Polarized Water Wires under Confinement in Chiral Channels - The

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Polarized Water Wires under Confinement in Chiral Channels Mihail Barboiu, Pierre-Andre Cazade, Yann Le Duc, YvesMarie Legrand, Arie van der Lee, and Benoit Coasne J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.5b03322 • Publication Date (Web): 19 Jun 2015 Downloaded from http://pubs.acs.org on June 24, 2015

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The Journal of Physical Chemistry

Polarized Water Wires under Confinement in Chiral Channels

Mihail Barboiu,†,* Pierre André Cazade,§ Yann Le Duc,† Yves Marie Legrand,† Arie van der Lee,† Benoit Coasne§,‡,*

1

Adaptive Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM-

UM-UMR-CNRS5635, Place Eugène Bataillon CC047, 34095 Montpellier Cedex 5, France. 2

Institut Charles Gerhardt Montpellier (ICGM), UMR 5253 CNRS/ENSCM/Université Montpellier 2, 8 rue de l’Ecole Normale, F-34296 Montpellier, France

3

MultiScale Materials Science for Energy and Environment, UMI 3466 CNRS-MIT and

Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

*To whom correspondence should be addressed. E-mail: [email protected] and [email protected] 1 ACS Paragon Plus Environment


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Abstract. The alignment of water molecules along chiral pores may activate proton/ion conduction along dipolar hydrophilic pathways. Here we show that a simple synthetic “Tchannel” forms a directional pore with its carbonyl moieties solvated by chiral helical water wires. Atom-scale simulations and experimental crystallographic assays reveal a dynamical structure of water and electrolyte solutions (alkali chlorides) confined in these organic Tchannels. Oscillations in the dipole orientation, which correspond to alternative ordering (dipole up – dipole down) of the water molecules with a period of about 4.2 Å (imposed by the distance between two successive carbonyl groups) are observed. When ions are added to the system, despite the strong coulombic water/ion interaction, confined water remains significantly ordered in the T-channel and still exhibits surface-induced polarization. Cation permeation can be achieved through alternated hydration-dehydration occurring along strongly oriented water-wires. The T-channel, which exhibits chirality with strong water orientation, provides an opportunity to unravel novel water-channels systems that share many interesting properties of biomolecular systems.

Keywords: Artificial water channels, Water wires, Ion channels, Molecular simulation

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1. Introduction Selective exchange of water, ions, and molecules between cells and their surrounding environment is at the heart of many biological processes. As far as transport along biological channels is concerned, the protein structure helps overcome the high energy barrier of translocation of metabolites which may be synergistically transported across the bilayer membrane.1 In such complex transport problems, electrostatic interactions are known to play a key-role in the functional properties of Gramicidin A,2,3 Aquaporin,4,5 KCsAK+,6 and M2Influenza A7,8,9 protein-channels. Water is also known to play a crucial role, owing to its complex behavior at the molecular level.10,11,12 Of particular interest, the orientational and positional ordering of water molecules induced by the atomic pore structure and water-water interactions can control ionic conduction as well as ion-valence selectivity, and may also prevail in the selective translocation of protons/ions through protein-channels.2,4,6,7

Molecular encapsulation of water in man-made materials allows exploring the behavior of water in conditions relevant to confined biological water as well as that of water with reduced dynamics in between those for liquid water and ice.13,14,15,16,17,18 Nevertheless, only few biomimetic membranes have been considered to selectively and efficiently conduct water.19,20,21,22 Within this context, unraveling the molecular dynamics of water trapped in artificial host channels is crucial for many scenarios relevant to biology, physics, chemistry, etc.. Specific interaction of water-wires with chiral synthetic pores may align the water molecules along their inner chiral surfaces, therefore presenting unique dipolar orientations.19,20,21 The chiro-induced dipolar moment of water wires is of great interest for electrostatic pumping within channels. It may also help design novel devices to mimic protein-channels and describe new scenarios of the polarization of chiral biological surfaces bio-lubricated with electrostatically active dipolar water aggregates.



