The atomic path for constructing single‐helical superstructure of AuCu bimetallic nanoclusters

Single‐helical or double‐helical structures are common in living organisms. Helical assembly has been found in the artificial nanoparticles, but how they do so remains poorly understood. Here, we exploit atomically precise Au6Cu6 bimetallic nanoparticles (or called nanoclusters) as building blocks to construct a single‐helical Au12Cu12 superstructure in an operative path, thereby providing access to currently elusive mechanistic pathways. We propose that the thermodynamically viable linear‐to‐bent process at a couple of Au6Cu6 nanoclusters imparted by the organic ligands seems to be critical for the helical‐nanostructured arrangement of Au12Cu12. This study could help to offer a new design rule for the exquisitely helical structure assembled from the artificial nanoparticles.


INTRODUCTION
Helicity in the world of matter is one of the most brilliant masterpieces of nature. Helical structures have been produced in artificial nanoparticles using nanofabrication techniques like self-assembly, but constructing the single-helical or double-helical superstructure remains a challenge, especially reaching the atomic-level precision as high as found in nature. [1][2][3] How these nanoscale building units are packed into helical nanostructures is a topic that has fascinated synthetic scientists. Another topic is whether the building blocks can act as "genes" carrying genetic codes and delivering their physicochemical properties into the nanostructured assemblies. Although a few seminal studies have revealed that chirality transfer or electron transfer can occur in the metal supercrystals, how they do so remains elusive. [4][5][6] We recently questioned if the combination of molecular self-assembly and atomically precise nanoparticles might be Ancheng Tang and Xiao Cai contributed equally to this work.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2022 The Authors. Aggregate published by SCUT, AIEI, and John Wiley & Sons Australia, Ltd. capable of unveiling the helical formation mechanism, which is a prerequisite for further understanding of physicochemical properties from the nanostructured assemblies.
Atomically precise metal nanoclusters have been recently attracted wide interest, since their crystal structures can be solved by single crystal X-ray crystallography. [7][8][9][10][11][12][13][14][15] They have absolutely precise formula and atomic-packing configurations like organic molecules, and even we can see the surface ligands on these nanoclusters, which are impossible for conventional nanoparticles, thereby providing access to currently inaccessible issues regarding helical-nanostructured arrangement and mechanism. [16][17][18][19][20][21] Despite major advances, which have been achieved in a few examples such as the double-and quadruple-helical assemblies of gold nanoclusters into superstructures, but the helical-assemblies remain a bottleneck for nanoclusters and corresponding driven-forces have been far understood. [1,3] More specifically, singlehelical superstructures formed using the metal nanoclusters as building units are highly desirable but remain a grand challenge.
In this work, we report a single-helical superstructure manipulated from AuCu bimetallic nanoclusters. The atomicscale precision of the total structure of the AuCu nanoclusters allows us to decipher the structural codes for the singlehelical-structured formation mechanism through a coupling study of experiment and theory, that is, the thermodynamically viable linear-to-bent process of Au 6 Cu 6 nanoclusters can favor the helical formation.

Synthesis of nanoclusters
Synthesis of Au 6 Cu 6 MBT 12 : 0.2 mmol of Au(SMe 2 )Cl was dissolved in a mixture of 4 mL dichloromethane and 5 mL acetone. Then, 0.4 mmol of 3-methylbenzenethiol was added to the above solution and stirred for 15 min, following 4-mL acetone dissolved 0.4 mmol of Et 3 N. After 45 min, 4-mL acetone solution with 0.2 mmol of Tetrakis (acetonitrile)copper(I) hexa-fluorophosph was added. The solution gradually turned golden yellow, indicating that the reaction was complete. The clusters were separated by thin-layer chromatography (TLC) and extracted with dichloromethane. The clusters dispersed and crystallized in diethyl ether and dichloromethane, yielding golden stripe crystals. Synthesis of Au 6 Cu 6 PET 12 and Au 6 Cu 6 PA 12 : Au 6 Cu 6 PET 12 and Au 6 Cu 6 PA 12 were prepared from 3-methylbenzenethiol of Au 6 Cu 6 MBT 12 in place of 2phenylethylmercaptan and phenylacetylene (PA) under otherwise identical conditions, respectively.
Synthesis of Au 12 Cu 12 PA 24 : 2.0 mg of Au 6 Cu 6 MBT 12 was dissolved in 20-mL acetonitrile under vigorous stirring. Then 1-mL Et 3 N and 165-μL PA were added. The solution changed from golden to orange at 60 • C for 5 h. The product was separated by TLC and extracted with dichloromethane. Dark red crystals were crystallized from CH 2 Cl 2 /Ethyl ether at ∼4 • C.

