Influence of Defects in Boron Nitride Nanotubes in the Adsorption of Molecules : Insights from B3LYP-D2* Periodic Simulations

The adsorption of H2O, NH3 and HCOOH as polar molecules and C6H6 and CH4 as non-polar ones on a series of zig-zag (6,0) single-walled boron nitride nanotubes (BNNTs) both being defect-free (P_BNNT) and containing defects at the nanotube walls has been studied by means of B3LYP-D2* periodic calculations. We focused on defects derived from monovacancies of B (N-rich_BNNT) and N (B-rich_BNNT) atoms and also on Stone-Wales defects (SW_BNNT). The adsorption of polar molecules with defective BNNTs is generally based on dative interactions and H-bonding, and their adsorption energies strongly depend on the type of BNNT. N-rich_BNNT is the most reactive nanotube towards adsorption of polar molecules, as in all cases deprotonation of the polar molecules is spontaneously given upon adsorption. The strength in the adsorption energies is followed by B-rich_BNNT, SW_BNNT and P_BNNT. Adsorption of non-polar molecules is mainly dictated by dispersion interactions, and, accordingly, the adsorption energies are almost constant for a given molecule irrespective of the type of nanotube

The (impossible?) formation of acetaldehyde on the grain surfaces: insights from quantum chemical calculations

Complex Organic Molecules (COMs) have been detected in the interstellar medium (ISM). However, it is not clear whether their synthesis occurs on the icy surfaces of interstellar grains or via a series of gas-phase reactions. As a test case of the COMs synthesis in the ISM, we present new quantum chemical calculations on the formation of acetaldehyde (CH3CHO) from the coupling of the HCO and CH3 radicals, both in gas phase and on water ice surfaces. The binding energies of HCO and CH3 on the amorphous water ice were also computed (2333 and 734 K, respectively). Results indicate that, in gas phase, the products could be either CH3CHO, CH4 + CO, or CH3OCH, depending on the relative orientation of the two radicals. However, on the amorphous water ice, only the CH4 + CO product is possible due to the geometrical constraints imposed by the water ice surface. Therefore, acetaldehyde cannot be synthesized by the CH3 + HCO coupling on the icy grains. We discuss the implications of these results and other cases, such as ethylene glycol and dimethyl ether, in which similar situations can occur, suggesting that formation of these molecules on the grain surfaces might be unlikely

Formation of interstellar silicate dust via nanocluster aggregation : Insights from quantum chemistry simulations

The issue of formation of dust grains in the interstellar medium is still a matter of debate. One of the most developed proposals suggests that atomic and heteromolecular seeds bind together to initiate a nucleation process leading to the formation of nanostructures resembling very small grain components. In the case of silicates, nucleated systems can result in molecular nanoclusters with diameters ≤ 2 nm. A reasonable path to further increase the size of these proto-silicate nanoclusters is by mutual aggregation. The present work deals with modeling this proto-silicate nanocluster aggregation process by means of quantum chemical density functional theory calculations. We simulate nanocluster aggregation by progressively reducing the size of a periodic array of initially well-separated nanoclusters. The resulting aggregation leads to a set of silicate bulk structures with gradually increasing density which we analyze with respect to structure, energetics and spectroscopic properties. Our results indicate that aggregation is a highly energetically favorable process, in which the infrared spectra of the finally formed amorphous silicates match well with astronomical observations

Gas-Phase and Microsolvated Glycine Interacting with Boron Nitride Nanotubes : a B3LYP-D2* Periodic Study

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

Computational Investigation on the Thermodynamics of H2CO + NH2 → NH2CHO + H on Interstellar Water Ice Surfaces

