Template-free synthesis of colloidal quantum dot assemblies with molecule-like architectures

Domain: physics
Published: 2026-03-13
Editorial outcome: minor_revision

Abstract
Designing colloidal assemblies with molecule-like architectures comprising more than two electronically coupled quantum dots has often required technologically complex, expensive, and top-down nanofabrication. Here we demonstrate a one-pot chemical synthesis of dimeric, trimeric, and tetrameric assemblies of coupled molecule-like quantum dots (CMQDs), using ZnSe@ZnS quantum dots as model. We show that the “valence” of these “artificial atoms” can be readily tuned by the amount of a suitable ligand in the reaction mixture, and that high-temperature fusion yields highly ordered oriented attachment and strong electron coupling between bound QDs. The shapes of the fused assemblies echo the canonical sp-, sp²-, and sp³-hybridization motifs and can be interpreted as appropriately shaped confining potential wells for electrons and holes. This work establishes an experimentally accessible entry point to related “artificial molecules” with controllable chemical composition, geometry, and electronic structure. The enhanced or emergent properties of such nanomaterials are anticipated to advance applications in optoelectronics, sensing, and quantum photonic technologies.

Introduction
All modern technology is unthinkable without scientists’ ability to arrange atoms into specific molecules/matter with precise control over chemical composition, geometry, and as a result, electronic structure. That same “control mindset” is now being transferred to nanoscale building blocks. For example, semiconductor quantum dots (QDs) are widely viewed as artificial atoms1-4 because quantum confinement gives them discrete, atom-like electronic structure, tunable by size, composition, and surface chemistry. Such paradigm has already inspired several applications of QDs as lasers,5single-photon sources,6 source of entangled photon pairs.7 However, fully exploiting the potential of artificial atoms requires learning how to synthesize quantum dot “molecules” with controlled stoichiometry, programmed geometry, and engineered electronic coupling between bound QDs. The latter generates emergent “molecular” electronic states and functions beyond those of isolated artificial atoms,8-13 thus enabling the design of new materials and devices for optoelectronics, quantum photonics, nanoscale energy/charge transport technologies and many other fields.

Molecule-like quantum dot assemblies can be differentiated by the nature of the inter-QD linkage. We define self-assembled quantum dot molecules as finite, stoichiometrically and geometrically distinct QD aggregates whose integrity is governed primarily by the interactions of function al groups on their periphery. To date, several successful strategies have been developed for the programmed synthesis of assembled quantum dot molecules, relying on DNA-encoded recognition motifs,14-16 electrostatic comple mentarity of charged polymer brushes,17 or templated multi-step procedure that allows to bind two QD particles with short covalent links (≈1 nm).18 All such linkages can provide exquisite control over the directionality, connectivity, and symmetry of assembled quantum dot molecules, but they inevitably impede inter-dot electronic communication.19

In contrast, in coupled colloidal molecule-like quantum dots (CMQDs),20 adjacent QD “atoms” form direct core–core junctions, yielding a rigid, chemically robust backbone of fused QDs and enabling direct electronic and energy coupling and, potentially, dopant exchange across the entire CMQDs. Yet, the reliable synthesis of such coupled dots21 remains considerably less straightforward than the assembly of assembled quantum dot molecules. Direct nanofabrication via molecular beam epitaxy,22, 23 though precise and compatible with convenient fabrication of CMQDs-based devices, is technologically complex, expensive, and difficult to scale. Much more practical is a templated approach24 in which assembled quantum dot molecules with short covalent linkages serve as intermediates for subsequent fusion into CMQDs. While reliable, this workflow is experimentally involved and was only extended to dimeric assembled quantum dot assembles.

In this work, we present a template-free, one-pot methodology for the synthesis of CMQDs via controlled fusion of two, three, or four QDs. ZnSe@ZnS quantum dots (Figure 1a) and their Cu- or Mn-doped variants were used to demonstrate our approach and to test the basic properties of the synthesized CMQDs. The exact outcome of the synthesis depends on the optimized amount of added oleylamine (OLAm). Atomic-resolution imaging corroborates face-to-face oriented attachment (OA) of the fused nanoparticles and allows us to postulate a dynamic combinatorial transformation of closely packed dimeric, triangular, and tetrahedral assembled quantum dot intermediates, as the connectivity (“valency”) of each individual QD increases with increasing OAm quantity. The fused CMQDs backbones can be viewed as continuous confining potential wells for electrons and holes, with overall geometries reminiscent of the canonical linear, trigonal, and tetrahedral motifs associated with sp, sp², and sp³ hybridization, respectively. In addition to advanced optical characterization, these quantum dot assemblies were evaluated as X-ray scintillators.

Results
Synthesis of colloidal molecule-like assemblies
The fabrication of CMQDs was derived from colloidal ZnSe/ZnS core/shell QDs25, 26 via modulation of the Ostwald ripening (OR), oriented attachment (OA), and multistep oriented attachment (MOA) process (Figure 1a and Supplementary Fig.1). Briefly, oleate and OLAm, as typical hard bases, exhibit strong coordination with zinc ions (borderline Lewis acids), resulting in effective passivation of the ZnSe/ZnS surface and the formation of monodisperse QDs.27 Meanwhile, OLAm acts as an amine-based anchor, whereas oleic acid (OLA) predominantly appears as a monodentate carboxylate that links the long-chain alkyl tail to the QD surface, with the carboxylate remaining more stable than the amine even in the monodentate form.28 Thus, when the solvent is exchanged from OLA/OLAm to pure OLAm, the passivation effect becomes insufficient, resulting in enhanced oriented attachment and the formation of ZnSe/ZnS dimers.29 When excess pure OLAm is introduced into the system, the viscosity of the reaction medium increases significantly,28 reducing the diffusion rate of the building blocks and promoting a MOA process, accompanied by Ostwald ripening and the formation of timer and tetramer ZnSe/ZnS molecules (Supplementary Figs. 2-5). Therefore, as the OLA concentration decreases and the OLAm amount increases, the self-organized, self-driven structure formed via multistep oriented attachment leads to the predominant formation of tetramer ZnSe/ZnS QDs.

Characterization and binding relationship analysis
We selected colloidal monomer ZnSe/ZnS QDs as the fundamental building blocks. The dimer, trimer, and tetramer colloidal molecules were fabricated in analogy with the sp, sp², and sp³ hybrid atomic orbitals, respectively (Figure 1b). The morphology of the ZnSe/ZnS CMQDs is depicted in Figure 1c-n and Supplementary Fig. 6. The monomer ZnSe/ZnS QDs were synthesized using the hot-injection method, with slight modifications based on refs.30-34 (see Methods). As depicted in Figure 1c-e, transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM), and high-angle annular dark-field (HAADF-STEM) imaging confirmed the fabrication of monomer QDs with low dispersity in size of 8.4 ± 1.9 nm (Supplementary Fig. 6). Selected area electron diffraction (SAED) pattern and X-ray powder diffraction (XRD) measurements indicate the zinc blende (ZB) structure of the ZnSe/ZnS QD building blocks (Supplementary Fig. 6). The dimer (Figure 1f-h), timer (Figure 1i-k), and tetramer (Figure 1l-n) structures were further characterized. HAADF-STEM images show that the fabricated monomer, dimer, trimer, and tetramer colloidal molecules closely resemble the hybridization atomic orbital model, including similarities in bond angles. Consequently, by decreasing the amount of OLA and increasing the amount of OLAm, the OR process is suppressed, allowing the OA and multistep OA processes to dominate, thereby facilitating the synthesis of ZnSe/ZnS CMQDs.

The fine structure of the ZnSe@ZnS CMQDs was further characterized using HAADF-STEM imaging and the corresponding 3D reconstructed structure. As shown in Figure 2a, the low index atomic planes (111), (020), and (202) are clearly visible, which facilitates identification of the boundary faces of the monomer crystal model (Figure 2b). Fast Fourier transform (FFT) analysis and the FFT-filtered reconstructed atomic structure (Supplementary Fig. 7) confirmed the zinc blende (ZB) ZnSe@ZnS structure along the [101] zone axis (ZA). To further validate the constructed monomer crystal model, structural analysis along the [01̅0] ZA was depicted in Supplementary Fig. 8. This analysis demonstrates the accurate reconstruction of cubic motifs35, which will serve as the model structure for subsequent oriented attachment relationship analysis.

The structure of the coupled colloidal ZnSe@ZnS dimer molecules (Figure 2c) was confirmed through HAADF-STEM imaging, which revealed a continuous atomic lattice formed between the two adjoined monomer QDs. This observation confirms the dimer structure through mutual modulation of the OA processes. A hetero-plane oriented attachment was observed, characterized by the connection of heteronymous faces: (022) ||(211) , matched well with the 3D ZnSe@ZnS dimer QD model (Figure 2d) derived from the STEM analysis. In this hetero-plane attachment scenario, both ZnSe@ZnS monomers in the conjunctive pair were further analyzed using separated FFT pattern analysis, revealing the fusion axes along [011] ZA and [213] ZA , respectively(Supplementary Fig. 9). Additionally, both homonymous (Supplementary Fig. 10) and heteronymous (misorientation) plane attachment relationships are observed in our system.

The sp2-analog trimer structure was characterized using HAADF-STEM (Figure 2e). It is clearly observed that the ternary structure is formed by connecting of a third monomer to a homonymous dimer QD. Both parts A and A of the trimer structure are aligned along the same [1̅21] zone axis, resulting in the formation of a homonymous plane attachment: (202) ||(202) (Figure 2f, and Supplementary Fig. 11). Notably, the size of the third monomer part (A ) in the ternary QDs is significantly smaller than that of the other two parts, attributed to the highly active vestigial monomer based on the incomplete inhibition of the Ostwald ripening effect. This phenomenon is also observed in the quaternary QD structures (Figure 2g, h, and Supplementary Fig. 12). It is evident that parts A toA exhibit similar geometric symmetry with a twisting or twirling effect along the [1̅21] ZA. Additionally, a fourth smaller monomer connects to the trimer structure along the [01̅1] ZA. This connection helps alleviate surface strain when forming trimer or tetramer colloidal ZnSe@ZnS assemblies with constrained attachment.

Significant surface defects are typically observed during the formation of trimer and tetramer CMQDs due to the combined modulation of the OR and OA processes. These defects36, 37 include stacking faults, edge dislocations, twin boundaries, and grain boundaries (details in Supplementary Fig. 13, 14), particularly in the tetramer structure. Additionally, multi-branched multimer QDs are observed during tetramer formation (Supplementary Fig. 15). Furthermore, energy dispersive X-ray spectroscopy (EDS) element mapping confirmed the core-shell architecture of the colloidal ZnSe@ZnS assemblies (Figure 2i-l), which indicating a continuous distribution of zinc in both the core and shell locations, while sulfur and selenium are distinctly located, signifying the shell and core positions, respectively. Thus, by precisely controlling the effects of the ligands via OR, and OA, and tuning them together, we synthesized monomer, dimer, trimer, and tetramer ZnSe@ZnS CMQDs.

Photophysical properties
The optical signatures of the assemblies were further explored as shown in Figure 3a,b. The coupled quantum dot assemblies exhibit significant red shifts in band-edge absorption and photoluminescence (PL) compared to the ZnSe@ZnS monomer. Additionally, according to the International Commission on Illumination (CIE) pattern, the formation of tetramer ZnSe@ZnS assemblies resulted in an almost pure blue emission (Figure 3c). This emission approaches the limits of ZnSe-based QDs, which still presents a challenge, requiring further investigation. Notably, a red shift of 71.3 meV was observed for the type-I ZnSe@ZnS tetramer compared to the monomer QDs. In contrast, our previous quasi-type II CdSe@CdS coupled dimer structure exhibited only a 26 meV red shift.38 Meanwhile, ensemble PL lifetime measurements revealed quenching of the lifetime (Figure 3d). The calculation results show that the electron and hole ground states in the monomer, dimer, trimer, and tetramer are confined to the core (Figure 3e, Supplementary Note 1, and Supplementary Table 1). The first excited state of the electron is confined to both the core and the shell. The red shift of the dimer, trimer, and tetramer relative to the monomer can be attributed to the coupling of the wave functions in the different quantum dots, analogous to the symmetry and antisymmetric of wave functions in conventional molecules (Figure 3f, g). We hypothesize that the formation of larger molecules and increased volume during the OA/OR combined process may lead to coupling with electron dislocation. This could result in observed red shifts in both absorption and PL, accompanied by lifetime quenching, reflecting the coupling among quantum dot assemblies and analogous to chemical bond-type hybridization seen in carbon-based systems.

To further validate our hypothesis, we conducted femtosecond transient absorption spectroscopy (fs-TAS) measurements, as depicted in Figure 3h-o. A prominent negative peak (ΔA<0) is observed around 430 nm and is attributed to ground-state bleaching (GSB). This reflects the depopulation of photo-generated electrons in the excitons of the ZnSe@ZnS QDs. When irradiated with a 365 nm pump laser, excitons are immediately generated and dissociated into free holes and electrons in the ZnSe@ZnS QDs. High-energy electrons then recombine with holes within 2.0 ps. Notably, ground state bleaching rapidly decays with the formation of colloidal ZnSe@ZnS CMQDs, indicating a fast exciton recombination rate. This rapid recombination may be due to energy transfer or surface defect trapping processes (Supplementary Fig. 16). Furthermore, a shift in GSB to longer wavelengths occurs as the decay time increases from 2.0 ps to 2.0 ns. This shift is likely due to the QDs’ significant volume increase, which results in enhanced electron dislocation and/or spatial separation rates 39-43and facilitates faster charge separation.

Single-particle photoluminescence spectroscopy
We investigate the PL properties of ZnSe@ZnS CMQDs at the single-particle level using single-particle PL spectroscopy. 44 As shown in Figure 4a-c, the single monomer, dimer and trimer CMQDs all exhibit stable PL intensity trajectories. The corresponding PL intensity histograms demonstrate that they all exhibit a significant proportion of bright states. This indicates that these monomers, dimers and trimers were prepared to a high standard. Due to the QDs' surfaces being passivated, the monomer exhibits a standard Auger blinking trajectory, as revealed by the nonlinear fluorescence lifetime-intensity distribution (FLID) 45 map shown in Supplementary Fig. 17. The corresponding PL decay curves which exhibit a multiexponential characteristic due to the influence of multi-excitons, ionized states, and surface non-radiative recombination, are shown in Figure 4d-f. A multi-exponential function fit yielded weighted average lifetimes of 19.7, 17.5, and 15.9 ns for the monomer, dimer and trimer assemblies, respectively. This gradual decrease in lifetime is attributed to an increase in multiple excitons and surface non-radiative recombination in the dimer and trimer assemblies. Single exciton lifetimes were obtained by fitting the PL decay curves extracted from the bright state of the PL intensity trajectories (Supplementary Fig. 18a-c), and the statistical results are summarized in Supplementary Fig 18d. The average single-exciton lifetimes in monomers, dimers and trimers are 25.3, 26.4, and 26.9 ns, respectively. This indicates that forming multimeric structures does not significantly alter the radiative recombination properties of single excitons.

