The H-Pd···N-H metal-ligand dual-atom sites synergistically catalyzed alkyne semi-hydrogenation with complete Z-selectivity

Domain: neuroscience
Published: 2026-01-23
Editorial outcome: minor_revision

Abstract
In single-atom catalysts, the coordination microenvironment surrounding transition-metal centers is widely recognized as a key factor shaping their electronic structures and geometries, thereby governing catalytic behaviors. However, the synergetic catalysis between metal center and ligating atoms remains underexplored in single-atom catalysis. Herein, we construct the Pd(II)-N4 sites on carbon nitride to achieve photocatalytic semi-hydrogenation of alkynes. Under light irradiation, the Pd-N4 sites could transform to H-Pd···N-H moieties. The Pd-H center enhances alkyne insertion while the adjacent N-H group facilitates intramolecular proton transfer. This metal-ligand cooperativity of H-Pd···N-H sites, together with the steric-hindrance imposed by carbon nitride scaffold, lowers the energy barrier for Z-alkene formation and ensures exclusive stereoselectivity. Simultaneously, the H-Pd···N-H sites exhibit stronger adsorption toward alkynes than alkenes, effectively suppressing over-hydrogenation to alkanes. Across all evaluated substrates, Z-alkenes are the only isomers detected, excluding E-isomer and alkane. Notably, in a 5:95 mixture of diphenylacetylene and Z-stilbene, this method selectively converts only the alkyne to the Z-isomer without over-hydrogenation, highlighting its potential for product purification.

Introduction
Z-olefinic structures are widespread in drugs and bioactive molecules1. Catalytic semi-hydrogenation of alkynes is among the most straightforward approaches to synthesize Z-alkenes2–5. However, formation of the corresponding E-isomer and over-hydrogenation to alkane is hard to avoid. Since Z- and E-isomers frequently exhibit distinct chemical or biological activities, but have nearly identical polarity and comparable molecular size, their separation is highly challenging3. Thus, achieving both high chemo- and stereo-selectivity in the alkyne semi-hydrogenation is of utmost significance. The Lindlar catalyst is a classical heterogeneous system for generating Z-alkenes and has been widely applied in the chemical industry6. However, the presence of adjacent metal-hydride (M-H) species or subsurface hydrogen species can lead to over-hydrogenation of the Z-alkene to alkane or formation of E-isomer via further β-H elimination (Fig. 1a). In single-atom catalysts (SACs), isolated transition-metal active sites could be built, eliminating interference from adjacent M-H species (Fig. 1b)7–11. The uniform chemical environment around metal active sites could deliver excellent chemoselectivity to prevent over-hydrogenation in alkyne semi-hydrogenation12–19. Nevertheless, trace amounts of E-isomers often remain in most of these catalytic systems (Table S1), highlighting the need for more sophisticated catalyst site architectures to replace mononuclear M-H species and improve the stereoselectivity.

In homogeneous catalysis, ligand engineering has enabled Ir-20, Ru-21, Mo-22, Co-23,24, and Mn-based25,26 pincer catalysts to achieve high stereoselectivity in semi-hydrogenation (Fig. 1c). Two primary catalytic mechanisms, inner-sphere and outer-sphere pathways, have been proposed to explain the origin of high stereoselectivity3. In these systems, either the unique H-N-M-H structure (outer-sphere) or steric hindrance on the ligand (inner-sphere) governs the attack spatial position of the alkyne, underscoring the crucial influence of the coordination microenvironment around the transition-metal center for stereoselectivity. Inspired by homogeneous pincer complexes, constructing a similar H-N-M-H microenvironment around single-atom sites on a bulky support offer the potential for precise regulation of stereoselectivity in heterogeneous catalysis (Fig. 1d). Herein, we build Pd(II)-N4 sites on graphitic carbon nitride (g-C3N4) through a photo-induced ligand exchange (PILE) method27. Meanwhile, the g-C3N4, a typical semiconductor with visible light absorption28–30, enables coupling of photocatalytic water splitting with the hydrogenation process for semi-hydrogenation of internal alkynes. Mechanistic studies (Fig. 1e) suggest that upon light irradiation, Pd(II) was initially reduced to Pd(0), which reacted with protons to form Pd(II)-H active intermediate. Simultaneously, N-H sites were formed adjacent to Pd(II)-H, forming H-Pd···N-H dual-atom sites. After alkyne insertion, the Pd···N-H sites, assisted by the steric-hindrance effect of the g-C3N4 scaffold, enabled intramolecular protonation along a lower energy pathway, facilitating the Z-alkene formation. Chemoselectivity was further controlled by the preferential adsorption of alkynes over alkenes on the H-Pd···N-H sites. Notably, using this method, the diphenylacetylene (1) could be converted to Z-stilbene (2) with >99% chemoselectivity and >99% stereoselectivity. In a 5:95 mixture of 1 and 2, selective reduction of alkyne impurities to Z-stilbene was achieved without over-hydrogenation. Remarkably, across all tested substrates, only Z-alkenes were detected, with no formation of E-isomer or alkane.

Results
Synthesis and characterization of Pd-N4/CN catalysts
The Pd(acac)2 was deposited onto g-C3N4 nanosheets by thoroughly mixing the two in dichloromethane (DCM), which was then followed by solvent evaporation. The resulting solid was dispersed in water and exposed to Xe lamp irradiation, during which ligand exchange occurred, enabling Pd to coordinate with N atoms on g-C3N4—a process referred to as the PILE strategy (Fig. 2a). After washing and drying, atomically dispersed Pd sites were successfully anchored on g-C3N4 framework. Inductively coupled plasma-emission spectrometry (ICP-OES) confirmed a Pd of 2.07 wt% (Table S2). Energy-dispersive X-ray spectroscopy (EDX) elemental mappings and aberration-corrected high-angle annular dark-field scanning transmission electron microscopy (AC-HAADF-STEM) imaging verified the uniform dispersion of Pd atoms without detectable aggregation (Figs. 2b and 2c). The atomic force microscopy (AFM) images revealed that the Pd-N4/CN maintained a two-dimensional structure with a thickness of ~2.2 nm (Fig. 2d). Compative X-ray photoelectron spectroscopy (XPS) analysis g-C3N4 and Pd-N4/CN revealed a shift of the C=N-C peak toward a higher binding energy, attributable to Pd-N bond formations (Fig. 2e). The Pd 3d peaks at 342.26 eV and 337.00 eV further confirmed the presence of Pd(II) species (Fig. S5). Synchrotron X-ray absorption spectroscopy (XAS) provided complementary electronic and structural insights. In the Pd K-edge X-ray absorption near-edge structure (XANES) spectra, the absorption edge of Pd-N4/CN closely resembled that of Pd(acac)2, correlating with a +2 oxidation state (Fig. 2f). In the R-space, Fourier transform extended X-ray absorption fine structure (FT-EXAFS) spectra, a distinct Pd-N coordination peak (~1.47 Å) appeared with no evidence of Pd-Pd scattering, excluding nanoparticle formation (Fig. 2g). Furthermore, EXAFS fitting results indicated that four N atoms coordinated with Pd to form the initial coordination shell, forming a Pd-N4 structure (Fig. S6). As shown in Fig. S8, the diffraction peaks (2θ = 13.5, 28.4) of Pd-N4/CN correlated with g-C3N4 in X-ray diffraction (XRD) analysis, indicating that the Pd nanoparticle did not exist in the catalyst. Subsequently, the carrier separation and migration were studied via the transient photocurrent, steady photoluminescence (PL) spectra, and electrochemical impedance spectroscopy (EIS). Under light irradiation, the Pd-N4/CN exhibited a higher photocurrent density (~0.2 μA•cm-2) compared with g-C3N4 (Fig. S9). A smaller series resistance of Pd-N4/CN (121 Ω) was detected through EIS (Fig. S10). The reduced PL intensity demonstrated that the photoexcited electron was hard to recombine in Pd-N4/CN (Fig. S11). These experimental results consistently indicated that the incorporation of Pd enhanced charge separation and carrier migration efficiency.

Photochemical semi-hydrogenation reactions
The photocatalytic semi-hydrogenation of 1 with Pd-N4/CN was selected as the model. A mixture of Pd-N4/CN (10 mg, 2 wt%), TEOA (0.5 mL), substrate 1 (0.1 mmol) in H2O/DCE (2/2 mL) was irradiated with 420 nm LEDs at room temperature for 4 h. After the reaction, only product 2 was detected in 99% yield, while E-1,2-diphenylethene (3) and 1,2-diphenylethane (4) were not detected by gas chromatography (GC) analysis. Control experiment results indicated that the Pd-N4/CN, light irradiation, and TEOA were all essential for the reaction. In the absence of the co-solvent DCE, the yield decreased to 77%, although selectivity remained >99% (Fig. 3a). As shown in Fig. 3b, g-C3N4 alone exhibited no catalytic activity. A physical mixture of Pd(acac)2 and g-C3N4 produced 2 in only 20% yield after 9 h. Notably, throughout the entire reaction, the selectivity for product 2 remained >99%, even after complete substrate conversion (Fig. 3b, pink and green lines), demonstrating that this method effectively suppressed over-hydrogenation.

Investigations of the reaction mechanism
Light-on/off experiments confirmed that continuous irradiation is required for catalysis (Fig. 4a). Subsequently, in-situ XPS revealed a shift of Pd 3d 5/2 and Pd 3d 3/2 to lower binding energies after 90 min of irradiation on Pd-N4/CN (Fig. 4b), indicating photo-induced reduction of Pd(II). Stern–Volmer quenching experiments demonstrated that both Pd(II) and TEOA could quench the excited-state of g-C3N4 (Fig. 4c). On the other hand, the excited-state of Pd-N4/CN could be quenched by water, but cannot be quenched by substrate 1 (Fig. 4d). This quenching behavior supported an electron transfer pathway in which TEOA donated electrons to photoexcited g-C3N4, and the resulting photogenerated electrons subsequently reduced the Pd(II)-N sites before being transferred to H2O. After four cycles of Pd-N4/CN, the yield decreased to 78% (Table S4). Furthermore, AC-HAADF-STEM revealed partial aggregation of Pd single atoms into nanoparticles (Fig. S13), providing an indirect evidence that Pd(II) can be reduced to Pd(0) during the reaction. Hydrogen evolution measurements further supported this conclusion: in the absence of alkyne, Pd-N4/CN could realize the hydrogen evolution reaction under light irradiation, whereas g-C3N4 alone exhibited no activity (Fig. 4e). It demonstrates that the single-atom Pd sites are the catalytic center of HER. In the presence of alkyne, no H2 was detected, suggesting either the hydrogenation of alkyne was faster compared with HER or that the generated H2 was rapidly consumed. Cyclic voltammetry (CV) curves of Pd-N4/CN exhibited a distinct oxidation peak with half-peak potential of −0.35 V (vs. Ag/AgCl), which decreased significantly upon alkyne addition (Fig. 4f)31,32. In contrast, g-C3N4 exhibited no such peak during CV test (Fig. S16). Based on literature reports33–35 and our experimental results, we propose that the proton reacted with Pd(0) to generate Pd-H species and subsequently reacted with alkyne.

