DOI: 10.6078/d19q3f
title: Gold Nanorods with PEG-Alkanethiol Ligands Etching in Graphene Liquid Cell Electron Microscopy-38 mM FeCl3

description: Premade gold nanorods with PEG-Alkanethiol ligands were etched in a
 graphene liquid cell and imaged using Transmission Electron Microscopy
 (TEM). An aqueous solution of gold nanorods, Tris Buffer-HCl, and
 FeCl3 was encapsulated between graphene sheets. The final
 concentration of FeCl3 was 38 mM. Through a combination of the
 electron beam-generated radiolysis products and the FeCl3, the nanorods
 underwent non-equilibrium etching. See associated papers for more
 details. 
description: The methods section taken from: Matthew R.
 Hauwiller, Xingchen Ye, Matthew R. Jones, Cindy M. Chan, Jason J. Calvin,
 Michelle F. Crook, Haimei Zheng, and A. Paul Alivisatos. Tracking the
 Effects of Ligands on Oxidative Etching of Gold Nanorods in Graphene
 Liquid Cell Electron Microscopy. ACS Nano, 2020. <b>Synthesis of Single Crystalline Gold Nanorods. </b>Single crystalline gold nanorods were synthesized followed previously reported seeded growth methods. Briefly, 0.3 mL of ice cold 0.01 M NaBH<sub>4</sub> were added to a solution of 5 mL of 0.1 M CTAB and 0.125 mL of 0.01 M HAuCl<sub>4</sub> and vigorously stirred for 2 minutes.  After 30 minutes, 24 µL of this seed solution was added to a solution of 20 mL of 100 mM CTAB, 1 mL of 10 mM HAuCl<sub>4</sub>, 0.3 mL of 10 mM AgNO<sub>3</sub>, and 0.114 mL of 100 mM ascorbic acid. To synthesize the higher aspect ratio gold nanorods, the synthesis was modified following previously reported protocol. The gold nanorods were spun down three times, and redispursed in Millipore filtered water for CTAB-based etching experiments and future ligand exchanges. <b>Exchanging to PEG-Alkanethiol Ligands. </b>Ligand exchange from CTAB to PEG-Alkanethiol followed previously reported synthetic protocols. Gold nanorods were spun down and resuspended in 100 µL of 5.7 mM HS-(CH<sub>2</sub>)<sub>11</sub>-(EG)<sub>6</sub>-OCH<sub>2</sub>-COOH. Then, 2 mL of H<sub>2</sub>O, 300 µL of 0.1% sodium dodecyl sulfate, and 600 µL of 1 M pH 8 phosphate buffer were added to the gold nanorod solution, resulting in a solution with 0.01% sodium dodecyl sulfate and 0.2 M phosphates buffered at pH 8 with 190 mM of PEG-Alkanethiol ligand. The amount of nanorods in the solution can vary as long as the amount PEG-Alkanethiol added is significantly in excess. The solution was sonicated for 10 seconds and then left to sonicate overnight at 35-40 degrees Celsius. After overnight sonication, the solution was centrifuged three times and resuspended in 0.01% sodium dodecyl sulfate solution. <b>Adding Cysteine to Gold Nanorod Tips For Graphene Liquid Cell Experiments. </b>21 µL of 1 nanomolar gold nanorods were mixed with 4.5 µL of 1 mM cysteine and incubated for 14 hours in the dark at room temperature. CTAB was not used in this exchange to avoid iron oxyhydroxide species from forming during liquid cell experiments. For the nanorods with full cysteine coverage, 20 uL of 1 nanomolar gold nanorods were mixed with 5 uL of 1 mM cysteine and incubated for 17 hours in the dark at room temperature. Gold nanorod solutions with full cysteine coverage showed aggregation at the bottom of the micro test tube. <b>Graphene Liquid Cell Fabrication. </b>The graphene liquid cells were fabricated following previous reported procedures. Briefly, 3-5 layer graphene was transferred to holey, amorphous carbon, gold quantifoil TEM grids (SPI Supplies, 300 Mesh, R1.2/1.3). These grids were used to encapsulate a solution of 38 mM FeCl<sub>3</sub>, 8 mM HCl, 58 mM Tris Buffer-HCl, and the gold nanorods of interest. All samples were imaged 30 minutes to 3 hours after encapsulation. <b>TEM Imaging Conditions. </b>All TEM imaging was performed on a FEI Tecnai T20 S-Twin TEM operating at 200 kV with a LaB<sub>6</sub> filament. Videos of nanocrystal dynamics were collected using a Gatan Orius SC200 camera utilizing a custom digital micrograph script with a full 2048x2048 readout with a binning of 2 pixels in each direction, at a nominal magnification of 71 kx resulting in a pixel resolution of 1.5 Å/pixel. The exposure time was 0.5 s, with a readout time of 0.8 s, yielding a frame rate of 0.77 fps. The electron dose rate was calibrated using our previously reported method. For the TEM electron beam dose rate calibration script, a conversion value of 6.7 counts/electron was used to convert CCD counts to electrons, consistent with our previous work.
description: The attached .dm3 and .avi files can be viewed using ImageJ
 (https://imagej.nih.gov/ij/index.html)