Characterization of the Adsorption of Nucleic Acid Bases onto Ferrihydrite via Fourier Transform Infrared and Surface-Enhanced Raman Spectroscopy and X-ray Diffractometry

The role of organic and inorganic substituents of roxarsone determines its binding behavior and mechanisms onto nano-ferrihydrite colloidal particles

The retention and fate of Roxarsone (ROX) onto typical reactive soil minerals were crucial for evaluating its potential environmental risk. However, the behavior and molecular-level reaction mechanism of ROX and its substituents with iron (hydr)oxides remains unclear. Herein, the binding behavior of ROX on ferrihydrite (Fh) was investigated through batch experiments and in-situ ATR-FTIR techniques. Our results demonstrated that Fh is an effective geo-sorbent for the retention of ROX. The pseudo-second-order kinetic and the Langmuir model successfully described the sorption process. The driving force for the binding of ROX on Fh was ascribed to the chemical adsorption, and the rate-limiting step is simultaneously dominated by intraparticle and film diffusion. Isotherms results revealed that the sorption of ROX onto Fh appeared in uniformly distributed monolayer adsorption sites. The two-dimensional correlation spectroscopy and XPS results implied that the nitro, hydroxyl, and arsenate moiety of ROX molecules have participated in binding ROX onto Fh, signifying that the predominated mechanisms were attributed to the hydrogen bonding and surface complexation. Our results can help to better understand the ROX-mineral interactions at the molecular level and lay the foundation for exploring the degradation, transformation, and remediation technologies of ROX and structural analog pollutants in the environment.

Unexpected Thiocyanate Adsorption onto Ferrihydrite Under Prebiotic Chemistry Conditions

The most crucial role played by minerals was in the preconcentration of biomolecules or precursors of biomolecules in prebiotic seas. If this step had not occurred, molecular evolution would not have occurred. Thiocyanate is an important molecule in the formation of biomolecules as well as a catalyst for prebiotic reactions. The adsorption of thiocyanate onto ferrihydrite was carried out under pH and ion composition conditions in seawater that resembled those of prebiotic Earth. The seawater used in this work had high Mg²⁺, Ca²⁺ and SO₄^2- concentrations. The most important result of this work was that ferrihydrite adsorbed thiocyanateata pH value (7.2 ± 0.2) that usually does not adsorb thiocyanate. The high adsorptivity of Mg²⁺, Ca²⁺ and SO₄^2-onto ferrihydrite showed that seawater ions can act as carriers of thiocyanate to the ferrihydrite surface, creating a huge outer-sphere complex. Kinetic adsorption and isotherm experiments showed the best fit for the pseudo-second-order model and an activation energy of 23.8 kJ mol^-1forthe Langmuir-Freundlich model, respectively. Thermodynamic data showed positive ΔG values, which apparently contradict the adsorption isotherm data and kinetic data that was obtained. The adsorption of thiocyanate onto ferrihydrite could be explained by coupling with the exergonic SO₄^2- adsorption onto ferrihydrite. The FTIR spectra showed no difference between the C≡N stretching peaks of adsorbed thiocyanate and free thiocyanate, corroborating the formation of an outer-sphere complex. All the results demonstrated the importance of the artificial seawater composition for the adsorption of thiocyanate and for understanding prebiotic chemistry.

Abiotic phosphorus recycling from adsorbed ribonucleotides on a ferrihydrite-type mineral: Probing solution and surface species

Iron (Fe) (oxyhydr)oxide minerals, which are amongst most reactive minerals in soils and sediments, are known to exhibit strong adsorption of inorganic phosphate (P_i) and organophosphate (P_o) compounds. Beyond synthetic P_o compounds, much still remains unknown about the reactivity of these minerals to transform naturally-occurring P_o compounds to P_i, particularly with respect to solution versus surface speciation of P_o hydrolysis. To investigate this reactivity with a ferrihydrite-type mineral and ribonucleotides, we employed high-resolution liquid chromatography-mass spectrometry (LC-MS), X-ray absorption near-edge structure (XANES), Fourier-transform infrared (FTIR) spectroscopy, and molecular modeling. Kinetic experiments were conducted with the mineral (1 g L^-1) reacted with adenosine monophosphate, diphosphate, or triphosphate (respectively AMP, ADP, ATP; 50 µM). Analysis of solution organic species by LC-MS implied that only adsorption occurred with AMP and ADP but both adsorption and dephosphorylation of ATP were evident. Maximum adsorption capacities per gram of mineral were 40.6 ± 0.8 µmol AMP, 35.7 ± 1.6 µmol ADP, and 10.9 ± 1.0 µmol ATP; solution dephosphorylated by-products accounted for 15% of initial ATP. Subsequent XANES analysis of the surface species revealed that 16% of adsorbed AMP and 30% of adsorbed ATP were subjected to dephosphorylation, which was not fully quantifiable from the solution measurements. Molecular simulations predicted that ADP and ATP were complexed mainly via the phosphate groups whereas AMP binding also involved multiple hydrogen bonds with the adenosine moiety; our FTIR data confirmed these binding confirmations. Our findings thus imply that specific adsorption mechanisms dictate the recycling and subsequent trapping of P_i from ribonucleotide-like biomolecules reacted with Fe (oxyhydr)oxide minerals.

Mineral Facilitated Horizontal Gene Transfer: A New Principle for Evolution of Life?

