First Principles Calculations of the Adsorption of NH3 on a Periodic Model of the Silica Surface

Unraveling the Intrinsic Biocidal Activity of the SiO2-Ag Composite against SARS-CoV-2: A Joint Experimental and Theoretical Study

The COVID-19 pandemic has emerged as an unprecedented global healthcare emergency, demanding the urgent development of effective materials to inactivate the SARS-CoV-2 virus. This research was planned to disclose the remarkable biocidal activity of SiO2-Ag composites incorporated into low-density polyethylene. For this purpose, a joint experimental and theoretical [based on first-principles calculations at the density functional theory (DFT) level] study is performed. Biological assays showed that this material eliminatesStaphylococcus aureusand SARS-CoV-2 virus in just 2 min. Here, we investigate a previously unexplored process that we postulate may occur along the O2 and H2O adsorption and activation processes of pure and defective SiO2-Ag surfaces for the generation of reactive oxygen species (ROS). The obtained results help us to predict the nature of ROS: superoxide anion radicals, •O2-, hydroxyl radicals, •OH, and hydroperoxyl radicals, •HO2, that destroy and degrade the structure of the SARS-COV-2 virus. This is consistent with the DFT studies, where the energetic, electronic, and magnetic properties of the intermediates show a feasible formation of ROS. Present findings are expected to provide new insights into the relationship among the structure, property, and biocidal activity of semiconductor/metal SiO2-Ag composites.

Acidity of SiO2-Supported Metal Oxides in the Presence of H2O Using the Adsorption Equilibrium Infrared Spectroscopy Method: 1. Adsorption and Coadsorption of NH3 and H2O on SiO2

The present study is dedicated to the characterization (identification, heats of adsorption, and coverages) of the adsorbed species formed by the adsorption and coadsorption of NH₃ and H₂O on two SiO₂ solids. Adsorption equilibrium infrared spectroscopy allowed us (a) to show that NH₃ and H₂O are mostly adsorbed on free SiOH groups via H bonds and (b) to determine their individual heats of adsorption: 53 and 49 kJ/mol, whatever be their coverages (Langmuir adsorption model), for NH_3ads and H₂O_ads, respectively. These values consistent with the microcalorimetry literature data explain that their coverages are decreased upon NH₃-H₂O coadsorption, considering a competitive Langmuir model. However, the temperature-programmed adsorption equilibrium procedure achieved from MS data indicated that a minor amount of other NH₃ species (not detected using Fourier-transform infrared) is more strongly adsorbed and that hydrolysis of SiOSi siloxane by H₂O could occur in parallel. NH₃-H₂O coadsorption leads to the formation of NH₄⁺ species, which involves H₂O adsorbed species. Both NH₃ and H₂O are not adsorbed above 450 K, which means that the SiO₂ contribution to the characterization of the acidity of metal oxide catalysts supported on SiO₂ using NH₃ as the probe molecule in the presence of H₂O is negligible above this temperature.

The Adhesion Mechanism of Marine Mussel Foot Protein: Adsorption of L-Dopa onα- and β-Cristobalite Silica Using Density Functional Theory

Marine mussels strongly adhere to various surfaces and endure their attachment under a variety of conditions. In order to understand the basic mechanism involved, we study the adsorption of L-dopa molecule on hydrophilic geminal and terminal isolated silanols of silica (001) surface. High content of modified amino acid L-dopa is found in the glue-like material secreted by the mussels through which it sticks to various surfaces under water. To understand the adsorption behavior, we have made use of periodic Density Functional Theory (DFT) study. The L-dopa molecule adheres to silica surfaces terminated with geminal and terminal silanols via its catechol part. In both cases, the adhesion is achieved through the formation of 4 H-bonds. A binding energy of 29.48 and 31.67 kcal/mol has been estimated, after the inclusion of dispersion energy, for geminal and terminal silanols of silica, respectively. These results suggest a relatively stronger adhesion of dopa molecule for surface with terminal isolated silanols.

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.

