Icosahedral Core Research Articles

Structure of anellovirus-like particles reveal a mechanism for immune evasion

Anelloviruses are nonpathogenic viruses that comprise a major portion of the human virome. Despite being ubiquitous in the human population, anelloviruses (ANVs) remain poorly understood. Basic features of the virus, such as the identity of its capsid protein and the structure of the viral particle, have been unclear until now. Here, we use cryogenic electron microscopy to describe the first structure of an ANV-like particle. The particle, formed by 60 jelly roll domain-containing ANV capsid proteins, forms an icosahedral particle core from which spike domains extend to form a salient part of the particle surface. The spike domains come together around the 5-fold symmetry axis to form crown-like features. The base of the spike domain, the P1 subdomain, shares some sequence conservation between ANV strains while a hypervariable region, forming the P2 subdomain, is at the spike domain apex. We propose that this structure renders the particle less susceptible to antibody neutralization by hiding vulnerable conserved domains while exposing highly diverse epitopes as immunological decoys, thereby contributing to the immune evasion properties of anelloviruses. These results shed light on the structure of anelloviruses and provide a framework to understand their interactions with the immune system.

Relationship between Structural Defects and Free Electrons in Icosahedral Nanoclusters.

According to the classic superatom model, metal nanoclusters with a "magic number" of free valence electrons display high stability, manifesting as the closed-shell-dependent electronic robustness. The icosahedral nanobuilding blocks containing eight free electrons were the most common in constructing metal nanoclusters; however, the structure defect-dependent variations of the free electron count in icosahedral configurations are still far from thorough research. Here, we reported a hydride-containing [Pt2Ag15(SAdm)4(DPPOE)4H]2+ nanocluster with two largely defective Pt1Ag8 icosahedral cores. Together with previously reported complete or slightly defective icosahedra in metal nanoclusters, the largely defective Pt1Ag8 core provided important clues to reveal the evolutionary mode of structural defects and free electrons in icosahedral nanoclusters; the free electron count of icosahedron was reduced two-by-two (i.e., from 8e to 6e and then to 4e) accompanied by the structure defection. Overall, the work presented a novel Pt2Ag15 nanocluster with a largely defective core structure that enables an atomic-level understanding of the relationship between structural defects and free electrons in icosahedral nanoclusters.

Leveraging RALI‐THINICE Observations to Assess How the ICOLMDZ Model Simulates Clouds Embedded in Arctic Cyclones

AbstractDespite their essential role in the high‐latitude climate, the representation of mixed‐phase clouds is still a challenge for Global Climate Models (GCMs)'s cloud schemes. In this study we propose a methodology for robustly assessing Arctic mixed‐phase cloud properties in a climate model using airborne measurements. We leverage data collected during the RALI‐THINICE airborne campaign that took place near Svalbard in August 2022 to evaluate the simulation of mid‐level clouds associated with Arctic cyclones. Simulations are carried out with the new limited‐area configuration of the ICOLMDZ model which combines the recent icosahedral dynamical core DYNAMICO and the physics of LMDZ, the atmospheric component of the IPSL‐CM Earth System Model. Airborne radar and microphysical probes measurements are then used to evaluate the simulated clouds. A comparison method has been set‐up to guarantee as much as possible the spatiotemporal co‐location between observed and simulated cloud fields. We mostly focus on the representation of ice and liquid in‐cloud contents and on their vertical distribution. Results show that the model overestimates the amount of cloud condensates and exhibits a poor cloud phase spatial distribution, with too much liquid water far from cloud top and too much ice close to it. The downward gradual increase in snowfall flux is also not captured by the model. This in‐depth model evaluation thereby pinpoints priorities for further improvements in the ICOLMDZ cloud scheme.

Polyhedral and Macropolyhedral Metal-Rich Cobaltaboranes: A 25-Vertex Hourglass-Shaped Cluster.

