms are important for the ν(OH) frequency, but are not significant for δ(OH). These results show that the effect of the tetrahedral sheet on the OH groups is constant for the different cation pairs joined to these OH groups.

Bubble Nucleation on Micro Line Heaters

Nucleation temperatures on micro line heaters were measured precisely by obtaining the I-R (current-resistance) characteristic curves of the heaters. The bubble nucleation temperature on the heater with 3 μm width is higher than the superheat limit, while the temperature on the heater with broader width of 5 μm is considerably less than the superheat limit. The nucleation temperatures were also estimated by using the molecular cluster model for bubble nucleation on the cavity free surface with effect of contact angle. The bubble nucleation process was observed by microscope/35 mm camera unit with a flash light of μs duration.

Single and regular hydrogenation and oxidation of carbon nanotubes: MNDO calculations

AbstractCalculations of electron energetic characteristics of atomic hydrogen adsorption processes on internal and external surfaces of single‐walled carbon nanotubes (tubulenes) of (6,6) “armchair” type having cylindrical symmetry have been carried out. This article reports also on the results of calculations of the atomic adsorption of oxygen on the surface of armchair and zigzag single‐walled carbon nanotubes. Ionic‐embedded covalent‐cyclic cluster (IECCC) and molecular cluster models within the framework of semiempirical quantum chemical scheme MNDO well shown in the theoretical researches of electronic molecular and periodic solid‐state structures have been used. The electronic and energy characteristics of the oxidation processes are analyzed, and the most energetically favorable oxide structure of the (6,6) nanotube is determined. It is found that narrow‐gap nanotubes show a tendency to metallic behavior as their surface is saturated with oxygen atoms. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

Fluorination of carbon nanotubes: Quantum chemical investigation within MNDO approximation

AbstractComputations of (6, 0), (8, 0), (6, 6), (7, 7), and (8, 8) single‐wall carbon nanotubes fluorination processes have been carried out within the framework of molecular cluster model and semiempirical quantum chemical MNDO scheme. The adsorption energy of fluorine atom as a function of distance from the surface carbon has been constructed. Chemical stable and van der Waals metastable stations of an F atom on nanotube surfaces have been found. The adsorption process of two fluorine atoms on adjacent surface carbons has been studied. It has been found that the second fluorine atom is adsorbing without van der Waals metastable station. The probability of the processes has been estimated in quasiclassic approaching. The greatest possible concentration ratio F/C of almost all investigated nanotubes have been obtained equal to 1 besides (8, 8) nanotube, for which the ratio is 0.75. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

Extreme Molecular Orientations in a Dimorphic System: Polar/Centric and Polar/Polar Cogrowth Crystal Architectures

(4-Pyrrolidinopyridyl)bis(acetylacetonato)zinc(II) forms perfectly polar as well as centrosymmetric crystal structures depending sensitively on the solvent and the rate of crystallization. Semiempirical computational modeling of molecular clusters, incorporating solvation effects, highlights the delicate balance of energetics involved in the solvent polarity preference of the extreme structures. A suitable choice of solvents provides crystals exhibiting an unusual cogrowth of polar/centric as well as polar/polar domains. This material provides a vivid illustration of the subtle nature of supramolecular assembly leading to extreme organizational motifs and opens up possibilities of realizing novel multidomain architectures in crystals.

Fluorination of carbon nanotubes within the molecular cluster method

Computations of single-wall carbon nanotube fluorination processes have been carried out within the framework of the molecular cluster model and semiempirical quantum-chemical MNDO scheme. The adsorption energy for the fluorine atom as a function of distance from the surface of the carbon has been calculated. Chemically stable and van der Waals metastable stations of F atoms on nanotube surfaces have been found. The adsorption process for two fluorine atoms on adjacent surface carbons has been studied. It has been found that the second fluorine atom is adsorbed without van der Waals metastable station. The probability of the processes has been estimated in the quasi-classical approach. The greatest possible concentration ratio F/C of almost all investigated nanotubes has been found to be 1 except for the (8,8) nanotube for which the ratio is 0.75.

Bubble nucleation on micro line heaters under steady or finite pulse of voltage input

Nucleation temperatures on micro line heaters under steady voltage input were measured precisely by obtaining the I– R (current–resistance) characteristic curves of the heaters having dimensions of 50 μm in length, 3 or 5 μm in width, and 0.583 μm in thickness. The bubble nucleation temperature on the heater with 3 μm width is higher than the superheat limit, while the temperature on the heater with broader width of 5 μm is considerably less than the superheat limit. The nucleation temperature under a finite voltage pulse input was also measured for 5-μm width heater. The nucleation temperatures were also estimated by using the molecular cluster model for bubble nucleation on the cavity free surface with effect of contact angle. The bubble nucleation process was observed by a microscope/35 mm camera unit with a flash light of μs duration.

A theoretical study of the electronic structure of O 2 interstitial impurities in silica

The electronic and molecular structure of interstitial O 2 in silica (SiO 2) has been theoretically investigated by coupling the molecular cluster model to density functional theory. Calculations include the evaluation of optimised geometrical parameters, guest–host interaction energies and impurity vibrational frequencies. Results indicate that the inclusion of O 2 in SiO 2 is an endothermic process scarcely affecting the impurity electronic and structural properties.

Application of molecular cluster models to study the amino acid L‐α‐alanine and its derived radicals in the crystalline state

AbstractIn this study, molecular cluster methods are used to simulate the crystalline environment of L‐α‐alanine. Two clusters are constructed based on neutron diffraction data, containing 7 and 14 molecules respectively. The geometry of a central alanine molecule is optimised at several levels of theory, while the surrounding molecules in the cluster are kept fixed in space. By evaluating the difference between the optimised and the experimental geometries, an assessment is made of the different levels of theory used. These vary from semi‐empirical to full DFT‐B3LYP treatments of the cluster. Special attention is paid to hybrid methods, involving the ONIOM scheme. These cluster methods are then used to study a radiation‐induced radical of alanine, since they allow unbiased geometry optimisation of the radical under study. The influence of the theoretical treatment is considered on several calculated hyperfine coupling constants. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003