17 research outputs found
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 N<sub>2</sub>, CO<sub>2</sub>, and H<sub>2</sub>O 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 DerjaguinâBroekhoffâDe 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 Siî¸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)<sub>2</sub>/(SiO)<sub>3</sub> 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 Siî¸Oî¸CÂ(îťO)î¸
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 Siî¸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>6<sub>3</sub> hexagonal HA bulk have been studied by periodic density functional
calculations using the hybrid B3LYP functional and Gaussian basis
set of polarized double-Îś 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<sup>â</sup> 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<sup>â2</sup>. No sign of âmetallizationâ
occurs as for the classical macroscopic polar zinc- or oxygen-terminated
ZnO (0001) surfaces, due to counterpolarization of the electronic
density of the Ca<sup>2+</sup> and PO<sub>4</sub><sup>3â</sup> moieties surrounding the monodimensional OH<sup>â</sup> 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 PROâs
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 CîťO
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 63â126 kJ¡mol<sup>â1</sup> 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 (H<sub>2</sub>) 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 Mg<sub>2</sub>SiO<sub>4</sub> forsterite, the Mg end-member of
olivines (Mg<sub>2<i>x</i></sub>Fe<sub>2â2<i>x</i></sub>SiO<sub>4</sub>), also a very common mineral on the
Earthâs crust. Energetic and structural features indicate that
CO is exclusively physisorbed with binding energy values in the 23â68
kJ mol<sup>â1</sup> 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 ânativeâ
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 ânativeâ
conformation for both peptides resulted in a random coil (RC) structure,
with the helix (H) conformation being â100 kJ mol<sup>â1</sup> higher in free energy. The two peptide conformations interact with
the HA (001) and (010) surfaces by CîťO groups via Ca<sup>2+</sup> ions, by hydrogen bond between NH<sub>2</sub> groups and the basic
PO<sub>4</sub><sup>3â</sup> 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<sub>2</sub>O per surface
Ca<sup>2+</sup> and, on the latter, also considering the adsorption
of microsolvated peptides with 4 H<sub>2</sub>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 â160 kJ/mol,
whereas the reverse is computed for P2, preferring the helix conformation
by â50 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., Mg<sub>2</sub>SiO<sub>4</sub> (Fo) and Mg<sub>1.5</sub>Fe<sub>0.5</sub>SiO<sub>4</sub> (Fo<sub>75</sub>). A detailed structural
analysis of the (010) Fo and Fo<sub>75</sub> surface models shows
the presence of coordinatively unsaturated metal cations (Mg<sup>2+</sup> and Fe<sup>2+</sup>, respectively) with shorter metalâO distances
compared to the bulk ones. Energetic analysis devoted to the Fe<sup>2+</sup> electronic spin configuration and to the ion position in
the surfaces reveals that Fe<sup>2+</sup> 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<sup>2+</sup> is coordinatively unsaturated.
Comparison of the simulated IR and the corresponding reflectance spectra
indicates that Fe<sup>2+</sup> 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 metalâO 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 (Fe<sub>2</sub>NiP) 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 cmâ1 attributed to the PâH 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)ÂR 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/nm<sup>2</sup>, 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 Ă
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 Îą-quartz, so that they
could exhibit similar catalytic activity toward the amide bond formation