The second-order photon correlation, (g(2)(τ)), curves are shown in Figure 4g-i and reveal the statistics of photons from single ZnSe@ZnS CMQDs. Under low excitation, the biexciton QY was approximately equal to g(2)(0).46 The g(2)(0) statistics for monomers, dimers, and trimers are in Figure 4j-l, with values clustering around 0.37, 0.58, and 0.65, respectively. Specifically, monomers show a narrow distribution due to high purity; dimers are broader, reflecting slightly lower purity, and trimers are also broad, consistent with STREM yields (Supplementary Table 2). Dimers and trimers have higher g(2)(0) than monomers due to segregated biexcitons (SBX), which are long-lived, spatially separated biexcitons with reduced Auger quenching.47 Biexciton PL decay was further analyzed from the first photon in two-photon events.48 Dimer decays fall into two types: (i) rapid decay fitted by a single exponential, from strongly coupled dimers where both excitons reside in one core (localized biexciton, LBX; Figure 4m and left panel of Figure 4o), and (ii) a double-exponential decay with a fast LBX and slow SBX component (Figure 4n). In strongly coupled dimers, SBX converts quickly to LBX; in weakly coupled dimers, SBX and LBX emissions coexist due to slower SBX to LBX conversion.47 Supplementary Fig. 19 shows SBX lifetimes are broadly distributed due to coupling heterogeneity. Supplementary Fig. 20 reports LBX lifetimes of 1.7 ns (monomer), 2.3 ns (dimer), and 2.7 ns (trimer), with longer LBX lifetimes in dimers/trimers arising from enhanced exciton delocalization that suppresses Auger recombination.

Supplementary Fig. 21 shows the power-dependent PL decay for single monomer, dimer, and trimer assemblies.49 As laser power increases, the decay becomes faster, indicating a larger fraction of biexcitons at higher excitation. Power-dependent decay measurements thus quantify both biexciton lifetimes and Auger recombination, by subtracting high- and low-power decays. The extracted biexciton lifetimes are 2.03 ns (monomer), 2.24 ns (dimer), and 2.33 ns (trimer) (Supplementary Fig. 21d-f), consistent with the LBX lifetimes from the first-photon analysis in Supplementary Fig. 20. It should be noted that the biexciton lifetime can reach up to 2 ns, likely due to an alloyed ZnSe/ZnS shell that reduces Auger recombination, in line with recent report50. Additionally, an excess carrier may occupy the second emission center in the dimer, forming a potential trion (Supplementary Fig. 22). Meanwhile, the dimer and trimer assemblies exhibit more blinking in their PL trajectories due to band-edge carrier (BC) blinking, which is induced by surface defects formed during synthesis.51 Auger and BC blinking are caused by non-radiative Auger recombination and non-radiative BC recombination, respectively (Figure 4p). Additionally, due to the weak PL features, it was difficult to investigate the PL properties of individual tetramer assemblies at the single-particle level; only fast PL decay lifetimes could be obtained (Supplementary Fig. 23).

X-ray scintillator application
To further explore the boundaries of ZnSe@ZnS QD-based CMQDs structures, we synthesized doped ZnSe@ZnS QDs. As shown in Supplementary Fig. 24, the effects of different Mn2+ doping concentrations were investigated. An optimal Mn doping concentration of around 8% was found to achieve the highest PL quantum yield (QY) (detailed in Supplementary Fig. 25). Additionally, Cu²⁺-doped ZnSe:Cu@ZnS was fabricated using a similar strategy (Supplementary Figs. 26, 27). The ZnSe:Mn@ZnS was then used as a building block to synthesize colloidal molecule-like structures.

As illustrated in Figure 5a-d and Supplementary Fig. 28, STEM imaging confirms the formation of monomer, dimer, trimer, and tetramer ZnSe:Mn@ZnS QDs. The XRD pattern depicted in Figure 5e indicates that the coupled assemblies maintain the typical ZB structure even after Mn²⁺ doping. Similar red shifts are observed in the absorption and emission spectra of the ZnSe:Mn@ZnS-based system (Figure 5f, g). Due to surface strain, the PL feature of the tetramer structure is diminished. Meanwhile, the coupled assemblies based on ZnSe:Mn@ZnS exhibit rapid quenching of the PL lifetime (Figure 5h). Thus, the synthesis of ZnSe:Mn@ZnS assemblies demonstrates their versatility and potential application in Cd or Pd-based molecular structures.

Inspired by their fast charge separation rate and potential to avoid re-absorption, we investigated their application in X-ray scintillation. ZnSe is known as a scintillator candidate, particularly in ZnSe:Ag@ZnS materials52. Currently, zinc-based structures are primarily used for α particle detection. However, their use in X-ray imaging or detection is limited due to issues such as in stability, susceptibility to deliquescence, and strong reabsorption effects. We propose that our surface-engineered strategy for colloidal assemblies, which facilitates a fast charge separation rate, will provide promising candidates for improved performance and address these challenges.

The X-ray radio-luminescence spectrum shown in Supplementary Fig. 29 exhibits a consistent trend with the UV-induced luminescence spectrum. This indicates that there is a similar efficient energy transfer process under both X-ray and UV excitation. To demonstrate the potential application of ZnSe:Mn@ZnS in X-ray scintillation, we evaluated the X-ray imaging properties of scintillation films using an X-ray imaging system (Supplementary Fig. 30). X-ray imaging of the ZnSe:Mn@ZnS dimer, compared with monomer samples, reveals that the designed structure can distinguish different spring and SUDA markers clearly (Figure 5i), whereas images produced by ZnSe@ZnS appear blurry and dark. Therefore, the ZnSe:Mn@ZnS dimer system inhibits self-absorption due to its large Stokes shift and exhibits X-ray scintillator imaging performance due to its high energy transfer efficiency. Figure 5j proposes a plausible mechanism for the radioluminescence of ZnSe:Mn@ZnS nanocrystals. During the initial conversion phase, X-ray photons primarily interact with the lattice atoms of the ZnSe:Mn@ZnS nanocrystals, generating a significant number of high-energy electrons and holes. Subsequently, secondary electrons and low-kinetic charge carriers are produced. These charge carriers dissipate thermally through interactions with phonons, resulting in the transport of secondary electrons and holes into the conduction and valence bands52, respectively. However, due to the presence of Mn²⁺, the conduction band electrons do not directly recombine with the holes. Instead, they recombine with Mn²⁺, shifting the luminescence center to Mn²⁺. This behavior highlights the potential application of colloidal artificial ZnSe:Mn@ZnS CMQDs.

In summary, we have demonstrated template-free, one-pot, solution-based route to complex CMQDs. The discovery that the “valence” of artificial atoms can be easily modulated by varying the concentration of suitable ligands enables the programmed formation and subsequent fusion of few-dot assemblies into rigid, electronically coupled backbones of the desired CMQDs. The synthesized dimeric, trimeric, and tetrameric ZnSe@ZnS CMQDs can be regarded as confining potential wells shaped analogously to canonical sp, sp², and sp³ hybridization, respectively. In future work, we will elucidate the molecular mechanism by which ligands with low molecular weight (in the present study, oleylamine and oleic acid) modulate the valence of ZnSe@ZnS CMQDs and adapt this methodology to the synthesis of CMQDs from chemically distinct artificial atoms. Overall, our findings provide an experimentally accessible entry point toward solution-based synthesis of complex-shaped CMQDs, opening opportunities for emergent properties and applications in optoelectronics, sensing, and quantum technologies.

Methods
Materials. Oleylamine (OLAm, 70%), 1-octadecene (ODE, 90%), oleic acid (OLA, 90%), zinc acetate (ZnAc , 2 99.99%), manganese acetate (MnAc , 99%) and 1-octanehiol (98%) were purchased from Thermo Scientific. Selenium powder (Se, 99.99%) was purchased from Tokyo Chemical Industry. Tri-n-octylphosphine (TOP 97%) and poly(methyl methacrylate) (PMMA, (C H O ) , M 35000 g mol-1) were purchased from Innochem. Toluene (C H , 5 8 2 n w 7 8 AR) and cyclohexane (C H , AR) were purchased from Beijing chemical works. All the reagents were used as 6 12 received without further purification

Synthesis of Zn(OLA) precursors. Zinc acetate dihydrate (1834.8 mg), oleic acid (OLA, 16 mL), and octadecene (ODE, 24 mL) were added to a 100 mL flask at room temperature under a nitrogen atmosphere. The mixture was then heated to 120 °C and degassed three times to remove residual water and oxygen. After degassing, nitrogen was reintroduced, and the mixture was maintained at 120 °C for 30 min, during which it gradually transformed from an initial white turbidity to a clear yellow solution. Once the reaction was complete, the mixture was cooled to 80 °C, and zinc oleate (Zn(OLA)₂) was obtained and transferred for further use. The Zn(OLA)₂ solution should be stored at 4 °C for subsequent experiments.

Synthesis of Mn(OLA) precursors. Manganese (II) acetate (MnAc₂, 865.2 mg), oleic acid (OLA, 9 mL), and 1-octadecene (11 mL) were added to a 100 mL flask at room temperature under a nitrogen atmosphere. The mixture was then heated to 120 °C and degassed three times to remove residual water and oxygen. After degassing, nitrogen was reintroduced, and the mixture was maintained at 120 °C for 30 min, during which it gradually transformed from an initial white turbidity to a clear yellow solution. Once the reaction was complete, the mixture was cooled to 80 °C, and manganese oleate (Mn(OLA)₂) was obtained and transferred for further use. The Mn(OLA)₂ solution should be stored at 4 °C for subsequent experiments.

Synthesis of ZnSe@ZnS QDs. A mixture of 1 mL OLAm, 1 mL oleic acid, 8 mL octadecene, and 1.6 mL Zn(OLA)₂ was added to a 50 mL four-neck flask and stirred at 800 rpm. After purging three times with nitrogen, it was heated to 120 °C for 30 min, then raised to 300°C under nitrogen53. A 1 mL Se stock solution was rapidly injected at 300 °C; after 5 min, the heater was removed to cool. When it reached 220 °C, 0.2 mL TOP was added, then cooled to 200 °C. When the temperature was raised back at 260 °C, two solutions were injected via pump over 2 h: 5 mL of 0.1 M Zn precursor and 5 mL of 0.13 M 1-octanethiol in ODE. The mixture was held at 295 °C for 30 min54, 55. The reaction was cooled to 180 °C, then 2 mL toluene was added. After cooling to room temperature, the product was centrifuged with ethanol, washed twice, and finally dissolved in 5 mL cyclohexane for storage.

Synthesis of ZnSe@ZnS dimers, trimers, and tetramers QDs. The procedure follows the same steps as the monomer synthesis, with variations only in the initial solvent composition56-58. For dimers, use 1 mL OLAm and 9 mL ODE; for trimers, 2 mL OLAm and 8 mL ODE; and for tetramers, 7 mL OLAm and 3 mL ODE. All other steps and reagent quantities remain consistent with the monomer protocol.

Synthesis of ZnSe:Mn@ZnS QDs. A mixture of 1 mL OLAm, 1 mL OLA, 8 mL ODE, 160 μL of 0.25 M manganese precursor, and 1.44 mL of 0.25 M zinc precursor was added to a 50 mL four-neck flask. The mixture was stirred at 800 rpm, then purged and degassed three times with nitrogen at room temperature. It was gradually heated to 120 °C and maintained for 30 min under nitrogen flow. The system was then switched to a nitrogen atmosphere and heated to 300 °C. Then, 1 mL selenium solution was rapidly injected and the reaction was maintained at 300 °C for 5 min before the heater was removed to cool the mixture. At 220 °C, 0.2 mL of TOP was injected, and the mixture was cooled to 200 °C59. When temperature was then increased to 240 °C, 0.6 mL of 0.25 M zinc precursor was slowly injected, followed by a 30-min reaction at 280 °C. The temperature was then raised to 295 °C. During heating, two solutions were pumped over 2 h: solution A, 0.1 M zinc precursor (5 mL with injection rate 2.5 mL h-1), and solution B, 0.13 M octanethiol in ODE (5 mL with injection rate 2.5 mL h-1). The mixture was maintained at 295 °C for 30 min, then cooled to 180 °C. 2 mL of toluene were added, and the solution was cooled to room temperature. The mixture was transferred to a centrifuge tube, mixed with ≈ 20 mL of anhydrous ethanol, and centrifuged at 11,000 × g for 10 min. The pellet was dissolved in 5 mL of cyclohexane, washed twice with ethanol, and the supernatant was collected for storage.

Synthesis of ZnSe:Mn@ZnS dimers, trimers, and tetramers QDs. The procedure follows the same steps as the monomer synthesis, differing only in the initial solvent composition: dimers use 2 mL OLAm and 8 mL ODE; trimers use 3.5 mL OLAm and 6.5 mL ODE; and tetramers use 7 mL OLAm and 3 mL ODE. All other steps and reagent quantities are identical to the monomer protocol reported in refs.60, 61.

Fabrication of QDs-PMMA. Briefly, 1.2 g of PMMA was dissolved in 8 mL of toluene and stirred at 50 °C for 1 h. Subsequently, the prepared QDs were added to the PMMA precursor and stirred at room temperature for an additional hour. The resulting mixture (QDs and PMMA colloid) was then poured onto a pre-fabricated template and dried either through annealing or air drying to produce the QDs@PMMA films.

Single-particle optical measurement. The optical measurement system based on a laser confocal microscopy platform was employed to investigate the single-photon properties of individual particles. Before the experiment, a quantum dot solution was applied to an acetone-cleaned slide after oscillation and spinning. During the measurement, a supercontinuum laser (NKT Photonics, EXW-12) with a central wavelength of 402 nm, a pulse width of 4 nm, and a repetition rate of 5 MHz served as the excitation source. The laser beam was reflected by a dichroic mirror and focused onto the sample through an oil immersion objective (OLYMPUS, 100×, 1.3 NA) to form a diffraction-limited spot. The emitted fluorescence from the quantum dots was collected by the same objective and directed to two single-photon detectors (Excelitas, SPCM-AQRH-16-FC) configured for Hanbury-Brown-Twiss measurements. Photon arrival times were recorded using a time-resolved, time-dependent single-photon counting (TTTR-TCSPC) data acquisition card (SImINICS, FT1040). The fluorescence decay curves, lifetimes, and second-order correlation functions were extracted from the data using MATLAB analysis software.