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We recently discovered that a bola-amphiphile bis-triazole compound (TCT) form selfassembly structures which consist of stable helical pores.22 The TCT forms stable T-channels in lipid bilayers with the hydrated carbonyl and amine moieties pointing toward the interior of the T-channel. Such pores possess diastereoisomeric chiral inner hypersurfaces with atomic details inducing strong orientational ordering of confined water (Figure 1). Experiments have shown that such a T-channel lead to high water flux, high cation/anion selectivity, and large open channel-conductance states when used as bilayer membranes.22 These observations have raised the following issues: (a) the role of such oriented water, especially its contribution to ion encapsulation and translocation through the T-channels and the stability of such confined water, especially under competitive cation-water transport? Here we build on our previous work with an advanced structural and theoretical analysis of water and ion dynamics within the T-channels. We observe that the T-channels associate supramolecular chirality with water alignment along the channels. As in the case of Gramicidin A, our results suggest that ion transport within the T-channels is governed by the subtle balance between hydration and complexation energies of the confined cations. Nevertheless, the large transport activities for the T-channel with respect to Gramicidin A suggests that the dipolar orientation of confined water acts as a lubricant for ion conduction.


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2. Methods 2.1. X-ray Crystal data. X-ray data were collected on an Agilent Technologies Gemini-S diffractometer using graphite monochromated Mo-radiation at 173 K. The structure was easily solved by the ab-initio charge flipping method using locally normalized structure factors as implemented in the program Superflip.23 The structure could be refined down to R1(I>2σ(I)) =0.0815 and wR2 (I>2σ(I))=0.0812). Refinements were carried out using nonlinear least-squares methods within CRYSTALS.24 Since the analysis of the structure showed empty T-channels with a total solvent accessible volume of 478 Å3, representing 23% of the total unit cell volume it was decided to inspect closely the inner contents of the T-channels. By assigning the major peaks in the difference Fourier maps to oxygen atoms and letting the occupancy of these atoms freely refine while keeping constrained to each other the isotropic displacement parameter, the model could be further refined with soft shift limiting restraints to (I>2σ(I)) =0.0485 and (I>2σ(I))=0.0330. The total occupancy of the 8 oxygen positions was 0.7528 corresponding to 6.0 water molecules in the unit cell with an overall isotropic displacement factor somewhat (0.066 Å2) higher than the average isotropic displacement parameter of the TCT molecule itself (0.035 Å2). The total electron count of the unit cell water molecules amounts thus to 60 electrons. Alternatively the electron density in the unit cell was modelled using the squeeze procedure25 in the program PLATON.26 This yielded 44 electrons in the unit cell, lower than the electron count resulting from the ad-hoc refinement of the peaks in the electron density map. The electron count resulting from the refinement of the site occupancy factors may, however, be slightly overestimated because of the high average atomic displacement parameter. The final agreement factors of the refinement using the squeeze-modified structure factors were (I>2σ(I)) =0.0402 and (I>2σ(I))=0.0431.



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2.2. Cation transport experiments. A volume of 100 µL of vesicles filled with pyranine (8hydroxypyrene-1,3,6-trisulphonic acid trisodium salt or HPTS) was suspended in 1.9 mL of a phosphate/sulfate buffer. HPTS emission at the wavelength λ = 510 nm was probed using simultaneous excitation wavelengths equal to 403 and 460 nm. In the course of these experiments, a stock solution containing the compound TCT in 20 µL of DMSO (final solution with concentrations equal to 0.10, 0.20 and 0.40 mM, Supplementary Table S1) was added at a time t = 0 s. Such additions were followed by the addition of 21 µL of aqueous NaOH (concentration 0.5 M) at a time t = 60 s. NaOH increases the pH by about 1 pH unit in the buffer. Important dye emission modifications were observed at a time t = 500 s by lysis of the liposomes with a detergent consisting of 40 µL of aqueous (5%) Triton X100. Transport trace was estimated as the ratio of the intensities emitted at 460 and 403 nm. Rate constants were estimated using the slopes of ln([H+in]-[H+out]) as a function of time, where [H+in] and [H+out] are respectively the intravesicular/extravesicular proton concentrations. [H+out] was supposed to be constant over the duration of the experiment, while [H+in] was estimated at each time from the HPTS emission intensities using the calibration relationship, pH = 1.1684·log(I0/I1)+6.9807. In this equation, I0 and I1 are the intensities emitted with the excitation wavelengths 460 nm and 403 nm, respectively.27

