Supporting Information
Car-Parrinello molecular dynamics study of the Uranyl behaviour at the
gibbsite/water interface.
Sébastien Lectez, Jérôme Roques, Mathieu Salanne and Eric Simoni
SI.1) Uranyl ion solvation
Simulations are performed in order to characterize the structural properties of uranyl ion in
water. The studied system is generated from a water cubic box of side L = 12.41 Å, which is
composed of 64 water molecules to ensure a density of water near to 1 g/cm3. The starting
positions of water molecules had been optimized using a classical molecular dynamics
calculation with a SPC/E water model. The initial configuration of the studied system
corresponds to the last configuration of the optimized water box, where 3 water molecules
have been replaced by one uranyl ion. Thus, this studied system consists of one uranyl ion and
61 water molecules in a cubic box (L = 12.41 Å). The total simulation time is 10.4 ps
(including an equilibration time of 2 ps). In agreement with previous works44, the plane wave
basis set is truncated using an optimized kinetic energy cut-off of 70 Ry. Finally, a time step
of 5 a.u. (0.121 fs) and a fictitious electronic mass of 600 a.u. are used in these simulations.
The radial distribution function, gu-o(r), and the running coordination number functions, nUO(r),
for the studied system (UO22+ + 61H2O) are presented in Fig. SI-1.
(UO22+ + 61 H2O)
Figure SI.1: Radial distribution function gU-O(r) and the running coordination number
functions nU-O(r).
Three peaks are observed in the radial distribution function. The first peak located in the
range of 1.7-1.9 Å can be attributed to the two U-Oyl (nU-O(r)=2) bonds. The second peak
located between 2.1 and 2.8 Å corresponds to the five water molecules of the first solvation
shell. Finally, the third peak, which can be attributed to the second solvation shell, is located
in the range of 3.8 - 4.9 Å. This second shell contains 14 water molecules on average.
Geometrical parameters are summarized in Table SI.1 and compared to the literature values.
The simulations show that the U-Oyl average distance is 1.83 Å, which is slightly superior to
experimental values1-4 and to the Car-Parrinello MD simulation result of Nichols et al.5 but
very close to another CPMD calculation6,7. The calculated average angle OylUOyl is 173.1°.
The first solvation shell is characterized by 5 water molecules in the equatorial plane of the UOyl axis with an U-OH2 average distance of 2.42 Å, which is in good agreement with X-ray
data1-4,8, others DFT studies5-8 and classical molecular dynamic studies9,10.
Temperature (K)
Equilibration time (ps)
Dynamic time (ps)
U-Oyl Bond
rU-Oyl (Å)
UO22+ + 61H2O
(This Work)
350
2.2
10.4
1.83
Oyl-U-Oyl (°)
First solvation shell
number of water molecules
rU-OI (Å)
Second solvation shell
average number of water molecules
5
2.42
rU-OII (Å)
4.5
rOI-H2OII (Å)
1.73
1.766c,d, 1.702e, 1.77g
5a, 5b
4.61c,d, 4.9e , 5.3f, 5g
2.48a, 2.44b
2.42c,d,g, 2.421e, 2.41f
4.59b
14e
4.46c, 4.5d, 4.37e
10
163.8
4.45b
164.7b
4
rU-OII (Å)
4.43
rOyl-H2OII (Å)
2.11

1.81a, 1.77b
14.8b
14
4.47
Oyl-H-OII (°)
Experimental
173.9b
173.1
rU-OII (Å)
Equatorial plane
average number of water molecules
OI-H-OII (°)
Apical plane
average number of water molecules
Calculated
148.2
4.43b
154.5b
Table SI.1. Average geometric parameters of the solvation shell of the uranyl ion. a:
Reference 6 et 7. b: Reference 5. c: Reference 2. d: Reference 3. e: Reference 4. f: Reference
8.g: Reference 1.
These five water molecules are oriented such as their oxygen atoms are directly
coordinated to the uranyl ion and their hydrogen atoms point toward the water molecules of
the second solvation shell (Fig. SI.2).