Characterization. The UV-vis-NIR absorption spectrum was measured using a Lambda 35 spectrophotometer. Photoluminescence and radioluminescence spectra were recorded with a QE Pro fluorescence spectrophotometer (Ocean Insight), equipped with a miniature X-ray source (AMPEK, mini-X2). X-ray-induced luminescence images were captured using a digital camera (Work Power WP-GS1200). Time-resolved photoluminescence measurements were conducted with a FL3-TCSPC system (HORIBA JOBIN YVON). Transmission electron microscopy (TEM) and high-resolution TEM (HRTEM) analyses were performed with a Talos F200S G2 microscope operated at 200 kV. High-resolution scanning transmission electron microscopy (STEM) imaging and elemental mapping were carried out using a Themis Z aberration-corrected STEM (Thermo Fisher Scientific) at 300 kV, equipped with a high angular annular dark field (HAADF) detector for STEM imaging and a Super-X energy dispersive X-ray spectroscopy (EDS) detector for elemental analysis. X-ray powder diffraction (XRD) measurements were performed with a D8 Advance diffractometer.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "The authors present a nice study of controllably assemble collodial Zn-based nanoparticles to (monomers,) dimers, trimers and tetramers. The final strucutres resemble molecular bonding in terms of (s,) sp, sp2, and sp3 bonding. They discuss the corresponding mechanisms (beyond basic characterization) by crystallographic considerations and facetting. Further they explore the resulting optical properties and mechanisms in detail (time-resolved etc.)\nI think this study can be published in Nature Communications since it is also well written.\nI have only once request: The authors should add statistics of how many particles end up in the desired configuration as dimers, trimers and tetramers; how reliable is they synthesis ... does every approach lead to the desired outcome of does the outcome determine purpose; how many synthesis lead to the same predefined result?", "reviewer_2": "The manuscript by Fan et al. presents a variation of colloidal molecules from ZnSe@ZnS nanocrystals. By slight modification of the synthesis that rebalances oriented attachment and Ostwald ripening, monomers, dimers, trimers and oligomers are created and studied with various TEM and optical spectroscopy methods. Furthermore, colloidal molecules from Mn-doped nanocrystals are investigated for their use as scintillator material. While the TEM studies appear clear and sound, I have several concerns on the spectroscopy results and interpretations, see further below.\nDespite the claims in the abstract and introduction, the assembly of nanocrystals into colloidal molecules is far from novel, as it has been established for many nanocrystal material systems over the past decades, e.g. extensive works by the Manna group, or particularly related, CdSe dimers by the Banin group https://doi.org/10.1021/acs.accounts.0c00691 . Given the little actual change in the optical properties that the evolution from monomer over dimer and trimer to tetramer brings about (Figs. 3,4), it is questionable what benefits and tuning capabilities the presented colloidal molecules offer. Moreover, it is well known that doping nanocrystals enhances their properties for the use in scintillators through energy transfer and reduced reabsorption (see e.g. https://doi.org/10.1016/j.opelre.2019.01.001 ), but the current manuscript does not present significant advantages from using colloidal molecules for this application.\nIn conclusion, I fail to recognize “significant impact on quantum optoelectronics, sensing and high-energy particle detection” as the authors claim or a significant advance for the field that I would expect from a publication in Nature Communications.\nApart from my reservations on novelty and impact, I have the following remarks:\n1) As the variation from dimer, trimer and tetramer is achieved through a relatively small concentration change of OLAm, the samples clearly have a mixture of all different kinds of colloidal oligomers (Fig. 1, Fig. S3). It is not discussed what the yield distribution of dimers/trimers/tetramers is and how their respective purity changes with the synthesis conditions.\n2) In view of 1), how can the authors attribute the optical measurements, both ensemble (Fig. 3) and single (Fig. 4), to a particular colloidal molecule configuration, as in the optical spectroscopy and time-resolved measurements they do not know what the actual crystalline structure of the emitter(s) they measure in these mixtures?\n3) What is the quantum yield of the produced materials? This is an important figure that impacts the interpretation of the time-resolved data and in the end all optical applications.\n4) Biexcitons:\na. The authors interpret the value of g(2)(t=0) as originating from the molecular nature of the colloids, but this is only true for single excitons. When biexcitons are included in the picture (which they are here in the measurement as no spectral filtering is possible at room temperature), the g(2)(t=0) value actually becomes a measure of the biexciton quantum yield, see https://doi.org/10.1021/nl104054t\nb. Why are the biexciton lifetimes so similar for the different species (monomer, dimer, trimer) (Fig. 4m) when long-lived, spatially separated biexcitons with reduced Auger quenching should be possible in the oligomers (Fig. 4o), as observed in CdSe dimers https://www.nature.com/articles/s41467-019-13349-1 ? The increase in biexciton quantum yield (see Fig. 4c,g and comment 4) ) would be in line with this.\nc. Additional decay measurements should be done as a function of excitation power. Then the particular power-dependencies would potentially allow the extraction of the Auger, trion and biexcitonic contributions in the decay.\n5) The first two sentences in the abstract as well as the first three introductory paragraphs and the concluding paragraph in the manuscript are overselling the work and confusing the readers by introducing doubtful connections to biology (“unresolved challenges in understanding the origins of life … prebiotic world”) and molecular chemistry (“expansion of the molecular library within the periodic table … molecular evolutionary chemistry … development of novel molecules”). The authors should not use undefined terms such as “proto-atom chemistry” or the like but stick consistently to the established term “colloidal molecules”.\n6) In Fig. 3 i-l, there is a consistent peak at ~410 nm. The authors should discuss where this comes from.", "reviewer_3": "This manuscript introduces a simple method to assemble ZnSe/ZnS nanocrystals into a colloidal suspension of predominantly dimers, trimers, or tetramers and reports the properties of these multimers using collective and single-particle spectroscopy. It also demonstrates that Mn-doped ZnSe/ZnS dimers can be used as x-ray scintillators. This work is certainly of interest to the colloidal quantum dot community, and achieving trimers and tetramers of fused nanocrystals without templating is a synthetic achievement. The characterization is thorough, but it does not show strong evidence of wavefunction hybridization between the nanocrystals as the introduction’s analogy to carbon chemistry suggests is the goal of the work. The manuscript also lacks theoretical calculations or discussion of the expected behavior of coupled core-shell nanocrystals with type-I band alignment. With revisions, this work may be suitable for the broad readership of Nature Communications, but it is likely more appropriate for a journal focused on nanoscience.\n1. The final paragraph of the introduction makes the claim that the experiments “elucidate the fundamental principles of artificial proto-atoms with specific bonding angles and lengths.” This claim would be better supported by providing statistics on the variation of bond lengths/distances and angles among the species obtained in each type of reaction (dimer, trimer, etc.).\n2. Given the heavy emphasis on the analogy with carbon chemistry, it would be helpful for the authors to discuss in one place the data that they believe indicate that their “artificial molecules” exhibit wavefunction hybridization (or as they put it, a “coherent electron delocalization analogy to hybridized atomic orbitals”): 1) The main evidence for hybridization is the redshift of the absorption and photoluminescence. The small size and y scale of Fig 3a-b make it difficult to see the absorption shift clearly. An absorption shift is the more critical evidence for hybridization than a PL shift because energy transfer to the largest nanocrystal in the assembly via exciton hopping or FRET (which don’t require hybridization) can yield the PL shift. Since the oleylamine used to generate the multimers can also lead to Ostwald ripening, would the authors please explain how they can rule out that the nanocrystal clusters are not actually hybridized and are just close enough together to facilitate FRET? 2) There are no theoretical calculations provided to support the idea that the atom-like orbitals of the ZnSe/ZnS nanocrystals are coupled strongly enough to create such hybridization. The authors do compare the redshift of their tetramer to that of the CdSe/CdS dimer in reference 28, but it makes more sense to compare their dimer to the CdSe/CdS dimer to determine if the redshift suggests coupling, as was demonstrated in reference 28 by comparing fused and unfused dimers (which could not be done here because of the synthetic method). Also, they do not specify whether their 71.3 meV value is the redshift of the absorption or the PL. For evaluating hybridization, an absorption redshift is more convincing because a PL redshift can have several other possible sources. Critical to this discussion is the thickness of the ZnS shell that forms a type-I alignment with the ZnSe core and will provide a barrier to wavefunction hybridization. The thickness of the ZnS shell should therefore be reported.\n3. The size of Fig 3b also makes it difficult to see the sub-bandgap defect emission around 580 nm. Also, there is a small peak in the tetramer around 380 nm – what is the source of this very blue emission?\n4. In the first paragraph of the Results section, “oleic acid” is referred to as a “typical hard base.” The authors likely meant that oleate, the conjugate base of oleic acid, is the hard base.\n5. The authors note that “ensemble PL lifetime measurements revealed a dramatic quenching of the lifetime” in Fig. 3d, but these curves appear to be on top of each other. The authors should provide lifetimes from fits to the curves to compare and should revise their description of this data. How do these ensemble lifetimes compare to the lifetimes measured in the single nanostructures? Please also include the excitation power density used for the lifetime measurements.\n6. There is a noticeable difference in the sharpness of the image produced using the Mn-doped ZnSe/ZnS monomers and the dimers embedded in PMMA as an x-ray scintillator (Fig. 5i). Can the authors comment on the source of this performance difference since both materials exhibit the same large Stokes shift that avoids reabsorption?\n7. It would be helpful to include the relative PL efficiency of the different structures – monomers, dimers, etc. either from single-particle spectroscopy or an ensemble measurement. Ideally this would be PL quantum yield in solution (as is presented in the SI for the Mn-doped ZnSe/ZnS), but relative PL at the same absorption would be acceptable."}, "author_response": "Response to the reviewers\nMajor Modifications at a glance:\n1. We provide a robust statistical analysis of synthesis outcomes (dimers, trimers,\ntetramers) to demonstrate reproducibility and reliability. In the repetition experiments, we\nperformed three independent syntheses for each target morphology following the detailed\nprotocols in the manuscript. With precisely controlled temperature, precursors, and ligands,\nthese repetitions yield high reproducibility as assessed by scanning transmission electron\nmicroscope (STEM) imaging. Additionally, we present histogram statistics of bonding lengths\nand angles among the monomer, dimer, trimer, and tetramer ZnSe@ZnS QD molecules,\nillustrating analogies to s, sp, sp2, and sp3 hybridization. Based on these histogram results, the\nsynthesized monomer, dimer, trimer, and tetramer ZnSe@ZnS QDs with well-defined bonding\nlengths and angles were successfully fabricated, displaying features analogous to carbon\nhybridization configurations. This supports the reproducibility and robustness of our synthetic\nprotocol (Reference#1).\n2. Clarify and substantiate conceptual novelty and impact, including clear evidence of\nadvantages in optical behavior and measured quantum yield: I, novelty statement, based on\nour knowledge, this work represents the first report of a one-pot synthesis of colloidal artificial\ncore-shell QD molecules (encompassing monomer, dimer, trimer, and tetramer) without the use\nof templating or an additional polymer-assisted self-assembly step into molecules with defined\nconfiguration, bonding lengths, and bond angles. II. Optical behavior, we provide corrected\nstatistics for biexciton lifetimes. In the revised manuscript, we discuss both localized biexcitons\n(LBX) and long-lived, spatially segregated biexcitons (SBXs) within the oligomeric structures,\nwith reduced Auger recombination. Additionally, excitation-power dependent decay\nmeasurements are presented to quantify the contributions from biexciton, trion, and Auger\nrecombination. III. Quantum yield and biexciton quantum yield, The revised manuscript\ndiscusses the photoluminescence quantum yield (PLQY) of ZnSe@ZnS QD molecules across\nthe monomer, dimer, trimer, and tetramer forms, as well as the relation to the g(2)(t=0)\nbiexciton quantum yield (Reference#2).\n3. Strengthen evidence for wavefunction hybridization with clearer spectroscopy data,\ntheoretical justification, and differentiation from FRET effects: The theoretical calculations\nfor the coupling and hybridization of ZnSe@ZnS QD molecules were presented in the revised\nmanuscript. We employed the well-established Schrödinger Poisson framework, including\nCoulomb interactions, and solved self-consistently to obtain the eigen-energies and eigen-states\nof the monomer, dimer, trimer, and tetramer. Our results indicate that the ground-state\nwavefunctions are predominantly confined within the core regions, while the excited-state\nwavefunctions extend and couple to neighboring QDs. This could result in observed red shifts\nin both absorption and PL, accompanied by lifetime quenching, reflecting the coupling effect\nand analogous to chemical bond-type hybridization seen in carbon-based systems\n(Reference#3).\nThe detailed responses to each concern are described as follows.\nReviewer: 1\nThe authors present a nice study of controllably assemble colloidal Zn-based nanoparticles to\n(monomers,) dimers, trimers and tetramers. The final structures resemble molecular bonding\nin terms of (s,) sp, sp2, and sp3 bonding. They discuss the corresponding mechanisms (beyond\nbasic characterization) by crystallographic considerations and faceting. Further they explore\nthe resulting optical properties and mechanisms in detail (time-resolved etc.). I think this study\ncan be published in Nature Communications since it is also well written.