X-ray crystallography measurement
The single crystal X-ray crystallography data for Au 6 Cu 6 PET 12 , Au 6 Cu 6 MBT 12 and Au 12 Cu 12 PA 24 nanoclusters were collected on a Bruker D8 VENTURE using Cu Ka radiation (λ = 1.54178 Å).

Computational methods
The monomer and dimer structures for the Au 6 Cu 6 PA n L 12-n monomers and [Au 6 Cu 6 PA n L 12-n ] 2 dimers were optimized using the full atomistic models. Vibrational frequencies calculations were performed for the optimized structures to evaluate the Gibbs free energies of the clusters at 298 and 333 K. Increasing the temperature from 298 to 333 K brings very small variations to the ligand exchange and dimerization energies, so the energies at 298 K were reported for clarity. For [Au 6 Cu 6 PA 12 ] 2 and [Au 6 Cu 6 PA 2 MBT 10 ] 2 , constrained optimizations were performed by fixing and scanning the inter monomer Au-Au distance from 2.6 to 7.0 Å with a step size of 0.2 Å, in order to explore the energy landscape of the dynamic dimerization process. At each Au-Au distance, the positions of all the atoms in the dimer except for the two Au atoms were fully relaxed. Natural population analyses [22] of the monomers and dimers were performed to seek the influence of the ligand types on the electronic structures, as well as their implication in dimerization. All of the optimization and frequencies calculations were carried out at the density functional theory (DFT) level with the Perdew-Burke-Ernzerhof [23] (PBE) exchange-correlation functional and a LANL2DZ basis set and pseudopotential, [24,25] implemented in Gaussian09. [26] Additional single-point calculations were performed for the optimized monomers and dimers at the PBE/LANL2DZ level with the Grimme's DFT-D3 method [27] to obtain the energy correction caused by the dispersion interactions.