First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets

The seven main crystal surfaces of forsterite (Mg2 SiO4 ) were modeled using various Gaussian-type basis sets, and several formulations for the exchange-correlation functional within the density functional theory (DFT). The recently developed pob-TZVP basis set provides the best results for all properties that are strongly dependent on the accuracy of the wavefunction. Convergence on the structure and on the basis set superposition error-corrected surface energy can be reached also with poorer basis sets. The effect of adopting different DFT functionals was assessed. All functionals give the same stability order for the various surfaces. Surfaces do not exhibit any major structural differences when optimized with different functionals, except for higher energy orientations where major rearrangements occur around the Mg sites at the surface or subsurface. When dispersions are not accounted for, all functionals provide similar surface energies. The inclusion of empirical dispersions raises the energy of all surfaces by a nearly systematic value proportional to the scaling factor s of the dispersion formulation. An estimation for the surface energy is provided through adopting C6 coefficients that are more suitable than the standard ones to describe O-O interactions in minerals. A 2 × 2 supercell of the most stable surface (010) was optimized. No surface reconstruction was observed. The resulting structure and surface energy show no difference with respect to those obtained when using the primitive cell. This result validates the (010) surface model here adopted, that will serve as a reference for future studies on adsorption and reactivity of water and carbon dioxide at this interface.

Facile functionalized of SBA-15 via a biomimetic coating and its application in efficient removal of uranium ions from aqueous solution

A novel dopamine-functionalized mesoporous silica (DMS), synthesized by grafting dopamine onto a mesoporous molecular sieve (SBA-15), was developed as a sorbent to extract U(VI) from aqueous solution. The method used to modify SBA-15 was simple, facile and cost-effective. The DMS was characterized by SEM, TEM, XRD and BET, showing that the material had an ordered mesoporous structure and a large surface area. The effect of contact time, pH, ionic strength, temperature, and solid-liquid ratio on the sorption process was investigated. It was demonstrated that the adsorption of U(VI) by DMS was fast and that it can be described by the pseudo-second order-equation where the equilibrium time was 20 min. Additionally, the adsorption isotherm data were fitted well by the Langmuir model with the maximum adsorption capacity of DMS of 196 mg/g at pH 6.0. Furthermore, the influence of the K(+) and Na(+) concentrations and solid-to-liquid ratio on the sorption was very weak, and the values of the thermodynamic parameters revealed that the sorption process was exothermic and spontaneous. All the results suggested that the DMS could be used as an excellent adsorbent to remove U(VI) from aqueous solution.

Hydrogen-induced rupture of strained Si─O bonds in amorphous silicon dioxide

Using ab initio modeling we demonstrate that H atoms can break strained Si─O bonds in continuous amorphous silicon dioxide (a-SiO(2)) networks, resulting in a new defect consisting of a threefold-coordinated Si atom with an unpaired electron facing a hydroxyl group, adding to the density of dangling bond defects, such as E' centers. The energy barriers to form this defect from interstitial H atoms range between 0.5 and 1.3 eV. This discovery of unexpected reactivity of atomic hydrogen may have significant implications for our understanding of processes in silica glass and nanoscaled silica, e.g., in porous low-permittivity insulators, and strained variants of a-SiO(2).

Grafting of lanthanide complexes on silica surfaces dehydroxylated at 200 °C: a theoretical investigation

The grafting reaction of lanthanide silylamide complexes has been studied, in the framework of the DFT, highlighting the different grafting modes on a silica surface dehydroxylated at 200 °C.