To elucidate the characteristics of active hydrogen species, a series of H sources was examined instead of H2O (Table 1). Upon utilizing g-C3N4 as the catalyst, the hydrogenation product was not detected under the H2 atmosphere (Table 1, Entries 1, 2). When using Pd-N4/CN as the catalyst and H2 as the H source, only the Z-isomer was detected and the yield of 2 could be significantly improved under light irradiation (Table 1, Entries 3, 4). It was proposed that H2 was activated by Pd(II)-N sites to form an H-Pd···N-H active center, which was accelerated under irradiation. Density functional theory (DFT) results supported this proposal, showing a spontaneous, low-energy barrier pathway (ΔG‡ = 4.5 kcal/mol, ΔG = −22.5 kcal/mol) (Fig. S17). Triethoxysilane, a typical hydride donor capable of generating M-H species, also yielded 2 as the sole hydrogenation product when used in place of H2O. These results collectively indicated that Pd-H was a key reactive intermediate. When D2O was utilized instead of H2O, deuterated Z-alkene was obtained in 95% yield with 59% deuterium incorporation rate. It was observed that the oxidized TEOA released protons and decreased the deuterated incorporation ratio. Thus, reducing the amount of TEOA led to an increase of 77% of the deuterium incorporation rate, but the yield decreased to 52% (Fig. S18). These data confirmed that the H source in the system was proton (from water or other proton donors).

Furthermore, the hydrogenation reactions were not completely inhibited by the addition of radical scavengers such as 2,2,6,6-tetramethyl-1-piperidinyloxy (22% yield) and 2,6-di-tert-butyl-4-methylphenol (89% yield), suggesting that a radical pathway was unlikely (Fig. S19). A Fourier transform infrared spectrometer (FTIR) was employed to monitor, structural changes of the catalyst under the photoexcitation state. Under a H2/Ar (5:95) atmosphere without light, the FTIR spectrum of Pd-N4/CN was collected as the background. Upon continuous light irradiation, a new vibrational band appeared at ~3480 cm-1, which was attributable to N-H stretching (Fig. 5a)36,37. In the control experiments, using g-C3N4 instead of Pd-N4/CN, no corresponding band appeared (Fig. 5b). These observations indicated that formation of the NH group required both illumination and the presence of Pd single-atom sites.

A series of kinetic experiments are used to reveal the rate-determining step. Via GC analysis, the yields were obtained at different times (0, 15, 30, 45, 60 min), which exhibited a linear relationship with reaction times. The slope stands for the initial reaction rate. Through experimental data, the initial rate vs. [1] and initial rate vs. light intensity both showed zero-order kinetics (Figs. S21 and S22). And the initial rates were positively correlated with [Pd] at low concentrations, while independent of [Pd] at higher concentrations (Fig. S23). Both the initial rate vs. [H2O] and initial rate vs. [TEOA] showed first-order kinetics (Figs. S24 and S25). Subsequently, we use D2O instead of H2O and stop the reaction at the initial stage (yield <30%). A significant reduction of yield was observed (Fig. S26). All hydrogen atoms of the H-Pd···N-H active species originate from H2O or TEOA. Hence, according to kinetic experiment results, the rate-determining step might be either the generation of Pd-H intermediate between the Pd(0) and proton, or the intramolecular proton transfer from the N-H moiety to the Pd-alkenyl intermediate.

To compare the interactions of substrates with the catalyst, the prop-1-yn-1-ylbenzene and Z-prop-1-en-1-ylbenzene, which have a similar boiling point (185 oC and 175 oC), were selected as model molecules. Temperature programmed desorption (TPD) measurements revealed that Pd single-atom sites interacted with both alkyne and alkene, improving the desorption temperatures. However, the increase in desorption temperature was much more pronounced for the alkyne than the alkene (Figs. 5c, 5d). Theoretical calculations indicated that the ligand exchange with alkyne was exergonic for both unhydrogenated (Int-3a) and hydrogenated (Int-5) single-atom Pd(II)-N4 sites (Fig. 5e). Hence, alkyne exhibited stronger adsorption strength compared with the alkene on Pd-N4/CN. The difference in adsorption capacity resulted in high chemoselectivity and the suppression of over-hydrogenation. Consistently, when pure substrate 2 was introduced into the catalytic system, no further conversion was observed under standard conditions (Fig. S27). In industrial steam cracking, trace amounts of alkyne impurities were often generated alongside valuable alkenes. It is important to develop efficient methods to selectively remove these alkynes without over-hydrogenating the alkenes21. Upon treating a 5:95 mixture of 1 and 2 under standard conditions resulted in complete conversion of the alkyne to Z-alkene, with no detectable by-product (Fig. 5f).

DFT calculations
To elucidate the reaction mechanism and the selectivity control of hydrogenation, DFT calculations were conducted. The experimental studies demonstrated that single-atom Pd(II)-N4 sites activated H2 and adsorbed diphenylacetylene. Therefore, Int-1 served as the zero point of the free energy profile (Fig. 6). Int-1 underwent a rapid alkyne migratory insertion into the Pd-H bond via TS-1 to generate Int-2a with an activation free energy of 2.9 kcal/mol. The intramolecular hydrogenation of the alkenyl palladium Int-2a occurred through TS-2a to form the Z-alkene. The activation free energy was 23.3 kcal/mol. The E-alkene formed through H transfer from the isomeric intermediate Int-2a. However, the activation free energy of TS-2b was 8.7 kcal/mol higher compared with that of TS-2a. As shown in the three-dimensional structure of TS-2b, the steric clash between the ligand and the phenyl group of the substrate rendered this transition state kinetically less favored. Conversely, TS-2a suppressed such steric clashes, elucidating the exclusive formation of the Z-isomer. Moreover, the DFT calculations also identify the intramolecular protonolysis transition state (TS-2a) had the highest barrier in the catalytic cycle, implying the intramolecular proton transfer process might be the rate-determining step. However, the possibility, which the formation of the Pd-H species was involved in the rate-determining step, also cannot be excluded.

Substrate scope
The substrate scope of semi-hydrogenation of alkynes was investigated to affirm the mechanism. Initially, the scale-up reaction (1 mmol) was conducted, and the high chemo- and stereo-selectivity was maintained (Fig. 7, entry 1). The TON value is 101. The introduction of either alkyl groups (5) or methoxy groups (6) did not affect the conversion or selectivity. Other electron-rich aryl groups decreased the yield to 50% (7) and 75% (8). When using alkyl-1-yn-1-ylbenzene derivatives, good yields with single Z-isomer selectivity were obtained (9, 10). For internal alkyne, such as dodec-6-yne (11) and oct-3-yne (12), good yields with >99% stereoselectivity could be gained. And then, we tried to explore the substrates with sensitive functional groups. The -F (13), -Br (15), amino (16), amide (17), carbonyl (18), and ester groups (19) could be compatible and the corresponding products were obtained with moderate to excellent yields. The 1-Chloro-4-(phenylethynyl) benzene (14) could only get a 38% yield. The norethindrone derivative with alkenyl and carbonyl was compatible and got a 65% yield (20). For substrates that are difficult to synthesize, the ‘Intermolecular Reaction Screening’ method was used to evaluate functional group tolerance38,39. We repeated the semi-hydrogenation reaction of 1 with adding different additives. The conversion of 1, the yield of 2 and the recovery amount of the additive after reaction were determined by GC analysis. In this way, alkyl chloride (Entry 18), alkyl ketone (Entry 19) and alkyl cyan groups (Entry 20) could be compatible. The alkyl aldehyde, which is easily reduced, could be retain with a 49% recovery rate (Entry 21). The alkyl alcohol (Entry 22) and alkyl amine (Entry 23), which are easily oxidized, could not be retained. The PhNH2 (Entry 24) could be compatible, but the -SO2NH2 group (Entry 25) could not be remained.

Based on the above substrate scope results, only the Z-isomer was detected in all cases, without neither E-isomers or alkanes. Compared with previous single-atom catalytic semi-hydrogenation reactions (Table S1), the metal-ligand cooperative catalytic site (H-N···Pd-H) replaces the isolated metal-hydride active site (M–H). And the intramolecular N-H proton transfer process results in a sufficiently large activation free energy difference between the Z- and E-isomers, demonstrating exclusive stereoselectivity. This novel synergistical catalysis highlights the strengths and distinguishing features of Pd-N4/CN catalytic system.

Conclusion
In summary, this study successfully established Pd(II)-N4 sites on g-C3N4 through the PILE strategy. The unique H-Pd···N-H microenvironment and steric constrants of g-C3N4 induce photocatalytic semi-hydrogenation of alkynes with exclusive stereoselectivity to Z-isomers. Additionally, the stronger adsorption capacity of alkynes on Pd-N4/CN helps suppress over-hydrogenation. This work highlighted the critical role of ligating atoms in single-atom catalysis and demonstrated that constructing coordination environments analogous to those in homogeneous metal complexes led to similar structure-activity relationships. These findings offered a novel perspective for designing single-atom catalysts and catalytic systems for organic transformations.

