H. Christopher Greenwell

Recent advances in large-scale atomistic and coarse-grained molecular dynamics simulation of clay minerals

We review the recent advances in large-scale and coarse-grained molecular dynamics applied to clay minerals. Recent advances in local and distributed high performance computational resources together with the development of efficient parallelized algorithms has enabled the simulation of increasingly realistic large-scale models of clay mineral systems. Using this improved technology, it is becoming possible to simulate realistic clay platelet sizes at an atomistic level. This has considerably extended the spatial dimensions of microscopic simulation into a domain normally encountered in mesoscopic simulation. The simulation of large-scale model systems is important to further study complex phenomena, such as the structural and mechanical properties of disordered layered materials such as clays. In order to achieve even larger length and longer time-scales coarse-grained methods are increasingly employed, capturing phenomena such as composite failure modes and intercalation.

Role of Host Layer Flexibility in DNA Guest Intercalation Revealed by Computer Simulation of Layered Nanomaterials

Layered double hydroxides (LDHs) have been shown to form staged intermediate structures in experimental studies of intercalation. However, the mechanism by which staged structures are produced remains undetermined. Using molecular dynamics simulations, we show that LDHs are flexible enough to deform around bulky intercalants such as deoxyribonucleic acid (DNA). The flexibility of layered materials has previously been shown to affect the pathway by which staging occurs. We explore three possible intermediate structures which may form during intercalation of DNA into Mg2Al LDHs and study how the models differ energetically. When DNA strands are stacked directly on top of each other, the LDH system has a higher potential energy than when they are stacked in a staggered or interstratified structure. It is generally thought that staged intercalation occurs through a Daumas-Herold or a Rudorff model. We find, on average, greater diffusion coefficients for DNA strands in a Daumas-Herold configuration compared to a Rudorff model and a stage-1 structure. Our simulations provide evidence for the presence of peristaltic modes of motion within Daumas-Herold configurations. This is confirmed by spectral analysis of the thickness variation of the basal spacing. Peristaltic modes are more prominent in the Daumas-Herold structure compared to the Rudorff and stage-1 structures and support a mechanism by means of which bulky intercalated molecules such as DNA rapidly diffuse within an LDH interlayer.

Selection for fitness at the individual or population levels: Modelling effects of genetic modifications in microalgae on productivity and environmental safety

A mechanistic model of microalgae is used to explore the implications of modifying microalgal chlorophyll content and photosynthetic efficiency with an aim to optimising commercial biomass production. The models show the potential for a 10 fold increase in microalgae productivity in genetically modified versus unmodified configurations, while also enabling the use of bioreactors of greater optical depth operating at lower dilution rates. Analysis suggests that natural selection of a trait benefiting the individual (high Chl:C(max), i.e., high antennae size) conflicts with artificial selection of a trait (low Chl:C(max)) of most benefit to production at the population level. The implication is that GM strains rather than strains selected from nature will be most beneficial for commercial algal biofuels production. Further, escaped GM algae populations may, depending on the specific nature of the modification, be quickly out-competed by the natural forms because individually a high Chl:C is beneficial in low light environments. However, it remains possible that changes in biochemical composition associated with genetic modification of photosystem competence, or with other selection processes to enhance commercial gain, may adversely affect the value of such organisms as prey for zooplankton, leading to the unwanted generation of future harmful algae.

Efficient synthesis of ordered organo-layered double hydroxides

Layered double hydroxides (LDHs) intercalated with terephthalate anions represent one of the most studied organo-LDH systems. We have prepared MgAl terephthalate-LDHs using an efficient hydrothermal approach from the respective metal hydroxide precursors. In contrast to terephthalate LDHs prepared by other methods, and as a result of the absence of competing anions, a large excess of terephthalate acid was not required, thereby allowing for an environmentally attractive synthetic route. The LDHs were prepared from starting reactant Mg/Al ratios of 2, 3, 4 and 5 and were found to exhibit unusually high degrees of order as evidenced from X-ray diffraction studies, especially at the Mg/Al ratio of 2. Further analysis of the X-ray diffraction data showed that, as in previous studies, three distinct interlayer arrangements could be identified. Scanning electron microscopy was used to compare and contrast the morphology of crystals formed with those prepared by other methods of LDH synthesis and confirms the high degree of structural integrity achieved by the synthetic method.

Determining materials properties of natural composites using molecular simulation

Layered double hydroxides (LDHs) have a wide range of potential uses due to their ability to intercalate anionic species, including poly-anionic biopolymers. Atomistic simulations can provide considerable insight into these nano-structured materials, particularly given the recent advance in high-performance computing facilities and scalable simulation codes that has enabled simulations virtually free of finite size effects. In this work we present our findings of large-scale (>100 000 atoms) molecular dynamics simulations of Mg–Al LDHs intercalated with alginate oligomers. We have investigated the effect of two different alginate oligomer chain lengths upon the materials properties of these LDH composites. In addition to this we have explored finite size effects through the use of three different system sizes for each alginate oligomer, the largest of which contains ∼240 000 atoms. We estimate the average bending modulus of the systems to be 3 × 10−19 J. However, we find the smallest alginate oligomer in our study dampens the undulations of the LDH sheets at long wavelengths, which confers a greater interlayer compressibility due to the small alginate molecules bridging the interlayer spacing. The initial orientation of larger alginate oligomers is found to have an impact on the Youngs moduli of the composite materials over the timescales considered in this work. We find the average in-plane Youngs modulus to be approximately 40 GPa for the total composite materials and 135 GPa for the LDH sheets alone.

