Does Silica Surface Catalyse Peptide Bond Formation? New Insights from First-Principles Calculations

Amino Acid Polymerization on Silica Surfaces

The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.

The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations

We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3'-C5' hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet-dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3'-C5' hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization.

Emergence of Order in Origin-of-Life Scenarios on Mineral Surfaces: Polyglycine Chains on Silica

The polymerization of amino acids (AAs) to peptides on oxide surfaces has attracted interest owing to its high importance in biotechnology, prebiotic chemistry, and origin of life theories. However, its mechanism is still poorly understood. We tried to elucidate the reactivity of glycine (Gly) from the vapor phase on the surface of amorphous silica under controlled atmosphere at 160 °C. Infrared (IR) spectroscopy reveals that Gly functionalizes the silica surface through the formation of ester species, which represent, together with the weakly interacting silanols, crucial elements for monomers activation and polymerization. Once activated, β-turns start to form as initiators for the growth of long linear polypeptides (poly-Gly) chains, which elongate into ordered structures containing both β-sheet and helical conformations. The work also points to the role of water vapor in the formation of further self-assembled β-sheet structures that are highly resistant to hydrolysis.

Contact Electrification of Biological and Bio-Inspired Adhesive Materials on SiO2 Surfaces: Perspectives from DFT Calculations

In this study, we investigate the contact electrification properties of glycine, cysteine, and dimethyl siloxane on silicon dioxide (SiO₂) surfaces using density functional theory calculations. Molecule contacting through the sulfhydryl group has stronger adhesion to the SiO₂-O and SiO₂-OH surfaces. The SiOH/SiO₂-Si system has the largest adhesion energy in all molecule/SiO₂-Si contact systems and charge transfers from the molecule to the SiO₂-O and SiO₂-Si surfaces. The molecule/SiO₂-OH systems have a reverse charge transfer direction. Molecules with their sulfhydryl and hydroxyl groups facing the SiO₂-O and SiO₂-OH surfaces have more transferred charges. The NH₂/SiO₂-Si system has a larger transferred charge than other molecule/SiO₂-Si systems. The direction of charge transfer is determined by the Bader charge of the isolated surface atoms. The respective energy difference in the lowest unoccupied occupied molecular orbitals between contacting atoms influences the charge transfer. The respective energy difference in the highest occupied molecular orbitals reflects the electron attraction and affects charge transfer. Finally, the quantitative relationship between the transferred charge and energy gaps is established to evaluate the charge transfer. The findings propose a new perspective and in-depth understanding of contact electrification and shed light on the bio-inspired adhesive materials design and fabrication for engineering applications.

Leucine on Silica: A Combined Experimental and Modeling Study of a System Relevant for Origins of Life, and the Role of Water Coadsorption

Leucine on silica constitutes an interesting system from the point of view of origins of life studies since leucine coadsorbed on SiO₂ together with glutamic acid can give rise to rather long linear polypeptides upon activation. It is also an ideal system to test methods of molecular characterization of biomolecules deposited on mineral surfaces since it combines a small-scale model of peptides and proteins, which are among the most important components of biodevices, with one of the most widely used inorganic materials. We have deposited l-leucine on a high surface fumed silica in the submonolayer range and characterized it by a multipronged approach including macroscopic information (thermogravimetry, X-ray diffraction), in situ spectroscopic methods (IR, multinuclear solid-state NMR including single-pulse and CP-MAS, 2-D HETCOR), and molecular modeling by density functional theory (DFT), including calculation of NMR parameters. Specific information can be obtained on the adsorption and interaction mechanism. Leucine is rather strongly adsorbed without any covalent bonds, through the formation of a specific lattice of H-bonds that often involve coadsorbed water molecules. Its state is indeed strongly dependent on the drying procedure: insufficient drying results in liquid-like surroundings for the leucine functional groups, while vacuum drying only retains a limited number of waters (of the order of 5 per leucine molecule). The most stable models have zwitterionic leucine interacting directly with surface silanols through their ammonium group, while the carboxylate interacts through bridging waters. Experimental NMR chemical shifts are satisfactorily predicted for these models, and leucine can be viewed as a probe for specific groups of surface sites known as silanol nests.

