Anab initiostudy of adsorption of alanine on the chiral calcite surface

Search for Chirality in Hydrogenated Magnesium Nanosilicates: A DFT and TD-DFT Investigation

The formation of silicate grains in the interstellar medium (ISM), especially those containing chiral surfaces such as clinopyroxenes, is poorly understood. Moreover, silicate interactions with various forms of hydrogen-proton (H+), neutral H (HI), and molecular hydrogen (H2) are of high importance as hydrogen comprises >90% of the ISM gas budget, and these species play important roles in the formation of new molecules in space. Furthermore, silicate surfaces catalyze the formation of H2 in the interstellar medium formed on dust grain surfaces by H-H association. The technical difficulty of in situ laboratory investigations of nanosilicate nucleation using astrophysically relevant environmental conditions makes computational chemistry a useful tool for studying potential nanosilicate structures. Furthermore, chiral surfaces interacting with chiral organic molecules could serve as templates that lead to the enantiomeric excess of l-amino acids and d-polyols detected in carbonaceous meteorites. However, in order for this effect to take place, an excess of one chiral form of a mineral is required to break the symmetry. This symmetry-breaking event could have been due to the asymmetric absorption of circularly polarized light by the nanosilicate as it traverses star-forming regions. We investigate this possibility using a metastable chiral form of an enstatite dimer as an input for density functional theory (DFT) and time-dependent (TD)-DFT calculations to obtain various properties and circular dichroism spectra. All in all, twenty-six magnesium nanosilicate structures were studied using varying degrees of hydrogenation: none, with HI, with H+, and with H2. The HSE06/aug-cc-pVQZ level of theory was used for the DFT calculations. TD-DFT calculations utilized the CAM-B3LYP/cc-pVQZ and ωB97X-D3/cc-pVQZ functional and basic set pairings. Results show that (1) all twenty-six structures have absorption bands that fall within the 0.6-28.3 μm range available with the newly launched James Webb Space Telescope and (2) there is a small enantioselective effect by UV-CPL on the eight chiral enstatite dimers (predicted g-values of up to 0.007). While the observed effect is small, it opens up the possibility that it is the inorganic material that becomes enantiomerically biased by UV-CPL, driving chiral enhancements in meteoric organic molecules.

Possible chemical and physical scenarios towards biological homochirality

The single chirality of biological molecules in terrestrial biology raises more questions than certitudes about its origin. The emergence of biological homochirality (BH) and its connection with the appearance of life have elicited a large number of theories related to the generation, amplification and preservation of a chiral bias in molecules of life under prebiotically relevant conditions. However, a global scenario is still lacking. Here, the possibility of inducing a significant chiral bias "from scratch", i.e. in the absence of pre-existing enantiomerically-enriched chemical species, will be considered first. It includes phenomena that are inherent to the nature of matter itself, such as the infinitesimal energy difference between enantiomers as a result of violation of parity in certain fundamental interactions, and physicochemical processes related to interactions between chiral organic molecules and physical fields, polarized particles, polarized spins and chiral surfaces. The spontaneous emergence of chirality in the absence of detectable chiral physical and chemical sources has recently undergone significant advances thanks to the deracemization of conglomerates through Viedma ripening and asymmetric auto-catalysis with the Soai reaction. All these phenomena are commonly discussed as plausible sources of asymmetry under prebiotic conditions and are potentially accountable for the primeval chiral bias in molecules of life. Then, several scenarios will be discussed that are aimed to reflect the different debates about the emergence of BH: extra-terrestrial or terrestrial origin (where?), nature of the mechanisms leading to the propagation and enhancement of the primeval chiral bias (how?) and temporal sequence between chemical homochirality, BH and life emergence (when?). Intense and ongoing theories regarding the emergence of optically pure molecules at different moments of the evolution process towards life, i.e. at the levels of building blocks of Life, of the instructed or functional polymers, or even later at the stage of more elaborated chemical systems, will be critically discussed. The underlying principles and the experimental evidence will be commented for each scenario with particular attention on those leading to the induction and enhancement of enantiomeric excesses in proteinogenic amino acids, natural sugars, and their intermediates or derivatives. The aim of this review is to propose an updated and timely synopsis in order to stimulate new efforts in this interdisciplinary field.

