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WOS:000342922100013; International audience; Water is the most abundant compound in interstellar and cometary ices. Laboratory experiments on ice analogues have shown that water has a great influence on the chemical activity of these ices. In this study, we investigated the reactivity of acetone-ammonia ices, showing that water is an essential component in chemical reactions with high activation energies. In a water-free binary ice, acetone and ammonia do not react due to high activation energy, as the reactants desorb before reacting (at 120 and 140 K, respectively). By contrast, our study shows that under experimental conditions of similar to 150 K, this reaction does occur in the presence of water. Here, water traps reactants in the solid phase above their desorption temperatures, allowing them to gather thermal energy as the reaction proceeds. Using infrared spectroscopy and mass spectrometry associated with isotopic labelling, as well as quantum chemical calculations, 2-aminopropan-2-ol (2HN-C(CH3)(2)-OH) was identified as the acetone-ammonia reaction product. The formation of this product may represent the first step towards formation of 2-aminoisobutyric acid (AIB) in the Strecker synthesis. The activation energy for the formation of 2-aminopropan-2-ol was measured to be 42 +/- 3 kJ mol(-1), while its desorption energy equalled 61.3 +/- 0.1 kJ mol(-1). Our work demonstrates that astrophysical water, rather than being a non-thermally reactive species, is crucial for the evolution of complex chemistry occurring in the Universe.

WOS:000340028400002; International audience; The thermal reactivity of a water-dominated cometary ice analog containing H2CO and NH3 is investigated by means of Fourier transform infrared spectroscopy, mass spectrometry, and B3LYP calculations. Three products are characterized by these techniques: aminomethanol (NH2CH2OH), methyleneglycol (HOCH2OH), and polyoxymethylene (POM, HO-(CH2-O)(n)-H). Their formation strongly depends on the initial NH3/H2CO ratio. In addition, the influence of the initial ice composition on the thermal stability of POM has also been investigated. It is shown that POM formed during warming of the ices consists of short-chain polymers (i.e., oligomers of formaldehyde HO-(CH2-O)(n)-H, n \textless 5), which are volatile at temperatures higher than 200 K. This suggests that gas-phase detection by the ROSINA instrument on board the Rosetta mission would be the most appropriate method to detect POM. Moreover, the mass spectra presented in this work might help in the interpretation of data that will be recorded by this instrument. Finally, a new scenario to explain the distributed source of formaldehyde observed in comets is discussed.

The adsorption of glycine (Gly) both in gas-phase conditions and in a microsolvated state on a series of zig-zag (n,0) single-walled boron nitride nanotubes (BNNTs, n = 4, 6, 9 and 15) has been studied by means of B3LYP-D2* periodic calculations. Gas-phase Gly is found to be chemisorbed on the (4,0), (6,0) and (9,0) BNNTs by means of a dative interaction between the NH2 group of Gly and a B atom of the BNNTs, whose computed adsorption energies are gradually decreased by increasing the tube radius. On the (15,0) BNNT, Gly is found to be physisorbed with an adsorption driving force mainly dictated by π-stacking dispersion interactions. Gly adsorption in a microsolvated environment has been studied in the presence of seven water molecules by progressively microsolvating the dry Gly/BNNT interface. The most stable structures on the (6,0), (9,0) and (15,0) BNNTs present the Gly/BNNT interface fully bridged by the water solvent molecules; i.e., no direct contact between Gly and the BNNTs takes place, whereas on the (4,0) BNNT the most stable structure presents a unique direct interaction between the COO− Gly group and a B atom of the nanotube. Further energetic analyses indicate that the (6,0), (9,0) and (15,0) BNNTs exhibit a low water affinity, which favors the Gly/water interactions upon BNNT coadsorption. In contrast, the (4,0) BNNT has been found to show a large water affinity, bringing the replacement of adsorbed water by a microsolvated glycine molecule as an unfavorable process.

