DOI: 10.6078/d14h46
title: Videos of Etching Gold Nanocubes and Nanorhombic Dodecahedra in Graphene Liquid Cell Transmission Electron Microscopy

description: Liquid cell Transmission Electron Microscopy (TEM) provides the
 opportunity to view nanocrystal dynamics in their native liquid
 environment with the necessary spatial resolution. In this dataset, gold
 nanocubes and nano-rhombic dodecahedra are etched inside graphene liquid
 cells while viewing using TEM. The initial gold nanocrystals are
 synthesized and then loaded in water pockets sandwiched between sheets of
 graphene. These graphene pockets protect the liquid from the vacuum of the
 TEM column while not preventing the electron beam from imaging the sample.
 The etching species in the reaction is a combination of FeCl3 preloaded in
 the liquid cell and oxidative radiolysis species generated by the electron
 beam. For this experiment, the initial concentration of FeCl3 was
 modulated to determine its effect on the etching process. A previously
 published paper using this dataset showed that the concentration of FeCl3
 acts as the potential in the system and this controls the intermediate
 facets on the nanocrystal. By watching nanocrystals as they undergo
 dynamic processes, the pathways and mechanisms of nanoscale processes can
 be better understood.
description: Taken from the Supporting Information of the previously published
 paper investingating the effect of the concentration of
 FeCl<sub>3</sub> on the intemediate facets:
 Hauwiller, M. R.; Frechette, L.; Jones, M.; Ondry, J.; Rotskoff,
 G.; Geissler, P.; Alivisatos, A. P. <em>Unraveling
 Kinetically-Driven Mechanisms of Gold Nanocrystal Shape Transformations
 using Graphene Liquid Cell Electron Microscopy. </em>Nano Letters.
 2018. <strong>Synthesis
 of Initial Gold Nanocrystals</strong> Gold cubes and rhombic dodecahedra were
 synthesized following a previously reported method for growing polyhedral
 nanocrystals from uniform seeds. To prepare the seeds, nanorods were
 synthesized and then etched down to spherical seeds. Briefly, 125 µL of 10
 mM HAuCl<sub>4</sub> was mixed with 5 mL of 100 mM CTAB before
 adding 300 µL of 10 mM ice cold NaBH<sub>4</sub>. This nanorod
 seed reaction mixture was stirred for 1 minute, and then let sit for 30
 minutes. A separate solution of 20 mL of 100 mM CTAB, 1 mL of 10 mM
 HAuCl<sub>4</sub>, 0.18 mL of 10 mM
 AgNO<sub>3</sub>, and 0.114 mL 100 mM Ascorbic Acid was
 prepared before injecting 24 µL of nanorod seed reaction mixture. The
 resulting growth solution sat in a water bath at 28° C for 2 hours.
 Nanorods were centrifuged two times for 15 minutes at 8,000 rpm,
 resuspending each time in 50 mM CTAB. The final nanorod solution was
 brought to 2 OD with 50 mM CTAB. Spherical gold seeds were synthesized
 from the nanorods by adding between 0.087 and 0.105 µL of 1 mM
 HAuCl<sub>4</sub> to each mL of nanorod solution and then let
 stir gently for 4 hours at 40° C. The exact amount of
 HAuCl<sub>4</sub> added to each rod sample was determined from
 small test batches to account for slight differences in the nanorod
 samples. The spherical seeds were centrifuged two times for 30 minutes at
 11,000 rpm, each time resuspending in 100 mM cetylpyridinium chloride
 (CPC) before bringing the final solution of spherical seeds to a 1 OD
 concentration.   Gold nanocubes were synthesized by mixing
 5 mL of 100 mM CPC, 500 µL of 100 mM KBr, 100 µL of 10 mM HAuCl4, and 150
 µL of 100 mM Ascorbic Acid before injecting between 350 µL and 400 µL of
 spherical seeds. The reaction was left to gently stir for 1 hour and then
 centrifuged twice at 10,000 rpm for 10 minutes before redispersing in
 Millipore-filtered water.   Gold rhombic dodecahedra were synthesized
 by mixing 5 mL of 100 mM CPC, 250 µL of 1 M HCl, 250 µL of 10 mM HAuCl4,
 13 µL of 10 mM AgNO3, and 30 µL of 100 mM of Ascorbic Acid before
 injecting between 50 and 100 µL of spherical seeds. The reaction was left
 to stir for 5.5 hours and then centrifuged twice at 10,000 rpm for 10
 minutes before redispersing in Millipore-filtered water.   <strong>Graphene Liquid Cell
 Fabrication</strong>   Graphene coated TEM grids were prepared
 by direct transfer of graphene onto holey quatifoil TEM grids. Breifly,
 CVD grown 3-5 layer Graphene on copper (ACS Materials) was washed three
 times in Acetone at 50° C for five minutes to dissolve any residual
 polymer on the graphene surface. After air drying, the graphene on copper
 was carefully flattened between two glass slides to smooth out bumps and
 rough areas. Holey carbon (1.2 µm diameter with 1.3 µM separation between
