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This cell follows the geometry of graphite in the x and y direc-
tions and allows for a large space above the solution in the z
direction to avoid spurious image interactions. The configuration
obtained after 10 ns of simulation at the two different tempera-
tures was employed as the starting point for our MD-ABF
production runs. Each ns of the NVT simulations has required
around 0.2 days running in 32 Itanium Montvale processors.
In our production runs, we have computed the equilibrium
free energy profiles (potentials of mean force) characterizing the
thermodynamic process of transfer of compound 2 molecules
from solution to the interface and vice versa (for an illustration,
see snapshots in Fig. 5). These free energy profiles were computed
using a new27 fast and efficient Adaptive Biasing Force (ABF)
methodology, implemented in version 2.7 of NAMD2. The
reaction coordinate for the ABF calculation was the z coordinate
of the centre of mass of the molecule being transferred. We have
performed two different simulation runs, corresponding to the
determination of the free energy profile at 20 ꢀC and 80 ꢀC with
€
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ꢂ
0.2 A resolution for the reaction coordinate. The force constant
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employed in the calculations was the default value of 10 kcal
molꢁ1
ꢁ2
ꢂ
A
and the simulations were typically run for 10 ns. All
ꢁ
P. Samorı, Angew. Chem., Int. Ed., 2009, 48, 2039–2043.
other parameters of the simulation were the same as employed in
the previous NVT simulation. Each ns of the MD-ABF simula-
tions has required around 1.57 days running in 32 Itanium
Montvale processors.
12 (a) S. Lei, K. Tahara, F. C. de Schryver, M. Van der Auweraer,
Y. Tobe and S. de Feyter, Angew. Chem., Int. Ed., 2008, 47, 2964–
2968; (b) G. Schull, L. Douillard, C. Fiorini-Debuisschert and
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Acknowledgements
14 A. Nion, P. Jiang, A. Popoff and D. Fichou, J. Am. Chem. Soc., 2007,
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15 N. Katsonis, A. Marchenko and D. Fichou, J. Photochem. Photobiol.,
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This work was partly funded by grants MAT 2009-13977-C03,
CTQ2007-60613/BQU, CTQ2010-15380/BQU, CONSOLIDER-
NANOSELECT-CSD2007-00041 and FIS2009-13370-C02-02.
J.S.-P. thanks the Generalitat de Catalunya for a FI predoctoral
ꢁ
Grant and the Institut Catala de Nanotecnologia for their
support. We also acknowledge the CESGA Supercomputing
Center for computational time at the Finisterrae Supercomputer
and technical assistance.
€
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