\nResponse: We sincerely appreciate the reviewer’s insightful and constructive feedback on\nour manuscript. The positive assessment of our work, particularly regarding its organization\nand innovation, is highly encouraging. Building on the fundamental atom-hybridization\nframework, we explore carbon-analogy concepts to construct new molecules and structures\nbased on “artificial QDs atom”. Therefore, achieving genuinely self-driven, self-organized\nassembly—unraveling the evolution of molecules from artificial atomic and molecular scales\nthat manifest specific symmetries and configurations, without relying on templating—\nremains a formidable challenge. We are grateful for the opportunity to address the\nsuggestions, which we believe will further strengthen the scientific rigor and clarity of our\nstudy. Below, we provide detailed, point-by-point responses to the comments.\nSpecific comments:\n1. I have only once request: The authors should add statistics of how many particles end up in\nthe desired configuration as dimers, trimers and tetramers; How reliable is they synthesis, does\nevery approach lead to the desired outcome of does the outcome determine purpose; how many\nsynthesis lead to the same predefined result?\nResponse: Thank you sincerely for your insightful comments and valuable suggestions. We\nconfirm that the precise histogram of the synthesized ZnSe@ZnS QD molecules’ configurations\nhas been added to the revised Supplementary Information. As depicted in Supplementary\nFigure 3 and Supplementary Table 2, the statistical distributions for the products\ncorresponding to monomer, dimer, trimer, and tetramer morphologies are 95.9%, 73.3%, 71.4%,\nand 76.7%, respectively. These results support that, based on our surface-engineered strategy,\nwe achieve ZnSe/ZnS QDs with distinct hybridization configurations corresponding to s, sp,\nsp2, and sp3 character, evidencing successful control over the synthesis and morphology.\nSupplementary Table 2. Statistics results for the different ZnSe@ZnS molecules configuration.\nRatio (%) monomer dimer trimer tetramer\nmonomer 95.9 18 3.5 0.5\ndimer 3.9 73.3 16.9 3.6\ntrimer 0.2 7.8 71.4 19.2\ntetramer 0 0.9 8.2 76.7\nSupplementary Figure 3. The statistics results for the monomer, dimer, trimer, and tetramer\nZnSe@ZnS molecules with s, sp, sp2, and sp3 hybridization configuration, respectively. Here\nthe total amount of QDs for the statistic was 80.\nFigure R1. Scanning transmission electron microscope (STEM) imaging of ZnSe@ZnS\nmonomer, dimer, trimer, and tetramer QDs, respectively. Here, the detailed synthesis date was\ndepicted for the three different time repetition experiment.\nRegarding the repetition experiment, which is of significant importance, we performed three\nindependent syntheses for each target morphology following the detailed protocols in the\nmanuscript. Under precisely controlled temperature, precursor, and ligand conditions, the\nmethod demonstrated high reproducibility (Figure R1). Detailed synthesis data and\nindependent STEM imaging results were highly consistent across all replicates, confirming the\nrobustness and repeatability of our synthesis protocol. Collectively, these findings establish the\nreliability of our approach for producing the target ZnSe@ZnS QD morphologies.\nChanges made: A detailed discussion of the statistical results for the specific configurations of\nZnSe@ZnS QD molecules has been provided in the revised Supplementary Information and\nSupplementary Table.\nReviewer: 2\nThe manuscript by Fan et al. presents a variation of colloidal molecules from ZnSe@ZnS\nnanocrystals. By slight modification of the synthesis that rebalances oriented attachment and\nOstwald ripening, monomers, dimers, trimers and oligomers are created and studied with\nvarious TEM and optical spectroscopy methods. Furthermore, colloidal molecules from Mn-\ndoped nanocrystals are investigated for their use as scintillator material. While the TEM\nstudies appear clear and sound, I have several concerns on the spectroscopy results and\ninterpretations, see further below. Despite the claims in the abstract and introduction, the\nassembly of nanocrystals into colloidal molecules is far from novel, as it has been established\nfor many nanocrystal material systems over the past decades, e.g. extensive works by the\nManna group, or particularly related, CdSe dimers by the Banin group\nhttps://doi.org/10.1021/acs.accounts.0c00691. Given the little actual change in the optical\nproperties that the evolution from monomer over dimer and trimer to tetramer brings about\n(Figs. 3, 4), it is questionable what benefits and tuning capabilities the presented colloidal\nmolecules offer. Moreover, it is well known that doping nanocrystals enhances their properties\nfor the use in scintillators through energy transfer and reduced reabsorption (see e.g.\nhttps://doi.org/10.1016/j.opelre.2019.01.001), but the current manuscript does not present\nsignificant advantages from using colloidal molecules for this application. In conclusion, I fail\nto recognize “significant impact on quantum optoelectronics, sensing and high-energy particle\ndetection” as the authors claim or a significant advance for the field that I would expect from\na publication in Nature Communications. Apart from my reservations on novelty and impact, I\nhave the following remarks.\nResponse: Thank you for the reviewer’s comments. We believe that our manuscript,\n“Evolution of self-organized colloidal artificial molecules” offers novel insights and is well\nsuited for publication in Nature Communications. In comparison with previous work that relied\non templating or an additional polymer-assisted self-assembly to form molecular structures, our\nstrategy provides three distinct advantages and advances:\nI, We employed a one-pot synthesis strategy with precisely controlled temperature, ligand\nconcentration, and reaction time, without using any template or polymer scaffolding, to produce\nmonomer, dimer, trimer, and tetramer ZnSe@ZnS QD molecules. Moreover, it’s true that the\nManna group has published extensive work on self-assembled nanostructures, particularly\nsingle-component tetrapod CdS systems, which exhibit high moisture and oxygen tolerance\n(e.g., Acc. Chem. Res. 2013, 46, 7, 1387-1396; Nat. Mater. 2011, 10, 872-876). In comparison,\nour ZnSe@ZnS core-shell QD molecules demonstrate robust assembly and functional\nproperties under comparatively stricter environmental conditions, highlighting a distinct route\ntoward core-shell QDs based “molecules” with controlled configurations.\nII, To date, achieving precise control over the fusion process to form well-defined core-shell\nunits from each component remains challenging. In particular, the precise, purely zinc-based\nQD synthesis is not yet as mature as that of cadmium-based systems. As for the progress for\nthe fusion of CdSe@CdS dimer molecules by Banin group (Nat. Commun., 2019, 10, 5401.\npioneering colloidal fusion CdSe@CdS dimer research). However, the synthesis step for the\nCdSe@CdS dimer relied on the silicon template with further HF etching and high temperature\nfusion process.\nIII, In our templating-free strategy, we achieve ZnSe@ZnS monomer, dimer, trimer, and\ntetramer molecule-like structures that exhibit carbon-atom based hybridization analogs (s, sp,\nsp2, and sp3) with well-defined bonding configurations, including specific bond angles, bond\nlengths, and hybridization.\nRegarding the optical properties of the ZnSe@ZnS molecule-like structures, the revised\nmanuscript presents corrected biexciton lifetimes, with discussion of both localized biexcitons\n(LBX) and long-lived, spatially segregated biexcitons (SBXs) in the oligomeric structures,\nindicating reduced Auger recombination. In addition, excitation-power dependent decay\nmeasurements are reported to quantify the contributions from biexciton, trion, and Auger\nrecombination. Meanwhile, the revised manuscript also discusses the photoluminescence\nquantum yield (PLQY) for ZnSe@ZnS QD molecules across the monomer, dimer, trimer, and\ntetramer forms, as well as the biexciton quantum yield associated with g(2)(t=0).\nTherefore, we believe the revised manuscript is well-suited for Nature Communications.\n1. As the variation from dimer, trimer and tetramer is achieved through a relatively small\nconcentration change of OLA , the samples clearly have a mixture of all different kinds of\nm\ncolloidal oligomers (Fig. 1, Fig. S3). It is not discussed what the yield distribution of\ndimers/trimers/tetramers is and how their respective purity changes with the synthesis\nconditions.\nResponse: Thank you sincerely for your insightful comments and valuable suggestions. We\nhave added the precise histogram results for the configurations of the synthesized ZnSe@ZnS\nQD molecules in the revised Supplementary Information. As shown in Supplementary Figure\n3 and Supplementary Table 2, the statistical distributions for the products corresponding to\nmonomer, dimer, trimer, and tetramer morphologies are 95.9%, 73.3%, 71.4%, and 76.7%,\nrespectively. These results demonstrate, based on our surface-engineered strategy, successful\nsynthesis of ZnSe/ZnS QDs exhibiting s, sp, sp2, and sp3 hybridization configurations.\nSupplementary Table 2 provides the statistics for the different ZnSe@ZnS configurations.\nSupplementary Figure 3. The statistics results for the monomer, dimer, trimer, and tetramer\nZnSe@ZnS molecules with s, sp, sp2, and sp3 hybridization configuration, respectively. Here\nthe total amount of QDs for the statistic was 80.\nSupplementary Table 2. Statistics results for the different ZnSe@ZnS molecules configuration.\nRatio (%) monomer dimer trimer tetramer\nmonomer 95.9 18 3.5 0.5\ndimer 3.9 73.3 16.9 3.6\ntrimer 0.2 7.8 71.4 19.2\ntetramer 0 0.9 8.2 76.7\nFigure R2. Synthetic scheme for proto colloidal artificial molecules including colloidal\nmonomer, dimer, trimer, and tetramer QDs. The type of ligands and concentration significantly\naffect the morphology of the QDs through precise modulation of the Ostwald ripening (OR),\noriented attachment (OA) and multistep Oriented attachment (M A) process.\nO\nAbout the mechanism and process for the purity changes with the synthesis conditions were\nrecognized as follow. Briefly, oleate and oleylamine (OLAm), typical hard bases, coordiante\nstrongly with zinc ions (borderline Lewis acids) and effectively passivate the ZnSe/ZnS surface,\npromoting monodispersed QDs (Figure R2). Oleylamine acts as an amine-based anchor,\nwhereas oleic acid (OLA) is associated with a long-chain alkyl tail linked to the QD surface via\ncarboxylate groups; the carboxylate remains more stable than the amine, even in monodentate\nform. When the solvent is exchanged from OLA/OAm to pure OAm, passivation becomes\ninsufficient, favoring oriented-attachment processes and the formation of ZnSe/ZnS dimers.\nIntroducing excess pure OAm increases the viscosity of the reaction medium, which reduces\nthe diffusion rate of building blocks. This facilitates multistep oriented attachment (MOA),\nOstwald ripening, and the formation of trimers and tetramers of ZnSe/ZnS. Consequently,\ndecreasing OLA concentration and increasing OLAm content promotes self-organized, self-\ndriven assembly through MOA, leading to predominant tetramer formation (Supplementary\nFigure.2-5).\nChanges made: A detailed discussion about the proposed mechanism for the formation of\nZnSe/ZnS QDs molecules in the revised manuscript.\nPrototypical evolution of proto colloidal artificial-molecules was derived from colloidal\nZnSe/ZnS core/shell QDs via precise modulation of the OR, OA, and M A process (Figure 1a\nO\nand Supplementary Figure.1). “Briefly, oleate and oleylamine (OLAm), as typical hard bases,\nexhibit strong coordination with zinc ions (borderline Lewis acids), resulting in effective\npassivation of the ZnSe/ZnS surface and the formation of monodisperse QDs. Meanwhile,\noleylamine acts as an amine-based anchor, whereas oleic acid (OLA) predominantly appears as\na monodentate carboxylate that links the long-chain alkyl tail to the QD surface, with the\ncarboxylate remaining more stable than the amine even in the monodentate form. Thus, when\nthe solvent is exchanged from OLA/OAm to pure OAm, the passivation effect becomes\ninsufficient, resulting in enhanced oriented attachment and the formation of ZnSe/ZnS dimers.\nWhen excess pure OAm is introduced into the system, the viscosity of the reaction medium\nincreases significantly, reducing the diffusion rate of the building blocks and promoting a\nmultistep oriented attachment (MOA) process, accompanied by Ostwald ripening and the\nformation of timer and tetramer ZnSe/ZnS molecules (Supplementary Figure.2-5). Therefore,\nas the OLA concentration decreases and the OLAm amount increases, the self-organized, self-\ndriven structure formed via multistep oriented attachment leads to the predominant formation\nof tetramer ZnSe/ZnS QDs.”\nA detailed statistic results with specific configuration ZnSe@ZnS molecules was provided in\nthe revised supplementary information and supplementary table. And also the related discussion\nfor the synthesis of ZnSe@ZnS molecules was added in the revised manuscript.\n2. In view of 1), how can the authors attribute the optical measurements, both ensemble (Fig.\n3) and single (Fig. 4), to a particular colloidal molecule configuration, as in the optical\nspectroscopy and time-resolved measurements they do not know what the actual crystalline\nstructure of the emitter(s) they measure in these mixtures?\nResponse: Thank you for the reviewer’s comments. As noted above for ZnSe@ZnS QD\nmolecules, our precisely controlled synthesis strategy enables purity yields of 95.9%, 73.3%,\n71.4%, and 76.7% for the monomer, dimer, trimer, and tetramer samples of ZnSe@ZnS QD\nmolecules, respectively. Thus, we believe that ensemble optical absorption,\nphotoluminescence (PL), and time-resolved fluorescence decay measurements are mainly governed by the specific\nconfiguration.\nFor single-particle measurements, we determine the presence of monomers, dimers, and trimers\nby examining the g(2)(0) values of the second-order photon correlation function g(2)(τ),\nas\ndepicted in Figure 4 of the revised manuscript main text. The g(2)(0) values differ among\nmonomers, dimers, and trimers due to the formation of a new type of biexciton, termed a\nsegregated biexciton, observed in dimers and trimers (Nat. Commun. 2019, 10, 5401; ACS\nNano, 2023, 17, 14990-15000). In our single-particle studies, we measured many individual\nparticles within each sample. The statistical distributions of g(2)(0) are shown in Figure R3.\nThe histograms indicate that g(2)(0) values cluster around approximately 0.37 for monomers,\n0.58 for dimers, and 0.65 for trimers. These distributions resemble the corresponding STEM\nresults summarized in Supplementary Table 2. The monomer distribution is narrow due to the\nhigh purity of the monomer samples, whereas the dimer distribution is broader due to slightly\nlower dimer purity. The trimer g(2)(0) values are higher than those of dimers, consistent with a\nhigher probability of segregated biexciton formation, and the trimer distribution is also broader,\nin agreement with the configuration yield shown in Supplementary Table 2.