In an effort to break the single-cage 16-vertex supraicosahedral barrier, we have explored the reaction of [Cp*CoCl2], 1 with [LiBH4·THF], followed by thermolysis with [BH3·SMe2] [Cp* = η5-C5Me5]. Although our objective to synthesize a high-nuclearity single-cage cluster was not achieved, we have isolated a 25-vertex macropolyhedral cluster [(Cp*Co)5Co2B18H17(CH3)S] (2). Cluster 2 is an exceptional fused hourglass-shaped macropolyhedral cluster composing two icosahedral cores ([Co3B9] and [Co4B8]) and three tetrahedral cores [Co2B2]. Although the fusion in cluster 2 is very complex, it follows Mingos fusion formalism, leading to an attractive hourglass-shaped cluster. Through subtle changes in reaction conditions, two new cobaltaborane clusters, nido-4,5,7-[(Cp*Co)3B7H11] (3) and nido-2,9-[(Cp*Co)2B8H12] (4), have been isolated. The observed core geometries of clusters 3 and 4 are similar to the parent deltahedra [B10H14] with (n + 2) SEP (SEP = skeletal electron pair, n = no. of vertices). All the synthesized cobaltaboranes have been characterized in solution by ESI-mass, nuclear magnetic resonance spectroscopy, infrared spectroscopy and structurally solved by single-crystal X-ray diffraction analysis.

Mechanism Insight into Metal Exchange between Au25(SR)18-/Ag25(SR)18- Clusters and Metal Ions from Ab Initio Molecular Dynamics Simulations.

The metal exchange reaction has emerged as an efficient method to synthesize ligand-protected alloy nanoclusters with precise compositions and structure. However, the understanding of the mechanism of these metal exchange processes is quite limited. Herein, the dynamic process of metal exchange of Au25(SR)18- and Ag25(SR)18- (R = CH3) nanoclusters with metal ions (Au+, Ag+, Cu2+, Cu+, Cd2+, and Hg2+) is investigated using ab initio molecular dynamics simulations. Computational results unveiled a multifaceted nature of the metal exchange process, dictated by several variables, including thermodynamic stability, electrochemical activity, metal affinity to ligand, and the coordination mode of metal ions. As a result of these factors, metal ions may either directly exchange with Au or Ag atoms on the icosahedral core surface by a "knock-off" mechanism or be stably adsorbed at the core-motif interface of Au25(SR)18- and Ag25(SR)18- nanoclusters. Meanwhile, we also discovered that counterions can promote adsorbed Ag and Cu atoms to diffuse into the gold core. Finally, the driving force of the galvanic reduction and antigalvanic reduction reactions is discussed. The formation of a more stable core-doping product nanocluster is the major driving force of metal exchange reactions.

Gas-Phase Structures of [Au21(SR)14]- and [Au17(SR)10]- with Eight Electrons: Can They Support an Icosahedral Au13 Core?

A prototypical thiolate (RS)-protected gold cluster [Au25(SR)18]- has high stability due to specific geometric and electronic structures: an icosahedral (Ih) Au13 core with a closed electronic shell containing eight electrons is completely protected by six units of Au2(SR)3. Nevertheless, collisional excitation of [Au25(SR)18]- in a vacuum induces the sequential release of Au4(SR)4 to form [Au21(SR)14]- and [Au17(SR)10]- both containing eight electrons. To answer a naive question of whether these fragments bear an Ih Au13(8e) core, the geometrical structures of [Au21(SC3H7)14]- and [Au17(SC3H7)10]- in the gas phase were examined by the combination of anion photoelectron spectroscopy and density functional theory (DFT) calculation of simplified models of [Au21(SCH3)14]- and [Au17(SCH3)10]-. We concluded that [Au21(SC3H7)14]- retains a slightly distorted Ih Au13(8e) core, while [Au17(SC3H7)10]- has an amorphous Au13 core composed of triangular Au3, tetrahedral Au4, and prolate Au7 units. DFT calculations on putative species [Au19(SCH3)12]- and [Au18(SCH3)11]- suggested that the Ih Au13(8e) core undergoes dramatic structural deformation due to mechanical stress from μ2 ligation of only one RS.

