Semiconductor SERS enhancement enabled by oxygen incorporation

Semiconductor-based surface-enhanced Raman spectroscopy (SERS) substrates represent a new frontier in the field of SERS. However, the application of semiconductor materials as SERS substrates is still seriously impeded by their low SERS enhancement and inferior detection sensitivity, especially for non-metal-oxide semiconductor materials. Herein, we demonstrate a general oxygen incorporation-assisted strategy to magnify the semiconductor substrate–analyte molecule interaction, leading to significant increase in SERS enhancement for non-metal-oxide semiconductor materials. Oxygen incorporation in MoS2 even with trace concentrations can not only increase enhancement factors by up to 100,000-fold compared with oxygen-unincorporated samples but also endow MoS2 with low limit of detection below 10−7 M. Intriguingly, combined with the findings in previous studies, our present results indicate that both oxygen incorporation and extraction processes can result in SERS enhancement, probably due to the enhanced charge-transfer resonance as well as exciton resonance arising from the judicious control of oxygen admission in semiconductor substrate.

This paper reports an exciting discovery, the kind of result that makes me want to try it out immediately myself (I will of course wait till publication!). First let me say that the paper is well presented, with clear and useful figures and, for the most part, very good and clear English, though some editorial attention is still required. The scientific content is comprehensive and thorough, with very few points where I wanted to ask for more information.
Importantly, the synthesis details (taking into account the SI) appear adequate for others to reproduce the work; this paper is certain to provoke attempts to reproduce its results and so this is essential. The detailed discussion of XPS spectra is useful as a very good way for others to compare their product materials.
The discussion of the sites occupied by oxygen in the lattice is very interesting and crediblethere are likely to be a lot of reports on ordering in alloy TMDs and there have already been some (mostly computational) discussions of related effects (for example, the ordering of vacancies). As ternary alloys attract more attention, the possibility of inducing ordering and of exercising control over their structure is very attractive -it will impact on many material properties besides SERS enhancements.
The charge transfer mechanism probably needs more work to prove this, but the comments here are valid and of course the paper would not be complete without attempting some understanding of the mechanism.
I would like to ask the authors if they can make some comments and provide any data on the following two scientific points: Firstly, the SERS community are always concerned with stability and reproducibility of SERS substrates; these issues have been the major obstacles to commercialisation of many promising ideas. Of course I am not saying that the authors should produce a recipe for a commerciallyviable SERS substrate here, but can they tell us anything already about the working lifetime and sensitivity to contamination of their material?
Secondly, I would be very interested to see (perhaps in the SI) the Raman spectra of the different materials without R6G, for two reasons: (i) this will be of assistance to others in reproducing the starting materials, and (ii) I'd expect it to be another indicator of the different types of incorporation of oxygen that the authors present. I was surprised these spectra were not presented. In this context, I note that there is a very strong peak in the Raman spectra at ~600 cm-1. This does more or less correspond to an R6G peak, though not a strong one. However, it is where I might also expect local vibrational modes of Mo-O to appear. Can the authors confirm explicitly that *all* the Raman peaks they show are due to R6G? I think it is implied but not said.

Other minor corrections:
Abstract -should spell out "LOD" in full p5 lines 110-111 "The significant difference between substitution and oxidation is Mo(VI) can be observed in partial oxidation process but not in oxygen substitution process" I misunderstood this sentence at first; I think it might help to say "is that Mo(VI) can be observed in the partial oxidation process but not in the oxygen substitution process" -authors please confirm! p6 line 114 "hydrothermal treatment of (NH4)6Mo7O24·4H2O is performed" Does this mean "treatment of thiourea in (NH4)..."? I think this is important enough to be absolutely clear in the main text even if it's in the SI. Same comment applies to the figure 1 caption. p14 line 303 "exhilaratingly" This is perhaps over the top! I think it's the first time in my career that I've seen this word in a scientific paper so, whilst I appreciated the authors' attempt to use interesting language, I'd tone it down a bit. p19 line 388 "through Fermi's golden rule" Not sure why it's necessary to mention FGR here -it's such a general principle that it doesn't add any information to say this.

Answer to reviewer's comments:
We would like to thank all the reviewers for their deep and thorough reviewing of our manuscript. In view of these constructive and helpful comments, we have carefully and substantially revised our manuscript. Here are the detailed responses to the comments of the reviewers.