RESULTS AND DISCUSSION
The total structures of the three Au 6 Cu 6 nanoclusters capped by different ligands of phenylethylthiolate (PET), 3-methylbenzenethiol (MBT) and PA, that is, Au 6 Cu 6 PET 12 , Au 6 Cu 6 MBT 12 and Au 6 Cu 6 PA 12 , were determined by Xray crystallography. Note that the crystal structure of the Au 6 Cu 6 PA 12 nanocluster has been reported; [28] and hence, the crystal data and structure refinement of the Au 6 Cu 6 PET 12 and Au 6 Cu 6 MBT 12 nanoclusters are only shown in Tables S1 and S2. As illustrated in Figure 1, the metal kernel in each Au 6 Cu 6 can be viewed as the three triangular layers of Cu 3 -Au 6 -Cu 3 . From the range of Au-Au/Cu-Cu distances in the Au 3 /Cu 3 plane ( Figure S1), the Au-Au bond and Cu-Cu bond can be excluded since these distances are far deviated from the normal Au-Au/Cu-Cu bond lengths (2.8 Å/2.7 Å). However, the Cu 3 layers are linked with the middle Au 6 layer through Cu-Au bond, since the Cu-Au average distances are 3.082, 3.007, and 2.843 Å for Au 6 Cu 6 PET 12 , Au 6 Cu 6 MBT 12 , and Au 6 Cu 6 PA 12 , respectively. Obviously, the shortest Cu-Au bond in Au 6 Cu 6 PA 12 arises from the exterior ligand of PA, which may give rise to the compact kernel due to its stronger binding affinity compared to the thiolate ligands.
To further reveal the structural discrepancy of the three Au 6 Cu 6 nanoclusters caused by different ligands, the dihedral angle between the slightly off-plane vertex and the central Au 3 triangle in Au 6 and the Au-Cu-Au angle in the Au 3 Cu 2 hexahedron were collected in Figure  S2. For example, the variances of Au-Cu-Au angle for Au 6 Cu 6 PET 12 , Au 6 Cu 6 MBT 12 , and Au 6 Cu 6 PA 12 are 8.21, 4.50 and 4.50, respectively. These results show that the kernel of Au 6 Cu 6 PET 12 undergoes larger distortion than those of another two Au 6 Cu 6 nanoclusters, which can be further confirmed by the variances for the three dihedral angles in Au 6 layers of the three clusters (4.33, 1.04, and 1.12; Figure  S2B). Of note, this distortion can be observed in Figure 1, the two Cu 3 layers are not overlapped as well as those in Au 6 Cu 6 MBT 12 and Au 6 Cu 6 PA 12 observed from the top view, which may be interpreted by the flexibility of PET ligand endowed by the −CH 2 CH 2 − group between phenyl and terminal S atom, while MBT and PA ligands are more rigid due to the direct linkage between phenyl and S or alkynyl. In addition, the packing modes of the two Au 6 Cu 6 MBT 12 and Au 6 Cu 6 PET 12 nanoclusters in their crystal lattices are shown in Figures S3 and S4. The Ultraviolet-visible (UV-Vis) spectra of the three Au 6 Cu 6 nanoclusters are also shown in Figure S5.
Notably, the crystal structure of another cluster Au 12 Cu 12 (denoted Au 12 Cu 12 PA 24 ) can be viewed from the dimerization of Au 6 Cu 6 PA 12 . Its crystal data are listed in Table S3, and the UV-Vis spectra of the Au 12 Cu 12 PA 24 clusters are shown in Figure S5. Specifically, two Au 6 Cu 6 PA 12 nanoclusters are dimerized by two triangular vertex Au atoms with the bond length of 3.025 Å. Note that two Au 6 planes are in an approximate vertical direction (Figure 2A). More interestingly, a helical packing mode of Au 12 Cu 12 nanoclusters is observed in the crystal lattice, which is reminiscent of the RNA chain in the biology due to the single helicity. As shown in Figure 2C,D, the helical chain of Au 12 Cu 12 (pitch: Å) contains four cluster molecules, which are marked with "α/β/γ/δ", as well as the bases of RNA. Further analysis shows that the shortest Au-H distance ranges from 2.814 to 3.333 Å, implying that Au-H interaction should play an important role in the helical packing of Au 12 Cu 12 nanoclusters rather than common weak interaction like π-H or π-π between phenyl and H atoms from neighbored Au 12 Cu 12 nanoclusters (Figure 3). It should be noted that this Au-H interaction is also found in the intramolecular Au 12 Cu 12 cluster ( Figure 3). For each Au 6 Cu 6 triangle in the Au 12 Cu 12 PA 24 crystal, one Au-vertex is bonded to the other triangle in the dimer with a Au-Au distance of 3.032 Å, the other two Auvertices are weakly associated with two neighboring dimers via Au⋅⋅⋅H interaction, with vertex-vertex distance of 7.502 Å. Such an assembly layout leads to a space group of P4 3 2 1 2 (number: 96). A helix is formed surrounding the fourfold screw axis 4 3 , and in longer range, multiple helices are placed around the twofold screw axis 2 1 (Figure 2B,C).
