Atomistic Model of Micelle-Templated Mesoporous Silicas: Structural, Morphological, and Adsorption Properties

The structural, morphological, and adsorption properties of MCM-41 porous silicas are investigated using a realistic numerical model obtained by means of <i>ab initio</i> calculations [Ugliengo, P.; et al. <i>Adv. Mater.</i> <b>2008</b>, <i>20</i>, 1]. Simulated X-ray diffraction, small angle neutron scattering, and electronic microscopy for the atomistic model are in good agreement with experimental data. The morphological features are also assessed from chord length distributions and porous volume and specific geometrical surface calculations, etc. The N₂, CO₂, and H₂O adsorption isotherms in the atomistic model of MCM-41 are also in reasonable agreement with their experimental counterpart. An important finding of the present work is that water forms a film adsorbed on specific hydrophilic regions of the surface while the rest of the surface is depleted in water molecules. This result suggests that the surface of MCM-41 materials is heterogeneous, as it is made up of both hydrophilic and hydrophobic patches. While adsorption and irreversible capillary condensation can be described using the thermodynamical approach by Derjaguin (also known as the Derjaguin–Broekhoff–De Boer model), the Freundlich equation fits nicely the data for reversible and continuous filling in small pores

Amide and Peptide Bond Formation: Interplay between Strained Ring Defects and Silanol Groups at Amorphous Silica Surfaces

The formation of amide and peptide bonds on plain amorphous silica surfaces was studied by DFT-D3 methods on cluster silica surface models involving strained SiO rings as sources of reactivity. The amide/peptide bond-formation reaction was found to be thermodynamically and kinetically favored compared to the gas-phase processes because of the copresence of surface (SiO)₂/(SiO)₃ strained ring defects, resulting from the high-temperature treatment of silica, and spatially close SiOH silanol groups. Preliminary extended calculations involving ammonia and formic acid provided insights into the most promising reaction paths for amide bond formation on defective silica surfaces. These paths were also employed to study glycine dipeptide formation. The reactions proceed through two steps: (i) silica ring opening by reaction with carboxylic acids to form a SiOC­(O) surface mixed anhydride (SMA) and (ii) reaction of the SMA with amines to form the amide product. The key point of the overall reaction is the synergy between the strained SiO rings and the spatially close silanol groups: SMA formation forces carboxylic acids to be immobilized on the surface, whereas SiOH groups act as effective mild Brønsted catalytic acidic sites through a silanol-assisted proton-relay mechanism in the second step. These results provide some atomistic insights into recent experimental findings on the formation of amides catalyzed by bare silica surfaces

Stability of the Dipolar (001) Surface of Hydroxyapatite

The features of the ferroelectric (proton ordered) hydroxyapatite HA (001) surface as derived from the <i>P</i>6₃ hexagonal HA bulk have been studied by periodic density functional calculations using the hybrid B3LYP functional and Gaussian basis set of polarized double-ζ quality. Geometry, surface energy, and electronic features of HA (001) slab models of thickness from 1 nm to almost 50 nm have been computed, by keeping under careful control numerical errors due to the very large system size. The present results reveal that the ferroelectric OH^– alignment does not compromise the stability of the HA (001) surface up to the nanometric scale. Indeed, a slab thickness of 43 nm, containing 2640 atoms in the unit cell, exhibits a dipole moment across the slab of 0.73 D, a wide band gap of 7.60 eV, and a surface energy of 1.344 J·m^–2. No sign of “metallization” occurs as for the classical macroscopic polar zinc- or oxygen-terminated ZnO (0001) surfaces, due to counterpolarization of the electronic density of the Ca²⁺ and PO₄^3– moieties surrounding the monodimensional OH^– polar arrays. These findings may be relevant to explain why, experimentally, HA nanocrystals orient along the main axis of the proto-collagen fibrils with their crystallographic <i>c</i> axis (perpendicular to the {001} crystal plane family)

How Does Collagen Adsorb on Hydroxyapatite? Insights From Ab Initio Simulations on a Polyproline Type II Model