Altres ajuts: "Ramón y Cajal" programFormamide has a key role in prebiotic chemistry as it is the simplest molecule containing the four most important atoms from a biological point of view: hydrogen, carbon, nitrogen and oxygen. Due to its importance, the formation of this molecule has been studied and different pathways have been considered both in gas-phase and on ices of dust grains since it was first detected. In the present work, the thermodynamics of the formation route of formamide starting from NH2 and H2CO, a reaction channel proposed to occur in the gas phase, has been theoretically investigated in the scenario taking place on icy dust grains modelled by both a cluster and a periodic approach. Different DFT functionals have been employed to obtain accurate energy values for the mechanistic steps involved in the reaction

Formation of Interstellar Silicate Dust via Nanocluster Aggregation: Insights From Quantum Chemistry Simulations

The issue of formation of dust grains in the interstellar medium is still a matter of debate. One of the most developed proposals suggests that atomic and heteromolecular seeds bind together to initiate a nucleation process leading to the formation of nanostructures resembling very small grain components. In the case of silicates, nucleated systems can result in molecular nanoclusters with diameters ≤ 2 nm. A reasonable path to further increase the size of these proto-silicate nanoclusters is by mutual aggregation. The present work deals with modeling this proto-silicate nanocluster aggregation process by means of quantum chemical density functional theory calculations. We simulate nanocluster aggregation by progressively reducing the size of a periodic array of initially well-separated nanoclusters. The resulting aggregation leads to a set of silicate bulk structures with gradually increasing density which we analyze with respect to structure, energetics and spectroscopic properties. Our results indicate that aggregation is a highly energetically favorable process, in which the infrared spectra of the finally formed amorphous silicates match well with astronomical observations

Prebiotic peptide bond formation through amino acid phosphorylation : insights from quantum chemical simulations

Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they present high activation energies. In living organisms, in the formation of peptides by condensation of amino acids, this issue is overcome by the participation of adenosine triphosphate (ATP), in which, previous to the condensation, phosphorylation of one of the reactants is carried out to convert it as an activated intermediate. In this work, we present for the first time results based on density functional theory (DFT) calculations on the peptide bond formation between two glycine (Gly) molecules adopting this phosphorylation-based mechanism considering a prebiotic context. Here, ATP has been modeled by a triphosphate (TP) component, and different scenarios have been considered: (i) gas-phase conditions, (ii) in the presence of a Mg2+ ion available within the layer of clays, and (iii) in the presence of a Mg2+ ion in watery environments. For all of them, the free energy profiles have been fully characterized. Energetics derived from the quantum chemical calculations indicate that none of the processes seem to be feasible in the prebiotic context. In scenarios (i) and (ii), the reactions are inhibited due to unfavorable thermodynamics associated with the formation of high energy intermediates, while in scenario (iii), the reaction is inhibited due to the high free energy barrier associated with the condensation reactions. As a final consideration, the role of clays in this TP-mediated peptide bond formation route is advocated, since the interaction of the phosphorylated intermediate with the internal clay surfaces could well favor the reaction free energies

Activation of amino acids and peptides by interaction of Cu+ and Cu2+ cations and aluminosilicate surfaces

Consultable des del TDXTítol obtingut de la portada digitalitzadaUna molècula està activada quan, per acció d'un agent extern, mostra una reactivitat diferent que en el seu estat normal. Vies d'activació freqüents són per interacció amb cations metàl·lics, per absorció de radiació ionitzant o ultraviolada com també per adsorció en superfícies sòlides. Aquest treball tracta sobre l'activació de petites biomolècules, en concret d'aminoàcids i pèptids, per interacció amb cations de coure i aluminosilicats. Avui en dia es poden generar sistemes metall-lligand en fase gas i estudiar-ne la reactivitat induïda per la interacció amb els cations metàl·lics gràcies a les tècniques d'espectrometria de masses, les quals són rellevants en àrees com la proteòmica o la bioquímica. Aquesta tesi, doncs, es centra en el context de la química metal·loiònica en fase gas on es combinen càlculs teòrics amb experiments d'espectrometria de masses. No obstant, també tracta des d'un punt de vista mecanoquàntic l'activació de biomolècules per interacció amb superfícies de minerals degut a la seva importància en la química prebiòtica.A molecule is activated when, owing to an external agent, it displays different reactivity than in its normal state. The activation can be given by interaction with metal cations, by absorption of ionizing or UV radiation as well as by adsorption on solid surfaces. This work addresses the activation of small biomolecules, in particular amino acids and peptides, by the interaction with copper cations and aluminosilicates. Nowadays generating metal-ligand systems in the gas phase and studying the reactivity induced by the metal cations is feasible by means of recent mass spectrometry techniques, which are relevant in the areas of proteomics and biochemistry. This thesis, thus, is focused on the gas phase metal ion chemistry, in which theoretical calculations are combined with mass spectrometry experiments. Nevertheless, the activation of biomolecules by interaction with mineral surfaces has also been addressed from a quantum mechanic point of view, since its importance in the prebiotic chemistry