It is worth pointing out that the Au 12 Cu 12 PA 24 nanocluster can be obtained from the dimerization of Au 6 Cu 6 MBT 12 accompanied by the ligand exchange but not from the dimerization of Au 6 Cu 6 PA 12 with the same PA ligand. To decipher the potential mechanism of Au 6 Cu 6 L 12 , where L represents PA, PET, and MBT, respectively, DFT calculations were carried out at the PBE + D3 level. First, we need to explain the lack of dimerization for the three Au 6 Cu 6 L 12 without the The Gibbs free energies (with dispersion corrections) for Reaction (1) are predicted to be −39.3, −18.8, and −29.6 kcal/mol for L = PA, PET, and MBT, respectively, implying that all three dimerization reactions are thermodynamically viable. Note that the empirically determined dispersion correction contributes significantly (−37.8, −29.4, and −41.2 kcal/mol for PA, PET, and MBT, respectively) to the reaction energy, being the thermodynamic driving force of the dimerization. Among the three [Au 6 Cu 6 L 12 ] 2 clusters only [Au 6 Cu 6 PA 12 ] 2 is a true dimer with a closest intermonomer Au-Au distance of 3.2 Å, compared with corresponding distances of 4.6 and 7.0 Å that are nonbonding for [Au 6 Cu 6 PET 12 ] 2 and [Au 6 Cu 6 MBT 12 ] 2 . This suggests that Au 6 Cu 6 PET 12 and Au 6 Cu 6 MBT 12 do not undergo dimerization that leads to potential crystallization. This also corroborates the experimental observation that [Au 6 Cu 6 PA 12 ] 2 does not dissociate into monomers under mild conditions. The lack of the dimerization reaction of Au 6 Cu 6 PA 12 via Reaction (1), therefore, can only be attributed to the kinetic effects.
Calculations show that in addition to the lowest-energy [Au 6 Cu 6 PA 12 ] 2 with a bent Au 6 -Au 6 alignment (involving the centers of the Au 6 triangles and the closest Au-Au intermonomer pair), b-[Au 6 Cu 6 PA 12 ] 2 , there also exists a vibrationally stable atomic configuration l-[Au 6 Cu 6 PA 12 ] 2 with a linear Au 6 -Au 6 alignment ( Figure S6), being 20.1 kcal/mol higher in energy. To understand the kinetic effects on the dimerization of Au 6 Cu 6 PA 12 , constrained structure optimizations were carried out for both the linear and bent configurations, during which dimer configurations are fully relaxed under a constraint with fixed intermonomer Au-Au distance; the Au-Au distance is scanned from 2.6 to 7.0 Å (Figure 4). A relatively smooth path ( Figure 4A) is found for dimerization toward b-[Au 6 Cu 6 PA 12 ] 2 . However, as the intermonomer Au-Au distance decreases from the nonbonding regime to the bonding regime, the Au 6 -Au 6 distance of the constrainedly optimized b-[Au 6 Cu 6 PA 12 ] 2 ( Figure 4B) becomes relatively short with a small variation, ranging from 9.8 to 10.6 Å. Since the Au 6 -Au 6 distance is related to the collision cross section of the monomer, the direct formation of b-[Au 6 Cu 6 PA 12 ] 2 via dimerization may require collision of monomers with small cross sections, which could be kinetically hindered by the steric effects of the PA ligands. On the other hand, the reaction path for the dimerization toward l-[Au 6 Cu 6 PA 12 ] 2 involves a rugged reaction energy change and several moderate energy barriers (15-20 kcal/mol), and there likely exist several local minima other than the l-[Au 6 Cu 6 PA 12 ] 2 with short Au-Au distance along the path. Hence, even though the l-[Au 6 Cu 6 PA 12 ] 2 path could initiate at a larger cross section (with Au 6 -Au 6 distance of ∼13 Å), the indirect dimerization path to b-[Au 6 Cu 6 PA 12 ] 2 via l-[Au 6 Cu 6 PA 12 ] 2 is also not viable.
Interestingly, none of the three pure Au 6 Cu 6 L 12 dimerizes but the exclusive combination of Au 6 Cu 6 MBT 12 and H-PA leads to formation of b-[Au 6 Cu 6 PA 12 ] 2 . To unravel this, the Au 6 Cu 6 PA n L 12-n (L = PET or MBT) with mixed ligands and their corresponding dimers [Au 6 Cu 6 PA n L 12-n ] 2 were modelled using the DFT-D3 method (Figures S7 and  S8). The formation energies of these Au 6 Cu 6 PA n L 12-n from Au 6 Cu 6 L 12 via L-PA ligand exchange (Reaction (2)) were calculated (Tables S4 and S5). Au 6 Cu 6 L 12 + nH − PA → Au 6 Cu 6 PA n L 12−n (2) The Gibbs free energy for substituting one PA for one L is ∼14 kcal/mol, with small fluctuation depending on the type and location of L (with PET > MBT and edge-L > vertex-L). In practice, the ligand exchange equilibrium is largely affected by the choice of the solvent, and the actual equilibrium may be more apt to the substitution than the DFT prediction indicates. The Gibbs free energy for the dimerization of Au 6 Cu 6 PA n L 12-n at 298 K were predicted (Reaction (3)), 2Au 6 Cu 6 PA n L 12−n → [ Au 6 Cu 6 PA n L 12−n ] and plotted against n ( Figure 4C). For Au 6 Cu 6 PA n PET 12-n , the correlation between the dimerization energy and n is found to be nonlinear, with two energy minima identified at n = 2 and 8. Such nonlinearity implies that the introduction of PA ligands may bring manifold effects on