Robust vibrational coherence protected by a core-shell structure in silver nanoclusters.

Vibrational coherence has attracted considerable research interests because of its potential functions in light harvesting systems. Although positive signs of vibrational coherence in metal nanoclusters have been observed, the underlying mechanism remains to be verified. Here, we demonstrate that robust vibrational coherence with a lifetime of 1 ps can be clearly identified in Ag44(SR)30 core-shell nanoclusters, in which an icosahedral Ag12 core is well protected by a dodecahedral Ag20 cage. Ultrafast spectroscopy reveals that two vibrational modes at around 2.4 THz and 1.6 THz, corresponding to the breathing mode and quadrupolar-like mode of the icosahedral Ag12 core, respectively, are responsible for the generation of vibrational coherence. In addition, the vibrational coherence of Ag44 has an additional high frequency mode (2.4 THz) when compared with that of Ag29, in which there is only one low frequency vibration mode (1.6 THz), and the relatively faster dephasing in two-layer Ag29 relative to that in Ag44 further supports the fact that the robust vibrational coherence in Ag44 is ascribed to its unique matryoshka-like core-shell structure. Our findings not only present unambiguous experimental evidence for a multi-layer core-shell structure protected vibrational coherence under ambient conditions but also offers a practical strategy for the design of highly efficient quantum optoelectronic devices.

Synthesis and crystallization of a carboxylate functionalized N-heterocyclic carbene-based Au13 cluster with strong photo-luminescence.

Here we report the synthesis and crystallization of a -COOH-capped N-heterocyclic carbene (NHC)-protected Au13 cluster. The single-crystal structure of the -COOH-capped NHC-Au13 cluster reveals a classic icosahedral core with one Au atom in its center. The icosahedral core is surrounded by five NHC ligands with pseudo C5 symmetry and exposed carboxyls in a pentagonal antiprism fashion. The detailed formula of the Au cluster was identified as Au13(bi-NHC carboxyl)5Cl2 (hereafter abbreviated as Au13-c). The density functional theory (DFT) calculations confirm that Au13-c is an electronically stable eight-electron super-atom cluster and elucidate its optical transitions in the UV-Vis range. The Au13-c cluster exhibits excellent thermal and chemical stability under bio-relevant conditions. Additionally, this cluster shows a strong red emission in DMF and H2O with an excellent quantum yield (QY) of 40% and 12.6%, respectively. The high QY of Au13-c enables its use in cell imaging on both cancer and noncancerous cells.

Tuning photoluminescence properties of Au clusters by surface modification and doping: lessons from case studies of icosahedral Au13

This review article focuses on the ubiquitous icosahedral Au13 core protected by organic ligands as a benchmark and derives empirical rules for tuning and enhancing photoluminescence properties through surface modification and heterometal doping.

Tailoring two magic number Au13 nanoclusters with N-containing diphosphine ligands: a classical icosahedral core vs. an unprecedented UFO- shaped core

Two magic number Au13 nanoclusters were tailored using two N-containing multidentate phosphine ligands with a classical icosahedral core and an unprecedented “UFO”-shaped polyhedral core, respectively.

Activity of Different AunSn+1 Staples in the Ligand Exchange of Au23(SR)16- with a Single Foreign Thiolate Ligand.

Ligand exchange has been widely used to synthesize novel thiolated gold nanoclusters and to regulate their specific properties. Herein, density functional theory (DFT) calculations were conducted to investigate the kinetic profiles of the ligand exchange of the [Au23(SCy)16]- nanocluster with an aromatic thiolate (2-napthalenethiol). The three types of staple motifs (i.e., trimetallic Au3S4, monometallic AuS2, and the bridging thiolates) of the Au23 cluster precursor could be categorized into eight groups of S sites with different chemical environments. The ligand exchange of all of them occurs favorably via the SN1-like pathway, with one site starting with the Au-S dissociation and seven other sites starting with the H-transfer steps. By contrast, the SN2-like pathway (i.e., the synergistic SCy-to-SAr exchange prior to the H-transfer step) is unlikely in the target systems. Meanwhile, the Au-S bond on the capping Au atom of the bicapped icosahedral Au15 core is the most active one, while the S sites on Au3S4 (except for the one remote from the metallic core) are all competitive exchanging sites. The ligand exchange activity of the bridging thiolate and the remote S site on Au3S4 is significantly less reactive. The calculation results correlate with the multiple ligand exchange within only a few minutes and the preferential etching of the AuS2 staple with the foreign ligands reported in earlier experiments. The relative activity of different staples might be helpful in elucidating the inherent principles in the ligand exchange-induced size-evolution of metal nanoclusters.