\nFigure R3. Statistical results of g(2)(0) values of (g(2)(τ)) curves of ZnSe@ZnS monomer (a),\ndimer (b), and trimer (c) molecules. The g(2)(0) values for the three samples are primarily\ndistributed around 0.37, 0.58, and 0.65, respectively.\nChanges made: A detailed discussion about the single particles measurement was added in the\nrevised Figure 4.\n“The second-order photon correlation, (g(2)(τ)), curves are shown in Figure 4g-i and reveal the\nstatistics of photons from single ZnSe@ZnS artificial molecules. Under low excitation, the\nbiexciton QY was approximately equal to g(2)(0). The g(2)(0) statistics for monomers, dimers,\nand trimers are in Figure 4j-l, with values clustering around 0.37, 0.58, and 0.65, respectively.\nSpecifically, monomers show a narrow distribution due to high purity; dimers are broader,\nreflecting slightly lower purity, and trimers are also broad, consistent with STEM yields\n(Supplementary Table 2).”\nFigure 4. Single particle measurements of colloidal artificial molecules. Time-tagged, time-\nresolved data for a single ZnSe@ZnS monomer, dimer, and trimer, including PL intensity\ntrajectories (a-c), PL decay curves (d-f), second-order photon correlation (𝑔(2)(𝜏)) curves (g-\ni), and statistical results of 𝑔(2)(0) values of (𝑔(2)(𝜏)) curves (j-l), respectively. (m) A\ntypical biexciton PL decay curve for a relatively strongly coupled dimer. A localized biexciton\n(LBX) lifetime value of 2.29 ns was obtained using a single exponential function fit. (n) A\ntypical biexciton PL decay curve for a relatively weakly coupled dimer. The LBX and\nsegregated biexciton (SBX) lifetime values obtained by fitting a double exponential function\nare 2.33 ns and 14.87 ns, respectively. (p) Schematic of LBX and SBX. (o) The on states in the\nPL trajectories correspond to single exciton emissions, while the grey states are caused by\nAuger blinking or band-edge carriers (BC) blinking.\n3. What is the quantum yield of the produced materials? This is an important figure that impacts\nthe interpretation of the time-resolved data and in the end all optical applications.\nResponse: Thank you for the suggestion. We measured PLQY for ZnSe@ZnS and\nZnSe:Mn@ZnS QDs molecules using a relative method. Results are shown in Figure 3b\n(revised manuscript) and Supplementary Table 2 (revised supplementary information).\nZnSe@ZnS PLQYs are 7.1%, 6.9%, 3.8%, and 0.6% for the monomer, dimer, trimer, and\ntetramer, respectively; ZnSe:Mn@ZnS PLQYs are 41.3%, 34.0%, 22.4%, and 0.1%,\nrespectively.\nFigure 3. Optical study of colloidal artificial-molecules. Absorption (a), emission spectra (b),\nstandard CIE pattern-1976 (c), and ensemble photoluminescence (PL) lifetime decay (d) of\nZnSe@ZnS monomer, dimer, trimer, and tetramer QDs. (e) the potential and the wave functions\nof the hole and electron of the dimer, (f) the electron clouds and hole clouds together with the\ncorresponding energy levels for the monomer, dimer, trimer, and tetramer (from left to right),\n(g) the red shift of the dimer, trimer, and tetramer relative to the monomer. The red line\ncorresponds to the experimental results, and the black line corresponds to the theoretical\ncalculation. The 2D transient absorption (TA) spectroscopy and corresponding TA spectroscopy\nwith different probe delay times under 365 nm excitation of ZnSe@ZnS monomer (h, l), dimer\n(i, m), trimer (j, n), and tetramer (k, o) QDs, respectively.\nChanges made: The PLQY for each ZnSe@ZnS and ZnSe:Mn@ZnS molecules was provided\nin the revised manuscript and Supplementary part.\nSupplementary Table 2. PLQY of the ZnSe@ZnS and ZnSe:Mn@ZnS molecules.\nPLQY(%) monomer dimer trimer tetramer\nZnSe@ZnS 7.1 6.9 3.8 0.6\nZnSe:Mn@ZnS 41.3 34.0 22.4 0.1\n4. Biexcitons:\na. The authors interpret the value of g(2)(t=0) as originating from the molecular nature of the\ncolloids, but this is only true for single excitons. When biexcitons are included in the picture\n(which they are here in the measurement as no spectral filtering is possible at room temperature),\nthe g(2)(t=0) value actually becomes a measure of the biexciton quantum yield,\nsee https://doi.org/10.1021/nl104054t.\nResponse: Thank you very much for your suggestions. Regarding colloidal artificial\nZnSe@ZnS molecules, the previous interpretation of g(2)(0) values was inappropriate.\nConsequently, we have removed the description linking g(2)(0) to n (the total number of photons\nemitted after a single excitation pulse) from the original manuscript. While the referenced paper\nprovides valuable insight for measuring biexciton quantum yields in single QDs, in the revised\nversion we use g(2)(0) to determine the biexciton quantum yields (QYs) of the monomer, dimer,\nand trimer molecules. The larger g(2)(0) values observed for dimers and trimers reflect the\nformation of segregated biexcitons in these structures.\nChanges made: The correction description for the g(2)(0) values in the revised manuscript.\nThe second-order photon correlation, (g(2)(τ)), curves are shown in Figure 4g-i and reveal the\nstatistics of photons from single ZnSe@ZnS artificial molecules. Under low excitation, the\nbiexciton QY was approximately equal to g(2)(0). The g(2)(0) statistics for monomers, dimers,\nand trimers are in Figure 4j-l, with values clustering around 0.37, 0.58, and 0.65, respectively.\nSpecifically, monomers show a narrow distribution due to high purity; dimers are broader,\nreflecting slightly lower purity, and trimers are also broad, consistent with STEM yields\n(Supplementary Table 2). Dimers and trimers have higher g(2)(0) than monomers due to\nsegregated biexcitons (SBX), which are long-lived, spatially separated biexcitons with reduced\nAuger quenching. Biexciton PL decay was further analyzed from the first photon in two-photon\nevents. Dimer decays fall into two types: (i) rapid decay fitted by a single exponential, from\nstrongly coupled dimers where both excitons reside in one core (localized biexciton, LBX;\nFigure 4m and left panel of Figure 4o), and (ii) a double-exponential decay with a fast LBX\nand slow SBX component (Figure 4n). In strongly coupled dimers, SBX converts quickly to\nLBX; in weakly coupled dimers, SBX and LBX emissions coexist due to slower SBX to LBX\nconversion. Supplementary Figure 19 shows SBX lifetimes are broadly distributed due to\ncoupling heterogeneity. Supplementary Figure 20 reports LBX lifetimes of 1.7 ns (monomer),\n2.3 ns (dimer), and 2.7 ns (trimer), with longer LBX lifetimes in dimers/trimers arising from\nenhanced exciton delocalization that suppresses Auger recombination.”\nb. Why are the biexciton lifetimes so similar for the different species (monomer, dimer, trimer)\n(Fig. 4m) when long-lived, spatially separated biexcitons with reduced Auger quenching should\nbe possible in the oligomers (Fig. 4o), as observed in CdSe dimers\nhttps://www.nature.com/articles/s41467-019-13349-1? The increase in biexciton quantum\nyield (see Fig. 4c,g and comment 4) ) would be in line with this.\nResponse: Thank you very much for your comments. In the previous version, only the localized\nbiexciton (LBX) lifetimes for the different species (monomer, dimer, and trimer) were reported.\nThe average LBX lifetimes are 1.7 ns (monomer), 2.3 ns (dimer), and 2.7 ns (trimer), as shown\nin Supplementary Figure 20. The progressively longer LBX lifetimes observed for dimers and\ntrimers reflect enhanced exciton delocalization in these larger oligomeric structures. The\ndetailed discussion has been added in the revised manuscript as follows:\nSupplementary Figure 20. Statistical results of LBX lifetimes for single monomers, dimers,\nand trimers. The respective average LBX lifetimes are 1.7 ns, 2.3 ns, and 2.7 ns. The increased\nLBX lifetimes observed in dimers and trimers are due to enhanced exciton delocalization within\nlarger multimeric structures, which suppresses nonradiative Auger recombination.\nIn the revised version, we added a discussion of segregated biexcitons (SBXs)—long-lived,\nspatially separated biexcitons with reduced Auger recombination in dimers and trimers. First-\nphoton analysis was used to obtain the biexciton photoluminescence (PL) decay curve by\nextracting the first photons from two-photon events identified in photon statistics (ACS Nano\n2014, 8, 7288-7296; J. Phys. Chem. Lett. 2018, 9, 6934-6940). The dimer biexciton decay\ncurves reveal two distinct types. One type exhibits rapid decay that can be fitted with a single-\nexponential function (Figure 4m and Figure R4), resembling the monomer biexciton decay\nand arising from LBXs generated by strongly coupled dimers. The other type yields a double-\nexponential decay (Figure 4n and Figure R4), comprising a fast and a slow component—the\nfast component corresponds to LBXs and the slow component to SBXs (ACS Nano 2023, 17,\n14990-15000). The lifetime distributions for LBXs and SBXs are summarized in\nSupplementary Figure 19, with SBX lifetimes showing a broad distribution due to\nheterogeneity in the coupling between the two emitting centers within the dimers.\nFigure R4. A typical biexciton PL decay curve for a relatively strongly coupled dimer. A\nlocalized biexciton (LBX) lifetime value of 2.29 ns was obtained by fitting a single exponential\nfunction. This is a typical biexciton PL decay curve for a relatively weakly coupled dimer. The\nLBX and segregated biexciton (SBX) lifetime values obtained by fitting a double exponential\nfunction are 2.33 ns and 14.87 ns, respectively. The on states in the PL trajectories correspond\nto single exciton emissions. The grey states are due to non-radiative Auger recombination and\nnon-radiative recombination of band-edge carriers (BC). PL blinking of single dimer, and trimer\nmolecules involves both Auger and BC blinking. Schematic of LBX and SBX.\nSupplementary Figure 19. Statistical results of lifetime values for localized biexcitons (LBXs)\nand segregated biexcitons (SBXs) in the ZnSe@ZnS dimer molecules.\nChanges made: The revised version includes revised Figure 4. The statistical results of the\nlifetime values for LBXs and SBXs are included in the revised manuscript and supplementary\ninformation.\n“Dimers and trimers have higher g(2)(0) than monomers due to segregated biexcitons (SBX),\nwhich are long-lived, spatially separated biexcitons with reduced Auger quenching. Biexciton\nPL decay was further analyzed from the first photon in two-photon events. Dimer decays fall\ninto two types: (i) rapid decay fitted by a single exponential, from strongly coupled dimers\nwhere both excitons reside in one core (localized biexciton, LBX; Figure 4m and left panel of\nFigure 4o), and (ii) a double-exponential decay with a fast LBX and slow SBX component\n(Figure 4n). In strongly coupled dimers, SBX converts quickly to LBX; in weakly coupled\ndimers, SBX and LBX emissions coexist due to slower SBX to LBX conversion.\nSupplementary Figure 19 shows SBX lifetimes are broadly distributed due to coupling\nheterogeneity. Supplementary Figure 20 reports LBX lifetimes of 1.7 ns (monomer), 2.3 ns\n(dimer), and 2.7 ns (trimer), with longer LBX lifetimes in dimers/trimers arising from enhanced\nexciton delocalization that suppresses Auger recombination.”\nc. Additional decay measurements should be done as a function of excitation power. Then the\nparticular power-dependencies would potentially allow the extraction of the Auger, trion and\nbiexcitonic contributions in the decay.\nResponse: Thank you very much for your suggestions. Excitation-power dependent decay\nmeasurements can quantify biexciton and Auger recombination by comparing PL decay curves\nobtained at high and low excitation powers (Nano Lett. 2016, 16, 2349-2362). In the revised\nmanuscript, we present the excitation-power dependent PL data for single monomers, dimers,\nand trimers (Supplementary Figure 21). We provide a detailed discussion of the contributions\nfrom Auger recombination, trion formation, and biexciton dynamics, organized into three\naspects:\nSupplementary Figure 21. (a-c) Excitation power-dependent decay curves for single\nmonomers, dimers and trimers. 〈N〉 represents the excitation condition and is defined as the\naverage number of photons absorbed per QD per pulse. The 〈N〉 value increases from top to\nbottom for the three PL decay curves. These decay curves were normalized to match the late-\ntime tails. (d-f) PL decay curves obtained by subtracting the PL decay at low excitation from\nthe PL decays at higher excitations. Fits to a single-exponential function yield biexciton\nlifetimes of 2.03 ns, 2.24 ns and 2.33 ns for monomers, dimers and trimers, respectively.\n(I) Biexciton contribution: To eliminate the influence of charged states on biexciton lifetime\nmeasurements, PL decay curves were extracted from the bright state of PL intensity trajectories\nof single monomer, dimer and trimer molecules, as shown in Supplementary Figure 21a-c.\nThese decay curves were first normalized to match the late-time tails. The late-time tails\ncorrespond to single-exciton recombination. Multiexcitons contributions can be isolated by\nsubtracting the PL decay at low excitation from the PL decays at higher excitations\n(Supplementary Figure 21d-f). The resulting PL decay curves can be fitted with a single-\nexponential function, yielding values of 2.03 ns and 2.24 ns for monomers and dimers,\nrespectively (Supplementary Figure 21d-e). These values are similar to the localized\nbiexciton lifetimes (τ ) obtained by first-photon analysis in Supplementary Figure 20.\nxx\nTherefore, these values correspond to localized biexciton lifetime. For trimer molecules, the PL\ndecay curves exhibit a double-exponential form (Supplementary Figure 21f). The long-lived\ncomponent can be fitted with a single-exponential function, yielding a value of 2.33 ns, which\nalso corresponds to the localized biexciton lifetime. The short-lived component may correspond\nto complex, higher-order excitons, which are not discussed here.\n(II) Auger recombination contribution: Biexciton Auger lifetime (τ ) can be calculated\nA,xx\nbased on the following formula:\n1/τ = 1/τ - 1/τ .\nA,xx xx r,xx\nWhere biexciton radiative lifetime (τ ) can be estimated using the single-exciton radiative\nr,xx\nlifetime (τ ), that is, τ = τ /4 (Annu. Rev. Condens. Matter Phys., 2014, 5, 285-316.). τ is\nr,x r,xx r,x r,x\nequal to the single exciton lifetime (τ ) because single excitons at bright states do not undergo\nx\nnonradiative recombination. The average τ is 25.3 ns, 26.4 ns and 26.9 ns for monomers,\nx\ndimers and trimers, respectively (Supplementary Figure 18). Based on the biexciton lifetimes\n(τ ) of 2.03 ns, 2.24 ns and 2.33 ns obtained above (Supplementary Figure 20), the biexciton\nr,xx\nAuger lifetime (τ ) can be calculated using the formula: 1/τ = 1/τ - 1/τ = 1/τ - 4/τ =\nA,xx A,xx xx r,xx xx r,x\n1/τ - 4/τ , which yields 2.99 ns, 3.39 ns and 3.57 ns for monomers, dimers and trimers,\nxx x\nrespectively. The corresponding non-radiative Auger recombination rates (k = 1/τ ) are\nA,XX A,xx\n0.33 × 109, 0.29 × 109 and 0.28 × 109, respectively. Consequently, the dimer and trimer\nmolecules exhibit smaller Auger recombination rates due to their larger volume.