Understanding water transport mechanisms at the nanoscale level remains a challenge for theoretical chemical physics. Major advances in chemical synthesis have allowed us to discover new artificial water channels, rivaling with or even surpassing water conductance and selectivity of natural protein channels. In order to interpret experimental features and understand microscopic determinants for performance improvements, numerical approaches based on all-atom molecular dynamics simulations and enhanced sampling methods have been proposed. In this study, we quantify the influence of microscopic observables, such as channel radius and hydrogen bond connectivity, and of meso-scale features, such as the size of self-assembly blocks, on the permeation rate of a self-assembled nanocrystal-like artificial water channel. Although the absolute permeation rate extrapolated from these simulations is overestimated by one order of magnitude compared to the experimental measurement, the detailed analysis of several observed conductive patterns in large assemblies opens new pathways to scalable membranes with enhanced water conductance for the future design.

1.
F.
Fornasiero
,
H. G.
Park
,
J. K.
Holt
,
M.
Stadermann
,
C. P.
Grigoropoulos
,
A.
Noy
, and
O.
Bakajin
, “
Ion exclusion by sub-2-nm carbon nanotube pores
,”
Proc. Natl. Acad. Sci. U. S. A.
105
,
17250
17255
(
2008
).
2.
Y.-x.
Shen
,
W.
Si
,
M.
Erbakan
,
K.
Decker
,
R.
De Zorzi
,
P. O.
Saboe
,
Y. J.
Kang
,
S.
Majd
,
P. J.
Butler
,
T.
Walz
,
A.
Aksimentiev
,
J.-l.
Hou
, and
M.
Kumar
, “
Highly permeable artificial water channels that can self-assemble into two-dimensional arrays
,”
Proc. Natl. Acad. Sci. U. S. A.
112
,
9810
9815
(
2015
).
3.
X.-B.
Hu
,
Z.
Chen
,
G.
Tang
,
J.-L.
Hou
, and
Z.-T.
Li
, “
Single-molecular Artificial transmembrane water channels
,”
J. Am. Chem. Soc.
134
,
8384
8387
(
2012
).
4.
X.
Zhou
,
G.
Liu
,
K.
Yamato
,
Y.
Shen
,
R.
Cheng
,
X.
Wei
,
W.
Bai
,
Y.
Gao
,
H.
Li
,
Y.
Liu
,
F.
Liu
,
D. M.
Czajkowsky
,
J.
Wang
,
M. J.
Dabney
,
Z.
Cai
,
J.
Hu
,
F. V.
Bright
,
L.
He
,
X. C.
Zeng
,
Z.
Shao
, and
B.
Gong
, “
Self-assembling subnanometer pores with unusual mass-transport properties
,”
Nat. Commun.
3
,
949
(
2012
).
5.
E.
Licsandru
,
I.
Kocsis
,
Y.-x.
Shen
,
S.
Murail
,
Y.-M.
Legrand
,
A.
van der Lee
,
D.
Tsai
,
M.
Baaden
,
M.
Kumar
, and
M.
Barboiu
, “
Salt-excluding artificial water channels exhibiting enhanced dipolar water and proton translocation
,”
J. Am. Chem. Soc.
138
,
5403
5409
(
2016
).
6.
Y. D.
Yuan
,
J.
Dong
,
J.
Liu
,
D.
Zhao
,
H.
Wu
,
W.
Zhou
,
H. X.
Gan
,
Y. W.
Tong
,
J.
Jiang
, and
D.
Zhao
, “
Porous organic cages as synthetic water channels
,”
Nat. Commun.
11
,
4927
(
2020
).
7.
J.
Shen
,
R.
Ye
,
A.
Romanies
,
A.
Roy
,
F.
Chen
,
C.
Ren
,
Z.
Liu
, and
H.
Zeng
, “
Aquafoldmer-based aquaporin-like synthetic water channel
,”
J. Am. Chem. Soc.
142
,
10050
10058
(
2020
).
8.
L. B.
Huang
,
M.
Di Vincenzo
,
Y.
Li
, and
M.
Barboiu
, “
Artificial water channels: Towards biomimetic membranes for desalination
,”
Chemistry
27
,
2224
(
2020
).
9.
A.
Horner
and
P.