Study of the Reactivity of CH3COOH+• and COOH+ Ions with CH3NH2: Evidence of the Formation of New Peptide-like C(O)-N Bonds

Acetamide, a small organic compound containing a peptide bond, was observed in the interstellar medium, but reaction pathways leading to the formation of this prebiotic molecule remain uncertain. We investigated the possible formation of a peptide-like bond from the reaction between acetic acid (CH₃-COOH) and methylamine (CH₃-NH₂) that were identified in the interstellar medium. From an experimental point of view, a quadrupole/octopole/quadrupole mass spectrometer was used in combination with synchrotron radiation as a tunable source of VUV photons for monitoring the reactivity of selected ions. Acetic acid was photoionized, and the reactivity of CH₃COOH^+• as well as COOH⁺ (produced from either acetic acid or formic acid) ions with neutral CH₃NH₂ was further studied. With no surprise, charge transfer, proton transfer, and concomitant dissociation processes were found to largely dominate the reactivity. However, a C(O)-N bond formation process between the two reactants was also evidenced, with a weak cross section reaction. From a theoretical point of view, results concerning reactivity and barrier heights were obtained using density functional theory, with the LC-ωPBE range-separated functional in combination with the 6-311++G(d,p) Pople basis set and are in perfect agreement with the experimental data.

A quantum mechanical study of dehydration vs. decarbonylation of formamide catalysed by amorphous silica surfaces

Formamide is abundant in the interstellar medium and was also present during the formation of the Solar system through the accretion process of interstellar dust. Under the physicochemical conditions of primordial Earth, formamide could have undergone decomposition, either via dehydration (HCN + H2O) or via decarbonylation (CO + NH3). The first reactive channel provides HCN, which is an essential molecular building block for the formation of RNA/DNA bases, crucial for the emergence of life on Earth. In this work, we studied, at the CCSD(T)/cc-pVTZ level, the two competitive routes of formamide decomposition, i.e. dehydration and decarbonylation, either in liquid formamide (by using the polarization continuum model technique) or at the interface between liquid formamide and amorphous silica. Amorphous silica was adopted as a convenient model of the crystalline silica phases ubiquitously present in the primordial (and actual) Earth's crust, and also due to its relevance in catalysis, adsorption and chromatography. Results show that: (i) silica surface sites catalyse both decomposition channels by reducing the activation barriers by about 100 kJ mol-1 with respect to the reactions in homogeneous medium, and (ii) the dehydration channel, giving rise to HCN, is strongly favoured from a kinetic standpoint over decarbonylation, the latter being, instead, slightly favoured from a thermodynamic point of view.

Water-assisted peptide bond formation between two double amino acid molecules in the gas phase

The gas phase mechanism of the peptide bond formation between two double amino acid (DAA) molecules described by the (NH₂)₂C(COOH)₂ formula is investigated in the presence of a water molecule. Formations of trans and cis DAA-DAA dipeptide products along both concerted and stepwise mechanisms have been studied at the CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ level. The results indicate that the activation energy barriers estimated for the water-assisted mechanisms are significantly reduced in comparison to the corresponding uncatalyzed reactions. The trans DAA-DAA isomer is expected to dominate in the final product due to its larger stability compared to the cis DAA-DAA product.

Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies

There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic⁻mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic⁻mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic⁻mineral interactions have been proposed. The present article aims at reviewing recent in silico works, mainly focusing on prebiotic processes occurring on the mineral surfaces of clays, iron sulfides, titanium dioxide, and silica and silicates simulated through quantum mechanical methods based on the density functional theory (DFT). The DFT is the most accurate way in which chemists may address the behavior of the molecular world through large models mimicking chemical complexity. A perspective on possible future scenarios of research using in silico techniques is finally proposed.