Bone has a hierarchical structure based on the mineralized fibril, an organic matrix envisaging collagen protein in tight interaction with hydroxyapatite mineral (HAP) and stabilized by water molecules. The tremendous complexity of this natural composite material hides the extraordinary features in terms of high compressive strength and elasticity imparted by the collagen protein. Clearly, understanding the nanoscale interface and mechanics of bone at atomistic level can dramatically improve the development of biocomposite and the understanding of bone related diseases. In this work, we aim at elucidating the features of the interaction between a model of a single-collagen-strand (COL) with the most common dried P-rich (010) HAP surface. The methods of choice are static and dynamic simulations based on density functional theory at PBE-D2, PBE-D3 and B3LYP-D3 levels. Collagen is made to a large extent by proline (PRO) and derivatives, and PRO’s side chain is known to affect the collagen triple helix stability dramatically. However, the role of the PRO side chain in the COL/HAP interface has never been studied so far at a quantum mechanical level. To decrease the enormous structural complexity of collagen itself, we employed a simple collagen model, i.e., a single strand based on the poly-l-proline type II polymer (PPII), which, for its composition, nicely suites our purposes. We discovered that during the HAP adsorption process, the polymer deforms to create a relatively strong electrostatic interaction between the PRO carbonyl CO group and the most exposed Ca ion of the P-rich (010) HAP surface. Both dynamic and static simulations agree that the HAP surface guides the formation of PPII conformers, which would be unstable without the support of the HAP surface. The PROs puckering and the polymer orientation affect the PPII affinity for the HAP surface with binding energies spanning within the 63–126 kJ·mol^–1 range. This work is the first step toward the development of a full collagen model envisaging a three-interlocked helical polymer interacting with the HAP surfaces

Forsterite Surfaces as Models of Interstellar Core Dust Grains: Computational Study of Carbon Monoxide Adsorption

Carbon monoxide (CO) is the second most abundant gas-phase molecule after molecular hydrogen (H₂) of the interstellar medium (ISM). In molecular clouds, an important component of the ISM, it adsorbs at the surface of core grains, usually made of Mg/Fe silicates, and originates complex organic molecules through the catalytic power of active sites at the grain surfaces. To understand the atomistic, energetic, and spectroscopic details of the CO adsorption on core grains, we resorted to density functional theory based on the hybrid B3LYP-D* functional inclusive of dispersion contribution. We modeled the complexity of interstellar silicate grains by studying adsorption events on a large set of infinite extended surfaces cut out from the bulk Mg₂SiO₄ forsterite, the Mg end-member of olivines (Mg_2<i>x</i>Fe_{2–2<i>x</i>}SiO₄), also a very common mineral on the Earth’s crust. Energetic and structural features indicate that CO is exclusively physisorbed with binding energy values in the 23–68 kJ mol^–1 range. Detailed analysis of data revealed that dispersive interactions are relevant together with the important electrostatic contribution due to the quadrupolar nature of the CO molecule. We performed a full thermodynamic treatment of the CO adsorption at the very low temperature typical of the ISM as well as a full spectroscopic characterization of the CO stretching frequency, which we prove to be extremely sensitive to the local nature of the surface-active site of adsorption. We also performed a detailed kinetic analysis of CO desorption from the surface models at different temperatures characterizing the colder regions of the ISM. Our computed data could be incorporated in the various astrochemical models of interstellar grains developed so far and thus contribute to improve the description of the complex chemical network occurring at their surfaces

Does Adsorption at Hydroxyapatite Surfaces Induce Peptide Folding? Insights from Large-Scale B3LYP Calculations

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 Ca²⁺ ions, by hydrogen bond between NH₂ groups and the basic PO₄^3– groups and by a relevant fraction due to dispersion forces. Peptide adsorption was studied on the dry (001) surface, the wet one envisaging 2 H₂O per surface Ca²⁺ and, on the latter, also considering the adsorption of microsolvated peptides with 4 H₂O 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

B3LYP Periodic Study of the Physicochemical Properties of the Nonpolar (010) Mg-Pure and Fe-Containing Olivine Surfaces

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 Mg_1.5Fe_0.5SiO₄ (Fo₇₅). A detailed structural analysis of the (010) Fo and Fo₇₅ surface models shows the presence of coordinatively unsaturated metal cations (Mg²⁺ and Fe²⁺, respectively) with shorter metal–O distances compared to the bulk ones. Energetic analysis devoted to the Fe²⁺ electronic spin configuration and to the ion position in the surfaces reveals that Fe²⁺ 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 Fe²⁺ is coordinatively unsaturated. Comparison of the simulated IR and the corresponding reflectance spectra indicates that Fe²⁺ 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