The physisorption/chemisorption of atomic hydrogen on a slab model of the Mg2SiO4 forsterite (010) surface mimicking the interstellar dust particle surface has been modeled using a quantum mechanical approach based on periodic B3LYP-D2* density functional calculations (DFT) combined with flexible polarized Gaussian type basis sets, which allows a balanced description of the hydrogen/surface interactions for both minima and activated complexes. Physisorption of hydrogen is barrierless, very weak and occurs either close to surface oxygen atoms or on Mg surface ions. The contribution of dispersion interactions accounts for almost half of the adsorption energy. Both the hydrogen adsorption energy and barrier to hydrogen jump between equivalent surface sites are overestimated compared to experimental results meant to simulate the interstellar conditions in the laboratory. The hydrogen atom exclusively chemisorbs at the oxygen site of the forsterite (010) surface, forming a SiOH surface group and its spin density being entirely transferred to the neighboring Mg ion. Barrier for chemisorption allows rapid attachment of H at the surface at 100 K, but prevents the same process from occurring at 10 K. From this H-chemisorbed state, the second hydrogen chemisorption mainly occurs on the neighboring Mg ion, thus forming a Mg-H surface group, giving rise to a surface species stabilized by favorable electrostatic interactions between the OHH-Mg pair. The formation of molecular hydrogen at the (010) forsterite surface adopting a Langmuir-Hinshelwood mechanism takes place either starting from two physisorbed H atoms with an almost negligible kinetic barrier through a spin-spin coupling driven reaction or from two chemisorbed H atoms with a barrier surmountable even at T higher than 10 K. We also suggest that a nanosized model of the interstellar dust built from a replica of the forsterite unit cell is able to adsorb half the energy released by the H2 formation by increasing its temperature by about 50 K which could then radiate in about 0.02 s.

The physisorption/chemisorption of atomic hydrogen on a slab model of the Mg2SiO4 forsterite (010) surface mimicking the interstellar dust particle surface has been modeled using a quantum mechanical approach based on periodic B3LYP-D2* density functional calculations (DFT) combined with flexible polarized Gaussian type basis sets, which allows a balanced description of the hydrogen/surface interactions for both minima and activated complexes. Physisorption of hydrogen is barrierless, very weak and occurs either close to surface oxygen atoms or on Mg surface ions. The contribution of dispersion interactions accounts for almost half of the adsorption energy. Both the hydrogen adsorption energy and barrier to hydrogen jump between equivalent surface sites are overestimated compared to experimental results meant to simulate the interstellar conditions in the laboratory. The hydrogen atom exclusively chemisorbs at the oxygen site of the forsterite (010) surface, forming a SiOH surface group and its spin density being entirely transferred to the neighboring Mg ion. Barrier for chemisorption allows rapid attachment of H at the surface at 100 K, but prevents the same process from occurring at 10 K. From this H-chemisorbed state, the second hydrogen chemisorption mainly occurs on the neighboring Mg ion, thus forming a Mg–H surface group, giving rise to a surface species stabilized by favorable electrostatic interactions between the OH⋯H–Mg pair. The formation of molecular hydrogen at the (010) forsterite surface adopting a Langmuir–Hinshelwood mechanism takes place either starting from two physisorbed H atoms with an almost negligible kinetic barrier through a spin–spin coupling driven reaction or from two chemisorbed H atoms with a barrier surmountable even at T higher than 10 K. We also suggest that a nanosized model of the interstellar dust built from a replica of the forsterite unit cell is able to adsorb half the energy released by the H2 formation by increasing its temperature by about 50 K which could then radiate in about 0.02 s.

WOS:000344249400008; International audience; Laboratory experiments devoted to simulate the chemistry occurring in interstellar and cometary ice analogues are of paramount importance to understand the formation of complex organic molecules that are detected throughout the universe. These laboratory simulations provide relevant hints on the fundamental physical and chemical steps associated with the increase of the molecular complexity in space and, moreover, give benchmark results for dedicated space missions. In the present work, we study the thermally promoted reactivity of H2O-dominated and D2O-dominated cometary ice analogues that contain various amounts of H2CO and NH3 by means of Fourier-transform infrared spectroscopy (FTIR), mass spectrometry and DFT calculations. Experimental measurements show that methyleneglycol (HOCH2OH) and D-2-methyleneglycol (DOCH2OD, the corresponding isotopologue) are formed from the H2O- and D2O-dominated ices, respectively, only if ammonia is present. We also reported for the first time the mass spectrum of methyleneglycol and D-2-methyleneglycol. B3LYP calculations have also been used to characterize the potential energy surface of the mechanistic steps associated with the formation of HOCH2OH as well as to simulate the IR spectrum of this compound. The fruitful interplay between theory and experiment has allowed us to elucidate the exact role of ammonia during the warming, which essentially stands for the formation and stabilization of the NH4+/OH- ion pair, thus enabling the OH- species to react with formaldehyde. The present results reproduce the heating of circumstellar ices in star formation regions and can be applied to the late thermal evolution of comets. In addition, the mass spectrum of methyleneglycol represents a benchmark for the analysis of the data coming from the ROSINA on-board instrument of the Rosetta mission.