Au13 Superatom Bearing Two Terpyridines at Coaxial Positions: Photoluminescence Quenching via Complexation with 3d Metal Ions

Abstract A gold cluster [Au13(dppe)5(EPTpy)2]3+ (dppe = 1,2-bis(diphenylphosphino)ethane, EPTpy-H = 4′-(4-ethynylphenyl)-2,2′:6′,2′′-terpyridine) was synthesized by ligand exchange reaction of [Au13(dppe)5Cl2]3+. Single-crystal X-ray diffraction analysis revealed that two terpyridyl moieties were σ-bonded to the coaxial positions of the icosahedral Au13 core. These two terpyridyl moieties were coordinated with 3d metal ions M2+ (M = Co, Ni, Cu, Zn) in acetonitrile solution under ambient conditions. The photoluminescence (PL) of [Au13(dppe)5(EPTpy)2]3+ with a quantum yield of 0.17 at ∼780 nm was almost completely quenched by coordination with Co2+, Ni2+, and Cu2+, while the PL was not affected by Zn2+ coordination. The metal-dependent PL quenching behavior is ascribed to the difference in the electronic structure of the metal ions. The energy transfer from the Au13 chromophore to the coordinated Co2+, Ni2+, or Cu2+ with an open electronic structure proceeds efficiently via an electron exchange mechanism, while the process is prohibited for Zn2+ with a closed electronic structure.

Insights into the growth law, electronic properties and spectra of Fenλ (n = 3–18; λ = 0, ±1) clusters

AbstractThe growth law, electronic properties and spectra of (n = 2–18; λ = 0, ±1) clusters have been examined by density functional theory (DFT) and an unbiased structure prediction method. Extensive geometry optimizations have been executed and show that the global minimum structures of clusters have a distinct growth law when n is 8–18. For n = 8–13 and 14–18, the iron atoms grow around a decahedral and icosahedral iron cluster core, respectively. Based on the present ground states, the calculated electronic parameters are in line with the experimental values. The thermal stability of charged iron cluster is higher than that of neutral iron cluster. The octahedral and icosahedral clusters are more stable than their neighbors. The former has low chemical activity and may be a superatom. The magnetic moment of Fe atom weakens in the cluster. The UV spectra, photoelectron spectra (PES) and infrared and Raman spectra of the clusters have been predicted and the global minimum structures of the clusters are determined by comparing the theoretical PES with the experimental results.

Hydride Doping Effects on the Structure and Properties of Eight-Electron Rh/Ag Superatoms: The [RhHx@Ag21-x{S2P(OnPr)2}12] (x = 0-2) Series.

Three hitherto unknown eight-electron rhodium/silver alloy nanoclusters, [RhAg21{S2P(OnPr)2}12] (1), [RhHAg20{S2P(OnPr)2}12] (2), and [RhH2Ag19{S2P(OnPr)2}12] (3), have been isolated and fully characterized. Cluster 1 contains a regular Rh@Ag12 icosahedral core, whereas 2 and 3 exhibit distorted RhH@Ag12 and RhH2@Ag12 icosahedral cores. The single-crystal neutron structure of 2 located the encapsulated hydride at the center of an enlarged RhAg3 tetrahedron. A similar position was found by neutron diffraction for one of the hydrides in 3, whereas the other hydride is trigonally coordinated to Rh and an elongated Ag-Ag edge. The solid-state structures of 1-3 possess C1 symmetry due to the asymmetric arrangement of the surrounding capping Ag atoms. Our investigation shows that the insertion of one hydride dopant provokes the elimination of one capping silver atom on the cluster surface, resulting in the general formula [RhHx@Ag21-x{S2P(OnPr)2}12] (x = 0-2), which maintains the same number of cluster electrons as well as neutral charge. Clusters 1-3 exhibit an intense emission band in the NIR region. Contrarily to their PdAg21 and PdHAg20 relatives, the 4d orbitals of the encapsulated heterometal are somewhat involved in the optical processes.