Computational Study on the Water Corrosion Process at Schreibersite (Fe₂NiP) Surfaces: from Phosphide to Phosphates

Phosphorus (P) is a fundamental element for whatever form of life, in the same way as the other biogenic macroelements (SONCH). The prebiotic origin of P is still a matter of debate, as the phosphates present on earth are trapped in almost insoluble solid matrixes (apatites) and, therefore, hardly available for inclusion in living systems in the prebiotic era. The most accepted theories regard a possible exogenous origin during the Archean Era, through the meteoritic bombardment, when tons of reactive P in the form of phosphide ((Fe,Ni)3P, schreibersite mineral) reached the primordial earth, reacting with water and providing oxygenated phosphorus compounds (including phosphates). In the last 20 years, laboratory experiments demonstrated that the corrosion process of schreibersite by water indeed leads to reactive phosphates that, in turn, react with other biological building blocks (nucleosides and simple sugars) to form more complex molecules (nucleotides and complex sugars). In the present paper, we study the water corrosion of different crystalline surfaces of schreibersite by means of periodic DFT (density functional theory) simulations. Our results show that water adsorbs molecularly on the most stable (110) surface but dissociates on the less stable (001) one, giving rise to further reactivity. Indeed, subsequent water adsorptions, up to the water monolayer coverage, show that, on the (001) surface, iron and nickel atoms are the first species undergoing the corrosion process and, in a second stage, the phosphorus atoms also get involved. When adsorbing up to three and four water molecules per unit cell, the most stable structures found are the phosphite and phosphate forms of phosphorus, respectively. Simulation of the vibrational spectra of the considered reaction products revealed that the experimental band at 2423 cm–1 attributed to the P–H stretching frequency is indeed predicted for a phosphite moiety attached to the schreibersite (001) surface upon chemisorption of up to three water molecules

Revealing Hydroxyapatite Nanoparticle Surface Structure by CO Adsorption: A Combined B3LYP and Infrared Study

The adsorption of CO at hydroxyapatite (HA) surfaces has been studied by combining quantum mechanical modeling with experimental IR results. To model the adsorption, the hybrid B3LYP-D*, inclusive of dispersive interactions, has been adopted within the periodic boundary conditions, using the CRYSTAL09 program and a polarized Gaussian type basis set. Four HA surfaces have been investigated using slabs of finite thickness: two stoichiometric HA(001) and HA(010)­R surfaces and two nonstoichiometric HA(010) in which the value of the Ca/P ratio was either higher (HA(010)_Ca-rich) or lower (HA(010)_P-rich) than the bulk value. Geometrical, energetic, and vibrational features of the adsorption process have been fully investigated, by considering CO coverage ranging from 1.5 to 6 CO/nm², respectively. By combining the results from the modeling study with experimental IR data, it was assessed that the vibrational features of adsorbed CO can be proposed as a potential tool for the recognition of types of surface terminations exposed by HA crystalline nanoparticles

How Does Silica Catalyze the Amide Bond Formation under Dry Conditions? Role of Specific Surface Silanol Pairs

The mechanism of the amide bond formation between nonactivated carboxylic acids and amines catalyzed by the surface of amorphous silica under dry conditions is elucidated by combining spectroscopic measurements and quantum chemical simulations. The results suggest a plausible explanation of the catalytic role of silica in the reaction. Both experiment and theory identify very weakly interacting SiOH surface group pairs (ca. 5 Å apart) as key specific sites for simultaneously hosting, in the proper orientation, ionic and canonical pairs of the reactants. An atomistic interpretation of the experiments indicates that this coexistence is crucial for the occurrence of the reaction, since the components of the canonical pair are those undergoing the amidation reaction while the ionic pair directly participates in the final dehydration step. Transition state theory based on quantum mechanical free energy potential energy shows the silica-catalyzed amide formation as being relatively fast. The work also points out that the presence of the specific SiOH group pairs is not exclusive of the adopted silica sample, as they can also be present in natural forms of silica, for instance as hydroxylation defects on α-quartz, so that they could exhibit similar catalytic activity toward the amide bond formation