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C Richard A Catlow

Publications and source records attributed to C Richard A Catlow.

At least 19 recordsLinked to original sources
PubMed2006

A computational investigation of the different intermediates during organoalkoxysilane hydrolysis.

Using a combination of atomistic molecular dynamics (MD) simulations and density functional theory (DFT) calculations, the four steps of hydrolysis of aminopropyl-, thiolpropyl-, and butyltrimethoxysilane have been studied. Large box MD simulations at constant pressure and temperature yield appropriate pair distribution functions--which allows us to quantify the number of surrounding water molecules--as well as the density of the systems. These densities serve as input for small box DFT calculations, which allow further geometry optimization and calculation of the electronic structure of the systems. The periodic DFT calculations are compared with gas-phase simulations. In all cases, the first step of hydrolysis is exothermic with the extent depending on the type of silane as well as on the number of hydrogen bonds in the initial stage.

Journal Article↗
PubMed2006

Unique organic-inorganic interactions leading to a structure-directed microporous aluminophosphate crystallization as observed with in situ Raman spectroscopy.

We report on the direct observation of key organic template-framework interactions leading to the formation of specific aluminophosphate structures. In particular, we show how MeAPO-34 formation was governed by an interaction between the divalent framework substituted metal ion and the template conformation, while for AlPO-5 the structure formation was determined by the template conformation alone. Understanding such interactions therefore appears to be important for the rationalization of microporous material formation.

Journal Article↗
PubMed2006

Adsorption of organosilanes at a Zn-terminated ZnO (0001) surface: molecular dynamics study.

Four different organosilanes (octyltrihydroxysilane, butyltrihydroxysilane, aminopropyltrihydroxysilane, and thiolpropyltrihydroxysilane) adsorbed at a reconstructed Zn-terminated polar ZnO (0001) surface are studied via constant temperature (298 K) molecular dynamics simulations. Both single adsorbed silane molecules as well as adsorbed silane layers are modeled, and the energy, distance, orientation, and alignment of these adsorbates are analyzed. The adsorbed silane molecules exhibit behavior depending on the chemical nature of their tail (nonpolar or polar) as well as on the silane concentration at the solid surface (single adsorption or silane layer). In contrast to the O-terminated ZnO surface studied previously, now adsorption can only occur at the vacancies of this reconstructed crystal surface, thus leading to an arched structure of the liquid phase near the crystal surface. Nevertheless, both nonpolar and polar single adsorbed silanes show a similar orientation and alignment at the surface (orthogonal in the former, parallel in the latter case) as for the O-terminated ZnO surface, although the interaction energy with the surface is considerably increased for nonpolar silanes while it is nearly unaffected for the polar ones. For adsorbed silanes within silane layers, the difference to single adsorbed silanes depends on the polarity of the tail: nonpolar silanes again show an orthogonal alignment, while polar silanes exhibit two different orientations at the solid surface-a head and a tail down configuration. This leads to two completely different but nevertheless stable orientations of these silanes at the Zn-terminated ZnO surface.

Journal Article↗
PubMed2006

Kinetic insights into the role of the solvent in the polymorphism of 5-fluorouracil from molecular dynamics simulations.

We investigate the fundamental factors controlling polymorphism in 5-fluorouracil by performing molecular dynamics simulations of solutions of the compound in water, nitromethane, and wet nitromethane. Analysis of the effect of solvent on the initial aggregation of 5-fluorouracil molecules shows that the strong binding of water to the 5-fluorouracil molecule hinders the formation of the doubly hydrogen-bonded dimer and, by default, promotes close hydrophobic F...F interactions that are a feature of the unusual (Z' = 4) structure of form I. In contrast, doubly hydrogen-bonded dimers are observed to form readily in solution in dry nitromethane, consistent with the crystallization of the doubly hydrogen-bonded ribbon structure of form II from this solvent. When nitromethane is doped with water, the water forms hydrogen bonds to the solute, interfering with the formation of the doubly hydrogen-bonded dimers, which is consistent with the crystallization of form I from this hygroscopic solvent when it is not dried. Overall, the molecular dynamics simulations provide an atomistic picture of how solvent-solute interactions can significantly affect the initial association of 5-fluorouracil molecules to the extent that they determine the polymorphic outcome of the crystallization.

Antimetabolites, Antineoplastic↗
PubMed2005

Structure-directing role of molecules containing benzyl rings in the synthesis of a large-pore aluminophosphate molecular sieve: an experimental and computational study.