Replies on comments of reviewer 1:
Comment 1: In this article, the authors present a new way of preparation of a semiconductor substrate for surface-enhanced Raman spectroscopy (SERS), which involves partial oxidation of an MoS 2 surface. Enhancements of up to 1.25 x 10 5 are obtained with Rhodamine 6G (R6G), and remarkably low limits of detection are also observed.
SERS on metal substrates has been found to support enhancement factors of over 10 11 , allowing single molecule detection. In semiconductors, due to the lack of a plasmon resonance, enhancements have been considerable smaller, at best on the order of 10 5 to 10 6 . However, even that is often adequate for construction of sensors.
Semiconductors have other advantages such as stability, and reproducibility, which in many cases make them superior to metals for certain applications, and are therefore currently a hot topic of research. The SERS enhancement in semiconductors relies on a charge-transfer mechanism rather than plasmon resonances, and the authors correctly identify this as the most important contribution to their remarkable observations. The experimental part of this paper is beautiful and of considerable interest in that it paves the way to construct semiconductor SERS substrates which are sensitive, stable and reproducible Author reply: Thanks for the referee's comments.

Comment 2:
Another important aspect of this work is the ability, by controlling the extent of oxidation, to adjust the energy levels of the substrate to allow specific molecules to be selected by means of adjusting the location of a charge-transfer transition. This aspect deserves more attention by the authors. The major weakness of this article is the authors' total misunderstanding of the theory of SERS in semiconductors, and therefore needs substantial revision.
Author reply: We greatly appreciate the valuable suggestion on the understanding of the theory behind semiconductor SERS! We have re-examined our experimental and simulation results very carefully. For example, to obtain more accurate simulation results, we apply the GW method with more computational cost than standard DFT to correct the band energies. Based on these efforts, we have rewritten the discussion section of mechanism studies in the manuscript, especially under the guidance of the reviewer, which emphasizes the importance of the coupling of charge transfer, and molecular and exciton resonances in our system. The revised words are marked in blue in the manuscript, and listed as below: The mechanism of oxygen-incorporation-assisted SERS enhancement. In our recent studies, it has been established that oxygen vacancies play an important role in enhancing semiconductor SERS effect (Nat. Commun. 2015, 6, 7800). The present findings unexpectedly show that the inverse process of making oxygen vacancies, oxygen incorporation, could also effectively magnify the SERS signals of semiconductor materials. Taken together, it is interesting to see whether the SERS enhancement effect induced by oxygen vacancies and oxygen incorporation reply on the same mechanism. Taking its cue from Lombardi et al.' pioneering theory on the SERS mechanism related to semiconductor materials (J. Phys. Chem. C 2014, 118, 11120-11130), we consider if some resonances such as charge-transfer, exciton and molecular resonances are involved in the mechanism.
Charge-transfer resonance is a resonance Raman-like process associated with the photon-induced charge transfer from the semiconductor band edges to the affinity levels of the adsorbed molecule. This results in a change of the polarizability of the molecule, and consequently amplifies the intensity of its Raman signal (Adv. Mater. 2017, 29, 1604797). For our partially-oxidized MoS 2 samples, there are considerable experimental evidences for charge-transfer through vibronic coupling. Note for example, in Fig. 4, the lines at 612 cm -1 and 773 cm -1 (corresponding to in-plane and out-of-plane bending motion of the hydrogen atoms of the xanthene skeleton, respectively) can be seen to be the most enhanced lines in the spectra. These lines are well-known to be vibronically coupled (J. Phys. Chem. 1984, 88, 5935-5944), and therefore tend to be highly enhanced in SERS wherever charge-transfer is important. Comparative analysis of the energy level structures of pristine MoS 2 , partially-oxidized MoS 2 , fully-oxidized MoO 3 and R6G further indicates that partially-oxidized MoS 2 provides significant advantages over other samples in charge transfer. As depicted in Fig. 6, when R6G is used as the target molecule, its HOMO and LUMO levels are at -5.7 eV and -3.4 eV, respectively. Examining the energy levels of the above three semiconductors, we find that the fully-oxidized MoO 3 has a relatively large band gap of 3.1 eV compared to other two materials, with two types of possible charge-transfer transitions from VB to LUMO at 3.96 eV and from HOMO to CB at 1.44 eV. Obviously, neither of charge-transfer transition energies is at or near the excitation laser energy (λ L =2.33 eV), thus leading to low SERS enhancement.
