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1. A single nucleobase tunes nonradiative decay in a DNA-bound silver cluster

   https://doi.org/10.1063/5.0056836  

   Zhang, Yuyuan ; He, Chen ; de La Harpe, Kimberly ; Goodwin, Peter M. ; Petty, Jeffrey T. ; Kohler, Bern ( September 2021 , The Journal of Chemical Physics)

   DNA strands are polymeric ligands that both protect and tune molecular-sized silver cluster chromophores. We studied single-stranded DNA C4AC4TC3XT4 with X = guanosine and inosine that form a green fluorescent Ag106+ cluster, but these two hosts are distinguished by their binding sites and the brightness of their Ag106+ adducts. The nucleobase subunits in these oligomers collectively coordinate this cluster, and fs time-resolved infrared spectra previously identified one point of contact between the C2–NH2 of the X = guanosine, an interaction that is precluded for inosine. Furthermore, this single nucleobase controls the cluster fluorescence as the X = guanosine complex is ∼2.5× dimmer. We discuss the electronic relaxation in these two complexes using transient absorption spectroscopy in the time window 200 fs–400 µs. Three prominent features emerged: a ground state bleach, an excited state absorption, and a stimulated emission. Stimulated emission at the earliest delay time (200 fs) suggests that the emissive state is populated promptly following photoexcitation. Concurrently, the excited state decays and the ground state recovers, and these changes are ∼2× faster for the X = guanosine compared to the X = inosine cluster, paralleling their brightness difference. In contrast to similar radiative decay rates, the nonradiative decay rate is 7× higher with the X = guanosine vs inosine strand. A minor decay channel via a dark state is discussed. The possible correlation between the nonradiative decay and selective coordination with the X = guanosine/inosine suggests that specific nucleobase subunits within a DNA strand can modulate cluster–ligand interactions and, in turn, cluster brightness. 

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2. Long-lived Ag106+ Luminescence and a Split DNA Scaffold

   J. T. Petty, S. Carnahan ( June 2021 , Journal of chemical physics)

   Molecular silver clusters emit across the visible to near-infrared, and specific chromophores can be formed using DNA strands. We study C4AC4TC3G that selectively coordinates and encapsulates Ag106+, and this chromophore has two distinct electronic transitions. The green emission is strong and prompt with ϕ = 18% and τ = 1.25 ns, and the near-infrared luminescence is weaker, slower with τ = 50 µs, and is partly quenched by oxygen, suggesting phosphorescence. This lifetime can be modulated by the DNA host, and we consider two derivatives of C4AC4TC3G with similar sequences but distinct structures. In one variant, thymine was excised to create an abasic gap in an otherwise intact strand. In the other, the covalent phosphate linkage was removed to split the DNA scaffold into two fragments. In relation to the contiguous strands, the broken template speeds the luminescence decay by twofold, and this difference may be due to greater DNA flexibility. These modifications suggest that a DNA can be structurally tuned to modulate metastable electronic states in its silver cluster adducts. 

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3. Large-scale investigation of the effects of nucleobase sequence on fluorescence excitation and Stokes shifts of DNA-stabilized silver clusters

   https://doi.org/10.1039/D0NR08300C  

   Copp, Stacy M. ; Gonzàlez-Rosell, Anna ( March 2021 , Nanoscale)

   null (Ed.)

   DNA-stabilized silver clusters (Ag N -DNAs) exhibit diverse sequence-programmed fluorescence, making these tunable nanoclusters promising sensors and bioimaging probes. Recent advances in the understanding of Ag N -DNA structures and optical properties have largely relied on detailed characterization of single species isolated by chromatography. Because most Ag N -DNAs are unstable under chromatography, such studies do not fully capture the diversity of these clusters. As an alternative method, we use high-throughput synthesis and spectroscopy to measure steady state Stokes shifts of hundreds of Ag N -DNAs. Steady state Stokes shift is of interest because its magnitude is determined by energy relaxation processes which may be sensitive to specific cluster geometry, attachment to the DNA template, and structural engagement of solvent molecules. We identify 305 Ag N -DNA samples with single-peaked emission and excitation spectra, a characteristic of pure solutions and single emitters, which thus likely contain a dominant emissive Ag N -DNA species. Steady state Stokes shifts of these samples vary widely, are in agreement with values reported for purified clusters, and are several times larger than for typical organic dyes. We then examine how DNA sequence selects Ag N -DNA excitation energies and Stokes shifts, comment on possible mechanisms for energy relaxation processes in Ag N -DNAs, and discuss how differences in Ag N -DNA structure and DNA conformation may result in the wide distribution of optical properties observed here. These results may aid computational studies seeking to understand the fluorescence process in Ag N -DNAs and the relations of this process to Ag N -DNA structure. 