When the Surface Matters: Prebiotic Peptide-Bond Formation on the TiO2 (101) Anatase Surface through Periodic DFT-D2 Simulations

The mechanism of the peptide-bond formation between two glycine (Gly) molecules has been investigated by means of PBE-D2* and PBE0-D2* periodic simulations on the TiO₂ (101) anatase surface. This is a process of great relevance both in fundamental prebiotic chemistry, as the reaction univocally belongs to one of the different organizational events that ultimately led to the emergence of life on Earth, as well as from an industrial perspective, since formation of amides is a key reaction for pharmaceutical companies. The efficiency of the surface catalytic sites is demonstrated by comparing the reactions in the gas phase and on the surface. At variance with the uncatalyzed gas-phase reaction, which involves a concerted nucleophilic attack and dehydration step, on the surface these two steps occur along a stepwise mechanism. The presence of surface Lewis and Brönsted sites exerts some catalytic effect by lowering the free energy barrier for the peptide-bond formation by about 6 kcal mol^-1 compared to the gas-phase reaction. Moreover, the co-presence of molecules acting as proton-transfer assistants (i.e., H₂ O and Gly) provide a more significant kinetic energy barrier decrease. The reaction on the surface is also favorable from a thermodynamic standpoint, involving very large and negative reaction energies. This is due to the fact that the anatase surface also acts as a dehydration agent during the condensation reaction, since the outermost coordinatively unsaturated Ti atoms strongly anchor the released water molecules. Our theoretical results provide a comprehensive atomistic interpretation of the experimental results of Martra et al. (Angew. Chem. Int. Ed. 2014, 53, 4671), in which polyglycine formation was obtained by successive feedings of Gly vapor on TiO₂ surfaces in dry conditions and are, therefore, relevant in a prebiotic context envisaging dry and wet cycles occurring, at mineral surfaces, in a small pool.

Thermal behavior, structure, dynamic properties of aqueous glycine solutions confined in mesoporous silica MCM-41 investigated by x-ray diffraction and quasi-elastic neutron scattering

Differential scanning calorimetry, X-ray diffraction, and quasi-elastic neutron scattering (QENS) measurements of aqueous glycine solutions confined in mesoporous silica (MCM-41) were performed at different glycine concentrations, pH, and loading ratio (=mass of glycine solution/mass of dry MCM-41) in the temperature range from 305 to 180 K to discuss the confinement effect on the thermal behavior, the structure, and the dynamic properties of the solutions. The freezing points of the confined glycine solutions decreased, compared with those of the bulk solutions. The corresponding exothermic peak due to ice formation became broader with an increase in the glycine concentration. By subtracting X-ray diffraction patterns of dry MCM-41 from those of glycine solution-loaded MCM-41, information about the structure of the confined glycine solutions was obtained. The radial distribution functions of the confined glycine solutions showed that the peaks assigned to the interaction between glycine molecules and the surface silanol (Si-OH) groups of MCM-41 at pH = 5 were observed, in contrast to the case at pH = 2. The QENS data on H/D substituted aqueous glycine solutions gave the translational diffusion coefficients and the residence time of glycine and water molecules confined in MCM-41 individually. The activation energy of the diffusion coefficient of a glycine molecule at pH = 5 was larger than that at pH = 2. These results imply that glycine molecules locate near the pore surface of MCM-41 due to the formation of hydrogen bonding between glycine molecules and the silanol group of the MCM-41 wall at pH = 5.

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.

Formation of Diastereoisomeric Piperazine-2,5-dione from DL-Alanine in the Presence of Olivine and Water

DL-Alanine (Ala) was heated with/without powdered olivine and water at 120 °C for 8 days to investigate the formation of the diastereoisomers of piperazine-2,5-dione (diketopiperazine, DKP). When only DL-Ala was heated with a small amount of water, 3.0 % of DL-Ala changed to cis- and trans-DKP after 8 days. DKPs were not detected after heating when no water was added. The presence of a small amount of water is important factor controlling peptide production rates under thermal conditions. When DL-Ala was heated with olivine powder for 8 days, the yields of cis- and trans-DKP were 6.8 and 4.9 %, respectively. The high yield of cis-DKP compared with trans-DKP was attributed to greater thermal stability of cis-DKP. After heating for 8 days, the diastereoisomeric excess of cis-DKP without olivine was 7.3 %, whereas a much higher value of 16.3 % was obtained in the presence of olivine. Taken together, these results show that olivine is not only an efficient catalyst for the formation of DKPs but that it also play a significant role in determining the diastereoisomer selectivity of these cyclic dipeptides.

Prebiotic RNA polymerisation: energetics of nucleotide adsorption and polymerisation on clay mineral surfaces

A set of experimentally measured and internally consistent Gibbs free energies of binding between different model nucleotides and mineral surfaces is reported.

