Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars

Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like merging, splitting, and isomerisation of molecules. It is often convenient, in particular in the analysis of larger systems, to summarize several subsequent reactions into a single composite chemical reaction. We use a generic approach for composing graph grammar rules to define a chemically useful rule compositions. We iteratively apply these rule compositions to elementary transformations in order to automatically infer complex transformation patterns. This is useful for instance to understand the net effect of complex catalytic cycles such as the Formose reaction. The automatically inferred graph grammar rule is a generic representative that also covers the overall reaction pattern of the Formose cycle, namely two carbonyl groups that can react with a bound glycolaldehyde to a second glycolaldehyde. Rule composition also can be used to study polymerization reactions as well as more complicated iterative reaction schemes. Terpenes and the polyketides, for instance, form two naturally occurring classes of compounds of utmost pharmaceutical interest that can be understood as "generalized polymers" consisting of five-carbon (isoprene) and two-carbon units, respectively

Incorporation of Nitrogen into Organics Produced by Fischer-Tropsch Type Chemistry

Laboratory simulations have demonstrated that hydrothermal systems have the potential to produce a range of organic compounds through Fischer-Tropsch type (FTT) chemistry. The distribution of products depends on several factors, including the abundance and composition of feed-stock molecules, reaction temperature, and the physical and chemical characteristics of catalytic materials included in the reactions. The majority of studies per-formed to date have focused solely on inclusion of CO2 or CO and H2 as the carbon, oxygen and hydrogen sources, which limits the possible products to hydro-carbons, alcohols and carboxylic acids. A few studies have included nitrogen in the form of ammonia, which led to the production of amino acids and nitrogenous bases; and a separate suite of studies included sulfur as sulfide minerals or H2S, which yielded products such as thiols and amino acids. Although these demonstrations provide compelling evidence that FTT reactions can produce compounds of interest for the origins of life, such reactions have been conducted under a very limited range of conditions and the synthetic reaction mechanisms have generally not been well-characterized. As a consequence, it is difficult to extrapolate these results to geologic systems or to evaluate how variations in reactant compositions would affect the distribution of products over time. We have begun a series of laboratory experiments that will incorporate a range of precursor molecules in varying compositions to determine how these variables affect the relative amounts and speciation of life-essential elements in organic molecules produced under FTT conditions. In the present work, we focus on systems containing C, H, O and N

A route to anionic hydrophilic films of copolymers of l-leucine, l-aspartic acid and l-aspartic acid esters

A series of copolymers of l-leucine and β-benzyl-l-aspartate [Leu/Asp(OBz)] covering the range 30–70 mol % of l-leucine, was synthesized by the N-carboxyanhydride (NCA) method. The copolymers were characterized by elemental analysis, infra-red spectroscopy and viscometry. For all compositions high molecular weight copolymers were prepared with excellent film-forming properties. Tercopolymers of l-leucine, β-benzyl-l-aspartate and β-methyl-l-aspartate [Leu/Asp(OBz)/Asp(OMe)] were obtained after an ester interchange reaction (conversion 85–95%) with the original copolymer systems. These tercopolymers were characterized by elemental analysis and i.r. spectroscopy. Films of the tercopolymers, cast from organic solvents, could be converted into hydrophilic films by saponification of the methyl ester groups using alkaline water/organic solvent media. The hydrophilic films, which will be further investigated for their use as haemodialysis membranes were characterized by potentiometric titration and i.r. spectroscopy

Assessment of the Al–Fe–Ti system

The Al–Fe–Ti system has been assessed and the limiting binary systems are shortly reviewed. Based on a thorough review of the literature, isotherms at 800, 900, and 1000 °C have been re-evaluated and a provisional isotherm at 1200 °C is presented for the first time. The effect of alloying the binary phases with the third component is reviewed with regard to the ternary homogeneity ranges, crystallography, order/disorder transformations, and site occupancies. Of the variously reported ternary compounds only the existence of “Al2FeTi” (τ2) and “Al8FeTi3” (τ3) is confirmed. The occurrence of the phases τ2*, τ′2, and of a new stacking variant of TiAl is still under discussion, while the existence of the phases Fe2AlTi (τ1) and Fe25Al69Ti6 (X) is ruled out. The presented reaction scheme corroborates the isothermal sections and also a representation of the liquidus surface is given. Magnetic, electrical, thermochemical, atomistic and diffusion data for Al–Fe–Ti alloys are summarised and an overview about studies on modelling of phase equilibria and phase transformations is given