In contrast, both pristine MoS 2 and partially-oxidized MoS 2 have much smaller bandgaps of 1.29 and 0.56 eV, respectively, but the CB and VB positions of partially-oxidized MoS 2 is remarkably downshifted compared to that of pristine MoS 2 (Fig. 6c,d), which then causes quite different charge-transfer transitions in two samples. For pristine MoS 2 , charge-transfer transitions from VB to LUMO and from HOMO to CB occur at 1.80 and 1.79 eV, respectively, whereas the corresponding charge-transfer transitions for partially-oxidized MoS 2 occur at 2.26 and 0.60 eV, respectively. Although the charge-transfer transitions from VB to LUMO of both materials are possible to induce a charge-transfer resonance (λ CT ≈λ L ), the downshifted VB position after oxygen incorporation in partially-oxidized MoS 2 makes its charge-transfer transition energy (2.26 eV) much closer to the excitation laser energy when compared with that for pristine MoS 2 (1.80 eV), thus a stronger charge-transfer resonance can be expected for partially-oxidized MoS 2 . Moreover, similar to the observation for amorphous ZnO (Angew. Chem. Int. Ed. 2017, 56, 9851-9855), the formation of large quantities of highly-localized dangling bonds upon partial oxidation such as Mo-S-O, S-O bonds in our samples can also weaken the constraint to the surface electrons by a redistribution of the electron density in MoS 2 , which effectively improve the charge-transfer efficiency and further contribute to the SERS enhancement.
Although crucial to the high Raman enhancement on partially-oxidized MoS 2 is the existence of a charge-transfer resonance, other resonances in the system also contribute to the enhancement. Exciton resonance, which depends on the electronic structure of semiconductors, is recently found to be likely to play a large role in semiconductor SERS (ACS Photonics 2016, 3, 1164-1169J. Phys. Chem. C 2014, 118, 11120-1113. In pristine MoS 2 , these are well-known A, B, C and D exciton  Fig. 12), which may be a signature of the metallic nature of partially-oxidized MoS 2 as often being observed in highly-doped semiconductor compounds (Adv. Mater. 2015, 27, 3152-3158). Based on the above analysis of direct excitonic transitions, only two allowed direct transitions at the K point are in the vicinity of the laser excitation to get effective resonances for pristine MoS 2 (Fig. 6a).
In comparison, besides K-point transitions, another three M-point transitions can also participate in resonance with incident laser for partially-oxidized MoS 2 (Fig. 6b), in which the increased population of exciton resonances may be an important contribution to the charge-transfer effects through vibronic coupling. In addition, note that the molecular transition between the HOMO and LUMO levels of R6G at 2.3 eV is also near the laser (in this case 532.8 nm or 2.33 eV), which provides another resonant pathway to further enhance SERS effect.
Significantly, it should be emphasized that the three resonances involved in semiconductor SERS don't work independently. Instead, the mechanism for Raman enhancement involves the coupling of the charge-transfer resonance with one of the other, more intensely allowed transitions in the molecule-semiconductor system, either molecular resonance or exciton resonance (J. Phys. Chem. C 2014, 118, 11120-1113. On coupling, the normally weak charge-transfer resonance borrows intensity from the stronger nearby resonances, which can be expressed by a  Based on the studies about the effect of oxygen incorporation (this work) and oxygen extraction (our previous work) on SERS, the observed SERS enhancement arising from oxygen incorporation and oxygen extraction seems to share a unified mechanism that involves: 1) additional energy levels facilitates the possibility of charge-transfer between semiconductor and analyte molecule, which is in resonance with incident photons, 2) the improvement of exciton resonances brings about stronger intensity borrowing to the charge-transfer resonance in the semiconductor-molecule system. Therefore, by manipulating oxygen atoms in the lattice of semiconductor substrate through either incorporation or extraction to adjust the energy levels of the substrate, the location of both charge-transfer transition and exciton transition would be modulated, which is important to the achievement of highly-enhanced SERS signals for specific molecules.