Eight-Electron Superatomic Cu31 Nanocluster with Chiral Kernel and NIR-II Emission

Owing to the inherent instability caused by the low Cu(I)/Cu(0) half-cell reduction potential, Cu(0)-containing copper nanoclusters are quite uncommon in comparison to their Ag and Au congeners. Here, a novel eight-electron superatomic copper nanocluster [Cu31(4-MeO-PhC≡C)21(dppe)3](ClO4)2 (Cu31, dppe = 1,2-bis(diphenylphosphino)ethane) is presented with total structural characterization. The structural determination reveals that Cu31 features an inherent chiral metal core arising from the helical arrangement of two sets of three Cu2 units encircling the icosahedral Cu13 core, which is further shielded by 4-MeO-PhC≡C- and dppe ligands. Cu31 is the first copper nanocluster carrying eight free electrons, which is further corroborated by electrospray ionization mass spectrometry, X-ray photoelectron spectroscopy and density functional theory calculations. Interestingly, Cu31 demonstrates the first near-infrared (750-950 nm, NIR-I) window absorption and the second near-infrared (1000-1700 nm, NIR-II) window emission, which is exceptional in the copper nanocluster family and endows it with great potential in biological applications. Of note, the 4-methoxy groups providing close contacts with neighboring clusters are crucial for the cluster formation and crystallization, while 2-methoxyphenylacetylene leads only to copper hydride clusters, Cu6H or Cu32H14. This research not only showcases a new member of copper superatoms but also exemplifies that copper nanoclusters, which are nonluminous in the visible range may emit luminescence in the deep NIR region.

Vertex‐Shared Linear Superatomic Molecules: Stepping Stones to Novel Materials Composed of Noble Metal Clusters

Extremely small metal clusters composed of noble metal atoms (M) have orbitals similar to those of atoms and therefore can be thought of as artificial atoms or superatoms. If these superatoms can be assembled into molecular analogs, it might be possible to create materials with new characteristics and properties that are different from those of existing substances. Therefore, the concept of superatomic molecules has attracted significant attention. The present review focuses on vertex‐shared linear M12n+1 superatomic molecules formed via the sharing of a single metal atom between M13 superatoms having icosahedral cores and summarizes the knowledge obtained to date in this regard. This summary discusses the most suitable ligand combinations for the synthesis of M12n+1 superatomic molecules along with the valence electron numbers, stability, optical absorption characteristics, and luminescence properties of the M12n+1 superatomic molecules fabricated to date. This information is expected to assist in the production of many M12n+1 superatomic molecules with novel structures and physicochemical properties in the future.

Exploration of the Atomic Pathway of Seed-Mediated Growth from Icosahedral [Au25(SR)18]− to Bi-Icosahedral Au38(SR)24 and Au44(SR)26 Clusters Based on the 2e– Hopping Mechanism