Methods
Synthesis of Pd-N4/CN photocatalyst
40 g of urea were placed into 50 mL crucibles, and transferred to a Muffle furnace. The temperature was increased to 550 °C at a rate of 0.5 °C/min, maintained for 5 h, and then allowed to cool naturally to room temperature, yielding a light-yellow powder (g-C3N4). First, 200 mg g-C3N4 and an appropriate amount of Pd(acac)2 were each dispersed in 10 mL dichloromethane (DCM), and ultrasonicated at room temperature for 2 h. Second, the homogeneous dispersions were then combined and vigorously stirred for 12 h to obtain precursor solution A. This precursor solution A was transferred to a 500 mL beaker and left in a fume hood for several hours to completely evaporate the DCM. Subsequently, 100 mL of deionized water was added, and evenly mixed to obtain dispersion solution B. As shown in Fig. S2, dispersion B (100 mL) was then placed into photo-reduction reactor. Under Xe lamp irradiation for 5 h, photo-reduction and ligand exchange of Pd(acac)2 adsorbed on the g-C3N4 framework occurred, resulting in the formation of isolated Pd atoms coordinated to the g-C3N4 matrix.

Photocatalytic semi-hydrogenation of alkynes
The semi-hydrogenation of diphenylacetylene was conducted in a 10 mL Schlenk tube. Photocatalyst (10 mg) and ultrapure water (2 mL) were initially added and sonicated for 5 min. Subsequently, dichloroethane (DCE, 2 mL), triethanolamine (TEOA, 0.5 mL), and alkyne (0.1 mmol) were introduced. The reactor was frozen using liquid nitrogen, evacuated, and purged with argon. This cycle was repeated three times. The reaction mixture was subsequently irradiated with a 410-420 nm blue LED at room temperature for 4 h under continuous stirring.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "The manuscript by Liu and co-workers (manuscript ID: NCOMMS-25-58664) describe a homogenized heterogeneous\ncatalys, based on single-atom Pd(II)-N₄ sites anchored on graphitic carbon nitride (g-C₃N₄), engineered to the selective\nphotocatalytic semihydrogenation of alkynes. In their design strategy, Liu and co-workers were inspired by pincer-type metal\ncomplexes, that frequently exhibit metal-ligand cooperativity to activate E-Y bonds (e.g., H2). Using these fundamental\nconcepts from homogeneous catalysis, the authors were able to demonstrate that under light irradiation, the Pd-N₄ moieties\ntransform into H–Pd···N–H dual-atom-like sites that synergistically mediate alkyne activation and intramolecular proton\ntransfer. This metal–ligand cooperativity, combined with the steric hindrance of the carbon nitride support, affords complete\nZ-selectivity across a series substrate scope. Limited mechanistic investigations, supported by in situ spectroscopy and DFT\ncalculations, confirm that Pd–H species are key intermediates and that the system exhibits strong preference for alkyne\nadsorption over alkene absorption, suppressing over-hydrogenation\nStructural characterization confirms the isolated Pd(II) single atoms coordinated to four nitrogen atoms. The catalyst exhibits\nhigh stability and photocatalytic activity under mild, aqueous conditions using visible light. Control experiments exclude\nradical pathways and validate the involvement of metal-hydride intermediates and adjacent N–H units. The protocol allows\nfor sustainable and stereoselective hydrogenation using water or silanes as hydrogen sources.\nOverall, the experimental work appears to be conducted carefully, and the data interpretation is generally sound. However,\nthe manuscript suffers from significant issues in clarity and presentation, with numerous unclear or awkwardly phrased\nstatements throughout the text. The title, in particular, is overly long, difficult to follow, and contains grammatical errors. More\nimportantly, the study lacks rigorous mechanistic investigation, offers a relatively narrow substrate scope, and does not\npresent a level of conceptual or methodological novelty that would meet the publication standards of Nature\nCommunications. For these reasons, I do not recommend the manuscript for publication in its current form. Detailed\ncomments and concerns are provided below.\n1. Lack of novelty. I do not believe that the current manuscript meets the novelty threshold required for publication in Nature\nCommunications. As the authors themselves note in the introduction, numerous homogeneous systems have already\nachieved exclusive or near-exclusive Z-selective semihydrogenation of alkynes. More critically, the use of Ni–N₄ sites on\ncarbon nitride, while allowing minor formation of E-isomers, follows a remarkably similar mechanistic paradigm (Angew.\nChem. Int. Ed. 2023, 62, e202216511). Specifically: (i) both systems involve a two-electron reduction of the metal center\nupon photoirradiation; (ii) both employ water as the proton source; (iii) both enable the formation of deuterated alkenes; (iv)\nin both studies, the formation of an N–H bond is essential for catalytic turnover; and (v) in both, steric effects at the active site\nsuppress formation of the E-isomer. Taken together, these mechanistic parallels significantly diminish the conceptual\nnovelty of the present study. While the work is competently executed and may offer some incremental value, it is better\nsuited for a specialized journal such as ACS Catalysis.\n2. Limited Mechanistic Investigations. Although the authors present some mechanistic data that support the involvement of\nPd–H and N–H functionalities in the catalytic cycle, further mechanistic investigations would significantly enhance the depth\nand rigor of the study. For example, kinetic studies, such as initial rate measurements under varying substrate or catalyst\nconcentrations could help identify the rate-determining step and differentiate between alternative mechanistic pathways.\nPerforming an Eyring analysis would allow the authors to extract activation parameters (ΔH‡ and ΔS‡), offering further\ninsight into the nature of the transition state and supporting their DFT-derived energy barriers.\nMoreover, the pathway for water activation remains poorly defined. Given that the reaction relies on water as the hydrogen\nsource, it is important to clarify whether direct photolysis, metal-mediated splitting, or involvement of a photo-generated\nreductant (e.g., reduced g-C₃N₄ or oxidized TEOA) is responsible for proton delivery. If the mechanism for water activation\nhas already been elucidated in previous reports involving similar Pd-N₄ systems, a concise summary and proper citation\nwould be helpful for the reader, which I might have overlooked.\nSince the authors employed D₂O in place of H₂O in one set of experiments, it would be valuable to report whether a kinetic\nisotope effect (KIE) was observed. A measurable KIE could support the hypothesis that proton transfer from water (or from\nthe N–H group) is involved in the rate-limiting step. In contrast, the absence of a KIE may suggest that hydride transfer or\nanother step governs the reaction rate. Additionally, investigating the order of reaction with respect to TEOA or performing\nexperiments under varying light intensities could help confirm whether the photogenerated electron transfer is kinetically\nsignificant.\nTaken together, these additional studies could greatly strengthen the mechanistic foundation of the work and provide greater\nconfidence in the proposed catalytic cycle.\n3. Limited Substrate scope. Given the strong mechanistic resemblance to previously reported systems (as outlined in point\n2), the limited substrate scope further reduces the overall impact and does not, in my view, justify publication in Nature\nCommunications. The current study focuses primarily on aromatic and aliphatic internal alkynes, with minimal exploration of\nsubstrates bearing diverse or sensitive functional groups. In contrast, many homogeneous systems in the literature have\ndemonstrated excellent functional group tolerance, including successful semihydrogenation in the presence of aldehydes,\nketones, esters, amides, and halides. Exploring such substrates would not only highlight the robustness and selectivity of\nthe catalyst but also help differentiate this system from prior work. In its current form, the scope feels more proof-of-concept\nthan comprehensive, and does not convincingly establish the generality or practical utility of the method. A broader and\nmore challenging substrate panel—particularly involving reducible or coordination-sensitive functionalities—would be\nnecessary to elevate the significance of this work to the level expected for Nature Communications.\n4. The scientific English in this manuscript would benefit from thorough polishing. Many sentences are overly long,\ninconsistently phrased, and contain redundancies or grammatical errors. A careful language edit is recommended to\nimprove readability and precision. Some examples\na. Title: The H-Pd···N-H on Supporter as a Formal Metal-Ligand Dual-atom Site Synergistically Catalyzed Alkyne\nSemihydrogenation with Complete Z-selectivity. The title appears as to separate sentences, semihydrogenation is not\ncorrectly spelled, the first few words are unclear, etc. etc.\nb. Abstract: However, the involvement of ligating atoms in the catalytic cycle remains underexplored. It is not clear what is\nmeant. Ligating atoms are atoms coordinated to the metal center. The previous statement makes it clear the coordination\nenvironment around the metal center are key determinants in controlling the electronic properties and structure. These are\ncontradictory.