Comment 3:
Firstly, the authors should be aware that there is considerable evidence for charge-transfer through vibronic coupling in their own spectra. Note for example, in figure 4, the lines at 612 cm -1 and 773 cm -1 can be seen to be the most enhanced lines in the spectra. These lines are well-known to be vibronically coupled (J. Phys. Chem. 1984, 88, 5935-5944), and therefore tend to be highly enhanced in SERS wherever charge-transfer is important. Vibronic coupling is very important to Raman enhancement due to proximity to a surface, and is intimately tied up with charge-transfer effects Author reply: Thanks for the referee's comments. As the most important contribution to our remarkable semiconductor SERS enhancement, charge-transfer resonance has been extensively discussed in the revised manuscript as follows: "Charge-transfer resonance is a resonance Raman-like process associated with the photon-induced charge transfer from the semiconductor band edges to the affinity levels of the adsorbed molecule. This results in a change of the polarizability of the molecule, and consequently amplifies the intensity of its Raman signal (Adv. Mater. 2017, 29, 1604797). For our partially-oxidized MoS 2 samples, there are considerable experimental evidences for charge-transfer through vibronic coupling. Note for example, in Fig. 4, the lines at 612 cm -1 and 773 cm -1 (corresponding to in-plane and out-of-plane bending motion of the hydrogen atoms of the xanthene skeleton, respectively) can be seen to be the most enhanced lines in the spectra. These lines are well-known to be vibronically coupled (J. Phys. Chem. 1984, 88, 5935-5944), and therefore tend to be highly enhanced in SERS wherever charge-transfer is important. Comparative analysis of the energy level structures of pristine MoS 2 , partially-oxidized MoS 2 , fully-oxidized MoO 3 and R6G further indicates that partially-oxidized MoS 2 provides significant advantages over other samples in charge transfer. As depicted in Fig. 6, when R6G is used as the target molecule, its HOMO and LUMO levels are at -5.7 eV and -3.4 eV, respectively. Examining the energy levels of the above three semiconductors, we find that the fully-oxidized MoO 3 has a relatively large band gap of 3.1 eV compared to other two materials, with two types of possible charge-transfer transitions from VB to LUMO at 3.96 eV and from HOMO to CB at 1.44 eV. Obviously, neither of charge-transfer transition energies is at or near the excitation laser energy (λ L =2.33 eV), thus leading to low SERS enhancement. Author reply: Thanks for the referee's comments. As mentioned before, the coupling of several resonances in our system has been extensively discussed in the revised manuscript as follows: "Significantly, it should be emphasized that the three resonances involved in semiconductor SERS don't work independently. Instead, the mechanism for Raman enhancement involves the coupling of the charge-transfer resonance with one of the other, more intensely allowed transitions in the molecule-semiconductor system, either molecular resonance or exciton resonance (J. Phys. Chem. C 2014, 118, 11120-1113. On coupling, the normally weak charge-transfer resonance borrows intensity from the stronger nearby resonances, which can be expressed by a I think this is what the authors are alluding to when they invoke "dipole-dipole" coupling, but their discussion of it is somewhat vague and disjointed. The way it is presented in this article sounds quite speculative. First note that in order to explain such a large enhancement, the charge-transfer energy should be near the laser (in this case 532.8 nm or 2.32 eV). As illustrated in their figure 6, it is nowhere near that (0.72 eV in 6c and 1.44 eV in 6d). It is, however, near the transition from the VB of MoS 2 (-5.90 eV) and the LUMO of R6G (-3.40 eV) which lies about 2.5 eV. Notice this is also close to the molecular transition at 2.3 eV (5.70-3.40). Thus, the coupling between the molecular transition and the CT transition should be strong and make a rather large contribution to the enhancement.
Author reply: Thanks for the referee's comments. As mentioned before, the following paraphs have been added in the revised manuscript as follows: "Comparative analysis of the energy level structures of pristine MoS 2 , partially-oxidized MoS 2 , fully-oxidized MoO 3 and R6G further indicates that partially-oxidized MoS 2 provides significant advantages over other samples in charge transfer. As depicted in Fig. 6, when R6G is used as the target molecule, its HOMO and LUMO levels are at -5.7 eV and -3.4 eV, respectively. Examining the energy levels of the above three semiconductors, we find that the fully-oxidized MoO 3 has a relatively large band gap of 3.1 eV compared to other two materials, with two types of possible charge-transfer transitions from VB to LUMO at 3.96 eV and from HOMO to CB at 1.44 eV. Obviously, neither of charge-transfer transition energies is at or near the excitation laser energy (λ L =2.33 eV), thus leading to low SERS enhancement. "In addition, note that the molecular transition between the HOMO and LUMO levels of R6G at 2.3 eV is also near the laser (in this case 532.8 nm or 2.33 eV), which provides another resonant pathway to further enhance SERS effect." Furthermore, according to referee 2's suggestions, we also discuss the role of dangling bond on charge-transfer transition and SERS performance. In a very recent study (Angew. Chem. Int. Ed. 2017, 56, 9851-9855) provide by referee 2, it has been found that the amorphous ZnO could effectively improve the charge transfer efficiency and magnify the molecular polarization. In particular, the absence of long-range order in the atomic positions can create dangling bonds and band tails, and their arbitrary arrangement makes the energy of the system at the metastable state. The metastable electronic states in amorphous materials, such as the localized band tail states and unpaired electrons in a hybrid orbital, could effectively facilitate the electron escape and transfer. Referee 2 believes that the dangling bonds in our partially-oxidized samples also have a similar effect on SERS with those in amorphous ZnO, so an additional paragraph is added in the revised manuscript as follows:  Supplementary Fig. 12), which may be a signature of the metallic nature of partially-oxidized MoS 2 as often being observed in highly-doped semiconductor compounds (Adv. Mater. 2015, 27, 3152-3158). Based on the above analysis of direct excitonic transitions, only two allowed direct transitions at the K point are in the vicinity of the laser excitation to get effective resonances for pristine MoS 2 (Fig. 6a).
In comparison, besides K-point transitions, another three M-point transitions can also participate in resonance with incident laser for partially-oxidized MoS 2 (Fig. 6b), in which the increased population of exciton resonances may be an important contribution to the charge-transfer effects through vibronic coupling." Comment 7: In any case, this article is potentially ground-breaking in its construction of a high-enhancement semiconductor for SERS. However, it is weak in its analysis of the mechanism of the enhancement and can be strengthened considerably by proper application of theory.
Author reply: Thanks for the referee's comments. Under your kind guidance, we believe that the analysis of SERS enhancement mechanism in the revised manuscript has been considerably strengthened on the basis of the coupling of charge transfer, and molecular and exciton resonances.

