SUPPLEMENTARY ONLINE INFORMATION
Appendix A : Pore generation and surface reconstruction
A cylindrical pore was built following a procedure similar to that developed by Brodka et al.1,2
First, a model of amorphous silica was constructed by melting a lattice of ideal -cristobalite, a hightemperature polymorph of quartz. In this allotrope, silicon atoms occupy the positions of the
diamond crystal structure, while O atoms form bridges between them. A small box of -cristobalite
composed of 64 Si atoms and 128 O atoms was melted at T = 6000 K, and then quenched down to T =
300 K at a cooling rate of 10 K/ps. The van Beest-Kramer-van Santen (BKS) potential3 was chosen to
model the silica matrix, because it reproduces satisfactorily many structural and dynamical
properties of bulk amorphous silica.4 A Lennard-Jones 30-6 correction has been added to this
potential because of its divergence at short separation distances,5 which might occur at high
temperatures. The simulations were performed in the microcanonical ensemble (N,V,E) with the
DLPOLY molecular dynamics program.6 The length L of the cubic simulation box was set to 14.2646 Å
to achieve a density of 2.2 g/cm3, which corresponds to the density of amorphous silica.7 A 1 fs
timestep was used and a cutoff of 6 Å was employed. Long-range electrostatics interactions were
treated using the Ewald summation method. Since the goal was to simulate a pore with a diameter D
of about 30 Å, the simulation box of amorphous silica was replicated four times in the X, Y and Z
directions to achieve a cubic simulation box centered at the origin with a side length L = 57.0584 Å
and containing 12,288 atoms. A cylindrical cavity was created in the amorphous silica matrix by
removing all of the atoms within 15 Å of the Z axis. Then, the pore surface was generated as
described previously.1,2 The pore obtained, referred to as PH, has a surface concentration of OH
groups of about 7.6 OH/nm2, in good agreement with most of the previous simulation studies using
this procedure1,2,8. However, this value is far above those observed in synthesized mesoporous silica,
which span the range 1-3 OH/nm2. To decrease the silanol density, an additional procedure that
mimicks the condensation process occurring during the thermal treatment was developed.
In examining the surface silanols, two main patterns were observed: isolated pairs and
triangular triplets. The two patterns were transformed with the scheme shown in Fig. 1. In the
isolated pairs (Fig. 1a), the hydroxyl group of one silanol and the H atom of the other silanol were
removed and the remaining O atom was translated to a position Onew in the plane formed by the two
silicon atoms and the center of mass of the two original O atoms with an Si-Onew-Si angle of 120°. For
the triplets (Fig. 1b), all three H atoms were removed and a Si and O were added with the Si and O
atoms lying on the line orthogonal to the (Sia,Sib,Sic) plane containing the center of mass of Sia, Sib and
Sic and distances of 1.6 Å.
1
Fig. 1: Schematic representation of the reconstruction of (a) a pair and (b) a triplet of silanol
groups.
The simulation of this modified pore was run at 0 K for 1ps with the BKS potential9 without H
atoms; the Ewald summation method was used to treat the long-range electrostatic interactions
(convergence parameter of 0.338 Å-1), and the cutoff distance for van der Waals and real-space
electrostatic interactions was taken as 8.5 Å. In the resulting configuration a few Si atoms surrounded
by five oxygen atoms, so, the bridging O atoms between pairs of the pentavalent Si atoms were
removed and a short (50 fs) equilibration at 0 K was carried out to relax the position of the newly
tetravalent Si atoms. Finally, hydroxyl groups were added as described previously. The pore
obtained, referred to as PL (Fig. 2), has a silanol surface concentration of about 3 OH/nm2, consistent
with the values of synthesized MCM-41 materials. It should be mentioned that the pore diameter of
PL (3.2 nm) is slightly larger than that of PH (3.0 nm) because of the relaxation of the surface atoms
during the first 1 ps simulation of the reconstruction.
2
Fig.2: Schematic representation of the inner surface of the pores (top) before and (bottom) after
the surface reconstruction procedure described in the text. The O and H atoms in silanol groups are
colored red and white, respectively, whereas all other atoms are colored blue. This figure was
generated using VMD10.