Pohl
, “
Single-file transport of water through membrane channels
,”
Faraday Discuss.
209
,
9
33
(
2018
).
10.
I.
Kocsis
,
M.
Sorci
,
H.
Vanselous
,
S.
Murail
,
S. E.
Sanders
,
E.
Licsandru
,
Y.-M.
Legrand
,
A.
van der Lee
,
M.
Baaden
,
P. B.
Petersen
,
G.
Belfort
, and
M.
Barboiu
, “
Oriented chiral water wires in artificial transmembrane channels
,”
Sci. Adv.
4
,
eaao5603
(
2018
).
11.
S.
Murail
,
T.
Vasiliu
,
A.
Neamtu
,
M.
Barboiu
,
F.
Sterpone
, and
M.
Baaden
, “
Water permeation across artificial I-quartet membrane channels: From structure to disorder
,”
Faraday Discuss.
209
,
125
148
(
2018
).
12.
J. B.
Klauda
,
R. M.
Venable
,
J. A.
Freites
,
J. W.
O’Connor
,
D. J.
Tobias
,
C.
Mondragon-Ramirez
,
I.
Vorobyov
,
A. D.
MacKerell
, and
R. W.
Pastor
, “
Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types
,”
J. Phys. Chem. B
114
,
7830
7843
(
2010
).
13.
W. L.
Jorgensen
,
J.
Chandrasekhar
,
J. D.
Madura
,
R. W.
Impey
, and
M. L.
Klein
, “
Comparison of simple potential functions for simulating liquid water
,”
J. Chem. Phys.
79
,
926
935
(
1983
).
14.
K.
Vanommeslaeghe
and
A. D.
MacKerell
, “
Automation of the CHARMM general force field (CGenFF) I: Bond perception and atom typing
,”
J. Chem. Inf. Model.
52
,
3144
3154
(
2012
).
15.
S.
Jo
,
T.
Kim
,
V. G.
Iyer
, and
W.
Im
, “
CHARMM-GUI: A web-based graphical user interface for CHARMM
,”
J. Comput. Chem.
29
,
1859
1865
(
2008
).
16.
S.
Kim
,
J.
Lee
,
S.
Jo
,
C. L.
Brooks
,
H. S.
Lee
, and
W.
Im
, “
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules
,”
J. Comput. Chem.
38
,
1879
1886
(
2017
).
17.
B.
Hess
,
H.
Bekker
,
H. J. C.
Berendsen
, and
J. G. E. M.
Fraaije
, “
LINCS: A linear constraint solver for molecular simulations
,”
J. Comput. Chem.
18
,
1463
1472
(
1997
).
18.
S. D.
Bond
,
B. J.
Leimkuhler
, and
B. B.
Laird
, “
The Nosé–Poincaré method for constant temperature molecular dynamics
,”
J. Comput. Phys.
151
,
114
134
(
1999
).
19.
M.
Parrinello
and
A.
Rahman
, “
Crystal structure and pair potentials: A molecular-dynamics study
,”
Phys. Rev. Lett.
45
,
1196
1199
(
1980
).
20.
L.
Wang
,
R. A.
Friesner
, and
B. J.
Berne
, “
Replica exchange with solute scaling: A more efficient version of replica exchange with solute tempering (REST2)
,”
J. Phys. Chem. B
115
,
9431
9438
(
2011
).
21.
G.
Stirnemann
and
F.
Sterpone
, “
Recovering protein thermal stability using all-atom Hamiltonian replica-exchange simulations in explicit solvent
,”
J. Chem. Theory Comput.
11
,
5573
5577
(
2015
).
22.
N.
Michaud-Agrawal
,
E. J.
Denning
,
T. B.
Woolf
, and
O.
Beckstein
, “
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
,”
J. Comput. Chem.
32
,
2319
2327
(
2011
).
23.
W.
Humphrey
,
A.
Dalke
, and
K.
Schulten
, “
VMD: Visual molecular dynamics
,”
J. Mol. Graphics
14
,
33
38
(
1996
).
24.
O. S.
Smart
,
J. G.
Neduvelil
,
X.
Wang
,
B. A.
Wallace
, and
M. S. P.
Sansom
, “
HOLE: A program for the analysis of the pore dimensions of ion channel structural models
,”
J. Mol. Graphics
14
,
354
360
(
1996
).