METHYLENE BLUE ADSORPTION ON THE BASAL SURFACES OF KAOLINITE: STRUCTURE AND THERMODYNAMICS FROM QUANTUM AND CLASSICAL MOLECULAR SIMULATION

Organic dyes such as methylene blue (MB) are often used in the characterization of clays and related minerals, but details of the adsorption mechanisms of such dyes are only partially understood from spectroscopic data, which indicate the presence of monomers, dimers, and higher aggregates for varying mineral surfaces. A combination of quantum (density functional theory) and classical molecular simulation methods was used to provide molecular detail of such adsorption processes, specifically the adsorption of MB onto kaolinite basal surfaces. Slab models with vacuum-terminated surfaces were used to obtain detailed structural properties and binding energies at both levels of theory, while classical molecular dynamics simulations of aqueous pores were used to characterize MB adsorption at infinite dilution and at higher concentration in which MB dimers and one-dimensional chains formed. Results for the neutral MB molecules are compared with those for the corresponding cation. Simulations of the aqueous pore indicate preferred adsorption on the hydrophobic siloxane surface, while charge-balancing chloride ions adsorb at the aluminol surface. At infinite dilution and in the gas-phase models, MB adsorbs with its primary molecular plane parallel to the siloxane surface to enhance hydrophobic interactions. Sandwiched dimers and chains are oriented perpendicular to the surface to facilitate the strong hydrophobic intermolecular interactions. Compared with quantum results, the hybrid force field predicts a weaker MB adsorption energy but a stronger dimerization energy. The structure and energetics of adsorbed MB at infinite dilution are consistent with the gas-phase binding results, which indicate that monomer adsorption is driven by strong interfacial forces rather than by the hydration properties of the dye. These results inform spectroscopic studies of MB adsorption on mineral surfaces while also revealing critical areas for development of improved hybrid force fields.

Chiral interactions of histidine in a hydrated vermiculite clay

Recent work shows a correlation between chiral asymmetry in non-terrestrial amino acids extracted from the Murchison meteorite and the presence of hydrous mineral phases in the meteorite [D. P. Glavin and J. P. Dworkin, Proc. Natl. Acad. Sci. U. S. A., 2009, 106, 5487-5492]. This highlights the need for sensitive experimental tests of the interactions of amino acids with clay minerals together with high level computational work. We present here the results of in situ neutron scattering experiments designed to follow amino acid adsorption on an exchanged, 1-dimensionally ordered n-propyl ammonium vermiculite clay. The vermiculite gel has a (001) d-spacing of order 5 nm at the temperature and concentration of the experiments and the d-spacing responds sensitively to changes in concentration, temperature and electronic environment. The data show that isothermal addition of D-histidine or L-histidine solutions of the same concentration leads to an anti-osmotic swelling, and shifts in the d-spacing that are different for each enantiomer. This chiral specificity, measured in situ, in real time in the neutron beam, is of interest for the question of whether clays could have played an important role in the origin of biohomochirality.

An Introduction to Pyrolysis and Catalytic Pyrolysis: Versatile Techniques for Biomass Conversion

A significant proportion of renewable feedstocks research has been devoted to the production of bio-fuels and bio-chemicals from biomass, primarily via thermochemical conversion processes. This chapter presents an overview of alternative pyrolysis methodologies, which can convert biomass directly into solid (char), liquid (bio-oil), and gaseous products. In this report, the influence of the pyrolysis conditions employed, the design of reactor, and the nature of the biomass feedstock used upon the chemical composition of the product fractions are surveyed. A summary of the mechanisms by which the pyrolysis of the principle biomass constituents occurs is given. This is accompanied by an indication of the complications that arise as a result of the complex and heterogeneous nature of biomass, including the potential roles of the various salts and minerals naturally present in such feeds. From a commercial standpoint, the multi-component nature, different forms and structures of biomass, all pose significant challenges for the utilization of biomass in the manufacture of fuels and chemicals. Consequently, the in and ex situ use of a host of additives and catalysts (including molecular sieves, metal oxides, and transition metal-modified oxides) is reviewed, which have been incorporated in order to provide selectivity in pyrolytic biomass upgrading.

Ab initio transition state searching in complex systems: fatty acid decarboxylation in minerals.

Because of the importance of mineral catalyzed decarboxylation reactions in both crude oil formation and, increasingly, biofuel production, we present a model study into the decarboxylation of the shortest fatty acid, propionic acid C(2)H(5)COOH, into an alkane and CO(2) catalyzed by a pyrophillite-like, phyllosilicate clay. To identify the decarboxylation pathway, we searched for a transition state between the reactant, comprised of the clay plus interlayer fatty acid, and the product, comprised of the clay plus interlayer alkane and carbon dioxide. Using linear and quadratic synchronous transit mechanisms we searched for a transition state followed by vibrational analysis to verify the intermediate found as a transition state. We employed a periodic cell, planewave, ab initio density functional theory computation to examine total energy differences, Mulliken charges, vibrational frequencies, and the frontier orbitals of the reactants, intermediates, and products. The results show that interpretation of vibrational data, Mulliken charges and Fermi-level orbital occupancies is necessary for the classification of a transition state in this type of mixed bulk surface plus interlayer species, clay-organic system.

Biodiesel production via trans-esterification using Pseudomonas cepacia immobilized on cellulosic polyurethane.

In this work, Pseudomonas cepacia lipase immobilized on cellulosic polyurethane was used as a catalyst for biodiesel production via trans-esterification reactions in order to provide cost-effective methods of enzyme recycling. The efficacy of the immobilized enzyme catalyst at low loading (6.2 wt %) and the effects of temperature, water content, and reaction time in model trans-esterification of glyceryl trioctanoate were investigated extensively. It was found that water was necessary for the reaction of glyceryl trioctanoate with ethanol to proceed. A high conversion of glyceryl trioctanoate (∼70%) was obtained at 35 °C, with only 5.0 wt % of water content over a reaction period of 12 h.