2008 Annual Science Report

Carnegie Institution of Washington Reporting  |  JUL 2007 – JUN 2008

4. Prebiotic Molecular Selection and Organization

Project Summary
4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

1. Molecular Selection and Organization on Mineral Surfaces

The group’s diverse studies in molecular selection focused on problems related to what molecules are adsorbed selectively onto what mineral surfaces. Collaborator Dimitri Sverjensky and coworkers conducted theoretical and experimental investigations of the surface properties of hydrous ferric oxide (HFO) and titanium dioxide, which form an end-member in the spectrum of mineralogical behavior corresponding to strong attachment of many adsorbates including biomolecules. Amino acids, the basic building blocks of proteins in all living matter, must have played a central role in life’s origins, but how were these small molecular building blocks selected, concentrated and assembled from the dilute prebiotic soup? The team’s research addresses how amino acids attach to mineral surfaces in the presence of water, about which very little is known. For decades, in studies of the origin of life on Earth, amino acid-mineral surface interactions have been suggested to play roles in determining chiral selection, i.e., the prominence of left-handed amino acids in proteins, and in facilitating the formation of the peptide bonds between amino acids that determine the backbone of proteins. In addition, the attachment of amino acids to mineral surfaces such as titanium dioxide plays a critical role in the viability of implants of metallic titanium in the human body. The first step of their research involves the integration of available experimental studies of amino acid attachment to metal oxide surfaces with separate spectroscopic studies that have aimed to identify the types of attached species. This is done by developing a quantitative theoretical model of the chemical reactions at the iron oxide-water interface involving the amino acid glutamate.
Sverjensky and coworkers find three different surface species of glutamate involved in the attachment (Figure 1). The proportions of these three vary according to the environmental conditions such as the pH and the amount of glutamate. Interestingly, at high levels of glutamate, their model predicts that the elongate glutamate molecules attach by one end only and “stand up” on the surface. The other ends of the glutamate molecules point away from the surface and are potentially able to interact with the free ends of adjacent glutamates. This alignment could provide a new mechanism of chiral selection and peptide bond formation. New experiments and calculations are underway to test this hypothesis.

In conjunction with the above work, Postdoctoral Fellow Caroline Jonsson, Doctoral Student Christopher Jonsson, and coworkers have studied the interaction of organic molecules on the surface of oxyhydroxide minerals in aqueous solution using titration methods. Previously published results utilizing attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS) showed that aspartic and glutamic acid adsorb on titanium dioxide in a similar manner. Both aspartic and glutamic acid bind predominantly in a bridging-bidentate fashion involving both carboxylate groups. However, a second species in which the ligand chelates titanium through the distal carboxylate group may be present at low pH and high surface coverage. Glutamic acid also forms a third mixed chelating-monodentate surface complex. New experimental adsorption data on a well-characterized titanium dioxide (rutile) surface support this theoretical model (Figure 2). The team concludes that adsorption of glutamate on the surface of rutile is strongest at low pH, and decreases with increasing pH. Adsorption on rutile can be explained by a surface complexation model using a chelating (“standing up”) and/or a mixed chelating-monodentate (“lying down”) surface complex. FTIR spectroscopic results suggest that glutamate adsorbs to the rutile surface through one or both of the carboxylate groups (COO) at pH 3.5, which supports the surface complexation model. This structural interpretation agrees with previous studies for glutamate on amorphous TiO2, which indicates a similarity between the two surfaces.

Throughout these studies the team’s central task has been to identify general trends in molecular adsorption on minerals. To this end, NAI Postdoctoral Fellow H. James Cleaves continued his ambitious program of “geochromatography,” which is the study of the differential adsorption of molecular mixtures onto polycrystalline rocks and minerals. The group’s preliminary results demonstrate dramatic selective adsorption of molecules in a complex suite of HCN polymers.
Cleaves and coworkers also have investigated the adsorption of nucleic acid components on rutile (TiO2) surfaces in water. Adsorption affinity varied greatly with molecular structure, with ribonucleotides > deoxyribonucleotides > ribonucleosides > deoxyribonucleosides > free nitrogenous bases, suggesting a role for both sugar and phosphate groups in adsorption. The base substituent also plays a role with pyrimidines > purines, and guanine derivatives > adenine derivatives. This suggests an interaction between the two-position substituent of the heterocyclic rings and the mineral surface, in addition to interactions between the sugar and phosphate moieties. We are continuing to study these phenomena as functions of pH as well as by FTIR spectroscopy and hope to eventually be able to fit these data to adsorption models.
In a continuation of studies on clay mineral adsorption of RNA trinucleotides, Collaborator GÖzen Ertem and coworkers investigated the possible catalytic role of minerals in the abiotic synthesis of biologically important molecules. In the presence of montmorillonite, a member of the phyllosilicate group minerals that are abundant on Earth and identified on Mars, activated RNA monomers, namely 5’-phosphorimidazolides of nucleosides (ImpNs), undergo condensation reactions in aqueous electrolyte solution producing oligomers with similar structures to short RNA fragments. Analysis of the linear trimer isomers formed in the reaction of binary mixtures of activated adenosine-cytidine and adenosine-uridine monomers (ImpA-ImpC and ImpA-ImpU, respectively) employing high-performance liquid chromatograpy (HPLC), selective enzymatic hydrolysis, and matrix-assisted laser desorption/ionization mass spectroscopy (MALDI-MS) molecular weight measurements demonstrate that montmorillonite catalysis facilitates the formation of hetero-isomers containing 56% A and 44% C-monomer and 61% A and 39% U monomer incorporated in their structure. 56-61% of the monomer units are linked together by RNA-like 3’,5’-phosphodiester bonds. These results support Bernal’s hypothesis proposing the possible catalytic role of minerals in the abiotic processes in the course of chemical evolution.

