Chloride Ligands on DNA-Stabilized Silver Nanoclusters

Abstract

DNA-stabilized silver nanoclusters (Ag_N-DNAs) are known to have one or two DNA oligomer ligands per nanocluster. Here, we present the first evidence that Ag_N-DNA species can possess additional chloride ligands that lead to increased stability in biologically relevant concentrations of chloride. Mass spectrometry of five chromatographically isolated near-infrared (NIR)-emissive Ag_N-DNA species with previously reported X-ray crystal structures determines their molecular formulas to be (DNA)₂[Ag₁₆Cl₂]⁸⁺. Chloride ligands can be exchanged for bromides, which red-shift the optical spectra of these emitters. Density functional theory (DFT) calculations of the 6-electron nanocluster show that the two newly identified chloride ligands were previously assigned as low-occupancy silvers by X-ray crystallography. DFT also confirms the stability of chloride in the crystallographic structure, yields qualitative agreement between computed and measured UV-vis absorption spectra, and provides interpretation of the ³⁵Cl-nuclear magnetic resonance spectrum of (DNA)₂[Ag₁₆Cl₂]⁸⁺. A reanalysis of the X-ray crystal structure confirms that the two previously assigned low-occupancy silvers are, in fact, chlorides, yielding (DNA)₂[Ag₁₆Cl₂]⁸⁺. Using the unusual stability of (DNA)₂[Ag₁₆Cl₂]⁸⁺ in biologically relevant saline solutions as a possible indicator of other chloride-containing Ag_N-DNAs, we identified an additional Ag_N-DNA with a chloride ligand by high-throughput screening. Inclusion of chlorides on Ag_N-DNAs presents a promising new route to expand the diversity of Ag_N-DNA structure-property relationships and to imbue these emitters with favorable stability for biophotonics applications.

Figure 1

ESI mass spectrum of (DNA)₂[Ag₁₆Cl₂]⁸⁺. Insets show calculated isotopic distributions (red lines) aligned with experimental peaks (black curve) at z = 5^– and z = 4^–, as indicated by red stars. Red arrows show the predicted position for (DNA)₂[Ag₁₈]^q+.

Figure 2

Mass spectra of (a) T5A-(DNA)₂[Ag₁₆Cl₂]⁸⁺, (b) T5C-(DNA)₂[Ag₁₆Cl₂]⁸⁺, (c) T5G-(DNA)₂[Ag₁₆Cl₂]⁸⁺, and (d) A10-(DNA)₂[Ag₁₆Cl₂]⁸⁺. Insets show isotopic distributions aligned with experimental peaks at z = 4^– for each sample. Stars indicate peaks corresponding to insets with calculated isotopic distributions. Full mass spectra and fits can be found in Figures S14 and S15.

Figure 3

(a) Absorbance, (b) emission, and (c) ESI mass spectra confirm ligand exchange in the presence of excess Br^–, yielding (DNA)₂[Ag₁₆Br₂]⁸⁺. All solutions were prepared using 12.5 μM (DNA)₂[Ag₁₆Cl₂]⁸⁺, equivalent to 25 μM chloride concentration. The original (DNA)₂[Ag₁₆Cl₂]⁸⁺ with no Br^– added is in black. Increasingly lighter shades of magenta indicate increased 10×, 50×, 100×, and 500× concentration of NaBr per chloride. (a, b) Arrows indicate red-shift in peak absorbance and peak emission with increasing [Br^–]. (c) Shading colors indicate mass spectral peaks for the different ligand compositions (calculated isotopic distributions and full mass spectra are shown in Figures S19 and S20).

Figure 4

Isolated cluster model [Ag₁₆X₂]^q+ for testing the stability of the two atoms X in the observed crystal structure with DFT calculations. Gray spheres show the crystallographic sites of the 16 Ag atoms. Red spheres show the crystallographic positions of the X atoms. Green spheres show the DFT-optimized positions for X = Cl with q = 8 (corresponding to N₀ = 6 delocalized electrons in the nanocluster). Yellow and blue spheres show the DFT-optimized positions of X = Ag by treating the total cluster charge as q = 6 and 8, respectively.

Figure 5

(a) Calculated UV–vis absorption spectrum of A10-(DNA)₂[Ag₁₆Cl₂]⁸⁺ (atom positions taken from ref (32)) as compared to the experimental data (inset). Although red-shifted with respect to the measured spectrum, the calculated spectrum reproduces the features 1–3 seen in experiment. (b) Induced transition density for the calculated peak 1. Blue and red denote oscillation phases (“charge sloshing”) creating the transition dipole.

Figure 6

(a) Experimental ³⁵Cl-NMR spectrum of (DNA)₂[Ag₁₆Cl₂]⁸⁺. The inset shows the area in the red box. The peak at 0 ppm corresponds to free chlorides in solution, in agreement with the reference used (NaCl in D₂O). (b) Proximity effect by Na⁺ cations on the ³⁵Cl-NMR shift. The calculations were made on the isolated [Ag₁₆Cl₂]⁸⁺ cluster (right) where two Na⁺ cations (blue spheres) were placed close to Cl atoms (green spheres) in the cluster. The computed ³⁵Cl shifts as a function of the Cl–Na distance are shown on the left, where the horizontal dotted line shows the observed experimental NMR peak at 430.44 ppm.

Figure 7

(a) Overall structure of (DNA)₂[Ag₁₆Cl₂]⁸⁺. (b) 2|F_o| – |F_c| map around an Ag-mediated C8–C8 base pair contoured at the 1.5σ level. (Silver: Ag atoms; green: Cl^– ions.) Structural details available at the PDB database using accession code 6M2P.