(a)
(b)
Figure SI.2: (a) and (b) represent the second solvation shell of the uranyl ion. (a): The
equatorial plane. (b): The apical plane. OI: Oxygen atom from water molecules in the first
solvation shell. OII: Oxygen atom from water molecules in the second solvation shell.
Finally, the second solvation shell was also characterized, with an U-OH2 average distance
of 4.47 Å. However, this second shell can be divided in two water molecules types (see Fig.
SI.2): some of them are located in an equatorial position (Fig. SI.2 panel a) and the others in
an apical position (Fig. SI.2 panel b). The running coordination number function predicts an
average number of 14 water molecules in the second solvation shell. The equatorial plane
contains 10 water molecules at an average distance U-OII of 4.50 Å (see Fig. SI.2 panel a).
Each of these water molecules is linked by an hydrogen bond to a water molecule of the first
solvation shell. The average hydrogen bond length is 1.73 Å and the OIHOII angle is 163.8°.
In the apical plane, 4 water molecules are observed the most frequently during the simulation.
The average distance between oxygen atom of these molecules and the uranium atom is 4.43
Å. They are linked by a weak hydrogen bond of 2.11 Å length to oxygen atoms of uranyl ion
and the OylHOII average angle is 148.2° (see Fig. SI.2 panel b). These first results show that
the interactions between the second water molecules shell and the uranyl ion are less intense
for apical molecules than for equatorial ones.
During the simulation time, some exchanges between water molecules of the second
solvation shell and the bulk water were observed. The exchange process can be described by a
dissociative step immediately followed by an associative one. A diagram modelling this
behaviour is presented in the panel b of Fig. SI.3 in which the water molecules labelled 1, 2
and 3 are the three closest molecules to the water molecule labelled 4 (located in the first
uranyl solvation shell).
(a)
d1
(b)
d2
d1>d2
d1=d2
d1<d2
(c)
Figure SI.3: Description of one exchange mechanism event between one water molecule
from the second solvation shell of the equatorial plane and one water molecule of the bulk.
(a): Variation of the distance O4-Ox during the dynamics time with x= 1, 2 and 3. (b):
illustration of this exchange. The water molecule named 4 is a water molecule of the first
solvation shell and the water molecules called 1, 2 and 3 are the three water molecules in
competition for staying in the second solvation shell. (c): Variation of the O4HOx angles
during the dynamics time with x= 1, 2 and 3.
Molecules 2 and 3 are in competition to be located in the second solvation shell. The
variations of the distances O4-Ox and the angles O4HOx (x being 1, 2 or 3) during the
simulation are respectively plotted in the panel a and c in Fig SI.3. The exchange between
water molecules 2 and 3 can be observed in Fig. SI.3 from the crossing point (occurring at t ≈
3100 fs) of O4-O2 and O4-O3 distance curves (panel a) and from O4HO2 and O4HO3 angle
curves (panel c).
The observed mechanism is in perfect agreement with the results from Nichols et al.5 who
have also observed such exchanges for molecules in the apical plane.
SI.2) Bulk structure of gibbsite
The gibbsite is one of the four aluminum hydroxide (Al(OH)3) polymorphs. It is organized
in the form of sheets and crystallizes in pseudohexagonal platelets with monoclinic symmetry
(see Figure SI.4).
(a)
(b)
Figure SI.4: Snapshots of the gibbsite bulk structure. (a): Lateral view. (b): Basal view.
All of the polymorphs of aluminium hydroxide are composed of aluminum atoms layers
located in two-third of the octahedral sites with hydroxyl groups on either side. The cohesion
between sheets takes place through hydrogen bonds. The difference between gibbsite and
other Al(OH)3 polymorphs is the stacking sequence of the layers. The one of the gibbsite has
been described by several authors11,12. The gibbsite structure adopts the P21/n (C2h5) space
group. These crystallographic parameters and the atomic positions were experimentally
determined in the study of Saalfeld et al.11 and also calculated using ab initio approches13-16.