2.3. Molecular simulation. The material is a monoclinic crystal whose space group is I12/a1. The cell parameters are a = 8.47 Å, b = 17.55 Å, c = 13.55 Å with β= 95.85°. We considered a simulation box of 3×2×2 replicas along the cell axes (Figure S1a in the Supplementary Information). The atomic partial charges of the material were estimated in the frame of the Mulliken approach from DFT calculations (B3LYP/6-21G) performed with the software CRYSTAL 06.28 This software, which considers periodic systems, is well adapted for


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crystalline structures. Thanks to symmetry operations, only 22 out of the 176 atoms in the unit cell are needed to perform the calculations (Figure S1b in the Supplementary Information).

The experimental structure was kept frozen when performing the Quantum Chemistry calculations of the electronic energy (i.e., the cell parameters and atomic positions were not optimized). The charges obtained in the present work are in good agreement with those used in the AMBER force field (Supplementary Table S2)29,30 and with similar calculations (B3LYP/6-311G(d, p)) performed on the constitutive molecule with the software Gaussian03.

The SPC model of Jorgensen et al.31 was used to describe the water molecule. This model describes the O and H atom of the rigid water molecule (assumed to be rigid) with a partial charge interacting through the Coulomb interaction. Moreover, the oxygen atom of the water molecule interacts through repulsion/dispersion interactions described using a Lennard-Jones potential. Cations and anions (LiCl, NaCl, and CsCl) of the electrolytes were treated as a sphere with a charge +1 and -1, respectively. In addition, each ion interacts through repulsion/dispersion interactions described using a Lennard-Jones potential. These Lennard – Jones parameters, which are presented in Supplementary Table S2 were taken from Refs.32,33,34 Interactions between the atoms of water, atoms of the T-channel, and the ions include the Coulombic interaction and the dispersion interaction together with a repulsive interaction. The energy U k ( rk ) of ion or atom k at position rk is: =

,!,",#$,,%,#,!&

4

− + 4

(1)

where X = Li, Na, or Cs and rkj is the distance between the atom or ion j (OW, HW, X, Cl, O, C, N, or H) and the atom k of the electrolyte. All interaction contributions were determined within a cutoff corresponding to one half of the smallest box length ~12 Å. The Coulombic



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interaction was computed using the Ewald sum method with α = 0.22 Å-1, kA = 5, kB= 7, kC= (((), , (() are the vectors of the simulation box. The interaction parameters for the (), + 6, where ' substrate atoms are taken from AMBER force field for proteins.

The structure of water and electrolyte solutions in the T-channel was investigated using Monte Carlo simulations in the Canonical ensemble (MC).35,36 This technique is a stochastic method that simulates a system having a constant volume V (the T-channel with the adsorbed electrolyte solution), in equilibrium with a thermostat imposing its temperature T. Monte Carlo trial moves in the Canonical ensemble are molecule translation or rotation and ion translation. These moves were attempted in the present work with an equal probability. Molecule translation and rotation and ion translation are accepted with a probability given in the frame of the Metropolis method: -., = min21, exp7−8Δ., :;

(2)

where β = 1/kBT is the reciprocal temperature (kB is the Boltzmann constant). ∆Ui,j is the change in the internal energy between the state i before the move and the state j after the move. The MC calculations were computed using a home-made program where the species are represented as rigid bodies. The atomic positions of the substrate are maintained fixed during the MC simulations. Periodic boundary conditions were applied along the x, y, and z directions in order to avoid finite size effects. MC simulations were carried out for 5×107 trials for pure water and for 2×107 trials for electrolyte solutions. Configurations were stored each 104 trials. When averaging the thermodynamic quantities, the first 2500/100 configurations were discarded as they correspond to an equilibration step.