The role of high- and low-temperature ocean crust alteration for the marine calcium budget

Calcium (Ca) is a key element for the understanding of the chemical evolution of the ocean and for the global climate on long geological time scales. This is because Ca is interacting with the carbon cycle and is a major constituent of continental weathering. Beside continental runoff, mid-ocean ridges are of quantitative importance for the marine Ca elemental and isotope budget. Variations of hydrothermal circulation of seawater through oceanic crust have been recognized to play a significant role for the oceanic Ca mass and isotope balance. Hydrothermal activity leads to a chemical alteration of the circulating seawater at low- and high temperatures during water-rock interaction, the formation of Ca-bearing minerals, and during phase separation. Within the framework of the subproject 'CARLA' in the 'Special Priority Program SPP 1144' Ca isotope ratios (d44/40Ca) in hydrothermal fluids sampled from the Logatchev hydrothermal field (15°N/45°W) and the Ascension area (4 11°S) have been investigated in detail in order to further constrain the global Ca cycling

PADAMOT : project overview report

Background and relevance to radioactive waste management International consensus confirms that placing radioactive wastes and spent nuclear fuel deep underground in a geological repository is the generally preferred option for their long-term management and disposal. This strategy provides a number of advantages compared to leaving it on or near the Earth’s surface. These advantages come about because, for a well chosen site, the geosphere can provide: • a physical barrier that can negate or buffer against the effects of surface dominated natural disruptive processes such as deep weathering, glaciation, river and marine erosion or flooding, asteroid/comet impact and earthquake shaking etc. • long and slow groundwater return pathways from the facility to the biosphere along which retardation, dilution and dispersion processes may operate to reduce radionuclide concentration in the groundwater. • a stable, and benign geochemical environment to maximise the longevity of the engineered barriers such as the waste containers and backfill in the facility. • a natural radiation shield around the wastes. • a mechanically stable environment in which the facility can be constructed and will afterwards be protected. • an environment which reduces the likelihood of the repository being disturbed by inadvertent human intrusion such as land use changes, construction projects, drilling, quarrying and mining etc. • protection against the effects of deliberate human activities such as vandalism, terrorism and war etc. However, safety considerations for storing and disposing of long-lived radioactive wastes must take into account various scenarios that might affect the ability of the geosphere to provide the functionality listed above. Therefore, in order to provide confidence in the ability of a repository to perform within the deep geological setting at a particular site, a demonstration of geosphere “stability” needs to be made. Stability is defined here to be the capacity of a geological and hydrogeological system to minimise the impact of external influences on the repository environment, or at least to account for them in a manner that would allow their impacts to be evaluated and accounted for in any safety assessments. A repository should be sited where the deep geosphere is a stable host in which the engineered containment can continue to perform according to design and in which the surrounding hydrogeological, geomechanical and geochemical environment will continue to operate as a natural barrier to radionuclide movement towards the biosphere. However, over the long periods of time during which long-lived radioactive wastes will pose a hazard, environmental change at the surface has the potential to disrupt the stability of the geosphere and therefore the causes of environmental change and their potential consequences need to be evaluated. As noted above, environmental change can include processes such as deep weathering, glaciation, river and marine erosion. It can also lead to changes in groundwater boundary conditions through alternating recharge/discharge relationships. One of the key drivers for environmental change is climate variability. The question then arises, how can geosphere stability be assessed with respect to changes in climate? Key issues raised in connection with this are: • What evidence is there that 'going underground' eliminates the extreme conditions that storage on the surface would be subjected to in the long term? • How can the additional stability and safety of the deep geosphere be demonstrated with evidence from the natural system? As a corollary to this, the capacity of repository sites deep underground in stable rock masses to mitigate potential impacts of future climate change on groundwater conditions therefore needs to be tested and demonstrated. To date, generic scenarios for groundwater evolution relating to climate change are currently weakly constrained by data and process understanding. Hence, the possibility of site-specific changes of groundwater conditions in the future can only be assessed and demonstrated by studying groundwater evolution in the past. Stability of groundwater conditions in the past is an indication of future stability, though both the climatic and geological contexts must be taken into account in making such an assertion