As part of ongoing studies of chiral selection on mineral surfaces, Hazen and coworkers investigated the selective adsorption of a chiral tricarboxylic acid on feldspar and calcite surfaces. Capillary electrophoresis (CE) with UV detection was used for the first time to determine the enantioselective adsorption of the short-chain tricarboxylic acid, 3-carboxy adipic acid on minerals as a means of investigating plausible mechanisms for the origin of biochemical homochirality on Earth. The use of vancomycine as chiral selector in the separation buffer using the partial filling technique enabled the separation of the two enantiomers of this low absorbent short-chain organic acid in about 12 min. In order to achieve the sensitivity needed to determine the enantiomeric excess of samples of 3-carboxy adipic acid adsorbed on minerals, Hazen and coworkers applied a strategy consisting of a field-amplified sample stacking together with the use of a bubble capillary and detection at low wavelengths (192 nm). This combination enabled the determination of the enantiomeric excess of 3-carboxy adipic acid adsorbed on calcite and feldspar mineral samples at concentration levels as low as a few nanomoles of compound.
2. Mineral Evolution
An essential question when examining the role of minerals in life’s origin is when specific minerals first appeared in Earth’s near-surface environments. For example, if borate minerals are invoked as essential templates for prebiotic chemical processes, then it is important to know when borate minerals first formed in evaporites. Accordingly, Hazen and coworkers have investigated “mineral evolution,” which is a new way to frame mineralogy in an historical context.
The mineralogy of terrestrial planets evolves as a consequence of a range of physical, chemical, and biological processes. In pre-stellar molecular clouds, widely dispersed microscopic dust particles contain approximately a dozen refractory minerals that represent the starting point of planetary mineral evolution. Gravitational clumping into a protoplanetary disk, star formation, and the resultant heating in the stellar nebula produce primary refractory constituents of chondritic meteorites, including chondrules and calcium-aluminum inclusions, with ~60 different mineral phases. Subsequent aqueous and thermal alteration of chondrites, asteroidal accretion and differentiation, and the consequent formation of achondrites result in a mineralogical repertoire limited to ~250 different minerals found in unweathered meteorite samples.
Following planetary accretion and differentiation, the initial mineral evolution of Earth’s crust depended on a sequence of geochemical and petrologic processes, including volcanism and degassing, fractional crystallization, crystal settling, assimilation reactions, regional and contact metamorphism, plate tectonics, and associated large-scale fluid-rock interactions. These processes produced the first continents with their associated granitoids and pegmatites, hydrothermal ore deposits, metamorphic terrains, evaporites, and zones of surface weathering, and resulted in an estimated 1500 different mineral species. According to some origin-of-life scenarios, a planet must progress through at least some of these stages of chemical processing as a prerequisite for life.
Biological processes began to affect Earth’s surface mineralogy by the Eoarchean (~3.85 – 3.6 Ga), when large-scale surface mineral deposits, including banded iron formations, were precipitated under the influences of changing atmospheric and ocean chemistry. The Paleoproterozoic “Great Oxidation Event” (~2.2 to 2.0 Ga), when atmospheric oxygen may have risen to >1% of modern levels, and the Neoproterozoic increase in atmospheric oxygen, which followed several major glaciation events, ultimately gave rise to multicellular life and skeletal biomineralization and irreversibly transformed Earth’s surface mineralogy. Biochemical processes may thus be responsible, directly or indirectly, for most of Earth’s 4300 known mineral species.
The ten stages of mineral evolution (Figure 3) arise from three primary mechanisms: (1) the progressive separation and concentration of the elements from their original relatively uniform distribution in the pre-solar nebula; (2) an increase in range of intensive variables such as pressure, temperature, and the activities of H2O, CO2, and O2; and (3) the generation of far from equilibrium conditions by living systems. The sequential evolution of Earth’s mineralogy from chondritic simplicity to Phanerozoic complexity introduces the dimension of geologic time to mineralogy and thus provides a dynamic alternate approach to framing, and to teaching, the mineral sciences. Of special interest to astrobiology, the concept of mineral evolution provides a way to categorize terrestrial planets and moons, and points to specific mineralogical targets, including biomarkers, of interest to planetary exploration.