The present contribution analyzes the binding of ThT and neutral ThT derivatives to a β-sheet model by means of quantum chemical calculations. In addition, we study the properties of four molecules: (2-(2-hydroxyphenyl)benzoxazole (HBX), 2-(2-hydroxyphenyl)benzothiazole (HBT) and their respective iodinated compounds, HBXI and HBTI, in binding to amyloid fibril models and Aβ1-40fibrils by using a combination of docking, molecular dynamics and quantum mechanics calculations.

B3LYP periodic simulations have been carried out to study some physicochemical properties of the bulk structures and the corresponding nonpolar (010) surfaces of Mg-pure and Fe-containing olivine systems; i.e., Mg2SiO4 (Fo) and Mg1.5Fe0.5SiO4 (Fo75). A detailed structural analysis of the (010) Fo and Fo75 surface models shows the presence of coordinatively unsaturated metal cations (Mg(2+) and Fe(2+), respectively) with shorter metal-O distances compared to the bulk ones. Energetic analysis devoted to the Fe(2+) electronic spin configuration and to the ion position in the surfaces reveals that Fe(2+) in its quintet state and placed at the outermost positions of the slab constitutes the most stable Fe-containing surface, which is related to the higher stability of high spin states when Fe(2+) is coordinatively unsaturated. Comparison of the simulated IR and the corresponding reflectance spectra indicates that Fe(2+) substitution induces an overall bathochromic shift of the spectra due to the larger mass of Fe compared to Mg cation. In contrast, the IR spectra of the surfaces are shifted to upper values and exhibit more bands compared to the corresponding bulk systems due to the shorter metal-O distances given in the coordinatively unsaturated metals and to symmetry reduction which brings nonequivalent motions between the outermost and the internal modes, respectively.

The adsorption of H2O, NH3 and HCOOH as polar probe molecules and C6H6 and CH4 as non-polar ones on a series of zig-zag (n,0) single-walled boron nitride nanotubes (BNNTs) and on a boron-nitride mono-layer (BNML) has been studied by means of B3LYP-D* periodic calculations. Computed electrostatic potential maps for the pristine BN nanomaterials indicate that the smaller the radius, the larger the polar character. Polar molecules are found to be strongly chemisorbed on small radius BNNTs by means of dative interactions between electron donor atoms of the molecules and B atoms of the BNNTs, H-bonding, as well as dispersive forces. Remarkably, for HCOOH interacting with the (4,0) BNNT, this dative interaction is accompanied by a proton transfer to the nanotube. The corresponding computed adsorption energies decrease sharply with increasing tube radius, gradually approaching the values for physisorption on the BNML. Adsorption of non-polar molecules, mainly dictated by π-stacking (C6H6) and CH–π (CH4) dispersion interactions, is found to be energetically more favorable when physisorbed on large radius BNNTs, the most stable adducts being formed on the BNML.

Thioflavin-T (ThT) is one of the most widely used dyes for staining and identifying amyloid fibrils, which share a common parallel in register β-sheet structure. Unfortunately, ThT is a charged molecule, which limits its ability to cross the blood brain barrier and its use as an efficient dye for in vivo detection of amyloid fibrils. For this reason, several uncharged ThT derivatives have been designed and their binding properties to Aβ fibrils studied by fluorescence assays. However, there are still many unknowns on the binding mechanism and the role of noncovalent interactions on the affinity of these ligands toward β-sheet structures. The present contribution analyzes the binding of ThT (1) and neutral ThT derivatives (2-7) to a β-sheet model by means of quantum chemical B3LYP-D calculations and including solvent effects with the continuum CPCM method. Results show that, in all cases, ligand binding is mainly driven by dispersion interactions. In addition, ligands with -NH groups display hydrogen bond interactions with CO groups of the peptide strand, increasing the intrinsic affinity toward the β-sheet surface. Solvent effects notably reduce the affinity of charged ThT, as compared to neutral systems, due to its larger solvation energy. As a result, neutral derivatives display significantly higher affinities than ThT in solution, in agreement with experimental observations. Analysis of the hydrogen bonding network of the β-sheet structure indicates that stacking interactions upon ligand binding induce a shortening of interstrand hydrogen bonding, suggesting a strengthening of the β-sheet.