dimerization. The drastic increase in dimerization exergonicity from n = 0 to n = 2 ( Figure 4C) is due to the transition of intermonomer Au-Au interaction from nonbonding MBT 2 Au…AuMBT 2 to the bonding PA 2 Au-AuPA 2 , evident from the reduced Au-Au distance from 7.0 to 3.3 Å ( Figure 4D). Unlike the case of [Au 6 Cu 6 PA 12 ] 2 , the lowest energy configuration of [Au 6 Cu 6 PA 2 MBT 10 ] 2 has an essentially linear Au 6 -Au 6 alignment, 23.5 kcal/mol more stable than the bent configuration ( Figure S6). The substitution of PA at the intermonomer interacting sites for Au 6 Cu 6 PA n MBT 12-n with n ≥ 2 significantly decreases the steric effects upon the dimerization caused by the bulkier MBT ligands. Meanwhile, the Au 6 -Au 6 distance of the equilibrium structure of Au 6 Cu 6 PA 2 MBT 10 ( Figure 4C) remains comparatively high (>12 Å), and the reaction is likely not to be kinetically hindered. To verify this, constrained structure optimizations were performed for the [Au 6 Cu 6 PA 2 MBT 10 ] 2 , with the intermonomer Au-Au distance scanned from 2.6 to 7.0 Å (Figure 4). The scanned dimerization path is essentially barrierless, and the intermonomer Au 6 -Au 6 distance decreases smoothly as Au-Au distance decreases, showing that the dimerization of Au 6 Cu 6 PA 2 MBT 10 is indeed both thermodynamically and kinetically favorable.
As n further increases from 2 to 6, the dimerization energy increases slightly but the dimerization remains exergonic; both the Au-Au and Au 6 -Au 6 intermonomer distance of the dimer are essentially unchanged. At n = 8, the dimerization energy dramatically decreases to −65 kcal/mol, accompanied by the transition of the Au 6 -Au 6 alignment from approximately linear to bent as well as the shrinkage of the Au 6 -Au 6 distance. The dimerization of Au 6 Cu 6 PA 8 MBT 4 is ∼25 kcal/mol more exergonic than Au 6 Cu 6 PA 12 , implying that the MBT ligands that are not on the bonding Au-Au pair favor the dimerization. Further natural population analyses ( Figures S8 and S9 and Figure 4F) reveal that the natural atomic charge on the positively-charged Au 6 Cu 6 kernel of the Au 6 Cu 6 PA n MBT 12-n monomer decreases linearly as the Based on these computational results, the reaction mechanism for the synthesis of [Au 6 Cu 6 PA 12 ] 2 from Au 6 Cu 6 MBT 12 is proposed ( Figure 5). First, the Au 6 Cu 6 MBT 12 precursor forms mixed-ligand cluster with a small number of PA ligands such as Au 6 Cu 6 PA 2 MBT 10 . Next, the mixed-ligand clusters with two PA ligands on the same vertex-Au dimerize in approximately linear configurations, which is kinetically more feasible due to their comparatively large cross sections. PA ligands continue to replace the MBT ligands in the [Au 6 Cu 6 PA n MBT 12-n ] 2 , and the linear-to-bent transition occurs at n = ∼8. Eventually, all of the MBT ligands are replaced with the PA ligands, forming the thermally stable b-[Au 6 Cu 6 PA 12 ] 2 . The crystallization of b-[Au 6 Cu 6 PA 12 ] 2 may shift the equilibrium and further advance the dimerization.
The lack of reaction of the Au 6 Cu 6 PET 12 can also be explained using the computational results. The dimerizations of Au 6 Cu 6 PA n PET 12-n , n = 0 and 1, are thermodynamically unfavorable ( Figure 4C), as the bonding of the two monomers is obstructed by the bulky PET on all vertices of triangle metal kernel. The dimerizations of Au 6 Cu 6 PA n PET 12-n , n ≥ 2, lead to bent dimers, which are difficult to form directly due to the small cross section ( Figure 4D). Therefore, even though PET shares some of the virtues of MBT that favor the dimerization, for example, it reduces the intermonomer repulsion, synthesizing b-[Au 6 Cu 6 PA 12 ] 2 from Au 6 Cu 6 PET 12 is unfeasible because the thermodynamically viable linear-to-bent mechanism is absent.

CONCLUSION
In summary, we have synthesized a single-helical Au 12 Cu 12 PA 24 superstructure from the dimerization of a couple of Au 6 Cu 6 MBT 12 nanoclusters imparted by PA.
We have demonstrated that the thermodynamically viable linear-to-bent process of Au 6 Cu 6 MBT 12 can favor the helical formation. This present approach not only represents a new strategy to explore the feasibility of single-helical bimetallic nanoclusters but also serves as starting opportunities for opening the possibility of artificial nanoparticles used as building blocks just like genetic codes to deliver the physicochemical properties into the nanostructured assemblies in the future.

C O N F L I C T O F I N T E R E S T
The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported.

D ATA AVA I L A B I L I T Y S TAT E M E N T
The data that support the findings of this study are available in the Supporting Material of this article.