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3. Results and Discussion 3.1. X-ray structure of TCT. The unit cell is made of 12 molecules of TCT and 6 water molecules. Analysis of the crystals reveals homomeric H-bonding associations of the triazole moieties.37 The intertwined TCT strands in the structure form double-helix by two – CONH···NIm H-bonds (dN--H =2.28 Å) of the terminal T units, which present an unusual tetrahedral geometry (since double H-bond motifs are usually planar) (Figure 1). The successive tetrahedral H-bonding sequences strongly enforce the double-helical winding of the strand, which allows considerable overlap between the central hydrophobic chains of the monomers. The stiffness of the double helix formed by the TCT molecules arises from a combination of H-bonding and hydrophobic interactions, and may be associated with the stable oligomers observed in solution over a large concentration domain.22



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Figure 1. a) Chemical formula and crystal structure of TCT compound self-assembling in Tchannels with a pore void of small (d = 2.5 Å) and large (d = 4 Å) pore mouths. b) Ellipsoidand-stick representation of the crystal matrix of TCT with superimposed electron density isosurfaces (red) at the 1.3 e/Å3 level as calculated by the Maximum Entropy Method38 for the unit cell part 0 ≤ x ≤ 1; 0.2 ≤ y ≤ 0.8; 0.2 ≤ z ≤ 0.8, and visualized by VESTA.39 The Maximum Entropy Method converged to reliability factors of RF = 0.0187 and wRF = 0.0179 using a 4th-order F-constraint. Most oxygen atoms in the channel are discrete entities, but this depends of course on the exact value of isosurface level.

The self-assembly of TCT molecules leads to hour-glass T-channels with alternating small (d = 2.5 Å) and large (d = 4 Å) pore mouths (Figure 1). The inner pore presents an inversion plane with hypersurfaces of opposite chirality (half-superior and half-inferior). The water molecules confined within the T-channel are ordered with two preferential adsorption sites corresponding to -C=O···Hw and -NH···Ow H-bonds. They are arranged into approximately helical arrays and their position is consistent with the diastereoisotopic pattern of the double helical T-channel. The electron density map of water within the crystal structure of TCT suggests that they should exhibit water disorder/motion (see Methods section for a detailed discussion). 10 ACS Paragon Plus Environment

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3.2. Molecular structure of water confined within T-channels. To shed light on the structure and ordering of water molecules within the T-channel we performed Monte Carlo molecular simulations of water adsorbed within the experimentally determined structure. Six water molecules were adsorbed per T-channel with a length of 25.41 Å, which corresponds to 3 times the crystallographic parameter a = 8.47 Å. The simulated axial and radial density profiles in Figure 2 reveals significant positional ordering of water within the T-channel. Figure 2 also shows the simulated contour plots in the planes (x,y) and (y,z) of the density of water to illustrate the positions of water confined in the T-channel (these contour plots are integrated over the third direction). For the sake of clarity, we also show in the contour plots the skeleton of the T-channel which is represented by silver, red, and blue sticks that correspond to the bonds between the C, O, and N atoms, respectively. The density at r = 0 is very low as there are nearly no water molecules in the center of the T-channel. The two marked density peaks observed at r ~ 1.0 and 2.1 Å correspond to two layers of confined water. These two preferential positional are referred to as site A (in strong H-bonding interaction with the –C=O groups) and site B (corresponding to water molecules interacting with the amino groups) (Figure 2).