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.

Calcite Scale Inhibition Using Environmental-Friendly Amino Acid Inhibitors: DFT Investigation

Scale prevention is a long-term challenge. It is essential for ensuring the optimum utilization of oil and gas wells and minimizing economic losses due to disruptions in the hydrocarbon flow. Among the commonly precipitated scales is calcite, especially in oilfield production facilities. Previous studies on scale inhibitors have focused on investigating the performance of several phosphonates and carboxylates. However, the increased environmental awareness has pushed toward investigating environmental-friendly inhibitors. Research studies demonstrated the potential of using amino acids as standalone inhibitors or as inhibitor-modifying reagents. In this study, 10 amino acids for calcite inhibitors have been investigated using molecular simulations. Eco-toxicity, quantum chemical calculations, binding energy, geometrical, and charge analyses were all evaluated to gain a holistic view of the behavior and interaction of these inhibitors with the calcite {1 0 4} surface. According to the DFT simulation, alanine, aspartic acid, phenylalanine, and tyrosine amino acids have the best inhibitor features. The results revealed that the binding energies were -2.16, -1.75, -2.24, and -2.66 eV for alanine, aspartic acid, phenylalanine, and tyrosine, respectively. Therefore, this study predicted an inhibition efficiency of the order tyrosine > phenylalanine > alanine > aspartic acid. The predicted inhibition efficiency order reveals agreement with the reported experimental results. Finally, the geometrical and charge analyses illustrated that the adsorption onto calcite is physisorption in the acquired adsorption energy range.

A Few Experimental Suggestions Using Minerals to Obtain Peptides with a High Concentration of L-Amino Acids and Protein Amino Acids

The peptides/proteins of all living beings on our planet are mostly made up of 19 L-amino acids and glycine, an achiral amino acid. Arising from endogenous and exogenous sources, the seas of the prebiotic Earth could have contained a huge diversity of biomolecules (including amino acids), and precursors of biomolecules. Thus, how were these amino acids selected from the huge number of available amino acids and other molecules? What were the peptides of prebiotic Earth made up of? How were these peptides synthesized? Minerals have been considered for this task, since they can preconcentrate amino acids from dilute solutions, catalyze their polymerization, and even make the chiral selection of them. However, until now, this problem has only been studied in compartmentalized experiments. There are separate experiments showing that minerals preconcentrate amino acids by adsorption or catalyze their polymerization, or separate L-amino acids from D-amino acids. Based on the [GADV]-protein world hypothesis, as well as the relative abundance of amino acids on prebiotic Earth obtained by Zaia, several experiments are suggested. The main goal of these experiments is to show that using minerals it is possible, at least, to obtain peptides whose composition includes a high quantity of L-amino acids and protein amino acids (PAAs). These experiments should be performed using hydrothermal environments and wet/dry cycles. In addition, for hydrothermal environment experiments, it is very important to use one of the suggested artificial seawaters, and for wet/dry environments, it is important to perform the experiments in distilled water and diluted salt solutions. Finally, from these experiments, we suggest that, without an RNA world or even a pre genetic world, a small peptide set could emerge that better resembles modern proteins.

Adsorption of organic molecules on mineral surfaces studied by first-principle calculations: A review

First-principle calculations, especially by the density functional theory (DFT) methods, are becoming a power technique to study molecular structure and properties of organic/inorganic interfaces. This review introduces some recent examples on the study of adsorption models of organic molecules or oligomers on mineral surfaces and interfacial properties obtained from first-principles calculations. The aim of this contribution is to inspire scientists to benefit from first-principle calculations and to apply the similar strategies when studying and tailoring interfacial properties at the atomistic scale, especially for those interested in the design and development of new molecules and new products.

