Solution-state behaviour of algal mono-uronates evaluated by pure shift and compressive sampling NMR techniques.

Sodium salts of the algal uronic-acids, d-mannuronic acid (HManA) and l-guluronic acid (HGulA) have been isolated and characterised in solution by nuclear magnetic resonance (NMR) spectroscopy. A suite of recently-described NMR experiments (including pure shift and compressive sampling techniques) were used to provide confident assignments of the pyranose forms of the two uronic acids at various pD values (from 7.5 to 1.4). The resulting high resolution spectra were used to determine several previously unknown parameters for the two acids, including their pKa values, the position of their isomeric equilibria, and their propensity to form furanurono-6,3-lactones. For each of the three parameters, comparisons are drawn with the behaviour of the related D-glucuronic (HGlcA) and D-galacturonic acids (HGalA), which have been previously studied extensively. This paper demonstrates how these new NMR spectroscopic techniques can be applied to better understand the properties of polyuronides and uronide-rich macroalgal biomass.

Decoupling a novel Trichormus variabilis-Synechocystis sp. interaction to boost phycoremediation.

To conserve freshwater resources, domestic and industrial wastewater is recycled. Algal systems have emerged as an efficient, low-cost option for treatment (phycoremediation) of nutrient-rich wastewater and environmental protection. However, industrial wastewater may contain growth inhibitory compounds precluding algal use in phycoremediation. Therefore, extremophyte strains, which thrive in hostile environments, are sought-after. Here, we isolated such an alga - a strain of Synechocystis sp. we found to be capable of switching from commensal exploitation of the nitrogen-fixing Trichormus variabilis, for survival in nitrogen-deficient environments, to free-living growth in nitrate abundance. In nitrogen depletion, the cells are tethered to polysaccharide capsules of T. variabilis using nanotubular structures, presumably for nitrate acquisition. The composite culture failed to establish in industrial/domestic waste effluent. However, gradual exposure to increasing wastewater strength over time untethered Synechocystis cells and killed off T. variabilis. This switched the culture to a stress-acclimated monoculture of Synechocystis sp., which rapidly grew and flourished in wastewater, with ammonium and phosphate removal efficiencies of 99.4% and 97.5%, respectively. Therefore, this strain of Synechocystis sp. shows great promise for use in phycoremediation, with potential to rapidly generate biomass that can find use as a green feedstock for valuable bio-products in industrial applications.

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.

Influence of surface chemistry and charge on mineral-RNA interactions.

We present the results of large-scale molecular simulations, run over several tens of nanoseconds, of 25-mer sequences of single-stranded ribonucleic acid (RNA) in bulk water and at the surface of three hydrated positively charged MgAl layered double hydroxide (LDH) minerals. The three LDHs differ in surface charge density, through varying the number of isomorphic Al substitutions. Over the course of the simulations, RNA adsorbs tightly to the LDH surface through electrostatic interactions between the charged RNA phosphate groups and the alumina charge sites present in the LDH sheet. The RNA strands arrange parallel to the surface with the base groups aligning normal to the surface and exposed to the bulk aqueous region. This templating effect makes LDH a candidate for amplifying the population of a known RNA sequence from a small number of RNAs. The structure and interactions of RNA at a positively charged, hydroxylated LDH surface were compared with those of RNA at a positively charged calcium montmorillonite surface, allowing us to establish the comparative effect of complexation and water structure at hydroxide and silicate surfaces. The systems were studied by computing radial distribution functions, atom density plots, and radii of gyration, as well as visualization. An observation pertinent to the role of these minerals in prebiotic chemistry is that, for a given charge density on the mineral surface, different genetic sequences of RNA adopt different configurations.

Theory, modelling and simulation in origins of life studies.

Origins of life studies represent an exciting and highly multidisciplinary research field. In this review we focus on the contributions made by theory, modelling and simulation to addressing fundamental issues in the domain and the advances these approaches have helped to make in the field. Theoretical approaches will continue to make a major impact at the "systems chemistry" level based on the analysis of the remarkable properties of nonlinear catalytic chemical reaction networks, which arise due to the auto-catalytic and cross-catalytic nature of so many of the putative processes associated with self-replication and self-reproduction. In this way, we describe inter alia nonlinear kinetic models of RNA replication within a primordial Darwinian soup, the origins of homochirality and homochiral polymerization. We then discuss state-of-the-art computationally-based molecular modelling techniques that are currently being deployed to investigate various scenarios relevant to the origins of life.

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.

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.

Clay minerals mediate folding and regioselective interactions of RNA: a large-scale atomistic simulation study.

Since a mineral-mediated origin of life was first hypothesized over 60 years ago, clays have played a significant role in origins of life studies. Such studies have hitherto rarely used computer simulation to understand the possible chemical pathways to the formation of biomolecules. We use molecular dynamics techniques, performed on supercomputing grids, to carry out large-scale simulations of various 25-mer sequences of ribonucleic acid (RNA), in bulk water and with aqueous montmorillonite clay over many tens of nanoseconds. Hitherto, there has only been limited experimental data reported for these systems. Our simulations are found to be in agreement with various experimental observations pertaining to the relative adsorption of RNA on montmorillonite in the presence of charge balancing cations. Over time scales of only a few nanoseconds, specific RNA sequences fold to characteristic secondary structural motifs, which do not form in the corresponding bulk water simulations. Our simulations also show that, in aqueous Ca(2+) environments, RNA can tether to the clay surface through a nucleotide base, leaving the 3'-end of the strand exposed, providing a mechanism for the regiospecific adsorption and elongation of RNA oligomers on clay surfaces.

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.

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.

A critical appraisal of polymer-clay nanocomposites.

The surge of interest in and scientific publications on the structure and properties of nanocomposites has made it rather difficult for the novice to comprehend the physical structure of these new materials and the relationship between their properties and those of the conventional range of composite materials. Some of the questions that arise are: How should the reinforcement volume fraction be calculated? How can the clay gallery contents be assessed? How can the ratio of intercalate to exfoliate be found? Does polymerization occur in the clay galleries? How is the crystallinity of semi-crystalline polymers affected by intercalation? What role do the mobilities of adsorbed molecules and clay platelets have? How much information can conventional X-ray diffraction offer? What is the thermodynamic driving force for intercalation and exfoliation? What is the elastic modulus of clay platelets? The growth of computer simulation techniques applied to clay materials has been rapid, with insight gained into the structure, dynamics and reactivity of polymer-clay systems. However these techniques operate on the basis of approximations, which may not be clear to the non-specialist. This critical review attempts to assess these issues from the viewpoint of traditional composites thereby embedding these new materials in a wider context to which conventional composite theory can be applied. (210 references).