Zwitterionic versus canonical amino acids over the various defects in zeolites: a two-layer ONIOM calculation

Chirality in Organic and Mineral Systems: A Review of Reactivity and Alteration Processes Relevant to Prebiotic Chemistry and Life Detection Missions

Chirality is a central feature in the evolution of biological systems, but the reason for biology’s strong preference for specific chiralities of amino acids, sugars, and other molecules remains a controversial and unanswered question in origins of life research. Biological polymers tend toward homochiral systems, which favor the incorporation of a single enantiomer (molecules with a specific chiral configuration) over the other. There have been numerous investigations into the processes that preferentially enrich one enantiomer to understand the evolution of an early, racemic, prebiotic organic world. Chirality can also be a property of minerals; their interaction with chiral organics is important for assessing how post-depositional alteration processes could affect the stereochemical configuration of simple and complex organic molecules. In this paper, we review the properties of organic compounds and minerals as well as the physical, chemical, and geological processes that affect organic and mineral chirality during the preservation and detection of organic compounds. We provide perspectives and discussions on the reactions and analytical techniques that can be performed in the laboratory, and comment on the state of knowledge of flight-capable technologies in current and future planetary missions, with a focus on organics analysis and life detection.

Amino acid encapsulation in zeolite MOR: Effect of spatial confinement

In this study the absorption of glycine, α-alanine and β-alanine amino acids into the pores of the synthetic zeolite Na-mordenite was investigated with the aim of: (i) evaluating the effectiveness of the MOR framework type in amino acid adsorption (via vapor and aqueous loading); (ii) understanding the host-guest and guest-guest interactions to possibly design a tailor made material and a loading procedure able to maximize the amino acid adsorption; (iii) studying the effect of pressure on the adsorbed amino acids such as, for instance, possible amino acid condensation. The structural characterization, carried out with the combination of diffractometric and infrared spectroscopy analyses, shows that MOR can adsorb amino acids, which are found both in protonated/deprotonated (possibly also generating zwitterions) form. Vapor loading is ineffective for α-alanine, while it is effective in β-alanine and glycine adsorption, even if using different loading degrees. The shape and size of MOR channels make this zeolite suitable to accommodate a peptide. In a glycine loaded sample some molecules condensate to form cyclic dimers, while linear oligomers are detected only in a β-alanine MOR hybrid. The sample loaded with α-L-alanine from aqueous solution does not show the presence of amide bond signals, indicating that the molecules are mostly hosted in zwitterionic form in Na-MOR channels. The application of external baric stimuli does not induce substantial modifications in the structure of the glycine loaded zeolite; this result may be explained by the low number of molecules hosted in the channels. The amino acid amount within the zeolite pores is the most important reactivity parameter and an increased loading could induce chemical modifications.

Active Sites of M(IV)-incorporated Zeolites (M = Sn, Ti, Ge, Zr)

M(IV)-incorporated zeolites have recently aroused wide interest due to outstanding catalytic effects while their active sites remain largely elusive. Here periodic density functional theory calculations are conducted finding that active sites are determined jointly by identity of M(IV) ions, topology of zeolites, type of framework species and choice of T sites. All M2(IV) active sites in BEA zeolites are penta-coordinated with chemisorption of one water while subsequent water molecules that form only H-bonds promote chemisorption of the first water, especially the second water possessing comparable or even higher adsorption strengths as the first water; Ti(IV) and Ge(IV) active sites at the intersection remain penta-coordinated and Sn(IV) and Zr(IV) active sites prefer to hexa-coordination although potentially expanded to hepta-coordination. Different from other zeolites, Ti(IV) active sites in FER zeolites are hexa-coordinated as Sn(IV) active sites, due to the promoting effect of the first water. Lewis acidic defects expand Ti(IV) active sites to hexa-coordination while inhibit the formation of hepta-coordinated Sn(IV) species. Two forms of Brϕnsted acidic defects exist for Sn(IV) sites instead of only one for Ti(IV) sites, and all M(IV) Brϕnsted acidic defects, regardless of different acidic forms and M(IV) ions, can chemisorb only one water.