Investigating the adsorption mechanism of glycine in comparison with catechol on cristobalite surface using density functional theory for bio-adhesive materials

Amino acid proteins exist in Mussel's adhesive (mefp's) of which glycine has a significant amount. A density functional theory simulation study was performed in a belief that all the proteins in mefp's are responsible for the versatile adhesion.

Single Molecule Investigation of Glycine-Chlorite Interaction by Cross-Correlated Scanning Probe Microscopy and Quantum Mechanics Simulations

In this work, we studied the interaction of glycine with the (001) surface of chlorite mineral at a single molecule level by cross-correlating scanning probe microscopy (SPM) and ab initio quantum mechanics (QM) investigations. Chlorite mineral is particularly interesting and peculiar for the interaction with organic molecules because it presents an alternated stacking of brucite-like (hydrophobic) and talc-like (hydrophilic) layers of different polarities. Brucite-like is positive, whereas talc-like is negative. The experimental atomic force microscopy (AFM) observations show that glycine is stably and selectively adsorbed on the brucite-like layer, organized in monolayers with different patterns. The sizes of single molecules of glycine measured by AFM are in agreement with those calculated by QM. Glycine molecules were found to align both at the edges and on the terraces of the brucitic surface. QM simulations confirmed the AFM observations that glycine molecule is adsorbed with high adsorption energy preferentially with its plane parallel to the (001) brucite-like surface. QM also provided the geometry conformation of the molecule and the bonding scheme between glycine and brucite surface. This kind of data can be very helpful both to biotechnological applications of this substrate and to depict some important processes that might have been occurred in prebiotic environments.

Propanoate grafting on (H,OH)-Si(0 0 1)-2 × 1

We have examined the reactivity of water-covered Si(0 0 1)-2 × 1, (H,OH)-Si(0 0 1)-2 × 1, with propanoic (C2H5COOH) acid at room temperature. Using a combination of spectroscopic techniques probing the electronic structure (XPS, NEXAFS) and the vibrational spectrum (HREELS), we have proved that the acid is chemisorbed on the surface as a propanoate. Once the molecule is chemisorbed, the strong perturbation of the electronic structure of the hydroxyls, and of their vibrational spectrum, suggests that the molecule makes hydrogen bonds with the surrounding hydroxyls. As we find evidence that surface hydroxyls are involved in the adsorption reaction, we discuss how a concerted or a radical-mediated reaction (involving the surface silicon dangling bonds) could lead to water elimination and formation of the ester.

Peptide formation mechanism on montmorillonite under thermal conditions

The oligomerization of amino acids is an essential process in the chemical evolution of proteins, which are precursors to life on Earth. Although some researchers have observed peptide formation on clay mineral surfaces, the mechanism of peptide bond formation on the clay mineral surface has not been clarified. In this study, the thermal behavior of glycine (Gly) adsorbed on montmorillonite was observed during heating experiments conducted at 150 °C for 336 h under dry, wet, and dry-wet conditions to clarify the mechanism. Approximately 13.9 % of the Gly monomers became peptides on montmorillonite under dry conditions, with diketopiperazine (cyclic dimer) being the main product. On the other hand, peptides were not synthesized in the absence of montmorillonite. Results of IR analysis showed that the Gly monomer was mainly adsorbed via hydrogen bonding between the positively charged amino groups and negatively charged surface sites (i.e., Lewis base sites) on the montmorillonite surface, indicating that the Lewis base site acts as a catalyst for peptide formation. In contrast, peptides were not detected on montmorillonite heated under wet conditions, since excess water shifted the equilibrium towards hydrolysis of the peptides. The presence of water is likely to control thermodynamic peptide production, and clay minerals, especially those with electrophilic defect sites, seem to act as a kinetic catalyst for the peptide formation reaction.