\nc. Introduction: Nevertheless, a few E-isomers still persist in the vast majority of above catalytic systems. What does this\nmean, a few molecules, a few percentage?", "reviewer_2": "In this manuscript, the authors report that the Pd(II)-N4 sites anchored on carbon nitride (Pd-N4/CN) successfully achieved\nalkyne semihydrogenation with complete Z-selectivity. While the semihydrogenation reactions have been extensively\nstudied on SACs (e.g., Angew. Chem. Int. Ed. 2025, 64, e202500389; Angew. Chem. Int. Ed. 2024, 63: e202410394;\nAngew. Chem. Int. Ed. 2023, 62, e202216511), this work revealed that the ligand N-atoms in Pd-N4 SACs directly\nparticipate in the catalytic cycle, going beyond merely electronic modulation. Specifically, the study highlights the metal-\nligand cooperativity mechanism involving H-Pd-N-H sites. The authors successfully elucidate the indispensable role of\nligating N-atoms in the catalytic cycle through a combined spectroscopic analysis, DFT calculations, and control\nexperiments. These findings provide important insights into the structure-activity relationships in single-atom catalysts and\npave the way for further exploration of coordination-environment engineering. I recommend this work for publication in\nNature Communications, pending the resolution of the following issues:\n1. Additional characterizations should be included to better demonstrate the formation of Pd-H species, such as solid-state\nNMR.\n2. Was E→Z isomerization ruled out during the transformation? Photochemical isomerization warrants explicit exclusion.\n3. Why were in-situ IR studies conducted under H₂(g) rather than aqueous-phase reaction conditions?\n4. What motivated the use of prop-1-yn-1-ylbenzene instead of diphenylacetylene for TPD experiments?\n5. This manuscript would benefit from a more comprehensive discussion of previous studies on semihydrogenation\nreactions performed on SACs. More previous reports should be included.", "reviewer_3": "This manuscript reports the photocatalytic conversion of alkynes to Z-alkenes (>99% selectivity) mediated by H-N…Pd-H,\nevolved from single atom Pd(II)-N4 on carbon nitride. Electrochemical measurements and infrared spectroscopy revealed\nadsorbed H and in situ formation of N-H. (Pd) H insertion cooperates with proton transfer from the adjacent N-H+\nstereoselectivity to achieve exceptional Z selectivity. The stereoselective hydrogenation was further elucidated by\nadsorption profile and energy barriers to Z/E isomers. However, several issues should be addressed for consideration of\npublication.\n1. Single atom Pd on carbon nitride were previously reported (Angew. Chem. Int. Ed. 2022, 61, e202207410) showing\nalkene hydrogenation under similar reaction condition. Could the authors provide discuss on their different reactivities?\n2. TON value should be reported\n3. Figure 4b, the Pd 3d 5/2 peak seems to split after 90 min irradiation, with one maintain the original binding energy and the\nother shift to lower value.\n4. By the S-V analysis, the excited state quenching rate constants can be extracted. What is the solvent in the quenching by\nTEOA or Pdacac? Figure 3 shows the quenching by water (again what is the solvent?). Could solvent effect be excluded?\n5. Figure 4f, it is mysterious that the cathodic catalytic current did not change after addition of 1, which indicate that\nhydrogenation of 1 is less competitive in compared to HER, despite that 1 consumes some surface H (shown by the reduced\nanodic peaks). This is inconsistent with Figure 3e.\n6. Both H2 and HSi(OEt)3 can serve as hydrogen source in DCE in the absence of water/TEOA for photocatalytic\nhydrogenation. This indicates the photoinduced heterolysis of H2 to give H-N…Pd-H. However, this chemistry hardly works\nfor HSi(OEt)3 in the absence of a proton donor.\n7. Could the N-H band（3480 cm-1）be observed in H2O/TEOA instead of in H2/Ar?\n8. Following 5 and 6, the activity in H2/H2O might be even higher, if water promoted proton/H transfer pathway is operative\n(J. Am. Chem. Soc. 2025, 147, 29702−29710)\n9. To support the metal ligand cooperativity, DFT calculation for Pd-H (H2O as proton donor) in the absence of the adjacent\nN-H is crucial"}, "author_response": "Response Letter\nReviewer #1 (Remarks to the Author):\nThe manuscript by Liu and co-workers (manuscript ID: NCOMMS-25-58664) describe\na homogenized heterogeneous catalyst, based on single-atom Pd(II)-N₄ sites anchored\non graphitic carbon nitride (g-C₃N₄), engineered to the selective photocatalytic\nsemihydrogenation of alkynes. In their design strategy, Liu and co-workers were\ninspired by pincer-type metal complexes, that frequently exhibit metal-ligand\ncooperativity to activate E-Y bonds (e.g., H2). Using these fundamental concepts from\nhomogeneous catalysis, the authors were able to demonstrate that under light irradiation,\nthe Pd-N₄ moieties transform into H–Pd···N–H dual-atom-like sites that synergistically\nmediate alkyne activation and intramolecular proton transfer. This metal–ligand\ncooperativity, combined with the steric hindrance of the carbon nitride support, affords\ncomplete Z-selectivity across a series substrate scope. Limited mechanistic\ninvestigations, supported by in situ spectroscopy and DFT calculations, confirm that\nPd–H species are key intermediates and that the system exhibits strong preference for\nalkyne adsorption over alkene absorption, suppressing over-hydrogenation.\nStructural characterization confirms the isolated Pd(II) single atoms coordinated to four nitrogen\natoms. The catalyst exhibits high stability and photocatalytic activity under mild,\naqueous conditions using visible light. Control experiments exclude radical pathways\nand validate the involvement of metal-hydride intermediates and adjacent N–H units.\nThe protocol allows for sustainable and stereoselective hydrogenation using water or\nsilanes as hydrogen sources.\nOverall, the experimental work appears to be conducted carefully, and the data\ninterpretation is generally sound. However, the manuscript suffers from significant\nissues in clarity and presentation, with numerous unclear or awkwardly phrased\nstatements throughout the text. The title, in particular, is overly long, difficult to follow,\nand contains grammatical errors. More importantly, the study lacks rigorous\nmechanistic investigation, offers a relatively narrow substrate scope, and does not\npresent a level of conceptual or methodological novelty that would meet the publication\nstandards of Nature Communications. For these reasons, I do not recommend the\nmanuscript for publication in its current form. Detailed comments and concerns are\nprovided below.\nOur response: At first, we would like to express our sincere gratitude to the reviewer\nfor the comprehensive and meticulous comments. These suggestions have greatly\ncontributed to improving the quality of our paper. We have revised the manuscript based\non reviewers' comments and hope that the updated version meets with your approval.\nWe are grateful to the reviewer for suggesting additional kinetic studies, KIE, substrate\nscope, etc. These results give us a deeper understanding of the reaction mechanism,\nwhich will be discussed in detail subsequently.\n1. Lack of novelty. I do not believe that the current manuscript meets the novelty\nthreshold required for publication in Nature Communications. As the authors\nthemselves note in the introduction, numerous homogeneous systems have already\nachieved exclusive or near-exclusive Z-selective semihydrogenation of alkynes. More\ncritically, the use of Ni–N₄ sites on carbon nitride, while allowing minor formation of\nE-isomers, follows a remarkably similar mechanistic paradigm (Angew. Chem. Int. Ed.\n2023, 62, e202216511). Specifically: (i) both systems involve a two-electron reduction\nof the metal center upon photoirradiation; (ii) both employ water as the proton source;\n(iii) both enable the formation of deuterated alkenes; (iv) in both studies, the formation\nof an N–H bond is essential for catalytic turnover; and (v) in both, steric effects at the\nactive site suppress formation of the E-isomer. Taken together, these mechanistic\nparallels significantly diminish the conceptual novelty of the present study. While the\nwork is competently executed and may offer some incremental value, it is better suited\nfor a specialized journal such as ACS Catalysis.\nOur response: Thanks for the comment. On the one hand, in most previous reports, the\nE-isomers were inevitably yielded during the semi-hydrogenation of alkynes.\nFor example, in Zhao’s work (Angew. Chem. Int. Ed. 2023, 62, e202216511), the optimal\nstereoselectivity was Z:E = 93:7, while the substrate scope was limited. Even in\nhomogeneous catalytic systems, it is difficult to guarantee that all the products possess\nexclusive stereoselectivity (J. Am. Chem. Soc. 2016, 138, 8588; J. Am. Chem. Soc. 2022,\n144, 13266). The Z- and E-isomers often show different chemical or biological\nactivities, but have nearly identical polarity and comparable molecular size, which\ncreates significant separation difficulties. And then, as the reviewer points out, ‘current\nheterogeneous systems focus primarily on aromatic and aliphatic internal alkynes, with\nminimal exploration of substrates bearing diverse or sensitive functional groups.’ Our\ncatalytic system not only has achieved the exclusive Z-selectivity for semi-\nhydrogenation of alkynes, but also has demonstrated excellent functional group\ntolerance, including halides, ketone, ester, and amide (following the suggestions of the\nreviewer).\nOn the other hand, although a similar reaction mechanism was proposed in Zhao's\nwork, aside from EPR experiments that can demonstrate changes in the Ni valence state,\nthere is a lack of additional experimental evidence regarding the mechanism, including\nthe generation of NH species, the synergistic effect between NH and MH, and the\nactivation mechanism of H₂O, among others. In our work, we try our best to reveal the\nmechanism of alkyne semi-hydrogenation in a single-atom catalytic system by using\nseveral in-situ technologies, dynamic experiments (following the suggestions of the\nreviewer), and DFT calculations. The significance of ligating N-atoms for regulating\nthe selectivity is highlighted in this work, which has often been overlooked in single-\natom catalysis but has been extensively studied in homogeneous catalysis. It establishes\na connection between single-atom catalysis and homogeneous catalysis at the level of\nstructure-property relationships. This would facilitate the rational design of single-atom\ncatalyst structures and expand the application scope of single-atom catalytic organic\nsynthesis.