\nSupplementary Figure 18. Statistical results of LBX lifetimes for single monomers, dimers,\nand trimers. The respective average LBX lifetimes are 1.7 ns, 2.3 ns, and 2.7 ns. The increased\nLBX lifetimes observed in dimers and trimers are due to enhanced exciton delocalization within\nlarger multimeric structures, which suppresses nonradiative Auger recombination.\n(III) Trion contribution: The lifetimes of trions (charged excitons) can be obtained by\nextracting the decay curves of the charged states from the intensity trajectories of PL\nmeasurements (Appl. Phys. Lett., 2025, 127, 052104.), or by comparing PL decays collected\nfrom stirred and unstirred samples in solution (Annu. Rev. Condens. Matter Phys., 2014, 5, 285-\n316.). However, trion lifetimes may be similar to those of the segregated biexciton, which\nmakes them difficult to distinguish. A new type of trion, the segregated trion, may form in\ndimer molecules (Supplementary Figure 22), further complicating this research. The situation\nin trimer molecules is even more complicated. Given these complexities, we will investigate\ntrions systematically in our subsequent work.\nSupplementary Figure 22. Schematic of a localized trion and a segregated trion. The\nsegregated trion is a new type of trion in which an excess carrier occupies the second emission\ncenter of the dimer.\nChanges made: The detailed discussion about the excitation power-dependent decay curves\nfor single monomers, dimers and trimers was added to the revised manuscript and\nsupplementary information.\n“Supplementary Figure 21 shows the power-dependent PL decay for single monomer, dimer,\nand trimer molecules. As laser power increases, the decay becomes faster, indicating a larger\nfraction of biexcitons at higher excitation. Power-dependent decay measurements thus quantify\nboth biexciton lifetimes and Auger recombination, by subtracting high- and low-power decays.\nThe extracted biexciton lifetimes are 2.03 ns (monomer), 2.24 ns (dimer), and 2.33 ns (trimer)\n(Supplementary Figure 21d-f), consistent with the LBX lifetimes from the first-photon\nanalysis in Supplementary Figure 20. And an excess carrier may occupy the second emission\ncenter in the dimer, forming a potential trion (Supplementary Figure 22).”\n5. The first two sentences in the abstract as well as the first three introductory paragraphs and\nthe concluding paragraph in the manuscript are overselling the work and confusing the readers\nby introducing doubtful connections to biology (“unresolved challenges in understanding the\norigins of life … prebiotic world”) and molecular chemistry (“expansion of the molecular\nlibrary within the periodic table … molecular evolutionary chemistry development of novel\nmolecules”). The authors should not use undefined terms such as “proto-atom chemistry” or\nthe like but stick consistently to the established term “colloidal molecules”.\nResponse Thank you very much for your suggestions. The “overselling” description in the\nabstract and introduction part was rewriting and removed in the revised manuscript.\nChanges made: The reorganized for the abstract and introduction part and depicted in the\nrevised manuscript.\n(1) “Unraveling how such complex, stable architectures emerged from basic chemical\ninteractions remains challenges.”\n(2) “On the top of it, the quest to understand hybridization and atomic interactions has driven\ngroundbreaking advances in chemistry, dynamic systems, and emergence.”\n(3) “This concept allows for the creation of diverse molecular structures and facilitate the\ndevelopment of novel molecules that, will significantly impact quantum optoelectronics,\nsensing, and high-energy particle detection.”\n(4) The tittle was corrected as “Evolution of self-organized colloidal artificial molecules”\n6. In Fig. 3 i-l, there is a consistent peak at ~410 nm. The authors should discuss where this\ncomes from.\nResponse: Thank you sincerely for your insightful comments and valuable suggestions on our\nmanuscript. To confirm the origin of the 410 nm peak observed in the transient absorption (TA)\nspectra, we performed a control TA measurement using pure cyclohexane as the solvent (Figure\nR5 and Figure R6). The signal at 410 nm appeared in the same early-time region (within the\nfirst ~0.2 ps) in the control measurement, indicating a solvent-related artifact rather than a\nsample-specific transient. Consequently, the 410 nm peak is attributed to solvent-related\ninterference with the excitation laser in the TA setup.\nFigure R5. The 2D transient absorption (TA) spectroscopy and corresponding TA spectroscopy\nwith different probe delay times under 365 nm excitation of hexane solvent.\nFigure R6. The 2D transient absorption (TA) spectroscopy and corresponding TA spectroscopy\nwith different probe delay times under 365 nm excitation of ZnSe@ZnS monomer, dimer,\ntrimer, and tetramer QDs, respectively.\nChanges made: The corrected TA spectrum was depicted in the revised manuscript.\nReviewer: 3\nThis manuscript introduces a simple method to assemble ZnSe/ZnS nanocrystals into a colloidal\nsuspension of predominantly dimers, trimers, or tetramers and reports the properties of these\nmultimers using collective and single-particle spectroscopy. It also demonstrates that Mn-\ndoped ZnSe/ZnS dimers can be used as x-ray scintillators. This work is certainly of interest to\nthe colloidal quantum dot community, and achieving trimers and tetramers of fused\nnanocrystals without templating is a synthetic achievement. The characterization is thorough,\nbut it does not show strong evidence of wavefunction hybridization between the nanocrystals\nas the introduction’s analogy to carbon chemistry suggests is the goal of the work. The\nmanuscript also lacks theoretical calculations or discussion of the expected behavior of coupled\ncore-shell nanocrystals with type-I band alignment. With revisions, this work may be suitable\nfor the broad readership of Nature Communications, but it is likely more appropriate for a\njournal focused on nanoscience.\nResponse: We acknowledge the reviewers' encouraging assessment of our manuscript and its\ninnovative contributions. We report a universal, template-free strategy for synthesizing\nquantum dot monomers, dimers, trimers, and tetramers. In response to the reviewers’ guidance,\nwe have incorporated theoretical simulations. The combined experimental and theoretical\nanalysis confirms the quantum-mechanical coupling properties of the assembled colloidal\nquantum dot molecules. This methodology can be broadly applied to construct polymeric\nlibraries of diverse semiconductor core-shell nanocrystals, with details provided in the\nfollowing sections.. Therefore, we believe the revised manuscript is well-suited for Nature\nCommunications.\n1. The final paragraph of the introduction makes the claim that the experiments “elucidate the\nfundamental principles of artificial proto-atoms with specific bonding angles and lengths.”\nThis claim would be better supported by providing statistics on the variation of bond\nlengths/distances and angles among the species obtained in each type of reaction (dimer, trimer,\netc.).\nResponse: Thank you for your suggestion. The precise histogram analyses of bonding lengths\nand angles among the ZnSe@ZnS QD monomers, dimers, trimers, and tetramers reveal\nanalogies to the carbon hybridization states (s, sp, sp2, and sp3). Supplementary Figure 4\npresents the bonding lengths for the dimer, trimer, and tetramer ZnSe@ZnS QD molecules as\n5.2 ± 1.1 nm, 4.9 ± 0.6 nm, and 6.3 ± 1.5 nm, respectively. Supplementary Figure 5 shows\nthe corresponding bond-angle statistics, with the observed percentages of sp (180o), sp2 (120o),\nand sp3 (109.5o) hybridization configurations being 91.7%, 77.3%, and 90.3% for the dimer,\ntrimer, and tetramer, respectively. Collectively, these histogram results indicate that the\nsynthesized monomer, dimer, trimer, and tetramer ZnSe@ZnS QD molecules exhibit bonding\nlengths and angles characteristic of configurations analogous to s, sp, sp2, and sp3 hybridization,\nconfirming successful fabrication of structurally distinct oligomeric species.\nSupplementary Figure 4. The statistics results for the bond length of monomer, dimer, trimer,\nand tetramer ZnSe@ZnS QDs molecules. Here the total amount of QDs for the statistic was 80.\nSupplementary Figure 5. The statistics results for the bond angle of monomer, dimer, trimer,\nand tetramer ZnSe@ZnS QDs molecules. Here the total amount of QDs for the statistic was 80.\nChanges made: The statistics results for the bond angle and length were added in the revised\nmanuscript and Supplementary information.\n2. Given the heavy emphasis on the analogy with carbon chemistry, it would be helpful for the\nauthors to discuss in one place the data that they believe indicate that their “artificial molecules”\nexhibit wavefunction hybridization (or as they put it, a “coherent electron delocalization\nanalogy to hybridized atomic orbitals”\nResponse: We sincerely thank the reviewers for their insightful comments. In the revised\nmanuscript, we include a detailed theoretical study of the wave function hybridization in our\n“artificial molecules.” We also add a comprehensive discussion of how coherent electron\ndelocalization induces a red shift and the related correlation with the hybridization mechanism.\n1): The main evidence for hybridization is the redshift of the absorption and photoluminescence.\nThe small size and y scale of Fig 3a-b make it difficult to see the absorption shift clearly. An\nabsorption shift is the more critical evidence for hybridization than a PL shift because energy\ntransfer to the largest nanocrystal in the assembly via exciton hopping or FRET (which don’t\nrequire hybridization) can yield the PL shift. Since the oleylamine used to generate the\nmultimers can also lead to Ostwald ripening, would the authors please explain how they can\nrule out that the nanocrystal clusters are not actually hybridized and are just close enough\ntogether to facilitate FRET?\nResponse: Thank you for the valuable suggestion. Compared with the fluorescence spectrum,\nthe absorption-spectrum redshift provides more robust evidence for hybridization. In the\nrevised manuscript, we provide high-magnification imaging alongside band-gap absorption\nmeasurements. As shown in the expanded view of Figure R7, the exciton absorption peak shifts\ngradually from the monomer to the tetramer, with redshifts of 14.6 meV (dimer), 57.4 meV\n(trimer), and 92.1 meV (tetramer) relative to the monomer. This experimental trend is in good\nagreement with the theoretically calculated values (Figure R8 and Figure R9). Taken together,\nthese results support hybridization of the QD molecules rather than mere physical aggregation.\nFigure R7. The absorption of monomer, dimer, trimer, and tetramer ZnSe@ZnS QDs molecules.\nFigure R8. The simulated theoretical and experimental red-shift of monomer, dimer, trimer,\nand tetramer ZnSe@ZnS QDs molecules.\nFigure R9. The possible coupling mechanisms for the red-shift and shortening of lifetime in\nZnSe@ZnS QDs molecules.\nChanges made: The discussion and experimental test for the red-shift of absorption and\nemission were added in the revised manuscript and Supplementary information.\nThe Schrödinger-Poisson equations are used to obtain the eigen-energies and eigen-states of\nthe quantum dot molecules under a self-consistent condition. The procedure can be summarized\nas follows: first, we solve the time-independent Schrödinger equation without the Coulomb\ninteraction between the electron and hole, namely:\nℏ2 1\n(− 𝛻( 𝛻)+𝑉(𝑟))𝜓 (𝑟)= 𝐸 𝜓 (𝑟),\n2 𝑚∗(𝑟) 𝑐 𝑒 𝑒 𝑒\n𝑒\nℏ2 1\n(− 𝛻( 𝛻)+𝑉(𝑟))𝜓 (𝑟)= 𝐸 𝜓 (𝑟),\n2 𝑚∗(𝑟) 𝑣 ℎ ℎ ℎ\nℎ\nSecondly, we solve the Poisson equations, employing the wave functions of the electron and\nhole:\n𝛻(𝜖 ⋅𝜖(𝑟)𝛻𝜙 (𝑟))= −𝑞〈𝜓 (𝑟)|𝜓 (𝑟)〉,\n0 𝑒 𝑒 𝑒\n𝛻(𝜖 ⋅𝜖(𝑟)𝛻𝜙 (𝑟))= 𝑞〈𝜓 (𝑟)|𝜓 (𝑟)〉.\n0 ℎ ℎ ℎ\nThirdly, we calculate the self-polarization as\n𝜙 𝑠𝑝 = 𝜙 −𝜙𝐻,\n𝑘 𝑘 𝑘\nwhere 𝑘 = 𝑒,ℎ for electron and hole. 𝜙𝐻 is homogenous potential, which can be obtained as\n𝑘\n∇(ϵ ⋅ϵ ∇𝜙𝐻(r))= ∓𝑞〈𝜓 (𝑟)|𝜓 (𝑟)〉.\nFinally, we solve the Schrodinger equations, until the eigen-energies converge\nℏ2 1\n(− 𝛻( 𝛻)+𝑉(𝑟)+𝑞(𝜙 +𝜙 𝑠𝑝 ))𝜓′ = 𝐸′𝜓′,\n2 𝑚∗(𝑟) 𝑐 ℎ 𝑒 𝑒 𝑒 𝑒\n𝑒\nℏ2 1\n(− 𝛻( 𝛻)−𝑉(𝑟)−𝑞(𝜙 +𝜙 𝑠𝑝 ))𝜓′ =𝐸′𝜓′.\n2 𝑚∗(𝑟) 𝑣 𝑒 ℎ ℎ ℎ ℎ\nℎ\nThe spectrum shift can be obtained as\n𝛥𝐸 = (𝐸 −𝐸 )𝑚𝑜𝑛𝑜𝑚𝑒𝑟−(𝐸 −𝐸 )𝑚𝑢𝑙𝑡𝑖𝑚𝑒𝑟\n𝑒 ℎ 𝑒 ℎ\nSupplementary Table 1. The parameters in the calculation\nZnSe ZnS Environment Units\n𝑽 0 0.35 5 eV\n𝒄\n𝑽 0 -0.68 -5 eV\n𝒗\n𝒎∗ 0.21 0.16 1 ϵ\n𝒆 0\n𝒎∗ 0.6 0.75 1 ϵ\n𝒉 0\n𝝐 8.6 8.73 1 𝑚\n⊥ 0\n𝛜 8.31 1 𝑚\n∥ 0\n“The calculation results show that the electron and hole ground states in the monomer, dimer,\ntrimer, and tetramer are confined to the core (Figure 3e, calculation Section, and\nSupplementary Table 1). The first excited state of the electron is confined to both the core and\nthe shell. The red shift of the dimer, trimer, and tetramer relative to the monomer can be\nattributed to the coupling of the wave functions in the different quantum dots, analogous to the\nsymmetry and antisymmetry of wave functions in conventional molecules (Figure 3f-g).”\n2): There are no theoretical calculations provided to support the idea that the atom-like orbitals\nof the ZnSe/ZnS nanocrystals are coupled strongly enough to create such hybridization. The\nauthors do compare the redshift of their tetramer to that of the CdSe/CdS dimer in reference\n28, but it makes more sense to compare their dimer to the CdSe/CdS dimer to determine if the\nredshift suggests coupling, as was demonstrated in reference 28 by comparing fused and\nunfused dimers (which could not be done here because of the synthetic method). Also, they do\nnot specify whether their 71.3 meV value is the redshift of the absorption or the PL. For\nevaluating hybridization, an absorption redshift is more convincing because a PL redshift can\nhave several other possible sources. Critical to this discussion is the thickness of the ZnS shell\nthat forms a type-I alignment with the ZnSe core and will provide a barrier to wavefunction\nhybridization. The thickness of the ZnS shell should therefore be reported.\nResponse: Thank you sincerely for your insightful comments and valuable suggestions on our\nmanuscript. The theoretical calculations for the coupling and hybridization of ZnSe@ZnS QD\nmolecules are depicted in Figure R10. We employed the well-established Schrödinger-Poisson\nframework, including Coulomb interactions, to self-consistently compute the eigenenergies and\neigenstates of the monomer, dimer, trimer, and tetramer. The results indicate that the ground\nstates are localized within the QD cores, while the excited states couple to neighboring QDs.\nThis coupling resembles the formation of chemical bonds between atoms and leads to a\nreduction of the eigen-energies, which manifest as red shifts in the photoluminescence (PL) and\nabsorption spectra.\nFigure R10. The detailed parameter (a) of ZnSe/ZnS monomer and dimer for the simulation.