Formation of activated biomolecules by condensation on mineral surfaces--a comparison of peptide bond formation and phosphate condensation

Many studies have reported condensation reactions of prebiotic molecules, such as the formation of peptide bonds between amino acids, to occur to some degree on mineral surfaces. We have studied several such reactions on the same divided silica. When drying steps are applied, the equilibria of peptide formation from glycine, and polyphosphate formation from monophosphate, are displaced to the right because these reactions are dehydrating condensations, accompanied by the emission of water. In contrast, the equilibrium of AMP dismutation is not significantly favored by drying. The silica surface plays little role (if any) in the thermochemistry of the condensation reactions, but is does play a significant kinetic role by acting as a catalyst, lowering the condensation temperatures with respect to bulk solids. Of course, the surface also catalyzes the inverse hydrolysis reactions.

A SELF-CONSISTENT-CHARGE DENSITY-FUNCTIONAL TIGHT-BINDING THEORY BASED MOLECULAR DYNAMICS SIMULATION OF A ZWITTERIONIC GLYCINE IN AN EXPLICIT WATER ENVIRONMENT

A zwitterionic glycine (zGLY) is adopted as an example to study the impact of water environment (310 H2O molecules) on the molecular structure and energetics using a self-consistent-charge density-functional tight-binding theory based molecular dynamics (SCC-DFTB/MD) method. It is found that maximal eight hydrogen bonds could be formed simultaneously between eight water molecules and the zGLY. The ability of the COO- terminal to adsorb water molecules is stronger than the [Formula: see text] terminal with respect to hydrogen bonding with more water molecules and exhibits lower adiabatic adsorption energies. The zGLY's intramolecular hydrogen bond appeared unpredictably, without involving any proton transfer and generally helpful for enhancing the system stability. Water molecules play an important role to stabilize the zwitterionic amino acids and restrain the proton migration from the [Formula: see text] to the COO− group. Our results show that the SCC-DFTB/MD method could successfully describe geometry dynamical evolutions and energetics of biomolecules in a nanoscale simulation with the presence of a large number of water molecules. Our study not only verified the feasibility of a QM level methodology for describing the aqueous states of biochemical molecules, but also gave a clear evidence for the impact of water environment on amino acids.

EFFECTS AND ROLE OF WATER ENVIRONMENT ON A GEMINAL HYDROXYLATED SILICA SURFACE — SELF-CONSISTENT CHARGE DENSITY FUNCTIONAL TIGHT BINDING THEORY BASED MOLECULAR DYNAMICS SIMULATION

The presence of aqueous solution is inevitable in complex systems involving biological and material components and could affect the interaction between them substantially. To properly simulate such an interaction system, it is necessary to quantitatively explore the effects and specific roles of the water environment on the material surface. In this work, a silica surface was adopted as an example to study the impact of water environment ( 144H2O ) on the structure and energetics using a self-consistent charge density functional tight binding/molecular dynamic method. First, we demonstrated that the silica surface in a vacuum involves a large deformation due to the formation of hydrogen bonds among the surface silanols; in contrast, the deformation is eased in water environment because water molecules could locate in between the silanols and form many hydrogen bonds with the silanols. Therefore, water molecules play an important role to maintain surface from not getting heavily deformed. Our work not only tested the feasible computational methodology of studying nanoscale large systems under water environment at a quantum-mechanical level of theory, but also provided clear evidence on the impact of water environment to the inorganic surface.

Formation versus hydrolysis of the peptide bond from a quantum-mechanical viewpoint: The role of mineral surfaces and implications for the origin of life

The condensation (polymerization by water elimination) of molecular building blocks to yield the first active biopolymers (e.g. of amino acids to form peptides) during primitive Earth is an intriguing question that nowadays still remains open since these processes are thermodynamically disfavoured in highly dilute water solutions. In the present contribution, formation and hydrolysis of glycine oligopeptides occurring on a cluster model of sanidine feldspar (001) surface have been simulated by quantum mechanical methods. Results indicate that the catalytic interplay between Lewis and Brønsted sites both present at the sanidine surface, in cooperation with the London forces acting between the biomolecules and the inorganic surface, plays a crucial role to: i) favour the condensation of glycine to yield oligopeptides as reaction products; ii) inhibit the hydrolysis of the newly formed oligopeptides. Both facts suggest that mineral surfaces may have helped in catalyzing, stabilizing and protecting from hydration the oligopeptides formed in the prebiotic era.

