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1 In the format provided by the authors and unedited. DOI: /NCHEM.2675 Real-time molecular scale observation of crystal formation Roy E. Schreiber, 1 Lothar Houben, 2 Sharon G. Wolf, 2 Gregory Leitus, 2 Zhong-Ling Lang, 3 Jorge J. Carbó, 3 Josep M. Poblet, 3 and Ronny Neumann 1 * Supplementary Movie Descriptions Supplementary Movie 1. Crystallization with addition of NaCl by molecular attachment. Real time aggregation of MnPFOM molecules in the presence of NaCl under illumination with the electron microscope beam in a cryo-tem experiment. Cumulative electron doses applied are shown as a running counter on the bottom left hand side. The scale bar is 50 nm. A dark dot is associated with the cluster of tungsten atoms in a single MnPFOM molecule. Supplementary Movie 2. Crystallization with addition of NaCl by molecular attachment. Snapshots of MnPFOM molecules in the presence of NaCl aggregating under illumination with the electron microscope beam in a cryo-tem experiment. The scale bar is 50 nm. A dark dot is associated with the cluster of tungsten atoms in a single MnPFOM molecule. Note the homogeneous formation of aggregates throughout the sample in absence of ice formation. Supplementary Movie 3. Crystallization with addition of NaCl by cluster attachment. Continuing the illumination with the electron microscope beam in a cryo-tem experiment after small aggregates were formed may induce a process of cluster attachment. Colliding aggregates can be observed on the top right hand side and center as well as on the bottom right hand side. Cumulative electron doses applied are shown as a running counter on the bottom left hand side. The scale bar is 50 nm. A dark dot is associated with the cluster of tungsten atoms in a single MnPFOM molecule. Supplementary Movie 4. TEM irradiation with no salt addition. Illumination of a MnPFOM solution without addition of other salts under the electron microscope beam in a cryo-tem experiment. This control experiment shows that MnPFOM molecules do not aggregate under these conditions without addition of cations to the solution. Cumulative electron doses applied are shown as a running counter on the bottom left hand side. The scale bar is 50 nm. A dark dot is associated with the cluster of tungsten atoms in a single MnPFOM molecule. Supplementary Movie 5. Tomography of proto-crystals with Na +. A three dimensional reconstruction of the formed proto-crystals shows that they generally grow only in two dimensions in our conditions. A yellow dot is associated with the cluster of tungsten atoms in a single MnPFOM molecule. Supplementary Movie 6. Molecular dynamics simulation of MnPFOM with NaCl. A molecular dynamics simulation of 20 MnPFOM, H 2 O, 160 K + and 330 NaCl molecules. Dimers and trimers of MnPFOM molecules are formed, mediated by Na + and K + cations. Na blue, K brown, W grey, Mn purple, O red, F green. Supplementary Movie 7. Molecular dynamics simulation of MnPFOM without addition of salt. A molecular dynamics simulation of 20 MnPFOM, H 2 O, 160 K +, but without addition of NaCl. This control simulation shows that no stable dimers or trimers of MnPFOM molecules are formed when additional cations are not added to the system. Na blue, K brown, W grey, Mn purple, O red, F green. NATURE CHEMISTRY 1