Replies on comments of reviewer 2:
Comment 1: This is an interesting paper, in which author clearly demonstrated the oxygen-incorporation-assisted approach in improving the SERS performance of non-metal-oxide semiconductors. The experimental results are convinced, which also agree well with the simulations.
In the previous study from this group (S. Cong, et al., Nature Comm. 2015, 6, 7800), the author have found that introducing the oxygen vacancies into semiconductor nanomaterials can effectively enhance the SERS effect. In this paper, the author showed its inverse process that oxygen incorporation could also effectively magnify the SERS signals of semiconductor materials.
Author reply: Thanks for the referee's comments.

Comment 2:
To obtain a general mechanism of those results, the author believes that both effects of oxygen incorporation and oxygen extraction can cause different degrees of lattice distortion, leading to increased electron-transition probability and symmetry-related perturbance. This is indeed the mechanism suggested by the authors, who suggest the lattice distortion can lead to the remarkable SERS activity of semiconductor nanomaterials.

Replies on comments of reviewer 3:
Comment 1: I cannot recommend the publication of this manuscript in Nature Communication mainly because the originality and novelty of the manuscript are insufficient. To be accepted in Nature Communication much higher originality and novelty are needed．Semiconductor SERS spectroscopy is not always new. Already many papers and reviews on it have been published. Compared with those previous works the present work may increase enhancement factor of semiconductor SERS but it is not so remarkable to justify the publication in Nature Communication. The theoretical discuss described is also just modified one not original one.
Author reply: Thanks for the referee's comments! Firstly, we would like to further emphasize the originality and novelty of our manuscript. Semiconductor materials as SERS substrates has already been widely studied, however, the application of these materials is still seriously impeded by their low SERS enhancement and inferior detection sensitivity, especially for non-metal-oxide semiconductor materials. To the best of our knowledge, there are few viable routes to enormously boosting the SERS signals of non-metal-oxide semiconductor materials. For the first time, we demonstrate that oxygen incorporation in MoS 2 even with trace concentrations can not only dramatically increase enhancement factors by up to 100,000 folds compared with oxygen-unincorporated samples, but also endow MoS 2 with low limit of detection below 10 -7 M. Perhaps the enhancement factors of our materials are not the topmost, but we believe that the unique oxygen-incorporation-assisted approach may provide new insights into the CM process in SERS between semiconductor substrates and probe molecules, and in our recent works we always hammer away at finding a universal methodology for the design and optimization of semiconductors as advanced SERS substrates.
Secondly, in the present work, we try to provide a unified mechanism for both oxygen-incorporation-assisted and oxygen-vacancies-assisted SERS enhancement at a much deeper level. The mechanism involves: 1) additional energy levels facilitates the possibility of charge-transfer between semiconductor and analyte molecule, which is in resonance with incident photons, 2) the improvement of exciton resonances brings about stronger intensity borrowing to the charge-transfer resonance in the semiconductor-molecule system. Therefore, by manipulating oxygen atoms in the lattice of semiconductor substrate through either incorporation or extraction to adjust the energy levels of the substrate, the location of both charge-transfer transition and exciton transition would be modulated, which is important to the achievement of highly-enhanced SERS signals for specific molecules.