Do H-bond features of silica surfaces affect the H2O and NH3 adsorption? Insights from periodic B3LYP calculations

The adsorption of a single H(2)O and NH(3) molecule on different fully hydroxylated α-quartz, cristobalite, and tridymite surfaces has been studied at the B3LYP level of theory, within a periodic approach using basis sets of polarized triple-ζ quality and accounting for basis set superposition error (BSSE). Fully hydroxylated crystalline silica exhibits SiOH as terminal groups whose distribution and H-bond features depend on both the considered silica polymorph and the crystallographic plane, which gives rise to isolated, H-bond interacting SiOH pairs or infinitely connected H-bond chains. A key point of the present study is to understand how the H-bond features of a dry crystalline silica surface influence its adsorption properties. Results reveal that the silica-adsorbate (H(2)O and NH(3)) interaction energy anticorrelates with the density of SiOH groups at the surface. This counterintuitive observation arises from the fact that pre-existing H-bonds of the dry surface need to be broken to establish new H-bonds between the surface and the adsorbate, which manifests in a sizable energy cost due to surface deformation. A simple method is also proposed to estimate the strength of the pre-existing H-bonds at the dry surfaces, which is shown to anticorrelate with the adsorbate interaction energy, in agreement with the above trends.

Atomistic simulations of materials for optical chemical sensors: DFT-D calculations of molecular interactions between gas-phase analyte molecules and simple substrate models

The structures of complexes of some small molecules (formaldehyde, acetaldehyde, ammonia, methylamine, methanol, ethanol, acetone, benzene, acetonitrile, ethyl acetate, chloroform, and tetrahydrofuran, considered as possible analytes) with ethylbenzene and silanol (C(6)H(5)C(2)H(5) and SiH(3)OH, considered as models of polystyrene and silica gel substrates) and with acridine (C(13)H(9)N, considered as a model of an indicator dye molecule of the acridine series) and the corresponding interaction energies have been calculated using the DFT-D approximation. The PBE exchange-correlation potential was used in the calculations. The structures of complexes between the analyte and the substrate were determined by optimizing their ground-state geometry using the SVP split-valence double-zeta plus polarization basis set. The complex formation energies were refined by single-point calculations at the calculated equilibrium geometries using the sufficiently large triple-zeta TZVPP basis set. The calculated interaction energies are used to assess the possibility of using dyes of the acridine series adsorbed on a polystyrene or silica substrate for detecting the small molecules listed above.

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.

Convergence of electric field and electric field gradient versus atomic basis sets in all-siliceous and Mg substituted phillipsites

Electrostatic potential (EP), electric field (EF), and electric field gradient (EFG) values are calculated in periodic models of magnesium substituted phillipsite (MgPHI) zeolite forms using periodic DFT (PDFT) hybrid B3LYP level with fourteen different basis sets. Relative root mean square differences between the EP, EF, or EFG values estimated between different basis sets are evaluated in several spatial domains available for adsorbate molecules in the zeolite. In these areas, the EF increase in MgPHI is evaluated relative to all-siliceous PHI types. The EP is interpreted in terms of framework ionicity for MgPHI and all-siliceous PHI models. Angular Si-O-Si dependence of the EFG asymmetry at (17)O atoms in all-siliceous zeolites is discussed.

Electric field convergence versus atomic basis sets in all-siliceous zeolites

The electrostatic potential (EP) and electric field (EF) are calculated in the TON and CHA zeolites using periodic hybrid B3LYP, PBE, and PW91 functionals considering eight basis sets. Relative root mean square differences between the EP or EF values estimated between the different basis sets are evaluated in several domains available for adsorbate molecules in both zeolites. The EP is interpreted in terms of ionicity of the framework.

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.