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The adsorption of glycine on the Ca-rich and P-rich HA(010) nonstoichiometric surfaces has been studied at B3LYP level using a polarized triple-ζ basis set within periodic boundary conditions. Although the Ca-rich and P-rich HA(010) nonstoichiometric surfaces exhibit different terminations, giving rise to different electrostatic features in the adsorption regions, glycine preferentially adsorbs as a zwitterion on both surfaces. When adsorbed in a canonical form, the proton of the COOH group is always transferred to the HA(010) surface except for one case, which, in turn, is also the least stable one. Glycine adsorbs by favorable electrostatic interactions between COO–/Ca2+ and NH3+/PO42– species, while dispersion interactions play a minor role. The harmonic B3LYP vibrational spectrum is in very good agreement with the experimental one and, when merged with contributions due to glycine adsorbed on stoichiometric HA(010) surfaces, allows one to explain the origin of the “squat shape” of the COO– stretching ...

In this chapter, it is shown how in silico modeling by quantum mechanical methods provides structures and energetic as well as mechanistic reaction details relevant to prebiotic chemistry. In particular, reactions of astrobiochemical interest and processes related to the polymerization of amino acids on the rocks are dealt with, in which the role of naturally occurring inorganic surfaces (icy particles and silica-based materials, respectively) as catalysts is highlighted.

WOS:000307648700033; International audience; There is convincing evidence that the formation of complex organic molecules occurred in a variety of environments. One possible scenario highlights the universe as a giant reactor for the synthesis of organic complex molecules, which is confirmed by numerous identifications of interstellar molecules. Among them, precursors of biomolecules are of particular significance due to their exobiological implications, and some current targets concern their search in the interstellar medium as well as understanding the mechanisms of their formation. Hexamethylenetetramine (HMT, C6H12N4) is one of these complex organic molecules and is of prime interest since its acid hydrolysis seems to form amino acids. In the present work, the mechanism for HMT formation at low temperature and pressure (i.e. resembling interstellar conditions) has been determined by combining experimental techniques and DFT calculations. Fourier transform infra-red spectroscopy and mass spectrometry techniques have been used to follow experimentally the formation of HMT as well as its precursors from thermal reaction of NH3:H2CO:HCOOH and CH2NH:HCOOH ice mixtures, from 20 K to 330 K. DFT calculations have been used to compute the mechanistic steps through which HMT can be formed starting from the experimental reactants observed in solid phase. The fruitful interplay between theory and experiment has allowed establishing that the mechanism in the solid state at low temperature is different from the one proposed in liquid phase, in which a new intermediate (1,3,5-triazinane, C3H9N3) has been identified. In the meantime, aminomethanol has been unambiguously confirmed as the first intermediate whereas the hypothesis of methylenimine as the second is further strengthened.

Large-scale periodic quantum mechanical calculations (509 atoms, 7852 atomic orbitals) based on the hybrid B3LYP functional focused on the peptide folding induced by the adsorption on the (001) and (010) hydroxyapatite (HA) surfaces give interesting insights on the role of specific interactions between surface sites and the peptide, which stabilize the helix conformation over the "native" random coil ones for in silico designed model peptides. The two peptides were derived from the 12-Gly oligomer, with one (P1, C-tGGKGGGGGGEGGN-t) and two (P2, C-tGGKGGKEGGEGGN-t) glutamic acid (E) and lysine (K) residue mutations. The most stable gas-phase "native" conformation for both peptides resulted in a random coil (RC) structure, with the helix (H) conformation being ≈100 kJ mol(-1) higher in free energy. The two peptide conformations interact with the HA (001) and (010) surfaces by C═O groups via Ca(2+) ions, by hydrogen bond between NH(2) groups and the basic PO(4)(3-) groups and by a relevant fraction due to dispersion forces. Peptide adsorption was studied on the dry (001) surface, the wet one envisaging 2 H(2)O per surface Ca(2+) and, on the latter, also considering the adsorption of microsolvated peptides with 4 H(2)O molecules located at sites responsible of the interaction with the surface. The P1 mutant does prefer to be adsorbed as a random coil by ≈160 kJ/mol, whereas the reverse is computed for P2, preferring the helix conformation by ≈50 kJ/mol. Adsorption as helix of both P1 and P2 mutants brings about proton transfer toward the HA surfaces with a large charge transfer component to the interaction energy.

