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Monolayer protected metal clusters comprise a rich class of molecular systems and are promising candidate materials for a variety of applications. While a growing number of protected nanoclusters have been synthesized and characterized in crystalline forms, their dynamical behavior in solution, including prenucleation cluster formation, is not well understood due to limitations both in characterization and first-principles modeling techniques. Recent advancements in machine-learned interatomic potentials are rapidly enabling the study of complex interactions such as dynamical behavior and reactivity on the nanoscale. Here, we develop an Au-S-C-H atomic cluster expansion (ACE) interatomic potential for efficient and accurate molecular dynamics simulations of thiolate-protected gold nanoclusters (Aun(SCH3)m). Trained on more than 30,000 density functional theory calculations of gold nanoclusters, the interatomic potential exhibits ab initio level accuracy in energies and forces and replicates nanocluster dynamics including thermal vibration and chiral inversion. Long dynamics simulations (up to 0.1 μs time scale) reveal a mechanism explaining the thermal instability of neutral Au25(SR)18 clusters. Specifically, we observe multiple stages of isomerization of the Au25(SR)18 cluster, including a chiral isomer. Additionally, we simulate coalescence of two Au25(SR)18 clusters and observe series of clusters where the formation mechanisms are critically mediated by ligand exchange in the form of [Au-S]n rings.

DNA-stabilized silver nanoclusters (AgN-DNAs) are known to have one or two DNA oligomer ligands per nanocluster. Here, we present the first evidence that AgN-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 AgN-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 AgN-DNAs, we identified an additional AgN-DNA with a chloride ligand by high-throughput screening. Inclusion of chlorides on AgN-DNAs presents a promising new route to expand the diversity of AgN-DNA structure-property relationships and to imbue these emitters with favorable stability for biophotonics applications.

Density functional theory is used to study geometric, energetic, and electronic properties of metal–ligand bonds in a series of group-11 metal complexes and ligand-protected metal clusters. We study complexes as the forms of M–L (L = SCH3, SC8H9, PPh3, NHCMe, NHCEt, NHCiPr, NHCBn, CCMe, CCPh) and L1–M–L2 (L1 = NHCBn, PPh3, and L2 = CCPh). Furthermore, we study clusters denoted as [M13L6Br6]− (L = PPh3, NHCMe, NHCEt, NHCiPr, NHCBn). The systems were studied at the standard GGA level using the PBE functional and including vdW corrections via BEEF-vdW. Generally, Au has the highest binding energies, followed by Cu and Ag. PBE and BEEF-vdW functionals show the order Ag–L > Au–L > Cu–L for bond lengths in both M–L complexes and metal clusters. In clusters, the smallest side group (CH3) in NHCs leads to the largest binding energy whereas no significant variations are seen concerning different side groups of NHC in M–L complexes. By analyzing the projected density of states and molecular orbitals in complexes and clusters, the M–thiolate bonds were shown to have σ and π bond characteristics whereas phosphines and carbenes were creating σ bonds to the transition metals. Interestingly, this analysis revealed divergent behavior for M–alkynyl complexes: while the CCMe group displayed both σ and π bonding features, the CCPh ligand was found to possess only σ bond properties in direct head-to-head binding configuration. Moreover, synergetic effects increase the average binding strength to the metal atom significantly in complexes of two different ligands and underline the potential of adding Cu to synthesize structurally richer cluster systems. This study helps in understanding the effects of different ligands on the stability of M–L complexes and clusters and suggests that PPh3 and NHCs-protected Cu clusters are most stable after Au clusters. [ABSTRACT FROM AUTHOR]

Hepatitis E Virus-like particles self-assemble in to noninfectious nanocapsids that are resistant to proteolytic/acidic mucosal delivery conditions. Previously, the nanocapsid was engineered to specifically bind and enter breast cancer cells, where successful tumor targeting was demonstrated in animal models. In the present study, the nanocapsid surface was modified with a solvent-exposed cysteine to conjugate monolayer protected gold nanoclusters (AuNC). Unlike commercially available gold nanoparticles, AuNCs monodisperse in water and are composed of a discrete number of gold atoms, forming a crystalline gold core. Au102 pMBA44 (Au102) was an ideal conjugate given its small 2.5 nm size and detectability in cryoEM. Au102 was bound directly to nanocapsid surface cysteines via direct ligand exchange. In addition, Au102 was functionalized with a maleimide linker (Au102_C6MI) for maleimide-thiol conjugation to nanocapsid cysteines. The AuNC-bound nanocapsid constructs were conjugated in various conditions. We found Au102_C6MI to bind nanocapsid more efficiently, while Au102 remained more soluble over time. Nanocapsids conjugated to Au102_C6MI were imaged in cryoEM for single particle reconstruction to localize AuNC position on the nanocapsid surface. We resolved five unique high intensity volumes that formed a ring-shaped density at the 5-fold symmetry center. This finding was further supported by independent rigid modeling.