25.
S. J.
Weiner
,
P. A.
Kollman
,
D. A.
Case
,
U. C.
Singh
,
C.
Ghio
,
G.
Alagona
,
S.
Profeta
, and
P.
Weiner
, “
A new force field for molecular mechanical simulation of nucleic acids and proteins
,”
J. Am. Chem. Soc.
106
,
765
784
(
1984
).
26.
X.
Daura
,
K.
Gademann
,
B.
Jaun
,
D.
Seebach
,
W. F.
van Gunsteren
, and
A. E.
Mark
, “
Peptide folding: When simulation meets experiment
,”
Angew. Chem., Int. Ed.
38
,
236
240
(
1999
).
27.
A.
Hardiagon
,
S.
Murail
,
L.
Huang
,
M.
Barboiu
,
F.
Sterpone
, and
M.
Baaden
, “
Stability and structure of adaptive self-organized supramolecular artificial water channels in lipid bilayers
,” in
New Trends in Macromolecular and Supramolecular Chemistry for Biological Applications
(
Springer
,
2020
).
28.
F.
Zhu
and
K.
Schulten
, “
Water and proton conduction through carbon nanotubes as models for biological channels
,”
Biophys. J.
85
,
236
244
(
2003
).
29.
A.
Alexiadis
and
S.
Kassinos
, “
Molecular simulation of water in carbon nanotubes
,”
Chem. Rev.
108
,
5014
(
2008
).
30.
O.
Beckstein
,
P. C.
Biggin
, and
M. S. P.
Sansom
, “
A hydrophobic gating mechanism for nanopores
,”
J. Phys. Chem. B
105
,
12902
12905
(
2001
).
31.
A.
Horner
,
F.
Zocher
,
J.
Preiner
,
N.
Ollinger
,
C.
Siligan
,
S. A.
Akimov
, and
P.
Pohl
, “
The mobility of single-file water molecules is governed by the number of H-bonds they may form with channel-lining residues
,”
Sci. Adv.
1
,
e1400083
(
2015
).
32.
A.
Kalra
,
S.
Garde
, and
G.
Hummer
, “
Osmotic water transport through carbon nanotube membranes
,”
Proc. Natl. Acad. Sci. U. S. A.
100
,
10175
10180
(
2003
).
33.
H.
Yoshida
,
S.
Marbach
, and
L.
Bocquet
, “
Osmotic and diffusio-osmotic flow generation at high solute concentration. II. Molecular dynamics simulations
,”
J. Chem. Phys.
146
,
194702
(
2017
); arXiv: 1703.02759.
34.
J.
Dzubiella
,
R. J.
Allen
, and
J.-P.
Hansen
, “
Electric field-controlled water permeation coupled to ion transport through a nanopore
,”
J. Chem. Phys.
120
,
5001
5004
(
2004
).
35.
C. I.
Lynch
,
S.
Rao
, and
M. S. P.
Sansom
, “
Water in nanopores and biological channels: A molecular simulation perspective
,”
Chem. Rev.
120
,
10298
10335
(
2020
).
36.
H.
Chan
and
P.
Král
, “
Nanoparticles self-assembly within lipid bilayers
,”
ACS Omega
3
,
10631
10637
(
2018
).
37.
M.
Kumar
,
J. E. O.
Habel
,
Y.-x.
Shen
,
W. P.
Meier
, and
T.
Walz
, “
High-density reconstitution of functional water channels into vesicular and planar block copolymer membranes
,”
J. Am. Chem. Soc.
134
,
18631
18637
(
2012
).
38.
Y.-x.
Shen
,
W.
Song
,
D. R.
Barden
,
T.
Ren
,
C.
Lang
,
H.
Feroz
,
C. B.
Hen-derson
,
P. O.
Saboe
,
D.
Tsai
,
H.
Yan
,
P. J.
Butler
,
G. C.
Bazan
,
W. A.
Phillip
,
R. J.
Hickey
,
P. S.
Cremer
,
H.
Vashisth
, and
M.
Kumar
, “
Achieving high permeability and enhanced selectivity for Angstrom-scale separations using artificial water channel membranes
,”
Nat. Commun.
9
,
2294
(
2018
).

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