Evidence supporting the role of metal ions in Alzheimer's disease (AD) has rendered metal ion chelation as a promising therapeutic treatment. The rational design of efficient chelating ligands requires, however, a good knowledge of the electronic and molecular structure of the complexes formed. In the present work, the coordinative properties of a set of chelating ligands toward Cu(II) have been analyzed by means of DFT(B3LYP) calculations. Special attention has been paid to the aromatic behavior of the metalated rings of the complex and its influence on the chelating ability of the ligand. Ligands considered have identical metal binding sites (through N/O coordination) and only differ on the kind and size of the aromatic moieties. Results indicate that there is a good correlation between the stability constants (log β(2)) and the degree of metalloaromaticity determined through the I(NG) and HOMA indices; that is, the higher the metalloaromaticity, the larger the log β(2) value. MOs and aromaticity descriptors confirm that present complexes exhibit Möbius metalloaromaticity. Detailed analysis of the nature of the Cu(II)-ligand bonding, performed through an energy decomposition analysis, indicates that ligands with less aromatic moieties have the negative charge more localized in the metalated ring, thus increasing their σ-donor character and the metalloaromaticity of the complexes they form.

The adsorption by chemical vapor deposition of glycine to nanohydroxyapatite, well characterized by electron microscopy, has been studied by infrared spectroscopy and density functional theory based on the B3LYP functional. The comparison of the IR features of the adsorbed glycine with that resulting from the modeling has allowed elucidating the structures assumed by glycine at the crystalline faces of nanohydroxyapatite. These results will improve the understanding of the biomolecules/biomaterials interactions.

A Strecker-type synthesis of glycine by reacting NH(3), H(2)C=O and HCN in presence of ice water (H(2)O-ice) as a catalyst has been theoretically studied at B3LYP/6-31+G(d,p) level within a cluster approach in order to mimic reactions occurring in the interstellar and circumstellar medium (ICM). Results indicate that, despite the exoergonic character of the considered reactions occurring at the H(2)O-ice surface, the kinetics are slow due to relatively high electronic energy barriers (ΔU(0)(≠)=15-45 kcal mol(-1)). Reactions occurring within H(2)O-ice cavities, in which ice bulk effects have been modeled by assuming a dielectric continuum (ε=78), show energy barriers low enough to allow NH(2)CH(2)OH formation but not NH=CH2 (ΔU(0)(≠)= 2 and 21 kcal mol(-1), respectively) thus hindering the NH(2)CH(2)CN formation, i.e. the precursor of glycine, through Strecker channels. Moreover, hydrolysis of NH(2)CH(2)CN to give glycine is characterized by high electronic energy barriers (ΔU(0)(≠)=27-34 kcal mol(-1)) and cannot readily occur at cryogenic temperatures. Nevertheless, the facts that NH=CH(2) formation can readily be achieved through the radical-radical HCN+2H - NH−−CH2 reaction [D. E. Woon, Astrophys. J., 2002, 571, L177-L180], and that present results indicate that the Strecker step of NH=CH(2)+HCN−−NH(2)CH(2)CN exhibits a relative low energy barrier (ΔU(0)(≠)=8–9 kcal mol(-1)), suggest that a combination of these two mechanisms allows for the formation of NH(2)CH(2)CN in the ICM. These results strengthen the thesis that NH(2)CH(2)CN could have been formed and protected by icy dust particles, and then delivered through micro-bombardments onto the early Earth, leading to glycine formation upon contact with the primordial ocean.

Combining X-ray data on thioflavin-T and theoretical calculations on its binding to a peptide model for Abeta(1-42) fibrils gives evidence of main stabilizing interactions, which influence the dihedral angle between the two moieties of thioflavin-T and thereby its fluorescence properties; these results shed new light on possible strategies for the design of dyes to bind amyloid fibrils more specifically.

The adsorption of benzene and benzene-1,4-diol on two all-silica surface models derived from the framework of sanidine mineral with either hydrophobic or hydrophilic properties has been studied by means of periodic calculations based on local Gaussian basis function and the B3LYP-D functional, which includes dispersion contribution as an empirical correction to the pure B3LYP energy. The aromatic molecules have been docked on different adsorption sites of the two surfaces using the electrostatic potential of the separate parts as a guide to ensure the best matching between electrophilic/nucleophilic regions. The inclusion of dispersion in the definition of the functional method dramatically affects both the intermolecular geometries and the adsorption energies, these latter being, in all cases, underestimated without the inclusion of the dispersive contribution. The adsorption of the aromatic molecules on the hydrophobic silica surface is dictated by dispersion and weak CH...O(Si)O interactions. The entity of the interaction for benzene on the hydrophilic surface is close to the value of the sublimation energy of the benzene molecular crystal, thus showing that adsorbate self-aggregation and adsorption to the silica surface are competing processes. For hydrophilic surfaces dispersion is still large despite the fact that adsorption energies are almost doubled with respect to the hydrophobic surface due to H-bonding interactions through either SiOH...pi (benzene case) or SiOH...OH (benzene-1,4-diol case). The computed infrared spectra of the adsorbed molecules reveal small perturbations in the CH, CCH and CCC ring modes, which are sensitive to the adsorbate/adsorbent features, so that these bands can be used as fingerprints for the interpretation of experimental spectra. The present work may contribute to a better understanding of the sorption of typical organic contaminants in common earth's inorganic soils, which is of relevance for environmental concerns.