Thermodynamic Study of Water Adsorption in High-Silica Zeolites

The joint use of microcalorimetric and computational approaches has been adopted to describe H2O interaction with cus Al(III) Lewis and Si(OH)+ Al- Brønsted acidic sites within H-BEA and H-MFI zeolites (both with approximately 6 Al/unit cell). Adsorption data obtained at 303 K were compared to experimental model systems, such as all-silica zeolites, amorphous silica, and silico-alumina, transition alumina. In parallel, ab initio molecular modeling was carried out to mimic, in a cluster approach, Lewis and Brønsted acidic sites, as well as a variety of Si-OH species either with H-bonding interacting (nests and pairs) or isolated. H-BEA and H-MFI water affinity values were found to be almost equivalent, in both quantitative and energetic terms, in that dominated by Al-containing sites population, more than by nanocavity topology or by acidic site nature. Both H-zeolites, saturated with approximately 5 Torr of H2O vapor, bind approximately 4 H2O per Al site, almost one of which is tightly bound and not eliminated by RT pumping-off. A 160 < q(diff) < 80 kJ/mol interval was measured for the adsorption up to 1H2O/Al. The zero-coverage heat of adsorption (q0 approximately 160 kJ/mol, for both H-zeolites) was assigned to H2O/Lewis complex formation, which dominates the early stage of the process, in agreement with the ab initio computed H2O/Lewis sites binding energy. The rather broad q(diff) interval was interpreted as due to the simultaneous adsorption of H2O on both structural Brønsted sites and strongly polarized H2O already adsorbed on Lewis sites. For this latter species, BE = 74 kJ/mol was computed, slightly higher than BE = 65 kJ/mol for H2O/Brønsted sites interaction, showing that H2O coordinated on cus Al(III) Lewis sites behaves as a structural Brønsted site. The investigated all-silica zeolites have been categorized as hydrophilic in that the measured heat of adsorption (100 < q(diff) < 44 kJ/mol) was larger than the heat of liquefaction of water (44 kJ/mol) in the whole coverage examined. Indeed, polar defects present in the hydrophobic Si-O-Si framework do form relatively stable H2O adducts. Crystalline versus amorphous aluminosilicate q(diff) versus n(ads) plots showed that the measured adsorption heat is lower than expected, due to the extraction work of Al atoms from the amorphous matrix to bring them in interaction with H2O. On the contrary, such an energy cost is not required for the crystalline material, in which acidic sites are already in place, as imposed by the rigidity of the framework. Modeling results supported the experimental data interpretation.

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

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 katoite hydrogarnet Si-free Ca3Al2([OH]4)3: A periodic Hartree–Fock and B3-LYP study

The structure of the Si-free katoite hydrogarnet (116 atoms in the unit cell) has been investigated at the periodic ab initio quantum mechanical level with the CRYSTAL program, by using a Gaussian type basis set and both the HF and the hybrid B3-LYP Hamiltonians. The structure has been fully optimized at various pressures in the 0-46 GPa range; the modifications of the structure, and in particular of the (OH)4 group, as a function of pressure are analyzed. At the B3-LYP level and P greater than 15 GPa, a O-H...O interaction of increasing strength appears, with important modifications in the local geometry of the tetrahedral site. The calculated omega01(O-H) fundamental vibrational frequency at zero pressure is in excellent agreement with experiment (3674 and 3663 cm(-1), respectively); the omega01(O-H) stretching frequency remains essentially constant in the 0-15 GPa interval, whereas it dramatically decreases at higher pressures with a corresponding anharmonicity increase, as a consequence of the formation of a strong hydrogen bond. The hydration energy of grossular and the formation energy of Si-free katoite have also been computed, and the B3-LYP results are in quite good agreement with experiment.

Calculation of the vibration frequencies of ?-quartz: The effect of Hamiltonian and basis set

The central-zone vibrational spectrum of alpha-quartz (SiO2) is calculated by building the Hessian matrix numerically from the analytical gradients of the energy with respect to the atomic coordinates. The nonanalytical part is obtained with a finite field supercell approach for the high-frequency dielectric constant and a Wannier function scheme for the evaluation of Born charges. The results obtained with four different Hamiltonians, namely Hartree-Fock, DFT in its local (LDA) and nonlocal gradient corrected (PBE) approximation, and hybrid B3LYP, are discussed, showing that B3LYP performs far better than LDA and PBE, which in turn provide better results than HF, as the mean absolute difference from experimental frequencies is 6, 18, 21, and 44 cm(-1), respectively, when a split valence basis set containing two sets of polarization functions is used. For the LDA results, comparison is possible with previous calculations based on the Density Functional Perturbation Theory and usage of a plane-wave basis set. The effects associated with the use of basis sets of increasing size are also investigated. It turns out that a split valence plus a single set of d polarization functions provides frequencies that differ from the ones obtained with a double set of d functions and a set of f functions on all atoms by on average less than 5 cm(-1).