We describe the synthesis of AlPO-5 and SAPO-5 materials (AFI topology) using five different tertiary amines or quaternary ammonium ions containing one or two benzyl rings as structure-directing agents (SDAs). All of the molecules successfully direct the crystallization of AlPO-5; however, only the most efficient templates are able to crystallize SAPO-5. The observed differences in template efficiency can be rationalized in terms of the interaction energy between these molecules and the AFI framework. In ranking the template molecules, we notice that a well-defined molecular shape enhances the templating ability, but molecules that are too rigid are not able to adapt to the AlPO framework, yielding an inferior templating ability. Results of atomic-level modeling show that templates with one benzyl ring self-assemble in the main AFI channel by forming dimers with the benzyl rings parallel to each other; templates with two benzyl rings assemble instead into longer chains in which the benzyl ring of one molecule faces the ring of the subsequent one. Both mono- and dibenzyl templates show a high space-filling ability in AFI. Kinetic and thermodynamic factors that might affect the structure-directing activity of the molecules are examined.

Aluminum Compounds↗
PubMed2005

Electronic structure study of the high-pressure vibrational spectrum of FeS2 pyrite.

Plane-wave density functional calculations are used to investigate the pressure dependence of the geometry and Gamma-point phonons of FeS(2) pyrite up to 150 GPa. The linear response method is employed to calculate the vibrational properties. Raman-active modes are in excellent agreement with the experimental data available up to 50 GPa,(1) and we predict the evolution with pressure of the IR-active modes for which no high-pressure spectroscopic data have been reported so far. Over the wide pressure range investigated here, all vibrational frequencies depend nonlinearly on pressure; their pressure dependence is quantified by determining the full set of mode Grüneisen parameters and their pressure derivatives.

Journal Article↗
PubMed2005

Computational study of a chiral supramolecular arrangement of organic structure directing molecules for the AFI structure.

Molecular mechanics computational methods have been employed to study the structure directing effect of S-(-)-1-benzyl-2-pyrrolidiniummethanol molecules towards microporous aluminophosphate materials with the AFI structure. These chiral molecules form dimers inside the one-dimensional AFI channel, which are the active structure-directing agents in the synthesis. Four different conformers of the S-(-)-1-benzyl-2-pyrrolidiniummethanol molecule are in principle available; of these, the S,S-trans shows a marked stability in dimeric form. Self-assembly between adjacent dimers generates a helicoidal, and hence chiral arrangement of the organic molecules, which extends with the same direction of rotation through the whole solid, and may thus be employed to introduce chirality in the microporous material.

Aluminum Compounds↗
PubMed2005

Generating MnO2 nanoparticles using simulated amorphization and recrystallization.

Models of MnO2 nanoparticles, with full atomistic detail, have been generated using a simulated amorphization and recrystallization strategy. In particular, a 25,000-atom "cube" of MnO2 was amorphized (tension-induced) under molecular dynamics (MD). Long-duration MD, applied to this system, results in the sudden evolution of a small crystalline region of pyrolusite-structured MnO2, which acts as a nucleating "seed" and facilitates the recrystallization of all the surrounding (amorphous) MnO2. The resulting MnO2 nanoparticle is about 8 nm in diameter, conforms to the pyrolusite structure (isostructural with rutile TiO2, comprising 1 x 1 octahedra) is heavily twinned and comprises a wealth of isolated and clustered point defects such as cation vacancies. In addition, we suggest the presence of ramsdellite (2 x 1 octahedra) intergrowths. Molecular graphical snapshots of the crystallization process are presented.

Crystallization↗
PubMed2005

Hole localization in [AlO4]0 defects in silica materials.

First-principles calculations based on cluster models have been performed to investigate the ground state and the optically excited states of the [AlO(4)](0) hole in alpha-quartz and in the siliceous zeolite ZSM-5. The structure and spectroscopic properties of this defect have been studied using the recently developed Becke88-Becke95 one-parameter model for kinetics (BB1K) functional of Zhao et al., [J. Phys. Chem. A 108, 2715 (2004)]. Our results show that the BB1K method is significantly more reliable and more accurate than the standard density-functional theory (DFT) functionals at reproducing the localized spin density on one oxygen atom and the hyperfine coupling constants associated with the hole. Furthermore, we find that the BB1K results are in close agreement with experiments, and with the self-interaction-free unrestricted Hartree-Fock (UHF) and unrestricted second-order Møller-Plesset perturbation theory (UMP2) calculations. For the first time, we present results of the ground-state paramagnetic properties of the Al defect in ZSM-5. Similar to the theoretical work for defective alpha-quartz, we find that the BB1K, UHF, UHFLee-Yang-Parr, and UMP2 calculations show a localized hole on one oxygen neighboring the Al, while even the best to date thermochemically derived hybrid generalized gradient approximation density-functional, B97-2, predicts a different model where the hole is distributed over two oxygen. We have further considered the optical transitions of the [AlO(4)](0) center in alpha-quartz and ZSM-5. In both systems, our BB1K time-dependent density-functional theory (TDDFT) and configuration interaction singles (CIS) calculations predict that the most likely transition involves electron transfer from the hole-bearing oxygen to other neighboring oxygen ions. This reinforces the experimental conclusions obtained for defective alpha-quartz. Notably, the two lowest, most dominant excitation energies calculated by BB1K-TDDFT (1.99 and 3.03 eV) show excellent agreement with experiment (1.96 and 2.85 eV [B. K. Meyer, J.M. Spaeth, and J.A. Weil, J. Phys. C: Solid State Phys. 17, L31 (1987)]) clearly outperforming the CIS method and other DFT calculations available in the literature.