Comment 2:
The authors did not cite many important papers on semiconductor SERS from Prof.
Bing Zhao group of Jilin University, China who is one of the leaders in this field. The authors should consider more fair citation.
Author reply: Thanks for the referee's valuable comments and suggestion. Prof. Bing Zhao is a respectable scientist and one of the leaders in semiconductor SERS field. We have cited several important papers on semiconductor SERS from Prof.
Bing Zhao group in the revised manuscript.

Replies to additional comments:
Comment 1: The editors have asked me to make additional comments on the advancement and novelty of this work in the light of a previously published article, apparently from the same laboratory (S. Cong, et al., Nature Commun. 2015, 6, 7800). There are several apparent similarities between the two articles. Both involve modification of a semiconductor surface, which shows a relatively weak Raman enhancement. The modification results in a considerable increase in enhancement and therefore is suggested as a ground-breaking improvement in our ability to exploit semiconductors as high quality SERS substrates. The differences between the two articles are that the substrates are quite different (WO 3 and MoS 2 ). One was modified by reduction, and the other by oxidation. Oddly, their theoretical interpretation of their results was quite good in the first article, and rather vague and unlikely in the second.
Author reply: Thanks for the referee's comments and suggestions. In this revised manuscript, we have rewritten the discussion section of mechanism studies to make our theoretical interpretation more plausible. Based on our experimental and DFT simulation results in this work, we have systematically analyzed the contributions to an enhanced SERS from several resonances, including charge transfer, molecular and exciton resonances, and emphasize the importance of the coupling of these resonances in our system. Furthermore, at the end of this paper, we have taken a unified view to illustrate the SERS enhancement of semiconductors upon either oxygen incorporation (present work) or oxygen-extraction (our previous work), which is original as theoretical discussions about semiconductor SERS. Charge-transfer resonance is a resonance Raman-like process associated with the photon-induced charge transfer from the semiconductor band edges to the affinity levels of the adsorbed molecule. This results in a change of the polarizability of the molecule, and consequently amplifies the intensity of its Raman signal (Adv. Mater. 2017, 29, 1604797). For our partially-oxidized MoS 2 samples, there are considerable experimental evidences for charge-transfer through vibronic coupling. Note for example, in Fig. 4, the lines at 612 cm -1 and 773 cm -1 (corresponding to in-plane and out-of-plane bending motion of the hydrogen atoms of the xanthene skeleton, respectively) can be seen to be the most enhanced lines in the spectra. These lines are well-known to be vibronically coupled (J. Phys. Chem. 1984, 88, 5935-5944), and therefore tend to be highly enhanced in SERS wherever charge-transfer is important. Comparative analysis of the energy level structures of pristine MoS 2 , partially-oxidized MoS 2 , fully-oxidized MoO 3 and R6G further indicates that partially-oxidized MoS 2 provides significant advantages over other samples in charge transfer. As depicted in Fig. 6, when R6G is used as the target molecule, its HOMO and LUMO levels are at -5.7 eV and -3.4 eV, respectively. Examining the energy levels of the above three semiconductors, we find that the fully-oxidized MoO 3 has a relatively large band gap of 3.1 eV compared to other two materials, with two types of possible charge-transfer transitions from VB to LUMO at 3.96 eV and from HOMO to CB at 1.44 eV. Obviously, neither of charge-transfer transition energies is at or near the excitation laser energy (λ L =2.33 eV), thus leading to low SERS enhancement.