In order to check the validity of the Troullier-Martins and the Vanderbilt pseudopotentials
for this system, two sets of geometry optimizations were performed: one with Vanderbilt
pseudopotentials (called in this work V simulations) and one with Trouillier-Martins
pseudopotentials (called TM simulations). The kinetic energy cutoffs were respectively
optimized at 28 and 120 Ry. Geometrical parameters were optimized with a convergence
criterion of 5.10-4 a.u. on the average force of the system. In both cases, the starting
simulation cell was built using the Saalfeld et al.11 crystallographic parameters. Geometrical
parameters, after optimization, are summarized in Table SI.2. All these results are in excellent
agreement with previous theoretical13 and experimental results11, which justify the use of
these two pseudopotentials sets to calculate gibbsite properties.
Vanderbilt
(CPMD)
TroullierMartins
(CPMD)
PAW
(VASP)a
Experimentalb
a (Å)
8.823
8.736
8.736
8.684
b (Å)
5.150
5.099
5.099
5.078
c (Å)
9.628
9.724
9.628
9.736
 (°)
92.83
92.83
92.83
94.54
dO1-H…04
2.751
2.750
2.706
2.739
dO2-H…05
2.803
2.803
2.749
2.829
dO3-H…06
2.846
2.851
2.807
2.885
dO-H(in plane)
0.982
0.981
0.981
-
dO-H(out of plane)
0.991
0.987
0.991
-
dAl1-Al2
2.957
2.962
2.969
2.948
dAl2-Al4
2.897
2.925
2.896
2.896
dAl2-Al3
2.929
2.945
2.940
2.936
dAl1-O
1.901
1.901
1.914
1.904
Crystallographic parameters
Interatomic distances (Å)
1.916
1.928
1.918
1.913
dAl2-O
Table SI.2. Average parameters of gibbsite bulk. a: Veilly and al.13, b: Saalfeld and Wedde11.
Références
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
C. Den Auwer, D. Guillaumont, P. Guilbaud, S. D. Conradson, J. J. Rehr, A.
Ankudinov, and E. Simoni, New J. Chem. 28, 929 (2004).
J. Neuefeind, L. Soderholm, and S. Skanthakumar, J. Phys. Chem. A 108, 2733
(2004).
L. Soderholm, S. Skanthakumar, and J. Neuefeind, Anal. Bioanal. Chem. 383, 48
(2005).
M. Aaberg, D. Ferri, J. Glaser, and I. Grenthe, Inorg. Chem. 22, 3986 (1983).
P. Nichols, E. J. Bylaska, G. K. Schenter, and W. D. Jong, J. Chem. Phys. 128,
124507 (2008).
M. Buhl, Diss and Wipff, J. Am. Chem. Soc. 127, 13506 (2005).
M. Buhl, H. Kabrede, R. Diss, and G. Wipff, J. Am. Chem. Soc. 128, 6357 (2006).
P. G. Allen, J. J. Bucher, D. K. Shuh, N. M. Edelstein, and T. Reich, Inorg. Chem. 36,
4676 (1997).
P. Guilbaud and G. Wipff, J. Phys. Chem. 97, 5685(1993)
P. Guilbaud and G. Wipff, J. Mol. Struct. 366, 55 (1996)
H. Saalfeld and M. Wedde, Z. Kristallogr. 139, 129 (1974).
R. F. Giese Jr, Acta Crystallogr. B 32, 1719 (1975).
E. Veilly, J. Roques, M.-C. Jodin-Caumon, B. Humbert, R. Drot, and E. Simoni, J.
Chem. Phys. 129, 244704 (2008).
S. Fleming, A. Rohll, M.-Y. Lee, J. Gale, and G. Parkinson, J. Cryst. Growth 209, 159
(2000).
S. D. Fleming, A. L. Rohl, S. C. Parker, and G. M. Parkinson, J. Phys. Chem. B 105,
5099 (2001).
J. D. Gale, A. L. Rohl, V. Milman, and M. C. Warren, J. Phys. Chem. B 105, 10236
(2001).