\nWe consider the H-Pd···N-H synergistical mechanism and outstanding\nstereoselectivity to be key innovations of our work and hope they are recognized by the\nreviewers.\nNo. Reference Conditions System Yields Stereoselectivity\nPd-N /CN, 420\n4\nnm LEDs, room Complete Z-\ntemperature, selectivity\n[H] = H+\nAngew.\nNi-N/CN, 420\nChem. Int.\nnm LEDs, room Z/E = 88:12 –\ntemperature, [H] 93:7\n62,\n= H O\n2\ne202216511\nNiCl , dppp,\nZ/E = 36:64 –\n3 2022, 4, LEDs, room Heterogeneous Up to 96%\n90:10\n2597 temperature, [H]\n= H O\nNi/C N , 420 nm\n3 4\nB Environ.\nLEDs, room Z/E = 82:18 –\ntemperature, [H] 86:14\n2022, 304,\n= MeOH\n121004\nJ. Am.\nChem. Soc. Co pincer, 50 oC, Z/E = 4:1\n2016, 138, [H] = NH -BH – >99:1\n3 3\nRu pincer, room\nChem. Soc. Z/E = 7:1\n6 temperature, [H] Homogeneous Up to 99%\n2022, 144, – >20:1\n= H (1 bar)\n2\n13266\nOrg. Lett. Mn pincer, 60\nZ/E = 89:11\n7 2020, 22, oC, [H] = H (20 Homogeneous Up to 96%\n2\n– >99:1\n5423 bar)\n2. Limited Mechanistic Investigations. Although the authors present some mechanistic\ndata that support the involvement of Pd–H and N–H functionalities in the catalytic cycle,\nfurther mechanistic investigations would significantly enhance the depth and rigor of the study.\nFor example, kinetic studies, such as initial rate measurements under varying substrate or catalyst\nconcentrations could help identify the rate-determining step and differentiate between alternative mechanistic pathways.\nPerforming an Eyring analysis would allow the authors to extract activation parameters (ΔH‡ and ΔS‡), offering\nfurther insight into the nature of the transition state and supporting their DFT-derived energy barriers.\nOur response: Thanks for the comments. At first, we have supplemented kinetic studies.\nBy GC analysis, the yields of each reaction can be obtained at different times (0, 15, 30,\n45, 60 min). They exhibit a linear relationship between the yield and reaction time.\nThe slope of the lines stands for the reaction rate.\nThe initial rate vs. [alkyne] showed a zero-order kinetics.\nThe initial rate vs. light intensity showed a zero-order kinetics.\nThe initial rates were positively correlated with [Pd] at relatively low concentrations,\nwhile independent of [Pd] at higher concentrations.\nThe initial rate vs. [H O] showed first-order kinetics.\nWhen using D O in lieu of H O, the deuterated Z-alkene could be obtained with a\n2 2\n95% yield, and the deuterated ratio is 59%. We consider that the oxidized TEOA could\nrelease protons and decrease the deuterated ratio. With the reduction of TEOA, the\ndeuterated ratio could improve to 77%, but the yield has fallen to 52%.\nAnd then, we use D O instead of H O and stop the reaction at the initial stage (yield\n2 2\n< 30%). Regardless of the amount of triethanolamine added, the reaction rate\nsignificantly decreased in D O. Although these KIE experiments are not entirely\n2\nrigorous due to the unavailability of deuterated triethanolamine, a significant decrease\nin reaction rate was still observed when using D₂O instead of H O. Thus, we propose\n2\nthat the activation of water is involved in the rate-determining step of this reaction.\nBased on all the experimental results mentioned above, we supposed that the\ngeneration of Pd-H intermediate from the reaction of Pd(0) with a proton (from\nwater or TEOA) should be the rate-determining step of the reaction.\nSubsequently, by varying the temperature, we have obtained the reaction rate\nconstants at different temperatures (273.15K, 298.15K, 308.15K, 318.15K). Through\nEyring analysis (In\n𝑘\n= In\n𝑘𝐵+ ∆𝑆‡\n−\n∆𝐻‡\n×\n1\n), we plotted ln(k/T) against 1/T and\n𝑇 ℎ 𝑅 𝑅 𝑇\nobtained its slope and intercept through linear fitting. The H‡ = 2.2 kcal/mol and S‡\n= -77.6 cal/(K*mol). We believe that the value of H‡ appeared obviously too small.\nTEM characterization of the post-reaction catalyst revealed that heating induced the\naggregation of Pd single atoms into nanoparticles. The formation of nanoparticles could\nalready be observed when the temperature was raised to 45°C. Therefore, we speculate\nthat after heating, the deactivation of the catalyst led to inaccurate measurement of the\nreaction rate constants, making it difficult to apply Eyring analysis to determine the\nH‡ and S‡ for this system. Additionally, conducting the test within a relatively narrow\ntemperature range (from 273 K to 318 K) inherently introduces significant experimental\nerror. This is our explanation for the mismatch between the experimental results and\ntheoretical calculations.\nAfter 390 nm LED irradiation for 1 h at 318K. The reaction image and TEM image.\nMoreover, the pathway for water activation remains poorly defined. Given that the\nreaction relies on water as the hydrogen source, it is important to clarify whether direct\nphotolysis, metal-mediated splitting, or involvement of a photo-generated reductant\n(e.g., reduced g-C₃N₄ or oxidized TEOA) is responsible for proton delivery. If the\nmechanism for water activation has already been elucidated in previous reports\ninvolving similar Pd-N₄ systems, a concise summary and proper citation would be\nhelpful for the reader, which I might have overlooked.\nOur response: Thanks for the comments. At first, we monitored the generation of\nhydrogen by GC analysis. Without adding the alkyne, the Pd-N /CN could realize the\n4\nhydrogen evolution reaction under light irradiation, whereas g-C N cannot. It\n3 4\ndemonstrates that the single-atom Pd sites are the catalytic center of HER.\n) ol 250 P\nP\nd\nd\n1 -\n-\nC\nC\nN\nN\nw\nw\ni\ni\nt\nt\nh\nh\nD\nu\ni\nt\np\nD\nhe\nip\nn\nh\ny\ne\nla\nn\nc\ny\ne\nla\nty\nc\nl\ne\ne\nt\nn\ny\ne\nlene\nm 1\nm\nμ\n( 150\nd 100\ne\nc\nu\nd 50\no\nr\nP\n0\n0 1 2 3 4 5\nt (h)\nIn previous reports, single-atom catalysts have shown great potential for\nphotocatalytic water splitting, providing effective sites for proton reduction (Solar RRL,\n2020, 4, 2000283). The metal single-atom site could gain electrons and be reduced,\nsubsequently interacting with protons to form the M-H species, which further reacts\nwith another proton to generate hydrogen gas. This is widely recognized as one of the\nprimary pathways in photocatalytic HER. For example, in Li’s work (Nano Energy\n2022, 95, 107045), they have built single-atom sites (including Pd, Ir, Rh, Ru, and Pt)\non ZnIn S and realized photocatalytic hydrogen production. Through theoretical\n2 4\nstudies, they proposed that the proton could react with metal sites to form M-H species.\nLi, X.* et al., Nano Energy 2022, 95, 107045\nIn another report, Jiang and co-workers have built Pd single-atom sites on g-C N\n3 4\nand realized the photocatalytic hydrogen evolution reaction. In this work, the authors\nalso proposed that protons can react with Pd to form the Pd-H species, which serves as\na key intermediate in hydrogen production.\nJiang, R.* et al., ACS Appl. Energy Mater. 2018, 1, 2866\nTherefore, based on literature reports and our experimental as well as theoretical\nfindings, we propose that protons can react with Pd(0) to generate the Pd-H species. We\nhave incorporated relevant references in the manuscript to substantiate this perspective.\nSince the authors employed D₂O in place of H₂O in one set of experiments, it would be\nvaluable to report whether a kinetic isotope effect (KIE) was observed. A measurable\nKIE could support the hypothesis that proton transfer from water (or from the N–H\ngroup) is involved in the rate-limiting step. In contrast, the absence of a KIE may\nsuggest that hydride transfer or another step governs the reaction rate. Additionally,\ninvestigating the order of reaction with respect to TEOA or performing experiments\nunder varying light intensities could help confirm whether the photogenerated electron\ntransfer is kinetically significant.\nOur response: Thanks for the comments. At first, we have experimentally demonstrated\nthat the protons generated from the oxidation of triethanolamine can also serve as a\nhydrogen source for the semi-hydrogenation reactions. Hence, the KIE experiment is\nnot entirely rigorous due to the unavailability of deuterated triethanolamine. However,\na significant decrease in reaction rate was still observed when using D₂O instead of H O.\ninvolved in the rate-determining step of this reaction.\nKinetic experiments indicate that the initial rate vs. [TEOA] showed first-order\nkinetics and the initial rate vs. light intensity showed zero-order kinetics.\nWe supposed that the generation of Pd-H intermediate from the reaction of Pd(0)\nwith a proton (from water or TEOA) should be the rate-determining step of the reaction.\nTaken together, these additional studies could greatly strengthen the mechanistic\nfoundation of the work and provide greater confidence in the proposed catalytic cycle.\nOur response: We highly appreciate the reviewer's comments and suggestions, which\nhave helped us deepen our understanding of the reaction mechanism.\n3. Limited Substrate scope. Given the strong mechanistic resemblance to previously\nreported systems (as outlined in point 2), the limited substrate scope further reduces the\noverall impact and does not, in my view, justify publication in Nature Communications.\nThe current study focuses primarily on aromatic and aliphatic internal alkynes, with\nminimal exploration of substrates bearing diverse or sensitive functional groups. In\ncontrast, many homogeneous systems in the literature have demonstrated excellent\nfunctional group tolerance, including successful semihydrogenation in the presence of\naldehydes, ketones, esters, amides, and halides. Exploring such substrates would not\nonly highlight the robustness and selectivity of the catalyst but also help differentiate\nthis system from prior work. In its current form, the scope feels more proof-of-concept\nthan comprehensive, and does not convincingly establish the generality or practical\nutility of the method. A broader and more challenging substrate panel—particularly\ninvolving reducible or coordination-sensitive functionalities—would be necessary to\nelevate the significance of this work to the level expected for Nature Communications.