IR Spectral Fingerprint of Carbon Monoxide in Interstellar Water Ice Models

Carbon monoxide (CO) is the second most abundant molecule in the gas-phase of the interstellar medium. In dense molecular clouds, it is also present in the solid-phase as a constituent of the mixed water-dominated ices covering dust grains. Its presence in the solid-phase is inferred from its infrared (IR) signals. In experimental observations of solid CO/water mixed samples, its IR frequency splits into two components, giving rise to a blue- and a redshifted band. However, in astronomical observations, the former has never been observed. Several attempts have been carried out to explain this peculiar behaviour, but the question still remains open. In this work, we resorted to pure quantum mechanical simulations in order to shed some light on this problem. We adopted different periodic models simulating the CO/H$_2$O ice system, such as single and multiple CO adsorption on water ice surfaces, CO entrapped into water cages and proper CO:H$_2$O mixed ices. We also simulated pure solid CO. The detailed analysis of our data revealed how the quadrupolar character of CO and the dispersive forces with water ice determine the energetic of the CO/H$_2$O ice interaction, as well as the CO spectroscopic behaviour. Our data suggest that the blueshifted peak can be assigned to CO interacting {\it via} the C atom with dangling H atoms of the water ice, while the redshifted one can actually be the result of CO involved in different reciprocal interactions with the water matrix. We also provide a possible explanation for the lack of the blueshifted peak in astronomical spectra. Our aim is not to provide a full account of the various interstellar ices, but rather to elucidate the sensitivity of the CO spectral features to different water ice environments.Comment: MNRAS, accepte

Can Formamide Be Formed on Interstellar Ice? An Atomistic Perspective

Interstellar formamide (NH2CHO) has recently attracted significant attention due to its potential role as a molecular building block in the formation of precursor biomolecules relevant for the origin of life. Its formation, whether on the surfaces of the interstellar grains or in the gas phase, is currently debated. The present article presents new theoretical quantum chemical computations on possible NH2CHO formation routes in water-rich amorphous ices, simulated by a 33-H2O-molecule cluster. We have considered three possible routes. The first one refers to a scenario used in several current astrochemical models, that is, the radical-radical association reaction between NH2 and HCO. Our calculations show that formamide can indeed be formed, but in competition with formation of NH3 and CO through a direct H transfer process. The final outcome of the NH2 + HCO reactivity depends on the relative orientation of the two radicals on the ice surface. We then analyzed two other possibilities, suggested here for the first time: reaction of either HCN or CN with water molecules of the ice mantle. The reaction with HCN has been found to be characterized by large energy barriers and, therefore, cannot occur under the interstellar ice conditions. On the contrary, the reaction with the CN radical can occur, possibly leading through multiple steps to the formation of NH2CHO. For this reaction, water molecules of the ice act as catalytic active sites since they help the H transfers involved in the process, thus reducing the energy barriers (compared to the gas-phase analogous reaction). Additionally, we apply a statistical model to estimate the reaction rate coefficient when considering the cluster of 33-H2O-molecules as an isolated moiety with respect to the surrounding environment, i.e., the rest of the ice