2 Supplementary Movie 8. Crystallization with addition of CsCl by dense phase mechanism. Real time aggregation of MnPFOM molecules in the presence of CsCl under illumination with the electron microscope beam in a cryo-tem experiment. Cumulative electron doses applied are shown as a running counter on the bottom left hand side. The scale bar is 50 nm. A dark dot is associated with the cluster of tungsten atoms in a single MnPFOM molecule. Supplementary Movie 9. Crystallization with addition of CsCl by dense phase mechanism. Snapshots of MnPFOM molecules in the presence of NaCl aggregating under illumination with the electron microscope beam in a cryo-tem experiment. The scale bar is 50 nm. A dark dot is associated with the cluster of tungsten atoms in a single MnPFOM molecule. Supplementary Methods Synthesis - The synthesis of K 8 [H 2 F 6 NaMn IV (OH)W 17 O 55 ] 15H 2 O was done according to a previously reported procedure 36. First the Zn(II) substituted PFOM was prepared by dissolving 44 g of Na 2 WO 4 2H 2 O in 100 ml of de-ionized water and heating to C. To this solution were added 14 ml of 40% HF bringing it to ph = 4.5. The solution was then stirred for 1 hour and filtered. The filtrate was reheated to 80 C and a solution of 7 g Zn(CH 3 CO 2 ) 2 2H 2 O in 10 ml de-ionized water was added dropwise. The solution was let stir for an additional 1 hour and filtered. Note that carefully controlling the temperature ensures that the zinc atom is substituted at the belt position only. This filtrate was precipitated by addition of 4.5 g KCl and the precipitate was recrystallized in 5.5 ml de-ionized water. Yield 3 g. Then 3 g Zn(II)PFOM dissolved in 27 ml acetate buffer, ph=5, were heated to 50 C and 324 mg MnSO 4 H2O in 2 ml acetate buffer, ph=5, were added dropwise. The solution turned brown, was stirred for 30 min and then cooled. Mn(II)PFOM was precipitated with a saturated solution of KCl. Yield g (80%). 2g of Mn(II)PFOM were dissolved in 35 ml de-ionized water; 2g of Oxone were added and the solution was heated to 80 C. The solution changed color from light brown to purple and finally to dark brown, where upon it was cooled in ice water and Mn(IV)PFOM was collected by precipitation with saturated KCl. Yield 1.2 g (60%). X-ray Crystallography - Na 2 K 6 MnPFOM: An aqueous solution of 27 mm Mn(IV)PFOM and 420 mm NaCl was crystalized at 3 C. The formed crystals were heat sensitive and therefore were kept in liquid N 2 until their measurement. B-level alerts: Isolated O31, O32, O33, O35, O36, O37, O38 atoms are water molecules, H-atoms are not localized. Cs 5.5 K 2.5 MnPFOM: 5.5 mg CsCl were added to an aqueous solution of 0.5 ml 4.7 mm MnPFOM at room temperature. The mixture was heated until dissolution and slowly cooled to room temperature yielding the desired crystals. B-level alerts: Isolated O21 atom is a water molecule, H-atoms are not localized. NATURE CHEMISTRY 2

3 Data collection was performed on a Bruker Apex2 KappaCCD diffractometer, MoKα (l= å), graphite monochromator. Frame scan width = 0.5, scan speed 1 per 360 sec for Na 2 K 6 MnPFOM and 1 per 180 sec for Cs 5.5 K 2.5 MnPFOM. The data were processed with the Bruker Apex2 software and the structure was solved with SHELXT. Full matrix leastsquares refinement was based on F 2 with SHELXL-2014/7. Supplementary Table 1. Crystallographic details and statistics. Na 2 K 6 MnPFOM Cs 5.5 K 2.5 MnPFOM Formula F 6 K 6 Na 3 Mn 1 W 17 O 76 F 12 K 5 Na 2 Cs 11 Mn 2 W 34 O 128 Moiety formula F 6 K 6 Na 1 Mn 1 W 17 O 56 +2*Na+ 20*O 2*F 6 Na 1 Mn 1 W 17 O *Cs+5 *K+ 44*O Formula wt (g mol -1 ) Crystal dimentions (mm 3 ) 0.05 x 0.12 x x 0.12 x 0.04 Typical peak mosaicity (deg) Cryst system Monoclinic Orthorhombic Space group C2/c Cmca T (K) 100(2) 100(2) a (Å) (5) (4) b (Å) (3) (4) c (Å) (6) (5) α (deg) β (deg) 92.34(3) 90 γ (deg) V (Å 3 ) 8161(3) 7395(3) Z 4 2 D calc (g cm -3 ) µ (mm -1 ) Collected reflections h -26 h h 15 k -7 k k 16 l 35 l l 25 Unique reflections R int Reflections [I > 2σ(I)] Parameters Restraints R(F) a [I > 2σ(I)] R(F) a (all data) wr(f 2 ) a (all data) GOF Largest density peak (A -3 ) Deepest hole (A -3 ) NATURE CHEMISTRY 3