QUANTUM CHEMICAL STUDY ON THERMAL DECOMPOSITION MECHANISM OF CALCIUM CARBONATE

A detailed quantum chemical calculation is performed at the MP2(full)/6-311G* level to explore the mechanism of calcium carbonate thermal decomposition. Four microscopic pathways are identified. The rate constants of rate-determining steps in four pathways are calculated over a temperature range 298–1200 K. The calculating results show that only path A (R( CaCO 3) → IM 1 → P( CaO + CO 2)) and path B (R( CaCO 3) → IM B1 → IM B2 → P( CaO + CO 2) have contributions to the CaCO 3 thermal decomposition, and path A may be more favorable than path B. The present theoretical studies may provide useful information in understanding reaction mechanism of metal carbonates at the molecular level.

Biomolecule-biomaterial interaction: a DFT-D study of glycine adsorption and self-assembly on hydroxylated Cr2O3 surfaces

The adsorption of glycine, the building block of amino acids, on hydroxylated (0001)-Cr2O3 model surfaces, representing the stainless steel passive film surface, was modeled by means of the GGA + U method. The roles of glycine coverage and surface termination (hydroxylated Cr- and O-terminated surfaces) on the adsorption mode and self-assembly properties were explored. The hydroxylated Cr-terminated Cr2O3 surface, which presents two types of (H)OH groups exhibiting different acidic character, is more reactive than the hydroxylated O-terminated surface, where one single type of OH group is present, for all adsorption modes and coverages considered. Outer sphere adsorption occurs in the zwitterion form, stabilized at low coverage through H-bond formation with coadsorbed water molecules, and at the monolayer coverage by glycine self-assembling. The OH substitution by glycinate is favored on the hydroxylated Cr-terminated surface and not on the O-terminated one. The inclusion of dispersion forces does not change the observed tendencies. An atomistic thermodynamics approach suggests that outer sphere adsorption is thermodynamically favored over inner sphere adsorption in the whole domain of glycine concentration. The obtained SAM's free energies of formation are rationalized in a model considering the balance between sublimation and solvation free energies, and extrapolated to other amino acids, to predict the SAMs formation above hydroxylated surfaces. It is found that hydrophobic AA tend to self-assemble at the surface, whereas hydrophilic ones do not.

Enantiospecific adsorption of amino acids on hydroxylated quartz (0001)

Density functional theory calculations have been used to study the adsorption of glycine, alanine, serine, and cysteine on the hydroxylated (0001) surface of alpha-quartz. We found negligible differences in adsorption energies for the most stable minima of enantiomers of alanine on this surface. There are, however, measurable energy differences between the two enantiomers of both serine and cysteine in their most stable states. The source of this enantiospecificity is mainly the difference in the strength of hydrogen bonds between the surface and the two enantiomers. Our results provide initial information on how amino acids can exhibit enantiospecific adsorption on hydroxylated quartz surfaces.

Monte Carlo modeling of chiral adsorption on nanostructured chiral surfaces and slit pores

Adsorptive separation of chiral molecules is a powerful technique that has long been used in the chemical and pharmaceutical industries. An important challenge in this field is to design and optimize new adsorbents to provide selective discrimination of enantiomers. In this article, we introduce an off-lattice model of chiral adsorption on nanostructured surfaces and slit pores with the aim of predicting their enantioslective properties. The concept presented here involves finding the optimal chiral pattern of active sites on the pore walls that maximizes the difference between the binding energies of the enantiomers. Our initial effort focuses on chiral molecules that do not have specific interactions with the pore surface. One candidate meeting this requirement is 1,2-dimethylcyclopropane (DMCP), a chiral hydrocarbon whose interaction with a model pore surface was described using the Lennard-Jones potential. To model the adsorption of DMCP, we used the Monte Carlo simulation method. It was demonstrated that the separation of the enantiomers of DMCP is hardly obtainable because of the smoothness of the potential energy surface for molecules physisorbed in the pore. However, the simulated results allowed the identification of key factors that influence the binding of the enantiomers of DMCP to the pore walls with a special distribution of active sites. This information will be useful in future considerations of the adsorption of more complex chiral molecules.