\nOur response: Thanks for the comments. As noted by the reviewer, exploring substrates,\nwhich have reducible or coordination-sensitive functionalities, could better highlight\nthe advantages of our catalytic system and help differentiate it from prior work.\nIn this catalytic system, the -F, -Br, amino, amide, carbonyl, and ester groups could\nbe compatible. The 1-Chloro-4-(phenylethynyl)benzene could only get a 38% yield.\nOn the other hand, because certain substrates containing specific functional groups\nare difficult to synthesize, we employed ‘Intermolecular Reaction Screening’ to\nevaluate functional group tolerance (following Nat. Chem. 2013, 5, 597; Acc. Chem.\nRes. 2015, 48, 619). To examine the functional group compatibility, we repeated the\nsemi-hydrogenation reaction of 1 with different additives. The conversion of 1, the yield\nof 2, and the recovery amount of the additive after reaction were determined by GC\nanalysis. In this way, alkyl chloride (Entry 18), alkyl ketone (Entry 19) and alkyl cyan\ngroups (Entry 20) could be compatible. The alkyl aldehyde, which is easily reduced,\ncould be retain with a 49% recovery rate (Entry 21). The alkyl alcohol (Entry 22) and\nalkyl amine (Entry 23), which are easily oxidized, could not be retained. The PhNH\n2\n(Entry 24) could be compatible, but the -SO NH group (Entry 25) could not be\n2 2\nremained.\n4. The scientific English in this manuscript would benefit from thorough polishing.\nMany sentences are overly long, inconsistently phrased, and contain redundancies or\ngrammatical errors. A careful language edit is recommended to improve readability and\nprecision. Some examples\nOur response: Thanks for the constructive suggestion. We have carefully checked the\nmanuscript. Subsequently, we have sent the manuscript to a specialized agency for\npolishing by a native speaker. Every sentence has been carefully polished and revised.\nThe certification has been attached to the revision.\na. Title: The H-Pd···N-H on Supporter as a Formal Metal-Ligand Dual-atom Site\nSynergistically Catalyzed Alkyne Semihydrogenation with Complete Z-selectivity. The\ntitle appears as to separate sentences, semihydrogenation is not correctly spelled, the\nfirst few words are unclear, etc. etc.\nOur response: Thanks for the comment. We have changed the title to ‘The H-Pd···N-H\nMetal-Ligand Dual-atom Sites Synergistically Catalyzed Alkyne Semi-hydrogenation\nwith Complete Z-selectivity’. We hope to draw attention to the critical role of ligating\natoms in the catalytic cycle, which can deepen the comprehension of single-atom\ncatalysts at the structure-activity relationship level and provide new insights.\nFor the spelling of ‘semihydrogenation’, we found the same writing in another article\n(Chem. Rev. 2025, 125, 4397). Should it be ‘semi-hydrogenation’? We have changed it\nto ‘semi-hydrogenation’ in our manuscript.\nb. Abstract: However, the involvement of ligating atoms in the catalytic cycle remains\nunderexplored. It is not clear what is meant. Ligating atoms are atoms coordinated to\nthe metal center. The previous statement makes it clear the coordination environment\naround the metal center are key determinants in controlling the electronic properties\nand structure. These are contradictory.\nOur response: Thanks for the comment. This sentence is indeed somewhat ambiguous.\nWe intend to highlight that synergetic catalysis involving ligating atoms and transition-\nmetal centers has received limited research attention in single-atom catalysis. We have\nchanged this sentence to ‘However, the synergetic catalysis between metal center and\nligating atoms remains underexplored in single-atom catalysis.’\nc. Introduction: Nevertheless, a few E-isomers still persist in the vast majority of above\ncatalytic systems. What does this mean, a few molecules, a few percentage?\nOur response: Thanks for the comment. In this sentence, we misused the word 'a few',\nwhich led to a misunderstanding. We have changed it to ‘Nevertheless, trace amounts\nof E-isomers often remain in most of these catalytic systems (Table S1), highlighting\nthe need for more sophisticated catalyst site architectures to replace mononuclear M-H\nspecies and improve the stereoselectivity.’\nWe sincerely thank the reviewer for all the comments and suggestions, which\nhave helped us gain deeper insights into the reaction mechanism and broaden the\nsubstrate scope. These contributions have significantly enhanced the quality of the\nmanuscript.\nReviewer #2 (Remarks to the Author):\nIn this manuscript, the authors report that the Pd(II)-N4 sites anchored on carbon nitride\n(Pd-N4/CN) successfully achieved alkyne semihydrogenation with complete Z-\nselectivity. While the semihydrogenation reactions have been extensively studied on\nSACs (e.g., Angew. Chem. Int. Ed. 2025, 64, e202500389; Angew. Chem. Int. Ed. 2024,\n63: e202410394; Angew. Chem. Int. Ed. 2023, 62, e202216511), this work revealed\nthat the ligand N-atoms in Pd-N4 SACs directly participate in the catalytic cycle, going\nbeyond merely electronic modulation. Specifically, the study highlights the metal-\nligand cooperativity mechanism involving H-Pd-N-H sites. The authors successfully\nelucidate the indispensable role of ligating N-atoms in the catalytic cycle through a\ncombined spectroscopic analysis, DFT calculations, and control experiments. These\nfindings provide important insights into the structure-activity relationships in single-\natom catalysts and pave the way for further exploration of coordination-environment\nengineering. I recommend this work for publication in Nature Communications,\npending the resolution of the following issues:\nOur response: Thanks for the reviewer’s appreciation of our work. We will take all\ncomments from reviewers seriously.\n1. Additional characterizations should be included to better demonstrate the formation\nof Pd-H species, such as solid-state NMR.\nOur response: Thanks for the comment. At first, we isolated the catalyst under standard\nconditions with nitrogen protection and performed solid-state 1H NMR analysis, but no\nPd-H signal was detected. Subsequently, we directly mixed HSi(OEt) with the Pd-\n4\nsolid-state 1H NMR testing time to 3 hours. However, only the signals corresponding\nto carbon nitride were observed in the spectrum. We speculate that this may be due to\nthe high reactivity of the Pd-H species, making it difficult to detect. Theoretical\ncalculations can also support this conclusion (Please refer to the various Pd-H\nintermediates, Int-8, Int-10 and Int-14, mentioned in the response to question 9 for\nreviewer 3). The free energy changes for generating these three Pd-H intermediates are\nall high, while the energy barriers for converting Pd-H intermediates into products or\nN-H are low (TS-4, TS-5, TS-6 and TS-8). This suggests the hypothesis that, even if\nalternative uncalculated pathways for generating Pd-H exist, their conversion processes\nare likely to be so rapid that they may not be detectable by experimental means.\nBy the way, the signals at -16.8 and -19.5 ppm are attributed to spinning sidebands\nof solid-state NMR.\n20250114_刘奕畅_1#_Norm_12KHz_1H_single_pulse_toss-1-2.jdf\nZ0 = -34.97[kHz] toss cogwheel\n0.26\n0\n0\n.\n.\n2\n2\n2\n4 -stzfppi -erefphb -xartmaa -ppo(\nss\n(ef\nee\nP zi1\n(_\nR2ol,\nc\nO0il\n-o\nC.d(T\n6r\nE03 R\n7r\nS[(4U\n.e\nSH ,E\n5c\nIz0 ,\n4t\nN][T\n3(\nG,%RT\n0\n]UR\n4,\nP0,EU\n,\nA. E\nF\nR08)\n1A\nA[0 )\n9L\nMs[\n1S\nE]%\n.E\nT ]\n1,\nE),\n1F\nS 1\n6A\n0\n2L\n- 0\n,S\n- [\nE\n- %\n5,\n- ]\n6 .F\n)\n1A5L7S4E9 [)%] )\n0.2\n0\n0\n.\n.\n1\n1\n6\nSn\nnd\nt_\nt\naT ri tm _e T i m e\n======= 2ds2N11 0ei0O44 2ln2N-- 5tg5EJJ 0al0\nAA\n1 e1\nNN\n1 _1\n--\n4 p4\n22\n_ u_\n00\nl\n22\n刘 刘s\n55\n奕 奕e _\n11\n畅 畅t\n17\n_ _o\n::\n1 1s\n32\n# #s\n05\n_ .\n::\nN j\n55\no x\n90\nrm\n0\n0\n0\n0\n0\n.\n.\n.\n.\n.\n0\n0\n1\n1\n1\n6\n8\n2\nFXXXXXXXXXBCST\noai_iiip\ni_________llco\nmtmDmmme\neADFOPPRSSaiat\nma_o__ec\nlcorforewwnpna\ne_SmTUnt\ndqmefieseekpsl\nnFiainsr\n__aqsnsoeeie\n_\ntozitiio\nSDi\netclppnd\nS\nrenltom\ntun\ntsau\n_g\nc\nm esne\nrr\nnt C\na\na\nst ea\nsi l\nn\nt\ne nt\no i\ns\nr gi\nn p\nto\np\nhn\ne d\n========\n==============\nZ16PP[XJ\n13P65202642F88\n0D5rrp\nN 44r0[0\n908[A88\n5oop\nM ..o0p4\n...uL\n=R4ttm\n- 00t.p8\n300sS\nE oo]\nE 97o1m\n497]E\n-A nn\nC 68n7]\n366\n3L\nZ 37\n2\n819\n4\n6 62\n3\n252\n.\n0 9[\n0\n533\n9\n0 2m\n4\n180\n6\n258\n[\n/ []\n[\n[[[\nk\nM T\nM\nHkk\nH\n1 ]\nH\nzHH\nz\nz\n]zz\n]\n(\n]\n]]\n6\nt\n0\no\n0\ns\n[\nabundance\n0\n0\n0\n.\n.\n0\n0\n2\nparts41.339\np\n4\ne40.264\n0\nr\n. 0\nMillion : Proton\n30.0\n23.066 22.015\n2\n20.426\n0.0 10.0\n8.973 4.316 3.228 0.612\n0\n-0.488\n-10.0\n-16.843\n-2\n-19.458\n0.0 -30.0\nRRTMTXXXOOOOOOOAAABCDDEI eeuae___bbbbbbb\ncu\nexn\nlcbsmADPsssssss\nqt\ncpi\nave_pcwu_______\no\niet\nxr_F_qelAAAAWWW\ns\nmri\na_DrG_lsmmntiii\nh\naia\ntGieeTleppgnddd\ni\ntml\niaaqti\n__l\nttt m\nie_\noimu\nm\nPTe\nhhh _\nonW\nnnee\ne\nuo_\n__ T\nnta\n_\ntn\nlsP\n9T r\n__i\nD\nec\nssr\n0o a\nRPt\ne\nry\ne\ne\ns c\naa\nl\np\ns k\ntt\na\neh\ny ======================== 52314310119422504A1230C1 [0.1646.000...[.\nU...\n:0\ns\n2.0..100[255u8\nT712\n\\[\n]\n[9.06[[[d[[[s1\nO683\nUm\nm9074u%%eduu]1\nS980\nss\nm8[8[s]]gBss\ne]\n][d7u]\n]]]]\nr\nkC2s\nM\ns\nH][]\n\\\nz\nm\nO\nd\n]\ns\nF\ne\n]\nF\nlta\\Deskt\n20250114_刘奕畅_1#_Norm_12KHz_1H_single_pulse_toss-1-2.jdf\nZ0 = -34.97[kHz] toss cogwheel\n9.0\n8.0 -stzfppi -erefphb -xartmaa -ppo(\nss\n(ef\nee\nP zi1\n(_\nR2ol,\nc\nO0il\n-o\nC.d(T\n6r\nE03 R\n7r\nS[(4U\n.e\nSH ,E\n5c\nIz0 ,\n4t\nN][T\n3(\nG,%RT\n0\n]UR\n4,\nP0,EU\n,\nA. E\nF\nR08)\n1A\nA[0 )\n9L\nMs[\n1S\nE]%\n.E\nT ]\n1,\nE),\n1F\nS 1\n6A\n0\n2L\n- 0\n,S\n- [\nE\n- %\n5,\n- ]\n6 .F\n)\n1A5L7S4E9 [)%] )\n7.0\n6.0 FAESSAR iuxaoce ltpmltv ehepvui norleas arienli m\nm_t_o\ne\neI\nSn\nnd\nt_\nt\naT ri tm _e T i m e\n======= 2ds2N11 0ei0O44 2ln2N-- 5tg5EJJ 0al0\nAA\n1\ne1\nNN\n1\n_1\n--\n4\np4\n22\n_\nu_\n00\nl\n22\n刘\n刘s\n55\n奕\n奕e _\n11\n畅\n畅t\n17\n_\n_o\n::\n1\n1s\n32\n#\n#s\n05\n_\n.\n::\nN\nj\n55\no\nx\n90\nrm\n4\n5\n.\n.\n0\nst\nt\ne r\n======== Z16PP[XJ 0D5rrp\nN\n5oop\nM\n=R4ttm\n-\nE oo]\nE\n-A nn\nC\n3L\nZ\n4\n6\n.