Journal Article↗
PubMed2005

Simulation of the embryonic stage of ZnS formation from aqueous solution.

We investigate the processes of cluster formation and growth of ZnS from aqueous solution using molecular dynamics simulation techniques. The influence of both temperature and concentration is studied. We show that, at lower temperatures, the crucial process is the transformation of an outer-sphere Zn/S complex to an inner-sphere ion pair. Further growth of the latter is fast to generate negatively charged planar clusters. These clusters interact to form more stable, closed structures, which are found to be the global minima configurations in vacuo. At higher temperatures, no outer-sphere ion pairs are formed, and the larger cluster configurations form much more quickly.

Journal Article↗
PubMed2005

Structure and properties of ZnS nanoclusters.

Earlier studies have shown that the most stable structures for (ZnS)n clusters with n = 10-47 are hollow polyhedral clusters ("bubbles"). We report a detailed study of larger clusters, where n = 50, 60, 70, and 80, for which onionlike or "double bubble" structures are predicted. We report calculations of the vibrational spectra and the electronic structure of bubble and double bubble clusters, which may assist in their experimental identification.

Journal Article↗
PubMed2004

Fine structures of zeolite-Linde-L (LTL): surface structures, growth unit and defects.

High-resolution electron microscopy (HREM) has been used to image the surface structure of nano- and micrometer-sized synthetic crystals of zeolite-Linde-L (LTL). Columnar holes and rotational, nano-sized, wheel-like defects were observed within the crystals, where the hole has a minimum size equal to that of the rotational defect. Predictions of surface structure from atomistic computer simulation concur with the observations from HREM and provide insight into the crystal growth mechanism of perfect and defective LTL. Analysis of the energetics of the formation of rotational defect structures reveals that the driving force for defect creation is thermodynamic and furthermore, the rotational defects could be created in high concentrations. Formation of a columnar hole is found to be slightly energetically unfavourable and therefore we speculate that the incidence of both rotational and nano-sized vacancy defects is strongly dependent on kinetic factors and reaction conditions. The morphology of nano- and microcrystalline LTL is contradistinct and we use insights from simulation to propose an explanation of the disparity in crystal shape.

Journal Article↗
PubMed2004

Computational study of the structure-directing effect of benzylpyrrolidine and its fluorinated derivatives in the synthesis of the aluminophosphate ALPO-5.

Using a combination of computer modeling techniques, we have investigated the ability of benzylpyrrolidine and its fluorinated derivatives in ortho, meta, and para positions of the phenyl ring to direct the synthesis of the aluminophosphate AlPO-5. The o- and p-fluoro derivatives are not good templates because of the poor packing of the template molecules inside the AlPO-5 pores, due to a repulsion provoked by the fluorine atoms. However, benzylpyrrolidine and the m-fluoro derivative do direct the synthesis of AlPO-5, the latter being a better template due to higher electrostatic interactions with the framework. We demonstrate that, at least when the synthesis is performed with an excess of template molecules, the ability of organic templating molecules to direct the synthesis of microporous materials depends not on the host-guest interaction energy per unit of template molecules, as usually calculated, but on the density of interaction energy, i.e., the energy per formula unit of the microporous network. The packing density of molecules inside the channel system must be taken properly into account. From the calculated location of the benzylpyrrolidine molecules and their m-fluoro derivative inside the inorganic network, we would expect the formation of stable dimers.

Journal Article↗
PubMed2004

ZnS bubble clusters with onion-like structures.

Following recent studies which showed that the most stable structures for (ZnS)(n) clusters (n= 10-47) are the so-called "bubble clusters", in which all the atoms are three-coordinated, we have used simulated annealing techniques to find the most stable structure for a larger cluster, (ZnS)(60). We find an onion-like structure, with one small cluster enclosed inside a bigger one. The inner cluster has the structure of a sodalite cage. Bonding between the inner and the outer clusters creates a network of four-coordinated atoms.

Journal Article↗
PubMed2003

The initial stages of aminosilanol polymerisation.

For polysiloxanes to be used as a protective coating it is important that proton transfer, a trigger to polymerisation, is a facile process. Here we investigate the initial stages of polycondensation and compare different silanol tail groups and the effect of solvent (isopropanol). In the case of (3-aminopropyl)trihydroxysilane we see the potential for self catalysis as the tail group is a proton acceptor, while thiolpropyltrihydroxysilane and isopropanol do not promote proton transfer.

Journal Article↗