 holes), gold 300 Mesh quantifoil TEM grids (Structure Probe, Inc.) were
 placed carbon-side down on the graphene. A couple droplets of isopropanol
 were placed on top of the grids on graphene and let dry to bring the holey
 carbon in close contact with the graphene. After drying, the TEM grids
 bonded to graphene/copper substrate were floated on sodium persulfate with
 the copper side down to etch the copper. Following overnight etching, the
 graphene coated TEM grids were floated on Millipore-filtered water three
 times to rinse off the sodium persulfate and placed graphene-side up on
 filter paper for future use.   Graphene liquid cell pockets were made by
 encapsulating the solution of interest between two graphene coated TEM
 grids. The solution contained 0.25 mL of a FeCl<sub>3</sub>
 and Tris Buffer-HCl mixture with 10 uL of highly concentrated
 nanoparticles. The ratio of FeCl<sub>3</sub> and Tris Buffer
 was tuned to yield the desired FeCl<sub>3</sub> concentration
 for each trial. Tris Buffer-HCl was used to stabilize pockets although the
 exact mechanism by which Tris Buffer-HCl increases pocket success is not
 well understood. An approximately 0.5 uL droplet of the
 FeCl<sub>3</sub>/Tris Buffer/gold nanoparticle mixture was
 deposited on the graphene side of one grid. A second graphene-coated grid
 with a corner cut off was quickly placed graphene side down on top of the
 droplet on the first grid using tweezers. After waiting a couple minutes,
 the grid was taken to the TEM for imaging.   <strong>TEM
 Imaging</strong>   TEM imaging was performed on a FEI Tecnai
 T20 S-Twin TEM operating at 200kV with a LaB<sub>6</sub>
 filament. All videos were taken between 30 minutes and 3 hours after
 encapsulation. Timeseries of TEM images were collected with a Gatan Orius
 SC200 camera using a custom digital micrograph script with full 2048 x
 2048 pixel readout with a binning of 2 pixels in each direction, at a
 nominal magnification of 71kx resulting in a pixel resolution of 1.6
 Å/pixel, an exposure time of 0.5 s, and a readout time of 0.8 s yielding a
 framerate of 0.77 fps. Since etching is beam initiated, care was taken to
 minimize electron dose prior to imaging. Searching for suitable
 nanoparticles in liquid pockets was performed with a spread beam. Once a
 etchable nanocrystal was found, a custom Digital Micrograph script was
 used to reproducibly condense the electron beam to the same dose rate and
 start the TEM movie acquisition.    Briefly, at the start of a TEM session,
 a calibration script was run which fits the excitation of the C2 condenser
 lens to the dose rate of electrons recorded on the camera. This was done
 without a sample in the beam path. The extrema (most condensed and most
 spread) of the beam at the desired magnification were input into the
 script, and the C2 excitation was recorded by the script for both those
 states.  The script divided this interval into 10 equally spaced C2 lens
 excitation values, then it cycled through the C2 lens values and recorded
 an image at each value.  The image was used to calculate the dose rate at
 the given C2 lens excitation.  This data was linearized by plotting the C2
 lens excitation vs. 1/sqrt(dose rate) and fit using a linear regression
 algorithm script.  The linear regression results were then saved as a
 persistent number in Digital Micrograph. The dose rate calibration results
 were then used by a separate data acquisition script which the user could
 input an arbitrary dose rate within the calibrated range for data
 acquisition. Then, the script would convert the desired dose rate to a C2
 lens excitation that would deliver the desired dose rate.  Once the script
 set the required C2 lens excitation, the script would begin collecting a
 timeseries of images to record the beam induced <i>in situ</i>
 reaction.  The C2 lens calibration script was run before each imaging
 session since the brightness of our LaB<sub>6</sub> source
 decreases over time. We estimate that the dose rate is reproducibly
 returned to the same value within ±10%.  We note that our dose rate
 control method reproducibly provides the same dose rate over months of
 experiments (assuming camera sensitivity does not change over time)
 although it’s absolute magnitude is limited by the accuracy of the
 detector sensitivity measurement. Dose rate during etching was 800
 e<sup>-</sup>/Å<sup>2</sup>s using an incident
 electron to counts conversion of 6.26 counts per incident
 electron.    <strong>Image
 Analysis</strong>   The .dm3 are the original video files
 from the TEM imaging. The .avi files were made by opening the .dm3 files
 in ImageJ and saving as an .avi with TIFF compression.