\n0\n9\n0\n[\n/\nk\nM\nH\n1\nz] tos\n2\n3\n.\n.\n0\n_\nSDi\netclppnd\nS\ntun\ntsau _g\nc\nrr\nnt C\na\nea\nsi l\nn\nnt\no i\ns\ngi\nn p\nto\np\nhn\ne d\n============== 13P65202642F88 44r0[0\n908[A88\n..o0p4\n...uL\n00t.p8\n300sS\n97o1m\n497]E\n68n7]\n366\n37\n2 819\n62\n3 252\n9[\n0 533\n2m\n4 180\n8s\n6 258\n[]\n[ [[[\nT\nM Hkk\n]\nH zHH z ]zz\n(\n] ]]\n600[\n(thousandths)\n0\n1.0\nX :\nparts41.339\np\n4\ne40.264\n0\nr\n. 0\nMillion : Proton\n30.0\n23.066 22.015\n2\n20.426\n0.0 10.0\n8.973 4.316 3.228 0.612\n0\n-0.488\n-10.0\n-16.843\n-2\n-19.458\n0.0 -30.0\nRRTMTXXXOOOOOOOAAABCDDEI eeuae___bbbbbbb\ncu\nexn\nlcbsmADPsssssss\nqt\ncpi\nave_pcwu_______\no\niet\nxr_F_qelAAAAWWW\ns\nmri\na_DrG_lsmmntiii\nh\naia\ntGieeTleppgnddd\ni\ntml\niaaqti\n__l\nttt m\nie_\noimu\nm\nPTe\nhhh _\nonW\nnnee\ne\nuo_\n__ T\nnta\n_\ntn\nlsP\n9T r\n__i\nD\nec\nssr\n0o a\nRPt\ne\nry\ne\ne\ns c\naa\nl\np\ns k\ntt\na\neh\ny ======================== 52314310119422504A1230C1 [0.1646.000...[.\nU...\n:0\ns\n2.0..100[255u8\nT712\n\\[\n]\n[9.06[[[d[[[s1\nO683\nUm\nm9074u%%eduu]1\nS980\nss\nm8[8[s]]gBss\ne]\n][d7u]\n]]]]\nr\nkC2s\nM\ns\nH][]\n\\\nz\nm\nO\nd\n]\ns\nF\ne\n]\nF\nlta\\Deskt\nThe 1H SSNMR result of the mixture of Pd-N /CN and HSi(OEt)\n4 3\n2. Was E→Z isomerization ruled out during the transformation? Photochemical\nisomerization warrants explicit exclusion.\nOur response: Thanks for the comment. Under light irradiation, only trace amounts of\nE-alkenes can convert to Z-alkenes. Therefore, we propose that the direct photoexcited\nE–Z isomerization is not the major pathway in this system.\n3. Why were in-situ IR studies conducted under H₂(g) rather than aqueous-phase\nreaction conditions?\nOur response: Thanks for the comment. During bubbling the aqueous solution of\ntriethanolamine (TEOA) to the catalyst surface, we did the in-situ IR testing under light\nirradiation. Unfortunately, the water and triethanolamine caused significant interference\nin the infrared measurements. For the Pd /CN, strong absorption signals were observed\n1\nin both the 2800-3000 cm⁻¹ and 3500-4000 cm⁻¹ ranges. It is challenging to distinguish\nbetween signals originating from the catalyst and those from triethanolamine-derived\nmolecules. Therefore, we consider the results obtained using H₂ for testing to be more\nreliable.\nSet-up diagram of in-situ IR using aqueous solution of triethanolamine\nBubbling the aqueous solution of TEOA to the Pd-N /CN and then light-on\n3 4\n4. What motivated the use of prop-1-yn-1-ylbenzene instead of diphenylacetylene for\nTPD experiments?\nOur response: Thanks for the comment. To minimize errors in TPD testing, it is\nessential to keep the boiling points of the product and the raw material as close as\npossible. So, we used prop-1-yn-1-ylbenzene instead of diphenylacetylene (b.p. of\nalkyne = 185 oC, b.p. of Z-alkene = 175 oC)\n5. This manuscript would benefit from a more comprehensive discussion of previous\nstudies on semihydrogenation reactions performed on SACs. More previous reports\nshould be included.\nOur response: Thanks for the comment. We have cited some articles and further refined\nthe introduction of semihydrogenation reactions performed on SACs.\nReviewer #3 (Remarks to the Author):\nThis manuscript reports the photocatalytic conversion of alkynes to Z-alkenes (>99%\nselectivity) mediated by H-N…Pd-H, evolved from single atom Pd(II)-N4 on carbon\nnitride. Electrochemical measurements and infrared spectroscopy revealed adsorbed H\nand in situ formation of N-H. (Pd) H insertion cooperates with proton transfer from the\nadjacent N-H+ stereoselectivity to achieve exceptional Z selectivity. The\nstereoselective hydrogenation was further elucidated by adsorption profile and energy\nbarriers to Z/E isomers. However, several issues should be addressed for consideration\nof publication.\n1. Single atom Pd on carbon nitride were previously reported (Angew. Chem. Int. Ed.\n2022, 61, e202207410) showing alkene hydrogenation under similar reaction condition.\nCould the authors provide discuss on their different reactivities?\nOur response: Thanks for the comment. In this previous report, the substrates were\npredominantly styrene derivatives, and the yield of internal olefins is very low (No. 8).\nMeanwhile, under standard conditions, our catalytic system is also capable of reducing\nstyrene. Therefore, we believe the difference stems from the substrate structure.\nAdditionally, although both are single-atom Pd catalysts, the synthetic methods are\ndifferent. The reaction conditions also vary slightly. We consider these differences\naccount for the discrepancy in yields.\n2. TON value should be reported\nOur response: Thanks for the comment. In the 1 mmol scale reaction, 50 mg Pd-N /CN\n4\n(2.07 wt%) was used and the yield is 98%. The TON value is 101. And we have added\nthe TON value in the manuscript.\n3. Figure 4b, the Pd 3d 5/2 peak seems to split after 90 min irradiation, with one\nmaintain the original binding energy and the other shift to lower value.\nOur response: Thanks for the comment. We have repeated the in-situ XPS tests. After\n90 min irradiation, the peak shift of Pd 3d 5/2 and Pd 3d 3/2 to lower binding energy\nhas been detected. Currently, the peaks are smooth. We proposed that due to the low\nloading of Pd, there were some errors in the previous tests. We have updated the data\nin the revised manuscript.\n4. By the S-V analysis, the excited state quenching rate constants can be extracted. What\nis the solvent in the quenching by TEOA or Pdacac? Figure 3 shows the quenching by\nwater (again what is the solvent?). Could solvent effect be excluded?\nOur response: Thanks for the comment. In these experiments, solvents are both DCE.\nTo exclude the solvent effect, we used the MeCN instead of DCE and did the S-V\nanalysis. The H O could also quench the excited Pd-N /CN.\n2 4\n5. Figure 4f, it is mysterious that the cathodic catalytic current did not change after\naddition of 1, which indicate that hydrogenation of 1 is less competitive in compared to\nHER, despite that 1 consumes some surface H (shown by the reduced anodic peaks).\nThis is inconsistent with Figure 3e.\nOur response: Thanks for the comment. During the electrolysis, the proton could gain\nelectrons and be reduced to form Pd-H species in this system. The catalytic current\nobserved is generated by this step. The addition of alkynes does not affect this process,\nso the catalytic current shows no significant change. However, the introduced alkynes\nconsume Pd-H species, leading to observable changes at a half-peak potential of -0.35\nV. In Figure 4e, the detection focuses on hydrogen generation. Since the addition of\nalkynes consumes Pd-H species, hydrogen production is inhibited. The conclusions\ndrawn from these two experiments are consistent.\n6. Both H2 and HSi(OEt)3 can serve as hydrogen source in DCE in the absence of\nwater/TEOA for photocatalytic hydrogenation. This indicates the photoinduced\nheterolysis of H2 to give H-N…Pd-H. However, this chemistry hardly works for\nHSi(OEt)3 in the absence of a proton donor.\nOur response: Thanks for the comment. In HSi(OEt) , the H exhibits a -1 oxidation\n3\nstate, which could not be a proton donor. So, in our opinion, the solvent, DCE, could\nbe the proton donor in this system, giving assistance to form H(+1)-N…Pd-H(-1).\nWhen we used 1,2-dichlorobenzene instead of DCE, the stereoselectivity changed\nsignificantly. It implies that the proton donor is very important in this catalytic system.\n7. Could the N-H band（3480 cm-1）be observed in H2O/TEOA instead of in H2/Ar?\nOur response: Thanks for the comment. During bubbling the aqueous solution of\ntriethanolamine (TEOA) to the catalyst surface, we did the in-situ IR testing under light\nirradiation. Unfortunately, the water and triethanolamine caused significant interference\nin the infrared measurements. For the Pd /CN, strong absorption signals were observed\n1\nin both the 2800-3000 cm⁻¹ and 3500-4000 cm⁻¹ ranges. It is challenging to distinguish\nbetween signals originating from the catalyst and those from triethanolamine-derived\nmolecules. Therefore, we consider the results obtained using H₂ for testing to be more\nreliable.\nSet-up diagram of in-situ IR using aqueous solution of triethanolamine\nBubbling the aqueous solution of TEOA to the Pd-N /CN and then light-on\n3 4\n8. Following 5 and 6, the activity in H2/H2O might be even higher, if water promoted\nproton/H transfer pathway is operative (J. Am. Chem. Soc. 2025, 147, 29702−29710)\nOur response: Thanks for the comment. When water is added as a solvent, the yield\nincreases significantly, regardless of whether light irradiation is applied. These results\nwill provide valuable insights for our subsequent research.\n9. To support the metal ligand cooperativity, DFT calculation for Pd-H (H2O as proton\ndonor) in the absence of the adjacent N-H is crucial\nOur response: Thanks for the comment, and 3 scenarios were calculated.\n(a) Initiating from the key intermediate Int-2a, the process of proton transfer from N-\nH to Pd-H to yield Int-8 entails a very high energy barrier and is endergonic. Thus,\nthis process is not possible.\n(b) Pd in Int-2a coordinates with H₂O to form Int-9. (1) Int-9 can generate the Pd-H\nintermediate Int-10 via TS-5, followed by rapid reductive elimination to yield\nproduct Int-11. (2) A kinetically favoured pathway has been observed to bypass the\nPd-H intermediate, with Int-9 directly generating the product via an O-H-C\ntransition state (TS-7). However, the energy barrier of 29.6 kcal/mol reported here\nis higher than the 23.3 kcal/mol value given in the main text.\n(c) The absence of an adjacent N-H bond was also considered. Both the direct\ndeprotonation of adjacent N-H from Int-2a and Int-9 to form Int-12 and Int-13,\nrespectively, are endergonic processes. The pathway for generating the final product\nby Int-13 is very similar to that of Int-9, with the direct O-H-C transition state (TS-\n9) being more favorable. However, its energy barrier is also excessively high. It is\nconcluded that even if a base-assisted deprotonation of the adjacent N-H group\nstabilizes Int-13, the energy barrier for the single step from Int-13 to TS-9 alone\nreaches 28.3 kcal/mol. This pathway remains kinetically less competitive than the\nprimary route described in the main text.