Appendix B : Pore filling
The pore filling is a crucial step for simulations of confined liquids performed in the canonical
(N,V,T) or in the microcanonical (N,V,E) ensemble. Indeed, the experimental density of confined
solutions is often not known accurately, and it has been often assumed that the density of confined
liquid is that of the corresponding bulk.8 However, simulations of confined water at full hydration led
to a density of about 0.9 g.cm-3 at the center of the pore.11 This is the reason why simulations in the
grand canonical or Gibbs ensemble, in which the chemical potential µ of water is constant, are
frequently performed.12,13
In this study, the pore filling was performed in several steps. First, a box of water at bulk
density was superimposed on the pores PH and PL. All water molecules whose oxygen atoms were
within 2.5 Å of any heavy atom of the silica pore were removed. The remaining water molecules
were then simulated for a duration of 1 ns to allow the hydration of silanols and the filling of small
surface cavities. Since these two processes are likely to decrease the water density in the center of
the pore, the initial water box was then again superimposed onto the final configuration, i.e. for t = 1
ns. Once again, each molecule of the new water box whose oxygen atom was within 2.8 Å of any
3
heavy atom of the silica pore or of the oxygen atoms of the equilibrated confined water molecules
was removed. This filling procedure leads to a density in the center of the studied pores lower than
bulk water density. Given that the simulations were performed at constant volume, it was difficult to
confirm that the obtained densities were consistent with the silica force fields used. Therefore, a
second filling procedure was then applied (Fig. 3). Two cubic water boxes, WR1 and WR2, of side
length L = 57.0584 Å filled with water at bulk density were added on the top and on the bottom of
the initial simulation box of confined water (step (1) of Fig. 3). A first simulation at 300 K in the
microcanonical ensemble was performed for 250 ps with periodic boundary conditions (PBC) in the X,
Y and Z directions to allow the equilibration of water molecules from the reservoirs WR1 and WR2.
Then, a second simulation of 500 ps was performed at constant temperature with only periodicity
applied in the X and Y directions (step (2) of Fig. 3). In such circumstances, the water density in the
pore can reach an equilibrium value that depends only on water-water and water-silica interactions.
Given the absence of periodicity in the Z direction, a few water molecules escaped during the
different simulations. The water/vacuum interface was also not flat, meaning that the water density
in this region slightly depends on the distance to this interface. Nonetheless, it became constant and
reached bulk water density for distances larger than ≈ 5 Å. Therefore, the simulation box in the final
configuration of the preceding simulation was cut far from the water/vacuum interface, i.e. at Z = ±
45 Å (step (3) in Fig. 3). Two new water boxes at bulk density, WR3 and WR4, were then added on
the top and bottom sides of this sliced box, respectively (step (4) in Fig. 3). The number of water
molecules in these two reservoirs, and, as a consequence, their size along the Z axis, was chosen so
that the total number of water molecules in the simulation box remained identical to that in steps (1)
and (2). A simulation at 300 K with periodicity in the X, Y and Z directions was performed for 250 ps
for equilibration. Finally, the last configuration of this simulation was cut at Z = ± L/2 = ± 28.5292 Å
(step (5) in Fig. 3). The number of water molecules obtained by this procedure should correspond
approximately to the number of water molecules that would be confined at chemical equilibrium.
4
Fig. 3: Schematic description of the pore filling procedure used to adjust the confined water
density. (1) Two bulk density water reservoirs WR1 and WR2 were added above and below the
pre-filled silica pore. A simulation of 250 ps was then performed for equilibration. (2) A 500 ps
simulation was run so that the density inside the pore can adjust to its equilibrium value. (3) The
resulting box was sliced at Z = ± 45 Å, where the density of water is constant along the Z axis. (4)
Two new bulk density water reservoirs WR3 and WR4 were added on each side of the sliced box,
and a 250-ps simulation was performed for equilibration. (5) The last configuration of the
preceding simulation was sliced at Z= ± L/2 = ± 28.5292 Å. This figure was generated using VMD10.
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