Several tools that allow molecules, polymers, slabs, and crystals to be optimized in valence coordinates as well as a suitable saddle point optimization technique to search for transition state structures for this kind of system have been implemented in the ab initio periodic CRYSTAL code. The adoption of these localized coordinate systems largely facilitates the study of chemical processes in periodic systems with atomic connectivity, as occurs in catalytic reactions on zeolites, clathrates, or oxidic surfaces. As a paradigmatic case, the new features have been illustrated to study the proton jump between oxygen atoms of the Bronsted site in the H-chabazite zeolite. The electronic and Gibbs free energy profiles of the most representative proton jump channels have been computed at the B3LYP level, both for a dry H-chabazite as well as in the presence of one H2O molecule acting as a proton transfer helper. Because of the accuracy allowed by the optimization technique, all stationary points located have bee...

Both glycine and water exhibit a high affinity towards the hydroxyapatite HA surfaces. What happens when they are co-adsorbed at the HA (001) surface? B3LYP periodic calculations reveal that glycine displaces the pre-adsorbed water interacting directly with the HA surface.

The reaction of glycine (Gly) with a strained (SiO)(2) four-membered ring defect (D2) at the surface of an interstellar silica grain dust has been studied at ONIOM2[B3LYP/6-31+G(d,p):MNDO] level within a cluster approach in the context of hypothetical reactions occurring in the interstellar medium. The D2 opens up exothermically for reaction with Gly (Delta(r)U(0)=-26.3 kcal mol(-1)) to give a surface mixed anhydride S(surf)-O-C([double bond, length as m-dash]O)-CH(2)NH(2) as a product. The reaction barriers, DeltaU( not equal)(0), are 0.1 and 10.4 kcal mol(-1) for reactive channels involving COOH and NH(2) as attacking groups, respectively. Calculations show the surface mixed anhydride to be rather stable under the action of interstellar processes, such as reactions with isolated H(2)O and NH(3) molecules or the exposure to cosmic rays and UV radiation. The hydrolysis of the surface mixed anhydride to release again Gly was modelled by microsolvation (from 1 to 4 H(2)O molecules) mimicking what could have happened to the interstellar dust after seeding the primordial ocean in the early Earth. Results for these calculations show that the reaction is exergonic and activated, the Delta(r)G(298) becoming more negative and the DeltaG( not equal)(298) being dramatically reduced as a function of increasing number of H(2)O molecules. The present results are relevant because they show that defects present at interstellar dust surfaces could have played a significant role in capturing, protecting and delivering essential prebiotic compounds on the early Earth.

How does glycine adsorb at hydroxyapatite surfaces? Ab initio simulations based on periodic B3LYP GTO calculations reveal the detailed mechanism of binding to the (001) and (010) surfaces by shedding light on how acid and basic amino acid residues of proteins interact with hydroxyapatite based biomaterials.

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.

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.

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.

The role that silica surface could have played in prebiotic chemistry as a catalyst for peptide bond formation has been addressed at the B3LYP/6-31+G(d,p) level for a model reaction involving glycine and ammonia on a silica cluster mimicking an isolated terminal silanol group present at the silica surface. Hydrogen-bond complexation between glycine and the silanol is followed by the formation of the mixed surface anhydride Si(surf)-O-C(=O)-R, which has been suggested in the literature to activate the C=O bond towards nucleophilic attack by a second glycine molecule, here simulated by the simpler NH3 molecule. However, B3LYP/6-31+G(d,p) calculations show that formation of the surface mixed anhydride Si(surf)-O-C(=O)-R is disfavoured (delta(r)G298 approximately 6 kcal mol(-1)), and that the surface bond only moderately lowers the free-energy barrier of the nucleophilic attack responsible for peptide bond formation (deltaG298(double dagger) approximately 48 kcal mol(-1)) in comparison with the uncatalysed reaction (deltaG298(double dagger) approximately 52 kcal mol(-1)). A further decrease of the free-energy barrier of peptide bond formation (deltaG298(double dagger) approximately 41 kcal mol(-1)) is achieved by a single water molecule close to the reaction centre acting as a proton-transfer helper in the activated complex. A possible role of strained silica surface defects on the formation of the surface mixed anhydride Si(surf)-O-C(=O)-R has also been addressed.