4 Supplementary Table 2. Definition of the simulated systems. System MnPFOM H 2 O K + NaCl Box size (nm nm nm) none Number of molecules for the different species and box size is in nm 3. Supplementary Figure 1. Space filling model of the MnPFOM anion showing its oblong shape. Na blue, W grey, O red, F green. Supplementary Figure 2. Tomogram voxel projection and ortho-slices of the TEM cryosample after aggregation of MnPFOM molecules. Aggregates were formed in the presence of NaCl under illumination with the electron beam in the electron microscope. The voxel projection (a) shows several clusters that formed after crystal nucleation primarily in the xy- NATURE CHEMISTRY 4

5 plane. The ortho-slices I and II in (b) and (c) show a cross-sectional view of the TEM sample after the aggregation reaction. The location of the vitrified water surface in the sample is marked by arrows. Note that the image of the surface that is marked with arrows is repeated in a sequence of ghost images due to the limited number of projections that were available for the tomographic reconstruction. The residual vitrified water thickness after aggregation reaction is about 30 nm. Supplementary Figure 3. Comparison of 2D and 3D crystal lattice for the (100) plane. The plane lattice formed by a <100> view of the (100) plane in the XRD crystal structure of MnPFOM. MnPFOM molecule centers are marked by circles. The plane symmetry formed by this projection belongs to the rectangular pg plane group. The projection of a monoclinic C2/c space unit cell a,b,c is shown together with the rectangular pg plane unit cell (dashed red): a p =29.421(6) Å; b p =12.292(3) Å. Molecule centers occupy 2-fold positions (0.75, 0.35). Shortest distances between the lattice points are shown. Supplementary Figure 4. Crystal structure of the Na, K salt of MnPFOM. a, b. <010> and <100> views respectively of the (100) plane in the XRD crystal structure of MnPFOM. Na blue, K brown, W grey, O red, F green. The anions in this (100) plane are bound by Na + counter cations and surrounded by K + counter cations. MnPFOM molecules are surrounded by a layer of water molecules that shield their large negative charge. NATURE CHEMISTRY 5

6 Supplementary Figure 5. Sodium counter-cation site in the crystal structure. Na dark blue, W grey, O in the PFOM anion red, structural water cyan. Supplementary Figure 6. Simulated structures of MnPFOM dimers and trimers. Representative snapshots for MnPFOM MnPFOM dimer (a) and trimer (b) formation in the presence of additional NaCl salt. They correspond to different RDF peaks displayed in Figure 3. The tilt angles between the long axes of each MnPFOM couple are 58º, 45º and 37º for dimers (from the left to the right in panel a); and 3º and 64º for the two interactions in the trimer (from the left to the right in panel b). The dimer snapshots correspond to the same MnPFOM couple, whose interaction occurred during the last 3 ns of the simulation. The trimer interaction lasted for ~400 ps. The hydrophilic Mn-OH moiety does not participate in the MnPFOM MnPFOM interaction and points towards the water solution. NATURE CHEMISTRY 6

7 Supplementary Figure 7. Molecular dynamics simulations for the system without NaCl. Radial distribution functions between MnPFOM K + (brown) and MnPFOM MnPFOM (dark grey) for simulations without additional salt. The internal Na atom of the MnPFOM structure was used as reference for MnPFOM MnPFOM RDF. Supplementary Figure 8. Crystal lattice overlayed on a cryo-tem image for the system with Cs. Left: TEM image with CsCl after aggregation. Right: overlapped grid marks the crystal lattice seen in the image. Supplementary Note 1. Comment on the assignment of Na2 - A reviewer commented that the Na cation site (Na2 in the cif file) should be a half occupied K site due to relatively long Na-O bond lengths associated with our assignment. We have carefully considered this crystallographically plausible suggestion, since such a refinement yields the same, but not better, R-factor and thermal parameters. Despite this reasonable doubt, we believe that our assignment of a fully occupied Na site is more likely to be correct for the following reasons. (1) Assignment as a half occupied K site will result in 7 counter-cations per PFOM anion instead of 8 that is commensurate with the charge summation. (2) Since there is no other half occupied cation in the vicinity of this site, this will cause a negatively charged vacancy in the crystal structure whenever K is absent. It should be also noted that (1) the Na-O bonds are long relative to the average in the literature, but not unknown; 672 examples can be found in the CCDC. (2) Longer Na-O distances are quite common in polyoxometalate structures perhaps because the crystal lattice is determined mostly by the large polyoxometalate clusters. See, for example, ICSD collection code and for polyoxometalates with Na cations only. NATURE CHEMISTRY 7