Size growth is ubiquitous in the gold nanocluster synthesis. However, the atomic-level mechanism of seed-mediated growth of gold clusters remains mysterious. In this study, the seed-mediated growth pathway from the icosahedral [Au25(SR)18]- cluster to the bi-icosahedral Au38(SR)24 and Au44(SR)26 clusters is studied based on the two-electron (2e-) hopping mechanism. First, atomic structures of three key intermediate clusters, [Au29(SR)20]-, [Au33(SR)22]-, and Au41(SR)25, are predicted based on the 2e--unit decomposition strategy. The theoretically simulated UV-Vis spectra based on the predicted structure model of [Au29(SR)20]- and [Au33(SR)22]- matched well with the experimental curves reported previously. Based on the predicted intermediate cluster structures, the size growth pathway from the eight-electron (8e-) [Au25(SR)18]- cluster to 14-electron (14e-) Au38(SR)24 and 18-electron (18e-) Au44(SR)26 clusters is determined. In the step of formation of bi-icosahedral Au38(SR)24 from icosahedral [Au25(SR)18]-, two Au4 units are first formed. The third 2e- hopping step results in formation of an icosahedron unit. The present studies offered new insights into the formation and size conversion mechanism of ligand-protected gold nanoclusters containing icosahedral cores.

Carbon-free sandwich compounds based on arsenic and antimony with icosahedral metal cores

Carbon-free sandwich compounds based on arsenic and antimony with icosahedral metal cores

The one/two atom size-reduction of [Au23SCy16]- induced by the [Au6(dppp)4]2+ cluster.

The recent progress in atomically precise metal (Au, Ag etc.) nanoclusters has greatly enriched the molecular-level mechanistic understanding of metal nanomaterials. Herein, using two meta-stable (easy formation, easy transformation) clusters, i.e. [Au23SCy16]- and [Au6(dppp)4]2+ (HSCy and dppp denote cyclohexanethiol and 1,3-bis(diphenylphosphino)propane), as the reaction precursors, the etching of Au23 occurs smoothly, giving the one/two-atom size-reduced [Au21SCy12(dppp)2]+ and [Au22SCy14(dppp)]2+ as the major products. Structural analysis and DFT calculations indicate that the active reaction site of Au23 lies in the core-shell interference of the bi-capped icosahedral Au15 core and the AuS2 motifs. The fluorescence, band gap, and thermostability of the Au21 cluster products are improved compared to that of the Au23 precursors.

Palladium cluster complex [Pd13(μ4-C7H7)6]2+ (C7H7 = tropylium) with an fcc-close-packed cuboctahedral Pd13 core and isomers: theoretical insight into ligand-control of the Pd13 core structure.

One of the challenging targets in today's chemistry is size-, shape- and metal-atom packing-controlled synthesis of nano-scale transition metal cluster complexes because key factors governing these features have been elusive. Here, we present a DFT study on a recently synthesized palladium cluster complex [Pd13(μ4-C7H7)6]2+ (named Cubo-μ4; C7H7 = tropylium) with an fcc-close-packed cuboctahedral Pd13 core and possible isomers. The stability decreases in the order Cubo-μ4 > [Pd13(μ3-C7H7)3(μ4-C7H7)3]2+ with an hcp-close-packed anticuboctahedral Pd13 core (Anti-μ3,4) > [Pd13(μ3-C7H7)6]2+ with a non-close packed icosahedral Pd13 core (Ih-μ3) > [Pd13(μ4-C7H7)6]2+ with an anticuboctahedral Pd13 core (Anti-μ4) > [Pd13(μ3-C7H7)6]2+ with a cuboctahedral Pd13 core (Cubo-μ3). This ordering disagrees with the stability of the Pd13 core. The key factor governing the stability and metal-atom packing manner of these Pd13 cluster complexes is not the stability of the Pd13 core but the interaction energy between the Pd13 core and the [(C7H7)6]2+ ligand shell. The interaction energy is mainly determined by the charge-transfer from the Pd13 core to the [(C7H7)6]2+ ligand shell and the coordination mode of the C7H7 ligand (μ3- vs. μ4-coordination bond). In the μ4-coordination, all seven C atoms of the C7H7 ligand interact with four Pd atoms of the Pd4 plane using two CC double bonds and one π-allyl moiety. On the other hand, in the μ3-coordination, one or two C atoms of C7H7 cannot form bonding interaction with the Pd atom of the Pd3 plane. Thus, the use of appropriate capping ligands is one of the key points in the synthesis of nano-scale metal cluster complexes.