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.

The role of Lewis and Bronsted catalysts on the NH3 + HCOOH -> NH2CHO + H2O reaction has been studied ab initio using hydrogen fluoride and trifluoroaluminum as model systems of Bronsted and Lewis catalysts, respectively. Both catalysts, either alone or in combination, have been adopted to activate the synthesis of formamide, the simplest model of a peptide bond containing molecule, by reacting formic acid and ammonia. It has been found that the synergy between both catalysts dramatically lowers the activation barrier for the amide bond formation, a fact relevant in the prebiotic synthesis of peptides on the surface of oxidic minerals rich in Lewis/Bronsted sites. (c) 2005 Elsevier B.V. All rights reserved

The ground and low-lying states of Cu2+−H2O have been studied using different density functional and post-Hartree−Fock methods. CCSD(T) results indicate that Cu2+−H2O has C2v symmetry and that the ground electronic state is a 2A1 state. At this level of theory the relative order of the electronic states is 2A1 < 2B1 < 2B2 < 2A2. However, density functional results show that the relative stabilities of these states vary depending on the degree of mixing of exact Hartree−Fock (HF) and density functional (DF) exchange. For pure generalized gradient approximation (GGA) functionals and also for hybrid functionals with percentages of HF mixing up to ∼20−25%, the 2B1 state becomes more stable than the 2A1 one. Moreover, with these functionals a Cs(2A‘) structure is found to be the ground-state structure of Cu2+−H2O. This is attributed to the fact that, for C2v(2B1) and Cs(2A‘), GGA functionals provide a delocalized picture of the electron hole, which is overstabilized due to a bad cancellation of the self-intera...

Context. Successive hydrogenation reactions of CO on interstellar icy grain surfaces are considered one of the most e cient mechanisms in interstellar environments for the formation of H2CO and CH3OH, two of the simplest organic molecules detected in space. In the past years, several experimental and theoretical works have been focused on these reactions, providing relevant information both at the macroscopic and atomic scale. However, several questions still remain open, such as the exact role played by water in these processes, a crucial aspect because water is the dominant constituent of the ice mantles around dust grain cores. Aims. We here present a quantum chemical description of the successive H additions to CO both in the gas phase and on the surfaces of several water clusters. Methods. The hydrogenation steps were calculated by means of accurate quantum chemical methods and structural cluster models consisting of 3, 18, and 32 water molecules. Results. Our main result is that the interaction of CO and H2CO with the water cluster surfaces through H-bonds with the O atoms increases the C O polarization, thus weakening the C O bond. Consequently, the C atoms are more prone to receiving H atoms, which in turn lowers the energy barriers for the H additions compared to the gas-phase processes. The calculated energy barriers and transition frequencies associated with the reaction coordinate were adopted as input parameters in our numerical model of the surface chemistry (GRAINOBLE) to simulate the distribution of the H2CO and CH3OH ice abundances (with respect to water). Our GRAINOBLE results based on the energy barriers and transition frequencies for the reactions on the 32 water molecule cluster compare well with the observed abundances in low-mass protostars and dark cores.

Glycine is the simplest amino acid, and due to the significant astrobiological implications that suppose its detection, the search for it in the interstellar medium (ISM), meteorites, and comets is intensively investigated. In the present work, quantum mechanical calculations based on density functional theory have been used to model the glycine formation on water-ice clusters present in the ISM. The removal of either one H atom or one electron from the water-ice cluster has been considered to simulate the effect of photolytic radiation and of ionizing particles, respectively, which lead to the formation of OH{sup .} radical and H{sub 3}O{sup +} surface defects. The coupling of incoming CO molecules with the surface OH{sup .} radicals on the ice clusters yields the formation of the COOH{sup .} radicals via ZPE-corrected energy barriers and reaction energies of about 4-5 kcal mol{sup -1} and -22 kcal mol{sup -1}, respectively. The COOH{sup .} radicals couple with incoming NH=CH{sub 2} molecules (experimentally detected in the ISM) to form the NHCH{sub 2}COOH{sup .} radical glycine through energy barriers of 12 kcal mol{sup -1}, exceedingly high at ISM cryogenic temperatures. Nonetheless, when H{sub 3}O{sup +} is present, one proton may be barrierless transferred to NH=CH{sub 2} tomore » give NH{sub 2}=CH{sub 2}{sup +}. This latter may react with the COOH{sup .} radical to give the NH{sub 2}CH{sub 2}COOH{sup +.} glycine radical cation which can then be transformed into the NH{sub 2}CHC(OH){sub 2}{sup +.} species (the most stable form of glycine in its radical cation state) or into the NH{sub 2}CHCOOH{sup .} neutral radical glycine. Estimated rate constants of these events suggest that they are kinetically feasible at temperatures of 100-200 K, which indicate that their occurrence may take place in hot molecular cores or in comets exposed to warmer regions of solar systems. Present results provide quantum chemical evidence that defects formed on water ices due to the harsh-physical conditions of the ISM may trigger reactions of cosmochemical interest. The relevance of surface H{sub 3}O{sup +} ions to facilitate chemical processes by proton transfer (i.e., acting as acidic catalysts) is highlighted, and plausible ways of their formation at the water-ice surface in the ISM are also discussed.« less