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4. pH Dependence of the speciation and optical properties of 4-benzoylbenzoic acid

   https://doi.org/10.1039/D3CP01520C  

   Karimova, Natalia ; Alija, Onita ; Mora García, Stephanie L. ; Grassian, Vicki H. ; Gerber, R. Benny ; Navea, Juan G. ( July 2023 , Physical Chemistry Chemical Physics)

   Organic chromophores initiate much of daytime aqueous phase chemistry in the environment. Thus, studying the absorption spectra of commonly used organic photosensitizers is paramount to fully understand their relevance in environmental processes. In this work, we combined UV-Vis spectroscopy, 1 H-NMR spectroscopy, quantum chemical calculations, and molecular dynamics simulations to investigate the absorption spectra of 4-benzoyl benzoic acid (4BBA), a widely used photosensitizer and a common proxy of environmentally relevant chromophores. Solutions of 4BBA at different pH values show that protonated and deprotonated species have an effect on its absorbance spectra. Theoretical calculations of these species in water clusters provide physical and chemical insights into the spectra. Quantum chemical calculations were conducted to analyze the UV-Vis absorbance spectra of 4BBA species using various cluster sizes, such as C 6 H 5 COC 6 H 4 COOH·(H 2 O) n , where n = 8 for relatively small clusters and n = 30 for larger clusters. While relatively small clusters have been successfully used for smaller chromophores, our results indicate that simulations of protonated species of 4BBA require relatively larger clusters of n = 30. A comparison between the experimental and theoretical results shows good agreement in the pH-dependent spectral shift between the hydrated cluster model and the experimental data. Overall, the theoretical and empirical results indicate that the experimental optical spectra of aqueous phase 4BBA can be represented by the acid–base equilibrium of the keto-forms, with a spectroscopically measured p K a of 3.41 ± 0.04. The results summarized here contribute to a molecular-level understanding of solvated organic molecules through calculations restricted to cluster models, and thereby, broader insight into environmentally relevant chromophores. 

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5. Structure and luminescence of DNA-templated silver clusters

   https://doi.org/10.1039/D0NA01005G  

   Gonzàlez-Rosell, Anna ; Cerretani, Cecilia ; Mastracco, Peter ; Vosch, Tom ; Copp, Stacy M. ( March 2021 , Nanoscale Advances)

   null (Ed.)

   DNA serves as a versatile template for few-atom silver clusters and their organized self-assembly. These clusters possess unique structural and photophysical properties that are programmed into the DNA template sequence, resulting in a rich palette of fluorophores which hold promise as chemical and biomolecular sensors, biolabels, and nanophotonic elements. Here, we review recent advances in the fundamental understanding of DNA-templated silver clusters (Ag N -DNAs), including the role played by the silver-mediated DNA complexes which are synthetic precursors to Ag N -DNAs, structure–property relations of Ag N -DNAs, and the excited state dynamics leading to fluorescence in these clusters. We also summarize the current understanding of how DNA sequence selects the properties of Ag N -DNAs and how sequence can be harnessed for informed design and for ordered multi-cluster assembly. To catalyze future research, we end with a discussion of several opportunities and challenges, both fundamental and applied, for the Ag N -DNA research community. A comprehensive fundamental understanding of this class of metal cluster fluorophores can provide the basis for rational design and for advancement of their applications in fluorescence-based sensing, biosciences, nanophotonics, and catalysis. 

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