The supported monolayer of Au that accompanies alkanethiolate molecules removed by polymer stamps during chemical lift-off lithography is a scarcely studied hybrid material. We show that these Au-alkanethiolate layers on poly(dimethylsiloxane) (PDMS) are transparent, functional, hybrid interfaces that can be patterned over nanometer, micrometer, and millimeter length scales. Unlike other ultrathin Au films and nanoparticles, lifted-off Au-alkanethiolate thin films lack a measurable optical signature. We therefore devised fabrication, characterization, and simulation strategies by which to interrogate the nanoscale structure, chemical functionality, stoichiometry, and spectral signature of the supported Au-thiolate layers. The patterning of these layers laterally encodes their functionality, as demonstrated by a fluorescence-based approach that relies on dye-labeled complementary DNA hybridization. Supported thin Au films can be patterned via features on PDMS stamps (controlled contact), using patterned Au substrates prior to lift-off (e.g., selective wet etching), or by patterning alkanethiols on Au substrates to be reactive in selected regions but not others (controlled reactivity). In all cases, the regions containing Au-alkanethiolate layers have a sub-nanometer apparent height, which was found to be consistent with molecular dynamics simulations that predicted the removal of no more than 1.5 Au atoms per thiol, thus presenting a monolayer-like structure.

DNA-stabilized silver nanoclusters with 10 to 30 silver atoms are interesting biocompatible nanomaterials with intriguing fluorescence properties. However, they are not well understood, since atom-scale high level theoretical calculations have not been possible due to a lack of firm experimental structural information. Here, by using density functional theory (DFT), we study the recently atomically resolved (DNA)2–Ag16Cl2 nanocluster in solvent under the lowest-lying singlet (S1) and triplet (T1) excited states, estimate the relative emission maxima for the allowed (S1 → S0) and dark (T1 → S0) transitions, and evaluate the transient absorption spectra. Our results offer a potential interpretation of the recently reported transient absorption and dual emission of similar DNA-stabilized silver nanoclusters, providing a mechanistic view on their photophysical properties that are attractive for applications in biomedical imaging and biophotonics. [ABSTRACT FROM AUTHOR]

DNA-stabilized silver nanoclusters with 10 to 30 silver atoms are interesting biocompatible nanomaterials with intriguing fluorescence properties. However, they are not well understood, since atom-scale high level theoretical calculations have not been possible due to a lack of firm experimental structural information. Here, by using density functional theory (DFT), we study the recently atomically resolved (DNA)2–Ag16Cl2 nanocluster in solvent under the lowest-lying singlet (S1) and triplet (T1) excited states, estimate the relative emission maxima for the allowed (S1 → S0) and dark (T1 → S0) transitions, and evaluate the transient absorption spectra. Our results offer a potential interpretation of the recently reported transient absorption and dual emission of similar DNA-stabilized silver nanoclusters, providing a mechanistic view on their photophysical properties that are attractive for applications in biomedical imaging and biophotonics. [ABSTRACT FROM AUTHOR]

The magnetic response of valence electrons in doped gold-based M @ A u 8 L 8 q superatoms (M = Pd, Pt, Ag, Au, Cd, Hg, Ir, and Rh; L = PPh3; and q = 0, +1, +2) is studied by calculating the gauge including magnetically induced currents (GIMIC) in the framework of the auxiliary density functional theory. The studied systems include 24 different combinations of the dopant, total cluster charge, and cluster structure (cubic-like or oblate). The magnetically induced currents (both diatropic and paratropic) are shown to be sensitive to the atomic structure of clusters, the number of superatomic electrons, and the chemical nature of the dopant metal. Among the cubic-like structures, the strongest aromaticity is observed in Pd- and Pt-doped M @ A u 8 L 8 0 clusters. Interestingly, Pd- and Pt-doping increases the aromaticity as compared to a similar all-gold eight-electron system A u 9 L 8 + 1 . With the recent implementation of the GIMIC in the deMon2k code, we investigated the aromaticity in the cubic and butterfly-like M@Au8 core structures, doped with a single M atom from periods 5 and 6 of groups IX–XII. Surprisingly, the doping with Pd and Pt in the cubic structure increases the aromaticity compared to the pure Au case not only near the central atom but encompassing the whole metallic core, following the aromatic trend Pd > Pt > Au. These doped (Pd, Pt)@Au8 nanoclusters show a closed shell 1S21P6 superatom electronic structure corresponding to the cubic aromaticity rule 6n + 2. [ABSTRACT FROM AUTHOR]