A number of studies have highlighted that adsorption to minerals increases DNA longevity in the environment. Such DNA-mineral associations can essentially serve as pools of genes that can be stored across time. Importantly, this DNA is available for incorporation into alien organisms through the process of horizontal gene transfer (HGT). Here we argue that minerals hold an unrecognized potential for successfully transferring genetic material across environments and timescales to distant organisms and hypothesize that this process has significantly influenced the evolution of life. Our hypothesis is illustrated in the context of the evolution of early microbial life and the oxygenation of the Earth's atmosphere and offers an explanation for observed outbursts of evolutionary events caused by HGT.

Salinity Effects on the Adsorption of Nucleic Acid Compounds on Na-Montmorillonite: a Prebiotic Chemistry Experiment

Any proposed model of Earth's primitive environments requires a combination of geochemical variables. Many experiments are prepared in aqueous solutions and in the presence of minerals. However, most sorption experiments are performed in distilled water, and just a few in seawater analogues, mostly inconsistent with a representative primitive ocean model. Therefore, it is necessary to perform experiments that consider the composition and concentration of dissolved salts in the early ocean to understand how these variables could have affected the absorption of organic molecules into minerals. In this work, the adsorption of adenine, adenosine, and 5'AMP onto Na+montmorillonite was studied using a primitive ocean analog (4.0 Ga) from experimental and computational approaches. The order of sorption of the molecules was: 5'AMP > adenine > adenosine. Infrared spectra showed that the interaction between these molecules and montmorillonite occurs through the NH2 group. In addition, electrostatic interaction between negatively charged montmorillonite and positively charge N1 of these molecules could occur. Results indicate that dissolved salts affect the sorption in all cases; the size and structure of each organic molecule influence the amount sorbed. Specifically, the X-ray diffraction patterns show that dissolved salts occupy the interlayer space in Na-montmorillonite and compete with organic molecules for available sites. The adsorption capacity is clearly affected by dissolved salts in thermodynamic terms as deduced by isotherm models. Indeed, molecular dynamic models suggest that salts are absorbed in the interlamellar space and can interact with oxygen atoms exposed in the edges of clay or in its surface, reducing the sorption of the organic molecules. This research shows that the sorption process could be affected by high concentration of salts, since ions and organic molecules may compete for available sites on inorganic surfaces. Salt concentration in primitive oceans may have strongly affected the sorption, and hence the concentration processes of organic molecules on minerals.

Interaction, at Ambient Temperature and 80 °C, between Minerals and Artificial Seawaters Resembling the Present Ocean Composition and that of 4.0 Billion Years Ago

Probably one of the most important roles played by minerals in the origin of life on Earth was to pre-concentrate biomolecules from the prebiotic seas. There are other ways to pre concentrate biomolecules such as wetting/drying cycles and freezing/sublimation. However, adsorption is most important. If the pre-concentration did not occur-because of degradation of the minerals-other roles played by them such as protection against degradation, formation of polymers, or even as primitive cell walls would be seriously compromised. We studied the interaction of two artificial seawaters with kaolinite, bentonite, montmorillonite, goethite, ferrihydrite and quartz. One seawater has a major cation and anion composition similar to that of the oceans of the Earth 4.0 billion years ago (ASW 4.0 Ga). In the other, the major cations and anions are an average of the compositions of the seawaters of today (ASWT). When ASWT, which is rich in Na+ and Cl-, interacted with bentonite and montmorrilonite structural collapse occurred on the 001 plane. However, ASW 4.0 Ga, which is rich in Mg2+ and SO42-, did not induce this behavior. When ASW 4.0 Ga was reacted with the minerals for 24 h at room temperature and 80 °C, the release of Si and Al to the fluid was below 1 % of the amount in the minerals-meaning that dissolution of the minerals did not occur. In general, minerals adsorbed Mg2+ and K+ from the ASW 4.0 Ga and these cations could be used for the formation of polymers. Also, when the minerals were mixed with ASW 4.0 Ga at 80 °C and ASWT at room temperature or 80 °C it caused the precipitation of CaSO4∙2H2O and halite, respectively. Finally, further experiments (adsorption, formation of polymers, protection of molecules against degradation, primitive cell wall formation) performed under the conditions described in this paper will probably be more representative of what happened on the prebiotic Earth.

A comparative study on the experimental and calculated results of mid-infrared and Raman vibrational modes of nucleic acid bases

The MIR (mid-infrared) and Raman spectra of the nucleic acid base powders were tested by Fourier transform infrared spectroscopy and laser Raman spectroscopy. The vibrational modes of nucleic acid base crystals were simulated by the generalized energy-based fragmentation approach under periodic boundary conditions (hereinafter referred as PBC-GEBF) together with Guassian09 software. Taking into account the intermolecular hydrogen bonds in the unit cell and the weak interactions between the unit cells, the PBC-GEBF method adopted by our group was for the first time used for calculating nucleic acid base crystals in the 400-2000cm^-1 band. The theoretical and experimental spectra turn out to be in good agreement with each other. Compared with the calculated results of the nucleic acid base monomer, the calculated results of crystals appear to be in better agreement with the experimental results. Some weak vibration peaks were reproduced by simulation, and the positions of the vibration peaks agree well. By analyzing the vibrational modes, it can be observed that the vibrational modes below 1000 cm^-1 are mainly characterized by the collective vibrations involving all the molecules in the unit cell. In addition to intramolecular interactions, weak intermolecular interactions (including Van der Waals force and weak hydrogen bond) and the lattice stacking force also contribute to the overall vibrations. This study is of great importance to the analysis of the stability of RNA/DNA structures and their genetic properties.