Neutral vs zwitterionic glycine forms at the water/silica interface: structure, energies, and vibrational features from B3LYP periodic simulations

B3LYP periodic calculations with a triple-xi-polarized Gaussian basis set have been used to study adsorption of glycine on a hydroxylated silica surface (2.2 OH/nm2) model derived from the (001) surface of edingtonite. The simulation envisages glycine adsorbed either as a gas-phase molecule or when microsolvated by up to five H20 molecules. Both neutral and zwitterionic forms of glycine have been considered and their structural, energetic, and spectroscopic vibrational features compared internally and with experiments. As a gas phase glycine sticks in its neutral form at the silica surface, the zwitterion being highly unstable and with transition-state character. When glycine is microsolvated at the silica interface, two H20 molecules render the zwitterion population comparable to that of the neutral form whereas with four H2O molecules the neutral glycine population is wiped out in favor of the zwitterion. With four H20 molecules the most stable structure shows no direct contact between glycine and the silica surface, H20 acting as a mediator via H-bond interactions. The B3LYP energies and structural data were also supported by comparing the scaled harmonic vibrational features with literature FTIR data of glycine adsorbed on an amorphous silica surface either from the gas phase or in water solution.

Adsorption and polymerization of amino acids on mineral surfaces: a review

The present paper offers a review of recent (post-1980) work on amino acid adsorption and thermal reactivity on oxide and sulfide minerals. This review is performed in the general frame of evaluating Bernal's hypothesis of prebiotic polymerization in the adsorbed state, but written from a surface scientist's point of view. After a general discussion of the thermodynamics of the problem and exactly what effects surfaces should have to make adsorbed-state polymerization a viable scenario, we examine some practical difficulties in experimental design and their bearing on the conclusions that can be drawn from extant works, including the relevance of the various available characterization techniques. We then present the state of the art concerning the mechanisms of the interactions of amino acids with mineral surfaces, including results from prebiotic chemistry-oriented studies, but also from several different fields of application, and discuss the likely consequences for adsorption selectivities. Finally, we briefly summarize the data concerning thermally activated amide bond formation of adsorbed amino acids without activating agents. The reality of the phenomenon is established beyond any doubt, but our understanding of its mechanism and therefore of its prebiotic potential is very fragmentary. The review concludes with a discussion of future work needed to fill the most conspicuous gaps in our knowledge of amino acids/mineral surfaces systems and their reactivity.

Aluminosilicate surfaces as promoters for peptide bond formation: an assessment of Bernal's hypothesis by ab initio methods

The role in prebiotic chemistry that Brønsted and Lewis sites, both present at the surface of common aluminosilicates, may have played in favoring the peptide bond formation has been addressed by ab initio methods within a cluster approach. B3LYP/6-31+G(d,p) free energy potential energy surfaces have been fully characterized for the model reaction glycine + NH3 --> 2-NH2 acetamide (mimicking the true 2 Gly --> GlyGly one) occurring on (i) a Lewis site, (ii) a Brønsted site, and (iii) a combined action of Lewis/Brønsted sites. Compared to the gas-phase (gp) activation free energy of 50 kcal/mol, the Lewis site alone reduces the gp barrier to 41 kcal/mol, whereas the activation by the Brønsted site dramatically reduces the barrier to about 18 kcal/mol. Nevertheless, formation of the prereactant complex in this latter case will rarely occur, since water will easily displace the glycine molecule interacting with the Brønsted site. However, if a realistic feldspar surface with neighboring Brønsted and Lewis sites is considered, the proper prereactant complex is highly stabilized by a simultaneous interaction with the Lewis and the Brønsted sites, in such a way that the Lewis site strongly attaches the glycine molecule to the surface whereas the Brønsted site efficiently catalyzes the condensation reaction, showing that the interplay between Lewis/Brønsted sites is an important issue. The free energy barrier computed for the realistic feldspar surface model is 26 kcal/mol. The role of dispersive interactions on the free energy barrier and the stabilization of the final product, not accounted for by the B3LYP functional, have been estimated and shown to be substantial. Speculations about further elongation of the formed dipeptide have been put forward on the basis of the relatively strong interaction energy of the formed GlyGly dipeptide with the aluminosilicate surface.