\nThe eigenvalues and the wave functions of the electron and hole (eigenstate 0) of the monomer\n(b), dimer (c), trimer (d), and tetramer (e).\nTo definitively attribute the spectral redshift to hybridization, we prepared control samples of\nphysically coupled dimers using a template method (Figure R11a). Transmission electron\nmicroscopy (TEM) characterization (Figure R11b-d) shows nanoparticles that are merely in\ncontact without any intrinsic fusion. Moreover, their absorption spectra (Figure R11e) exhibit\nno appreciable redshift in the band-edge absorption peaks relative to the monomer. Collectively,\nthese results provide direct evidence that the redshifts observed in our samples arise from inter-\nparticle hybridization rather than aggregation or Ostwald ripening.\nFigure R11. (a) Scheme for fabrication of physical coupling ZnSe/ZnS dimer without fusion\nstep based on the templating method. The TEM imaging with low (b), high magnification (c-\nd), and (e) absorption spectrum of ZnSe/ZnS dimer QDs molecules.\nMeanwhile, the red-shift about “71.3 meV value” in the previously version of the manuscript\nwas for the PL emission peaks. This was fully discussed in the revised manuscript combined\nwith the theoretical calculations.\nAs for the detailed parameter for the synthesized ZnSe/ZnS QDs molecules, it was depicted in\nthe Figure R12. It’s true that usually the coupling based on the type-I ZnSe/ZnS QDs would\nbe difficulty compared with the type-I QDs. But in our new type ZnSe/ZnS QDs molecules\nsystem, the barrier and thickness is thin, that is, both energy transfer, Tunneling, biextion, and\ntrion formation (Figure R12) can lead to the obviously electron dislocation resulting in\nsignificant red-shift.\nFigure R12. The possible coupling mechanisms for the red-shift and shortening of lifetime in\nZnSe@ZnS QDs molecules.\nChanges made: The theoretical calculations for the coupling and hybridization of the\nZnSe@ZnS QDs molecules were added in the revised manuscript and Supplementary\ninformation.\n“We hypothesize that the formation of larger molecules and increased volume during the\nOA/OR combined process may lead to coupling with electron dislocation. This could result in\nobserved red shifts in both absorption and PL, accompanied by lifetime quenching, reflecting\nthe coupling among quantum dot molecules and analogous to chemical bond-type hybridization\nseen in carbon-based systems.”\n3. The size of Fig 3b also makes it difficult to see the sub-bandgap defect emission around 580\nnm. Also, there is a small peak in the tetramer around 380 nm – what is the source of this very\nblue emission?\nResponse: Thank you for the suggestion. We re-measured the samples with proper background\ncorrection, and the revised spectrum is presented in Figure R13. In the coupled ZnSe@ZnS\nQD system, the photoluminescence quantum yield (PLQY) decreases markedly with the\nformation of the higher-order assemblies: monomer, dimer, trimer, and tetramer. The reduction\nin PLQY for the trimer and tetramer is attributed to surface defects arising during the coupling\nprocess, which can give rise to defect-related emission near 580 nm. Additionally, the small\npeak near 380 nm observed for the tetramer is attributed to residual excitation signal and is\nconsistent with the low PLQY of the ZnSe@ZnS tetramer QDs.\nFigure R13. The emission spectra of ZnSe@ZnS monomer, dimer, trimer, and tetramer QDs.\nChanges made: The corrected PL spectrum of the ZnSe@ZnS monomer, dimer, trimer, and\ntetramer QDs was provided in the revised manuscript.\n4. In the first paragraph of the Results section, “oleic acid” is referred to as a “typical hard\nbase.” The authors likely meant that oleate, the conjugate base of oleic acid, is the hard base.\nResponse: Thank you for the suggestion. It’s true, the description in the manuscript about\n“oleic acid” should be corrected as “oleate”.\nChanges made: A correction about the “oleic acid” was added in the revised manuscript.\nPrototypical evolution of proto colloidal artificial-molecules was derived from colloidal\nZnSe/ZnS core/shell QDs via precise modulation of the OR, OA, and M A process (Figure 1a\nO\nand Supplementary Figure.1). “Briefly, oleate and Oleylamine (OLAm), as typical hard base,\nexhibits strong coordination and affinity with zinc ions (borderline Lewis acids), resulting in\neffective passivation of the ZnSe/ZnS surface and the formation of monodispersed QDs.”\n5. The authors note that “ensemble PL lifetime measurements revealed a dramatic quenching\nof the lifetime” in Fig. 3d, but these curves appear to be on top of each other. The authors\nshould provide lifetimes from fits to the curves to compare and should revise their description\nof this data. How do these ensemble lifetimes compare to the lifetimes measured in the single\nnanostructures? Please also include the excitation power density used for the lifetime\nmeasurements.\nResponse: Thank you for the suggestion. The localized, time-resolved photoluminescence (PL)\nlifetime decays for ZnSe@ZnS monomer, dimer, trimer, and tetramer QDs are presented in\nFigure R14. A faster decay rate (shorter lifetimes) is observed as the QD assemblies form,\ncompared with the ZnSe@ZnS monomer. Notably, the change in PL lifetime for single-particle\nmeasurements (Figure 4) is even more pronounced. Consequently, we have revised the\nmanuscript to describe the effect as a dramatic quenching of the lifetime, rather than a minor or\ninsignificant change.\nFigure R14. The ensemble photoluminescence (PL) lifetime decay of ZnSe@ZnS monomer,\ndimer, trimer, and tetramer QDs.\nFigure 4. Single particle measurements of colloidal artificial molecules. Time-tagged, time-\nresolved data for a single ZnSe@ZnS monomer, dimer, and trimer, including PL intensity\ntrajectories (a-c), PL decay curves (d-f), second-order photon correlation (𝑔(2)(𝜏)) curves (g-\ni), and statistical results of 𝑔(2)(0) values of (𝑔(2)(𝜏)) curves (j-l), respectively. (m) A\ntypical biexciton PL decay curve for a relatively strongly coupled dimer. A localized biexciton\n(LBX) lifetime value of 2.29 ns was obtained using a single exponential function fit. (n) A\ntypical biexciton PL decay curve for a relatively weakly coupled dimer. The LBX and\nsegregated biexciton (SBX) lifetime values obtained by fitting a double exponential function\nare 2.33 ns and 14.87 ns, respectively. (p) Schematic of LBX and SBX. (o) The on states in the\nPL trajectories correspond to single exciton emissions, while the grey states are caused by\nAuger blinking or band-edge carriers (BC) blinking.\nMeanwhile, excitation power-dependent decay curves for single monomers, dimers and trimers\nwas added in the revised manuscript (Supplementary Figure 21). And the 〈N〉 represents the\nexcitation condition and is defined as the average number of photons absorbed per QD per pulse\nfor PL lifetime of monomer, dimer and trimer depicted in the revised manuscript.\nSupplementary Figure 21. (a-c) Excitation power-dependent decay curves for single\nmonomers, dimers and trimers. 〈N〉 represents the excitation condition and is defined as the\naverage number of photons absorbed per QD per pulse. The 〈N〉 value increases from top to\nbottom for the three PL decay curves. These decay curves were normalized to match the late-\ntime tails. (d-f) PL decay curves obtained by subtracting the PL decay at low excitation from\nthe PL decays at higher excitations. Fits to a single-exponential function yield biexciton\nlifetimes of 2.03 ns, 2.24 ns and 2.33 ns for monomers, dimers and trimers, respectively..\nChanges made: Both ensemble and single particle photoluminescence (PL) lifetime decay\ncurves was added in the revised the manuscript. And the excitation power-dependent decay\ncurves for single monomers, dimers and trimers was added in the revised Supplementary\ninformation.\n“Meanwhile, ensemble PL lifetime measurements revealed quenching of the lifetime (Figure\n3d).”\n6. There is a noticeable difference in the sharpness of the image produced using the Mn-doped\nZnSe/ZnS monomers and the dimers embedded in PMMA as an x-ray scintillator (Fig. 5i). Can\nthe authors comment on the source of this performance difference since both materials exhibit\nthe same large Stokes shift that avoids reabsorption?\nResponse: Thank you for the suggestion. In X-ray imaging, the luminescence decay rate of a\nscintillator is a critical parameter. Although its impact is most pronounced for dynamic imaging,\na faster decay rate is also advantageous for static imaging: it enables more efficient signal\ncollection within a shorter exposure window, reduces motion blur, supports low-dose rapid\nradiography (ACS Appl. Mater. Interfaces 2019, 11, 7522-7528), and minimizes afterglow\nartifacts during high-speed sequential static acquisitions (Nat. Commun. 2024, 15(1), 8870). In\nour work, we find that the dimer and monomer scintillator materials have comparable quantum\nyields, but the dimer exhibits a significantly faster luminescence decay rate than the monomer.\nThis advantageous property suggests that, for static imaging applications requiring short\nexposure times, high throughput, or reduced afterglow, the dimer could provide a purer signal\nunder identical exposure conditions, thereby enhancing the final image signal-to-noise ratio and\nclarity. Our results offer a new design strategy for developing scintillator materials optimized\nfor efficient and rapid static imaging.\n7. It would be helpful to include the relative PL efficiency of the different structures – monomers,\ndimers, etc. either from single-particle spectroscopy or an ensemble measurement. Ideally this\nwould be PL quantum yield in solution (as is presented in the SI for the Mn-doped ZnSe/ZnS),\nbut relative PL at the same absorption would be acceptable.\nResponse: Thank you for the suggestion. We have measured the photoluminescence quantum\nyield (PLQY) of the ZnSe@ZnS and ZnSe:Mn@ZnS molecules employing a relative method,\nand the results are summarized in Supplementary Table 2. And the PLQY of monomer, dimer,\ntrimer, and tetramer ZnSe@ZnS was 7.1%, 6.9%, 3.8%, and 0.6%, respectively. And the PLQY\nof monomer, dimer, trimer, and tetramer ZnSe:Mn@ZnS was 41.3%, 34.0%, 22.4%, and 0.1%,\nrespectively. It was clear found that the coupled molecules structure formation can significant\ndecrease the PLQY, which was maybe induced by the surface defect among the coupled\nstructure formation process. Meanwhile, the Mn doping strategy could significant enhanced the\nPLQY.\nChanges made: The PLQY of both ZnSe@ZnS and ZnSe:Mn@ZnS molecules was provided\nin the revised manuscript.\nFigure 3. Optical study of colloidal artificial-molecules. Absorption (a), emission spectra (b),\nstandard CIE pattern-1976 (c), and ensemble photoluminescence (PL) lifetime decay (d) of\nZnSe@ZnS monomer, dimer, trimer, and tetramer QDs. (e) the potential and the wave functions\nof the hole and electron of the dimer, (f) the electron clouds and hole clouds together with the\ncorresponding energy levels for the monomer, dimer, trimer, and tetramer (from left to right),\n(g) the red shift of the dimer, trimer, and tetramer relative to the monomer. The red line\ncorresponds to the experimental results, and the black line corresponds to the theoretical\ncalculation. The 2D transient absorption (TA) spectroscopy and corresponding TA spectroscopy\nwith different probe delay times under 365 nm excitation of ZnSe@ZnS monomer (h, l), dimer\n(i, m), trimer (j, n), and tetramer (k, o) QDs, respectively."}, {"round": 2, "reviewer_comments": {"reviewer_1": "I think the authors answered my questions and revised the manuscript sufficiently. In my opinion the manuscript is ready for publication in Nature Communications.", "reviewer_2": "The authors did an excellent job in addressing all the comments with a lot of new, convincing data and providing a much-improved manuscript. A particular, fundamental concern was the specificity of the synthesis variants for the dimer/trimer/tetramer. Now the new statistics confirms that it is high, proving that the results are not obtained from uncontrolled mixtures, and furthermore, also highlighting the quality and significance of this template-free approach. In conclusion, I now fully support publication in Nature Communications.\nThe authors might want to consider the following minor formal points for their final version:\n- Both in Supplementary Figure 3 and Supplementary Table 2 it should be made clear that the x-axis labels and the column labels, respectively, are referring to the synthesis variant (“target”), whereas the identical labels for the bars / table-rows are referring to the measured fraction.\n- In the caption of Supplementary Figure 21 it is stated that “<N> increases from top to bottom for the three decay curves”. However, this is only true for their ordering in the figure legend, not the curves themselves. Therefore, I recommend adapting the legend and the description.\n- I like the revised title much better, but it may be good to include the nanocrystal aspect in order to avoid ambiguity, e.g. “Self-organized artificial molecules from colloidal nanocrystals”.", "reviewer_3": "The authors have addressed my concerns and significantly strengthened their manuscript with theory and key experiments.\nIn my opinion, there is sufficient novelty in their template-free approach to synthesizing colloidal quantum dot molecules and comprehensive characterization to merit publication in Nature Communications. The abstract and introduction would benefit from further language editing, however.\nA few minor revisions:\n1. One aspect that Reviewer 2’s emphasis on biexciton lifetimes brought to my attention was the relatively long biexciton lifetimes of ~2 ns measured in even the individual ZnSe/ZnS nanocrystals (localized biexciton lifetime). This was not commented upon by the authors but has been recently explained in the literature by an unintentionally alloyed ZnSe and ZnS shell that reduces Auger recombination and therefore lengthens the biexciton lifetime. I would suggest that the authors include a brief note about this and cite Lin, X. et al. Nature Nanotech. 20, 229-236, 2025 (doi: 10.1038/s41565-024-01812-0).\n2. Please define the bond length more exactly in Figure S4 – your nanocrystals are not elongated, so is the measurement center-to-center or center-to-edge, as suggested by the cartoon?\n3. The authors demonstrate quite high structural purity of their samples with regard to dimer, trimer, etc., so it remains puzzling that their ensemble lifetimes (Fig. 3d) are so similar when their single-structure lifetimes are not (Fig. 4d-f). The lifetime is likely quite sensitive to the strength of the coupling, so perhaps while the structural purity is there, the uniformity in coupling within the structures is not? Perhaps the authors can comment on the dispersion of single-structure lifetimes they observed to resolve the apparent discrepancy between the ensemble and single-structure measurements.\n4. Ostwald is missing from the initial definition of OR in the text\n5. Oleylamine in Fig. 1 is misspelled\n6. Figure 3f could use an energy scale/labels on the y-axis. Please label the y-axis of Fig 3g - Absorption Red Shift (to distinguish from PL)."