\nIn addition to the three pathways described above for generating Pd-H species, it is\npossible that other pathways exist. However, calculations reveal that Int-8 can generate\nN-H species via TS-4 with an extremely low energy barrier. Consequently, we\nhypothesise that the formation of Pd-H species is improbable in the absence of an\nadjacent N-H species, or if formed, would undergo rapid conversion into other species."}, {"round": 2, "reviewer_comments": {"reviewer_1": "The revised manuscript (NCOMMS-25-58664A) by Liu and co-workers satisfactorily addresses the vast majority of my\nprevious concerns. I commend the authors for the substantial effort invested in performing additional experiments and\nrestructuring key parts of the manuscript. In view of these improvements, together with the detailed responses provided, I\nbelieve the study is now suitable for publication in Nature Communications. A few remaining minor points should, however,\nbe considered before acceptance.\n1. Comparison relative to state-of-the-art\nAlthough the authors demonstrate in their response to the reviewers that their method offers advantages over recent state-of-\nthe-art approaches (for example Angew. Chem. Int. Ed. 2023, 62, e202216511), the manuscript would benefit from a\ndedicated paragraph clearly articulating how the present system differs mechanistically and conceptually from existing\nmethods. A comparison that goes beyond E/Z selectivity – for instance, detailing how the proposed PdH–NH dual reactivity\ncontributes to the enhanced performance – would significantly strengthen the broader impact and mechanistic positioning of\nthe work.\n2. Mechanistic discussion\nThe authors have carried out substantial kinetic and mechanistic experiments, yet the corresponding discussion in the main\ntext remains relatively brief. In particular, the conclusion that Pd–H formation is rate-limiting is stated rather quickly and is not\nfully integrated with the DFT results. At present, the mechanistic experiments and the computed reaction profile are\ndescribed somewhat independently, without a unifying narrative. The manuscript would clearly benefit from a better\nintegration between the two sections.\nImportantly, an alternative interpretation should be acknowledged: proton transfer from the NH moiety to the Pd-alkenyl\nintermediate (int2a → int3a) could also constitute the rate-determining step. This pathway is compatible with the observed\nfirst-order dependencies on H₂O, TEOA, and Pd if the buildup of the NH species originates from H2O or TEOA. Moreover,\nthe DFT calculations identify the protonolysis transition state as the highest barrier in the cycle.\nI therefore suggest that the authors either (i) include additional calculations evaluating the barrier for Pd–H formation to\nsupport the mechanistic assignment, or (ii) briefly discuss this alternative NH-transfer-limited pathway in the main text,\nindicating that both interpretations are plausible on the basis of the current data.\n3. Manuscript readability\nSeveral parts of the manuscript – including portions of the abstract – still contain awkward phrasing that makes the text\ndifficult to follow. A light editorial revision focused on clarity and flow would greatly improve readability and ensure\naccessibility to a broad readership.", "reviewer_2": "The authors have addressed all my points. The revised submission can be accepted.", "reviewer_3": "The authors have done an excellent job to address questions/issues. The revised manuscript is now suitable for publication\non Nature Communications"}, "author_response": "Response Letter\nReviewer #1 (Remarks to the Author):\nThe revised manuscript (NCOMMS-25-58664A) by Liu and co-workers satisfactorily\naddresses the vast majority of my previous concerns. I commend the authors for the\nsubstantial effort invested in performing additional experiments and restructuring key\nparts of the manuscript. In view of these improvements, together with the detailed\nresponses provided, I believe the study is now suitable for publication in Nature\nCommunications. A few remaining minor points should, however, be considered before\nacceptance.\n1. Comparison relative to state-of-the-art\nAlthough the authors demonstrate in their response to the reviewers that their method\noffers advantages over recent state-of-the-art approaches (for example Angew. Chem.\nInt. Ed. 2023, 62, e202216511), the manuscript would benefit from a dedicated\nparagraph clearly articulating how the present system differs mechanistically and\nconceptually from existing methods. A comparison that goes beyond E/Z selectivity –\nfor instance, detailing how the proposed PdH–NH dual reactivity contributes to the\nenhanced performance – would significantly strengthen the broader impact and\nmechanistic positioning of the work.\nOur response: Thanks for the comment. To highlight the advantages of this catalytic\nsystem, we add a dedicated paragraph following the substrate scope study.\nBased on the above substrate scope results, only the Z-isomer was detected in all cases,\nwithout neither E-isomers or alkanes. Compared with previous single-atom catalytic\nsemi-hydrogenation reactions (Table S1), the metal-ligand cooperative catalytic site\n(H-N···Pd-H) replaces the isolated metal‑hydride active site (M–H). And the\nintramolecular N-H proton transfer process results in a sufficiently large activation free\nenergy difference between the Z- and E-isomers, demonstrating exclusive\nstereoselectivity. This novel synergistical catalysis highlights the strengths and\ndistinguishing features of Pd-N /CN catalytic system.\n4\n2. Mechanistic discussion\nThe authors have carried out substantial kinetic and mechanistic experiments, yet the\ncorresponding discussion in the main text remains relatively brief. In particular, the\nconclusion that Pd–H formation is rate-limiting is stated rather quickly and is not fully\nintegrated with the DFT results. At present, the mechanistic experiments and the\ncomputed reaction profile are described somewhat independently, without a unifying\nnarrative. The manuscript would clearly benefit from a better integration between the\ntwo sections.\nImportantly, an alternative interpretation should be acknowledged: proton transfer\nfrom the NH moiety to the Pd-alkenyl intermediate (int2a → int3a) could also constitute\nthe rate-determining step. This pathway is compatible with the observed first-order\ndependencies on H₂O, TEOA, and Pd if the buildup of the NH species originates from\nH2O or TEOA. Moreover, the DFT calculations identify the protonolysis transition\nstate as the highest barrier in the cycle.\nI therefore suggest that the authors either (i) include additional calculations\nevaluating the barrier for Pd–H formation to support the mechanistic assignment, or (ii)\nbriefly discuss this alternative NH-transfer-limited pathway in the main text,\nindicating that both interpretations are plausible on the basis of the current data.\nOur response: Thanks for the comment and valuable suggestions, which have helped\nrefine our understanding of the mechanism. Indeed, based on the current experimental\ndata and DFT calculation results, we cannot identify which elementary reaction is the\nrate-determining step. Therefore, we fully agreed with the reviewer's suggestion and\nadded a brief discussion of both interpretations.\nThe revised version:\nAll hydrogen atoms of the H-Pd···N-H active species originate from H₂O or TEOA.\nHence, according to kinetic experiment results, the rate-determining step might be\neither the generation of Pd-H intermediate between the Pd(0) and proton, or the\nintramolecular proton transfer from the N-H moiety to the Pd-alkenyl intermediate.\nMoreover, the DFT calculations also identify the intramolecular protonolysis\ntransition state (TS-2a) had the highest barrier in the catalytic cycle, implying the\nintramolecular proton transfer process might be the rate-determining step. However,\nthe possibility, which the formation of the Pd-H species was involved in the rate-\ndetermining step, also cannot be excluded.\n3. Manuscript readability\nSeveral parts of the manuscript – including portions of the abstract – still contain\nawkward phrasing that makes the text difficult to follow. A light editorial revision\nfocused on clarity and flow would greatly improve readability and ensure accessibility\nto a broad readership.\nOur response: Thanks for the comment. To improve readability, we have used some\nsimple sentences in place of clause structures.\nThe revised Abstract:\nIn single-atom catalysts, the coordination microenvironment surrounding transition-\nmetal centers is widely recognized as a key factor shaping their electronic structures\nand geometries, thereby governing catalytic behaviors. However, the synergetic\ncatalysis between metal center and ligating atoms remains underexplored in single-\natom catalysis. Herein, we construct the Pd(II)-N sites on carbon nitride to achieve\n4\nphotocatalytic semi-hydrogenation of alkynes. Under light irradiation, the Pd-N sites\ncould transform to H-Pd···N-H moieties. The Pd-H center enhances alkyne insertion\nwhile the adjacent N-H group facilitates intramolecular proton transfer. This metal-\nligand cooperativity of H-Pd···N-H sites, together with the steric-hindrance imposed by\ncarbon nitride scaffold, lowers the energy barrier for Z-alkene formation and ensures\nexclusive stereoselectivity. Simultaneously, the H-Pd···N-H sites exhibit stronger\nadsorption toward alkynes than alkenes, effectively suppressing over-hydrogenation to\nalkanes. Across all evaluated substrates, Z-alkenes are the only isomers detected,\nexcluding E-isomer and alkane. Notably, in a 5:95 mixture of diphenylacetylene and Z-\nstilbene, this method selectively converts only the alkyne to the Z-isomer without over-\nhydrogenation, highlighting its potential for product purification."}]

Decision letter