Is the Peptide Bond Formation Activated by Cu2+ Interactions? Insights from Density Functional Calculations

The catalytic role that Cu(2+) cations play in the peptide bond formation has been addressed by means of density functional calculations. First, the Cu(2+)-(glycine)2 --> Cu(2+)-(glycylglycine) + H2O reaction was investigated since mass spectrometry low collision activated dissociation (CAD) spectra of Cu(2+)-(glycine)2 led to the elimination of a water molecule, which suggested that an intracomplex peptide bond formation might have occurred. Results show that this intracomplex condensation is associated to a very high free energy barrier (97 kcal mol(-1)) and reaction free energy (66 kcal mol(-1)) because of the loss of metal coordination during the reaction. Second, on the basis of the salt-induced peptide formation theory, the condensation reaction between two glycines was studied in aqueous solution using discrete water molecules and the conductor polarized continuum model (CPCM) continuous method. It is found that the synergy between the interaction of glycines with Cu(2+) and the presence of water molecules acting as proton-transfer helpers significantly lower the activation barrier (from 55 kcal/mol for the uncatalyzed system to 20 kcal/mol for the Cu(2+) solvated system) which largely favors the formation of the peptide bond.

Interaction of glycine with isolated hydroxyl groups at the silica surface: first principles B3LYP periodic simulation

The adsorption of a glycine molecule on a model silica surface terminated by an isolated hydroxyl group has been studied ab initio using a double-zeta polarized Gaussian basis set, the hybrid B3LYP functional, and a full periodic treatment of the silica surface/glycine system. The hydroxylated silica surface has been simulated using either a 2D slab or a single polymer strand cut out from the (001) surface of an all-silica edingtonite. A number of B3LYP-optimized structures have been found by docking glycine on the silica surface exploiting all possible hydrogen bond patterns. Whereas glycine is generally adsorbed in its neutral form, two structures show glycine adsorbed as a zwitterion, the surface playing the role of a "solid solvent" whereas intrastrand hydrogen bond cooperativity stabilizes the zwitterions. The adsorbed zwitterionic structures are no longer formed at a lower glycine coverage as simulated by enlarging the unit cell so as to break intrastrand hydrogen bonds, showing the importance of H-bond cooperativity in stabilizing the zwitterionic forms. Each structure has been characterized by computing its harmonic vibrational spectrum at the Gamma point, which also allowed us to calculate the free energy of adsorption. The experimental infrared features of chemical-vapor-deposited glycine on a silica surface are in agreement with those computed for glycine adsorbed in its neutral form and engaging three hydrogen bonds with the surface silanols, two of them involving the C=O bond and one originating from the glycine OH group. The NH(2) group plays only a minor role as a weak hydrogen bond donor.

Imidazo[1,2-a]pyrazine-3,6-diones derived from alpha-amino acids: a theoretical mechanistic study of their formation via pyrolysis and silica-catalyzed process

Imidazo[1,2-a]pyrazine-3,6-diones are unusual compounds composed of three alpha-amino acid fragments. These bicyclic amidines (BCAs) form under high temperatures or with the use of strong dehydrating reagents. We gave insight into the mechanisms of BCA formation via gas-phase pyrolytic and silica-catalyzed reactions of glycine (Gly) and alpha-aminoisobutyric acid (AIB) with related diketopiperazines (DKPs), using quantum chemical calculations. The entire process requires four steps: (1) O-acylation of DKP with free or silica-bonded amino acid, (2) acyl transfer from the oxygen to the nitrogen atom, (3) intramolecular condensation of the N-acyl DKP into a cyclol, and (4) elimination of water. To study step (1) at silica surface (modeled by H7Si8O12-OH cluster), we employed two-level ONIOM calculations (AM1:UFF, B3LYP/3-21G:UFF and B3LYP/6-31G(d):UFF); all gas-phase reactions were studied at the AM1, B3LYP/3-21G and B3LYP/6-31G(d) levels. The catalytic effect of silica was observed for both Gly and AIB: the activation energy in the O-acylation at the surface was lower by more than 9 kcal mol(-1) as compared to the gas-phase process. Contrary to the exothermic O-acylation, the gas-phase transfer reaction (step 2) was exothermic in both cases, but more favorable for Gly. The cyclocondensation of N-acylated DKPs into BCAs (steps 3 and 4) is endothermic for Gly and exothermic for AIB.