The mechanism of oxygen-incorporation-assisted SERS
In contrast, both pristine MoS 2 and partially-oxidized MoS 2 have much smaller bandgaps of 1.29 and 0.56 eV, respectively, but the CB and VB positions of partially-oxidized MoS 2 is remarkably downshifted compared to that of pristine MoS 2 (Fig. 6c, d) Supplementary Fig. 12), which may be a signature of the metallic nature of partially-oxidized MoS 2 as often being observed in highly-doped semiconductor compounds (Adv. Mater. 2015, 27, 3152-3158). Based on the above analysis of direct excitonic transitions, only two allowed direct transitions at the K point are in the vicinity of the laser excitation to get effective resonances for pristine MoS 2 (Fig. 6a).
In comparison, besides K-point transitions, another three M-point transitions can also participate in resonance with incident laser for partially-oxidized MoS 2 (Fig. 6b), in which the increased population of exciton resonances may be an important contribution to the charge-transfer effects through vibronic coupling. In addition, note that the molecular transition between the HOMO and LUMO levels of R6G at 2.3 eV is also near the laser (in this case 532.8 nm or 2.33 eV), which provides another resonant pathway to further enhance SERS effect.
Significantly, it should be emphasized that the three resonances involved in semiconductor SERS don't work independently. Instead, the mechanism for Raman enhancement involves the coupling of the charge-transfer resonance with one of the other, more intensely allowed transitions in the molecule-semiconductor system, either molecular resonance or exciton resonance (J. Phys. Chem. C 2014, 118, 11120-1113. On coupling, the normally weak charge-transfer resonance borrows intensity from the stronger nearby resonances, which can be expressed by a  Based on the studies about the effect of oxygen incorporation (this work) and oxygen extraction (our previous work) on SERS, the observed SERS enhancement arising from oxygen incorporation and oxygen extraction seems to share a unified mechanism that involves: 1) additional energy levels facilitates the possibility of charge-transfer between semiconductor and analyte molecule, which is in resonance with incident photons, 2) the improvement of exciton resonances brings about stronger intensity borrowing to the charge-transfer resonance in the semiconductor-molecule system. Therefore, by manipulating oxygen atoms in the lattice of semiconductor substrate through either incorporation or extraction to adjust the energy levels of the substrate, the location of both charge-transfer transition and exciton transition would be modulated, which is important to the achievement of highly-enhanced SERS signals for specific molecules.
Comment 2: In retrospect, now reading the first article, the current article does not seem as novel or ground-breaking as I previously thought. There are differences, as I pointed out above, and they are important, as part of the overall narrative of SERS in semiconductors, and together they represent important and novel advances in these materials. They should definitely be published in some journal, but I am not so convinced as to whether they are of sufficient novelty for Nature Communications.
Author reply: Thanks for the referee's comments. Firstly, we would like to further emphasize the originality and novelty of our manuscript. Semiconductor materials as SERS substrates has already been widely studied, however, the application of these materials is still seriously impeded by their low SERS enhancement and inferior detection sensitivity, especially for non-metal-oxide semiconductor materials. To the best of our knowledge, there are few viable routes to enormously boosting the SERS signals of non-metal-oxide semiconductor materials. For the first time, we demonstrate that oxygen incorporation in MoS 2 even with trace concentrations can not only dramatically increase enhancement factors by up to 100,000 folds compared with oxygen-unincorporated samples, but also endow MoS 2 with low limit of detection below 10 -7 M. Perhaps the enhancement factors of our materials are not the topmost, but we believe that the unique oxygen-incorporation-assisted approach may provide new insights into the CM process in SERS between semiconductor substrates and probe molecules, and in our recent works we always hammer away at finding a universal methodology for the design and optimization of semiconductors as advanced SERS substrates.
Secondly, in the present work, we try to provides a unified mechanism for both oxygen-incorporation-assisted and oxygen-vacancies-assisted SERS enhancement at a much deeper level. The mechanism involves: 1) additional energy levels facilitates the possibility of charge-transfer between semiconductor and analyte molecule, which is in resonance with incident photons, 2) the improvement of exciton resonances brings about stronger intensity borrowing to the charge-transfer resonance in the semiconductor-molecule system. Therefore, by manipulating oxygen atoms in the lattice of semiconductor substrate through either incorporation or extraction to adjust the energy levels of the substrate, the location of both charge-transfer transition and exciton transition would be modulated, which is important to the achievement of highly-enhanced SERS signals for specific molecules.