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Figure 2. (top) Axial (left) and radial (right) density profiles of water confined in the Tchannel as obtained by means of molecular simulation. The pink solid and dashed vertical lines correspond to the positions of the –C=O and NH2 groups, respectively, along the Tchannel. The density ρ is in arbitrary unit. For the axial density profile, ρ corresponds to the probability of finding a water molecule in a slice of volume unity at a position x along the pore axis. For the radial profile, ρ corresponds to the probability of finding a molecule in a volume unity between r and r + dr. (bottom) The absolute density in nm-3 is given by the density profile multiplied by the number of water molecules per T-channel. Contour plots show the average density of water within the T-channel with the following color code: blue < green < yellow < orange < red.

This situation corresponding to a water molecule interacting with an oxygen atom of the carbonyl groups is clearly seen in the contour plot in the (y,z) plane shown in Figure 2 12 ACS Paragon Plus Environment

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(position a). The second set of density peaks along the pore axis shows smaller peaks located between two successive sets of carbonyl groups. The subtle local ordering of water confined in the T-channel, which is characteristic of water confined in nanopores or in the vicinity of surfaces,40,41,42,43,44 suggests that its properties significantly differ from their bulk counterpart.

Figure 3 shows the pair correlation functions g(r)45,46 between the Ow and Hw of water (OW and HW atoms) and between the atoms of water and the oxygen atoms of the T-channel (OS). The g(r) between two atoms A and B is proportional to the probability of having A between r and r+dr from B. The g(r) function is related to the inverse Fourier transform of the structure factor S(q) as determined from neutron or X-ray scattering.47



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Figure 3. Pair correlation functions g(r) between the Hw of water and the O of the T-channel surface (solid blue line), between the Ow and Hw of confined water (solid black line), and between the Ow and Hw of bulk water (dashed black line).

The pair correlation functions between OW and HW exhibit short-range positional order which is characteristic of a liquid phase. The first peak observed at a distance about r ~ 1.8 Å corresponds to hydrogen bonding. As seen in Figure 3, such a distance is identical to what is obtained for bulk water. The first peak at a distance about r ~ 1.8 Å in the g(r) function between HW and OS atoms in water corresponds to the formation of hydrogen bonds between the water molecules and the oxygen atoms of the carbonyl groups of the T-channel. The amplitude of this peak ~0.7 is much smaller than that observed in confined water ~8 between OW and HW. The less significant hydrogen bonding for water with the oxygen atoms of the carbonyl groups is due to steric effects that prevent more than one water molecule from approaching the T-channel surface (steric interaction with other surface atoms). Moreover, these results suggest larger correlations between water molecules interacting with the neighboring water than for those interacting with carbonyl groups at the T-channel surface. The g(r) function between OS and HW exhibits a second peak at a distance of 4 Å, 14 ACS Paragon Plus Environment

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corresponding to the correlation between water molecules. The number N2S ~ 1 of water molecules in interaction with the first closest carbonyl groups is readily obtained from the number of water in a sphere of radius r = 4.5 Å. Given that a T-channel contains 12 oxygen atoms and N = 6 adsorbed water molecules, the fact that N2S ~ N/6 shows that each molecule is able to interact with two oxygen atoms.

We also investigated the dielectric structure and ordering of water within the T-channel. The density contour plots of water show two possible orientations: a) in the upper part of the Tchannel, the dipole of the water molecules is orientated along the positive axis and b) in the lower part of the T-channel, the dipole of the water molecules is orientated along the negative axis (Figure 4). The dipolar orientation of the confined water molecules is mostly imposed by the –C=O groups at the surface of the channel. Indeed, due to the inversion centers located between two successive sets of –C=O groups, the oxygen atoms in the lower part of the pore towards the positive axis while the oxygen atoms in the upper part point towards the negative axis. Of course, this result was expected since confined water must respect the inversion center symmetry imposed by the host structure. Consequently, this finding should not be considered as a result in itself but as a consistency check to validate the molecular simulations.



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Figure 4. a) Density contour plot of water (left) with µx < 0 (i.e. dipole towards the direction -

0 (i.e. dipole pointing towards the direction

Polarized Water Wires under Confinement in Chiral Channels - The

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