Stabilization of zwitterionic versus canonical proline by water molecules

At physiological conditions, a majority of biomolecules (e.g., amino acids, peptides and proteins) exist predominantly in the zwitterionic form that usually decides the biological functions. However, zwitterionic amino acids are not geometrically stable in gas phase and this seriously hampers the understanding of their structures, properties and biological functions. To this end, one of the recent research focuses is to demonstrate the stabilization effects of zwitterionic amino acids. Relative stabilities of canonical conformers are dependent on water contents, while zwitterionic stability improves monotonously and pronouncedly with increase of water contents. We find that one water molecule can render zwitterionic proline geometrically stable, and stabilities of different zwitterionic amino acids increase as glycine  Collapse

Key Words

• Conformational analysis
• Density functional calculations
• H-bonds
• Zwitterionic stabilization

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MESH Headings Collapse

Grants

• National Natural Science Foundation of China

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Affiliation(s)

Gang Yang />College of Resource and Environment and Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, Southwest University, 400715 Chongqing, People’s Republic of China
Lijun Zhou />College of Resource and Environment and Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, Southwest University, 400715 Chongqing, People’s Republic of China
Yang Chen />College of Chemistry Chemical Engineering and Environmental Engineering, Liaoning Shihua University, 113001 Fushun, Liaoning People’s Republic of China

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Adsorption of fructose in Sn-BEA zeolite from periodic density functional calculations

Sn-BEA zeolite selects fructose conformers from biochemically relevant polysaccharides rather than gas phase, and dispersion effects contribute significantly during interactions.

Disruptive catalysis by zeolites

Emerging concepts and novel possibilities in catalysis by zeolites for a new scenario in chemical and energy vector production.

Promoting the Adsorption of Metal Ions on Kaolinite by Defect Sites: A Molecular Dynamics Study

Defect sites exist abundantly in minerals and play a crucial role for a variety of important processes. Here molecular dynamics simulations are used to comprehensively investigate the adsorption behaviors, stabilities and mechanisms of metal ions on defective minerals, considering different ionic concentrations, defect sizes and contents. Outer-sphere adsorbed Pb²⁺ ions predominate for all models (regular and defective), while inner-sphere Na⁺ ions, which exist sporadically only at concentrated solutions for regular models, govern the adsorption for all defective models. Adsorption quantities and stabilities of metal ions on kaolinite are fundamentally promoted by defect sites, thus explaining the experimental observations. Defect sites improve the stabilities of both inner- and outer-sphere adsorption, and (quasi) inner-sphere Pb²⁺ ions emerge only at defect sites that reinforce the interactions. Adsorption configurations are greatly altered by defect sites but respond weakly by changing defect sizes or contents. Both adsorption quantities and stabilities are enhanced by increasing defect sizes or contents, while ionic concentrations mainly affect adsorption quantities. We also find that adsorption of metal ions and anions can be promoted by each other and proceeds in a collaborative mechanism. Results thus obtained are beneficial to comprehend related processes for all types of minerals.

Origin of Hofmeister Effects for Complex Systems

Hofmeister effects have been recognized as important as Mendel’s work was to genetics while remain largely controversial, especially for the mechanistic aspects. Here we demonstrated that complex colloids in electrolyte solutions show resembling aggregation kinetics as model colloid, and then quantitatively evaluated the resulting Hofmeister effects. Mechanism for the aggregation of complex colloids has been proposed that is closely associated with the charges of their constituents; despite that, electrostatic interactions play a minor role while polarization effect is evidenced to be the driving force for the aggregation processes. Polarization effect is further ascribed to arouse the resulting Hofmeister effects, which is supported by the fine correlation of activation energies vs. polarizability data of different alkali ions and the calculations of dipole moments for minerals with different charges and adsorbed alkali ions. Because of neglecting polarization effect, the prevailing DLVO theory is not sufficient to describe Hofmeister effects that are ubiquitous in nature. We speculate that polarization effect should also be responsible for Hofmeister effects of other charged systems such as proteins and membranes.