Replies on comments of reviewer 4:
Comment 1: This paper reports an exciting discovery, the kind of result that makes me want to try it out immediately myself (I will of course wait till publication!). First let me say that the paper is well presented, with clear and useful figures and, for the most part, very good and clear English, though some editorial attention is still required. The scientific content is comprehensive and thorough, with very few points where I wanted to ask for more information.
Importantly, the synthesis details (taking into account the SI) appear adequate for others to reproduce the work; this paper is certain to provoke attempts to reproduce its results and so this is essential. The detailed discussion of XPS spectra is useful as a very good way for others to compare their product materials.
The discussion of the sites occupied by oxygen in the lattice is very interesting and credible -there are likely to be a lot of reports on ordering in alloy TMDs and there have already been some (mostly computational) discussions of related effects (for example, the ordering of vacancies). As ternary alloys attract more attention, the possibility of inducing ordering and of exercising control over their structure is very attractive -it will impact on many material properties besides SERS enhancements.
The charge transfer mechanism probably needs more work to prove this, but the comments here are valid and of course the paper would not be complete without attempting some understanding of the mechanism.
Author reply: Thanks for the referee's comments! Comment 2: I would like to ask the authors if they can make some comments and provide any data on the following two scientific points: Firstly, the SERS community are always concerned with stability and reproducibility of SERS substrates; these issues have been the major obstacles to commercialisation of many promising ideas. Of course I am not saying that the authors should produce a recipe for a commercially-viable SERS substrate here, but can they tell us anything already about the working lifetime and sensitivity to contamination of their material?
Author reply: Thanks for the referee's kind comments and suggestion. We have carefully examined the working lifetime as well as sensitivity to contamination of our partially-oxidized samples as SERS substrates. Detailed experimental process and results are added in the SI, and also listed as follows: SERS performances of partially-oxidized samples obtained at 300 °C for 40 mins upon contamination with (a) methyl green (MG) or (c) methylene blue (MB). Another major concern in using SERS substrate is whether there will be interferences caused by the interaction of the contaminants. R6G-MG and R6G-MB solutions are prepared as model systems by mixing 1 mL of the 1 × 10 −4 M solution of R6G with 9 mL of the 1 × 10 −5 M solution of MG or MB solution. (a) shows the SERS spectra of R6G, MG and R6G-MG mixture, while (c) shows the SERS spectra of R6G, MB and R6G-MB mixture. As evident from these figures, the SERS spectrum of R6G seems not to be inhibited by the presence of MG or MB, showing good selectivity and sensitivity for R6G detection.

Comment 3:
Secondly, I would be very interested to see (perhaps in the SI) the Raman spectra of the different materials without R6G, for two reasons: (i) this will be of assistance to others in reproducing the starting materials, and (ii) I'd expect it to be another indicator of the different types of incorporation of oxygen that the authors present. I was surprised these spectra were not presented. In this context, I note that there is a very strong peak in the Raman spectra at ~600 cm -1 . This does more or less correspond to an R6G peak, though not a strong one. However, it is where I might also expect local vibrational modes of Mo-O to appear. Can the authors confirm explicitly that *all* the Raman peaks they show are due to R6G? I think it is implied but not said.
Author reply: Thanks for the referee's valuable suggestion. We have systematically examined the Raman spectra of R6G, pristine MoS 2 without R6G loading and partially-oxidized MoS 2 samples without R6G loading. With an increase of the oxidation temperature, the Raman spectra undergo obvious changes for MoS 2 samples.
Specifically, the Raman bands of the samples at low-temperature treatment (MoS 2 -200 °C and MoS 2 -300 °C) indicate the coexistence of Mo-S and Mo-O bonds, while for MoS 2 -350 °C sample after high-temperature treatment, the disappearance of A 1g (405 cm -1 ) band evidences a decreased amount of S component as well as the phase transition from pristine MoS 2 towards fully-oxidized MoO 3 (a). Furthermore, by comparing the Raman spectra of R6G and partially-oxidized MoS 2 samples without R6G loading (b), it is concluded that the peak in the Raman spectra at ~600 cm -1 corresponds to R6G peak but not the local vibrational mode of Mo-O bond.
More detailed information has been provided in the revised manuscript, and also listed as follows:  Comment 4:

Supplementary
Abstract -should spell out "LOD" in full Author reply: Thanks for the referee's comments. We have added a full expression for this.
"…., but also endow MoS 2 with low limit of detection (LOD) below 10 -7 M." Comment 5: p5 lines 110-111 "The significant difference between substitution and oxidation is Mo(VI) can be observed in partial oxidation process but not in oxygen substitution process" I misunderstood this sentence at first; I think it might help to say "is that Mo(VI) can be observed in the partial oxidation process but not in the oxygen substitution process" -authors please confirm! Author reply: Thanks for the referee's comments. We have rewritten this sentence as follows: "The significant difference between substitution and oxidation is that Mo(VI) can be observed in the partial oxidation process but not in the oxygen substitution process." This is perhaps over the top! I think it's the first time in my career that I've seen this word in a scientific paper so, whilst I appreciated the authors' attempt to use interesting language, I'd tone it down a bit.