The reactivity of the strained (SiO)(2)-four atom ring defect at the silica surfaces has been studied in a cluster approach adopting the ONIOM2[B3LYP6-31+G(d,p):MNDO] method to compute the ring opening reaction by interaction with H(2)O and NH(3). The vibrational "fingerprints" of the isolated defect are computed at 921, 930, and 934 cm(-1) in reasonable agreement with experimental evidence on amorphous silica outgassed at T900 K. The opening of the (SiO)(2)-four-member ring by the considered molecules is exergonic and the actual value depends on the possible constraints enforced on the reaction products by the silica surrounding. The free kinetic energy barriers result from the interplay between the nucleophilic/electrophilic character of the adsorbed molecule and are 22 and 25 kcal mol(-1) for NH(3) and H(2)O, respectively. All free energy profiles envisage an activated complex in which the nucleophilic part of the molecule interacts on the coordinatively strained silicon atom of the (SiO)(2) defect followed by the proton transfer from the coordinated molecule towards the oxygen of the defective ring. Calculations show that this step can be speed up by the presence of more than one adsorbed molecule or even more (about seven orders of magnitude), by the copresence of water molecules acting as "proton transfer helpers." In these cases, the free energy barriers decrease to approximately 13 and 15 kcal mol(-1) for NH(3) and H(2)O, respectively. For the case of H(2)O adsorption, benchmark test calculations reveal that MP2, BLYP, and B3LYP energy profiles are in very good agreement with each other, whereas for PBE, both the reaction energy and the activation barrier are underestimated. Present data also show that the molecular model mimicking the (SiO)(2) defect is far less reactive than what appears to occur on the real defect at the surface of amorphous silica. So, only a combination of some further geometrical strains imparted by the solid on the (SiO)(2) defect, not accounted for by the cluster models, and higher adsorbate loadings are needed to reharmonize experiment and simulation. Notwithstanding, the vibrational features of the reaction products have been characterized and support the available experimental measurements.

The structure, vibrational frequencies and binding energies of the complexes formed by the interaction of Cu+(d10, 1S), Ni+(d9, 2D) and Co+(d8, 3F and 1G) with glycylglycine have been theoretically determined. The most stable structure of Cu+–glycylglycine is bicoordinated with the Cu+ cation interacting with the terminal carbonyl oxygen and the amino group. However, for Ni+–glycylglycine and Co+–glycylglycine the lowest energy structures are tricoordinated, the interaction of the metal cation given by the same groups of Cu+-glycylglycine plus the nitrogen or oxygen atoms of the peptide bond. As for glycine, De values follow the order Ni+ > Co+ (triplet) ∼ Cu+, but the interaction energies are about 11–13 kcal mol−1 larger. Differences on the coordination properties of the metal cations are discussed and interpreted according to their electronic structure.

Phosphorous is ubiquitous in planet Earth and plays a fundamental role in all living systems. Finding a reasonable prebiotic source of phosphorous is not trivial, as common sources where it is present nowadays are in the form of phosphate minerals, which are rather insoluble and non-reactive materials, and, accordingly, unavailable for being readily incorporated in living organisms. A possible source of phosphorous is from the exogenous meteoritic bombardment and, in particular, in iron/nickel phosphites. These materials, by simple interaction with water, produce oxygenated phosphorous compounds, which can easily react with organic molecules, thus forming C-O-P bonds. In the present work, periodic ab-initio simulations at PBE level (inclusive of dispersive interactions) have been carried out on metallic Fe2NiP-schreibersite, as a relative abundant component of metallic meteorites, in order to characterize structural, energetics and vibrational properties of both bulk and surfaces of this material. The aim is to study the relative stability among different surfaces, to characterize both the nanocrystal morphology and the reactivity towards water molecules.