}, "author_response": "Response to the reviewers\nList of changes:\n(1), A revised Supplementary Fig 3 and Supplementary Table 2 with clearer labels.\n(2), Supplementary Fig 21 has been corrected to maintain the same order of decay curves, and\na description has been added in the revised manuscript.\n(3), The tittle was revised as “Self-organized artificial molecules from colloidal nanocrystals”.\n(4), The discussion of ZnSe/ZnS monomer biexciton lifetimes and the additional references\nwere cited in the revised manuscript.\n(5), The detailed description of the statistics results for the bond length was added in the revised\nSupplementary Information.\n(6), The Statistical results of single-structure lifetimes curves of ZnSe@ZnS monomer, dimer,\nand trimer molecules were added.\n(7), A definition of Ostwald ripening (OR) was corrected in the revised manuscript.\n(8), The misspelled for “Oleylamine” in the Figure 1 was corrected in the revised manuscript.\n(9), A revised Figure 3 with corrected y-axis was added in the manuscript.\nReviewer: 1\nI think the authors answered my questions and revised the manuscript sufficiently. In my\nopinion the manuscript is ready for publication in Nature Communications.\nResponse: We acknowledge the reviewers' encouraging assessment of our manuscript and\nits positive comments on our manuscript. To date, there has been no satisfactory method for\nprecisely fabricating colloidal semiconductor molecules via a template-free approach. We\nbelieve our self-organized, template-free artificial molecule synthesis strategy is significant\nfor the field of coupled colloidal semiconductor molecules, with potential applications in\nsuper-lattice luminescent devices, sensing, and scintillators.\nReviewer: 2\nThe authors did an excellent job in addressing all the comments with a lot of new, convincing\ndata and providing a much-improved manuscript. A particular, fundamental concern was the\nspecificity of the synthesis variants for the dimer/trimer/tetramer. Now the new statistics\nconfirms that it is high, proving that the results are not obtained from uncontrolled mixtures,\nand furthermore, also highlighting the quality and significance of this template-free approach.\nIn conclusion, I now fully support publication in Nature Communications. The authors might\nwant to consider the following minor formal points for their final version:\nResponse: Thank you for the reviewer’s comments. I greatly appreciate your rigorous reviewer\nfeedback, valuable suggestions, and positive comments. You’re right that the previous\nmanuscript version did not clearly present the single-particle measurements. In the revised\nmanuscript, we discuss both localized biexcitons and long-lived, spatially segregated biexcitons\nwithin the artificial-molecule structures, accompanied by reduced Auger recombination.\nAdditionally, excitation-power dependent decay measurements are presented to quantify the\ncontributions from biexciton, trion, and Auger recombination. Moreover, the revised\nmanuscript reports the photoluminescence quantum yield of ZnSe@ZnS QD molecules across\nthe monomer, dimer, trimer, and tetramer forms, and analyzes its relationship to the biexciton\nquantum yield. Thanks again for your significant suggestions on the revised manuscript. And\nwe believe the revised manuscript is well-suited for Nature Communications.\n1. Both in Supplementary Figure 3 and Supplementary Table 2 it should be made clear that the\nx-axis labels and the column labels, respectively, are referring to the synthesis variant\n(“target”), whereas the identical labels for the bars / table-rows are referring to the measured\nfraction.\nResponse: Thank you sincerely for your insightful comments and valuable suggestions. It’s\ntrue, in the current version, the x-axis labels and the column labels are similar in the\nSupplementary Fig 3 and Supplementary Table 2. Thus, in the revised version, the x-axis were\ncorrected as “Synthesized colloidal molecules” and the column were corrected as “measured\nfraction” in both revised Supplementary Fig 3 and Supplementary Table 2.\nChanges made:\nSupplementary Table 2. Statistics results for the different ZnSe@ZnS molecules configuration.\nRatio (%) Measured Measured Measured Measured\nmonomer dimer trimer tetramer\nSynthesized monomer 95.9 18 3.5 0.5\nSynthesized dimer 3.9 73.3 16.9 3.6\nSynthesized trimer 0.2 7.8 71.4 19.2\nSynthesized tetramer 0 0.9 8.2 76.7\nA revised Supplementary Fig 3 and Supplementary Table 2 with clear labels were added in the\nrevised manuscript.\nSupplementary Fig 3. The statistics results for the measured fraction percentage in the\nsynthesized monomer, dimer, trimer, and tetramer ZnSe@ZnS molecules with s, sp, sp2, and\nsp3 hybridization configuration, respectively. Here the total amount of QDs for the statistic was\n80.\n2. In the caption of Supplementary Figure 21 it is stated that “<N> increases from top to bottom\nfor the three decay curves”. However, this is only true for their ordering in the figure legend,\nnot the curves themselves. Therefore, I recommend adapting the legend and the description.\nResponse: Thank you for the reviewer’s comments. The order for the decay curves and\ndescription are corrected in the revised Supplementary Fig 21.\nSupplementary Fig 21. (a-c) Excitation power-dependent decay curves for single monomers,\ndimers and trimers. 〈N〉 represents the excitation condition and is defined as the average number\nof photons absorbed per QD per pulse. The 〈N〉 value increases from low to high for the three\nPL decay curves. These decay curves were normalized to match the late-time tails. (d-f) PL\ndecay curves obtained by subtracting the PL decay at low excitation from the PL decays at\nhigher excitations. Fits to a single-exponential function yield biexciton lifetimes of 2.03 ns,\n2.24 ns and 2.33 ns for monomers, dimers and trimers, respectively.\nChanges made: A revised Supplementary Fig 21 was provided in the revised manuscript.\n3. I like the revised title much better, but it may be good to include the nanocrystal aspect in\norder to avoid ambiguity, e.g. “Self-organized artificial molecules from colloidal\nnanocrystals”.\nResponse: Thank you for the suggestion. Combination both your and editorial comments, we\ncorrect the tittle as “Self-organized artificial molecules from colloidal nanocrystals”.\nChanges made: Revised tittle “Self-organized artificial molecules from colloidal\nnanocrystals” was provided in the newest manuscript.\nReviewer: 3\nThe authors have addressed my concerns and significantly strengthened their manuscript with\ntheory and key experiments. In my opinion, there is sufficient novelty in their template-free\napproach to synthesizing colloidal quantum dot molecules and comprehensive characterization\nto merit publication in Nature Communications. The abstract and introduction would benefit\nfrom further language editing, however, a few minor revisions:\nResponse: We acknowledge the reviewers' high evaluation of our manuscript and the\ninnovative comments about our template-free approach to synthesizing colloidal quantum dot\nmolecules. In the revised manuscript, we present a universal, template-free method for\nsynthesizing colloidal quantum dot monomers, dimers, trimers, and tetramers. The abstract and\nintroduction have also been re-edited. We believe this approach can be broadly applied to\nconstruct polymeric libraries of diverse semiconductor core–shell nanocrystals, with a wide\nrange of potential applications.\n1. One aspect that Reviewer 2’s emphasis on biexciton lifetimes brought to my attention was\nthe relatively long biexciton lifetimes of ~2 ns measured in even the individual ZnSe/ZnS\nnanocrystals (localized biexciton lifetime). This was not commented upon by the authors but\nhas been recently explained in the literature by an unintentionally alloyed ZnSe and ZnS shell\nthat reduces Auger recombination and therefore lengthens the biexciton lifetime. I would\nsuggest that the authors include a brief note about this and cite Lin, X. et al. Nature Nanotech.\n20, 229-236, 2025 (doi: 10.1038/s41565-024-01812-0).\nResponse: Thank you for your suggestion. In zinc-based colloidal quantum dot synthesis\nsystems, zinc diffusion is usually unavoidable. Therefore, your suggestion to form an alloyed\nZnSe/ZnS shell is entirely reasonable. As reported in the literature, once the alloy shell forms,\nit reduces Auger recombination and lengthens the biexciton lifetime. Our single-particle\nbiexciton lifetime measurements for the ZnSe@ZnS monomer yield a lifetime of 2 ns, which\nis consistent with the most recent work (Nature Nanotech. 2025, 20, 229-236). The discussion\nof these relatively long biexciton lifetimes has been included in the revised manuscript.\nChanges made:\nThe extracted biexciton lifetimes are 2.03 ns (monomer), 2.24 ns (dimer), and 2.33 ns (trimer)\n(Supplementary Fig 21d-f), consistent with the LBX lifetimes from the first-photon analysis\nin Supplementary Fig 20. It should be noted that the biexciton lifetime can reach up to 2 ns,\nlikely due to an alloyed ZnSe/ZnS shell that reduces Auger recombination, in line with recent\nreports 50. Additionally, an excess carrier may occupy the second emission center in the dimer,\nforming a potential trion (Supplementary Fig 22).\n50. Lin, X. et al. Blue lasers using low-toxicity colloidal quantum dots. Nat Nanotechnol 20,\n229-236 (2025)\n2. Please define the bond length more exactly in Figure S4 – your nanocrystals are not\nelongated, so is the measurement center-to-center or center-to-edge, as suggested by the\ncartoon?\nResponse: We sincerely thank the reviewers for their comments. The bond length was\ndetermined by the center-to-center distance in the dimer, trimer, and tetramer ZnSe@ZnS QDs\nmolecules as shown in Supplementary Fig 4 with cartoon.\nSupplementary Fig 4. The statistics results for the bond length of dimer, trimer, and tetramer\nZnSe@ZnS QDs molecules. Here the total amount of QDs for the statistic was 80. The related\nbond length for the statistic histogram was determined by the center-to-center distance as shown\nin the cartoon.\nChanges made: The revised Supplementary Fig 4 was added with defined description of bond\nlength statistic result.\n3. The authors demonstrate quite high structural purity of their samples with regard to dimer,\ntrimer, etc., so it remains puzzling that their ensemble lifetimes (Fig. 3d) are so similar when\ntheir single-structure lifetimes are not (Fig. 4d-f). The lifetime is likely quite sensitive to the\nstrength of the coupling, so perhaps while the structural purity is there, the uniformity in\ncoupling within the structures is not? Perhaps the authors can comment on the dispersion of\nsingle-structure lifetimes they observed to resolve the apparent discrepancy between the\nensemble and single-structure measurements.\nResponse: Thank you very much for your insightful suggestion. The similar ensemble lifetimes\nfor the monomer, dimer, and trimer may arise from two main factors. First, ensemble lifetimes\nwere measured under lower excitation conditions. Comparing the PL decay curves of single\nstructures (Figure. 4d-f) with those of their ensembles (Figure. 3d) shows that the main\ndifference lies in the short-lived region, which is predominantly due to biexcitons. Ensemble\nmeasurements use very low excitation, making biexciton generation scarce even in dimers and\ntrimers. In contrast, single-structure measurements require higher excitation to elicit more\nphotons and thus more biexcitons, especially in dimers and trimers. Hence, the disparity\nbetween single-structure and ensemble lifetimes reflects the differing biexciton contributions\nunder varying excitation.\nSecond, the shorter biexciton lifetimes contribute less to the weighted average PL lifetimes.\nFor single monomer, dimer, and trimer molecules, the biexponential fits in Figure. 4d-f yield\nlifetimes of 2.12 ns (17.0%) and 23.10 ns (83.0%) for the monomer; 2.67 ns (31.6%) and 24.34\nns (68.4%) for the dimer; and 3.20 ns (59.7%) and 33.38 ns (40.3%) for the trimer. The\nbracketed values are amplitude weights. Consequently, the weighted average lifetimes are 19.7\nns, 17.5 ns, and 15.9 ns for the monomer, dimer, and trimer, respectively. Despite higher\nbiexciton amplitude weights in the dimer and trimer, their short biexciton lifetimes limit their\ncontribution to the weighted average. This explains why the weighted average lifetimes for\nsingle structures do not vary greatly and, in turn, why ensemble lifetimes are relatively uniform.\nWe also added the statistical results for the weighted-average lifetimes of single monomer,\ndimer, and trimer molecules, shown in Figure R1 (see below). The single-structure lifetimes\nexhibit noticeable dispersion, which may reflect isomeric diversity and varying coupling\nstrengths in the dimers and trimers. In contrast, the histograms for the dimers and trimers cluster\naround shorter lifetimes. The mean values are 23.25 ns (monomer), 21.21 ns (dimer), and 18.85\nns (trimer). The shorter averages for the dimers and trimers arise from increased biexciton\nformation in these structures, driven by the coupled dimer/trimer configurations that promote\nrapid conversion of segregated biexcitons (SBXs) into localized biexcitons (LBXs).\nConsequently, dispersion in the weighted-average lifetimes highlights heterogeneity in\ncoupling within these colloidal artificial molecules.\nFigure R1. Statistical results of the weighted average lifetimes of the single-structure decay\ncurves of ZnSe@ZnS monomer (a), dimer (b), and trimer (c) molecules. The respective average\nvalues are 23.25 ns, 21.21 ns, and 18.85 ns for the monomer, dimer, and trimer molecules.\n4. Ostwald is missing from the initial definition of OR in the text.\nResponse: Thank you for the suggestion. The definition of Ostwald ripening (OR) was\ncorrected in the revised manuscript.\nChanges made: A definition of Ostwald ripening (OR) was corrected in the revised manuscript.\n“Hence, we propose the concept of “surface-engineered self-organized proto-atom chemistry”,\nfocusing on the fusion of core/shell ZnSe@ZnS proto-atoms to synthesize colloidal artificial\nmolecules through precisely Ostwald ripening (OR), oriented attachment (OA), and multistep\noriented attachment (M A), which elucidate the fundamental principles of artificial proto-\nO\natoms with specific bonding angles and lengths.”\n5. Oleylamine in Fig. 1 is misspelled.\nResponse: Thank you for the suggestion. The misspelled for “Oleylamine” in the Figure 1 was\ncorrected in the revised manuscript.\nChanges made: A correction about the misspelled for “Oleylamine” of Figure 1 was added in\nthe revised manuscript.\n6. Figure 3f could use an energy scale/labels on the y-axis. Please label the y-axis of Fig 3g -\nAbsorption Red Shift (to distinguish from PL).\nResponse: Thank you for the suggestion. The energy scale was labelled on the y-axis of Figure\n3f. And the y-axis of Figure 3g was corrected as “Absorption Red Shift” in the revised\nmanuscript.\nChanges made: A revised Figure 3 was added in the manuscript."}]

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