The Behavior of NH3+ Torsional Vibration in Amino Acids: A Raman Spectroscopic Study
, Ricardo Jorge Cruz Lima 2 and Paulo Tarso Cavalcante Freire 3Round 1
Reviewer 1 Report
Reviewed manuscript deals with low temperature Raman spectroscopy of four amino acids - i.e. L-valine, L-isoleucine, taurine and L-arginine hydrochloride monohydrate. The authors focused on temperature dependence of the positions of the bands of NH3+ torsional vibration. They try to correlate this position with changes in hydrogen bonding in studied crystal structures. The topic is quite interesting but there are several issues to be clarified. I have following questions and comments:
1) I am missing clear motivation why particular amino acids were selected for the study. They differ by many aspects (functional groups, ionic state, hydrogen bonding, etc.).
2) The temperature behaviour of the selected Raman bands is discussed but all the explanations are only hypotheses without any experimental confirmation. I am missing DSC data (which may clarify questions concerning phase transitions) and low temperature X-ray diffraction experiments. Moreover, precision of the determination of discussed hydrogen bonds lengths is negatively influenced by the fact that particular crystal structures mentioned in the manuscript were solved almost 50 years ago.
3) Why are the spectra in Figure 1 presented at different temperatures?
Finally, I am recommending extending the list of experimental techniques at least to liquid nitrogen temperature to obtain more relevant data for discussion of the spectroscopic results.
Author Response
Reviewer #1
Reviewed manuscript deals with low temperature Raman spectroscopy of four amino acids - i.e. L-valine, L-isoleucine, taurine and L-arginine hydrochloride monohydrate. The authors focused on temperature dependence of the positions of the bands of NH3+ torsional vibration. They try to correlate this position with changes in hydrogen bonding in studied crystal structures. The topic is quite interesting but there are several issues to be clarified. I have following questions and comments:
1) I am missing clear motivation why particular amino acids were selected for the study. They differ by many aspects (functional groups, ionic state, hydrogen bonding, etc.).
A: The motivation of the investigation is to show how to obtain qualitative information about the hydrogen bonds in a large range of temperature (or other thermodynamics parameter) just analyzing data from vibrational spectroscopy. One reason to chose these amino acids is because there are some studies related to them. Beyond this, the methodology should be valid for amino acids in general, and this is another reason why we have chosen samples differing in several aspects as functional groups.
2) The temperature behaviour of the selected Raman bands is discussed but all the explanations are only hypotheses without any experimental confirmation. I am missing DSC data (which may clarify questions concerning phase transitions) and low temperature X-ray diffraction experiments. Moreover, precision of the determination of discussed hydrogen bonds lengths is negatively influenced by the fact that particular crystal structures mentioned in the manuscript were solved almost 50 years ago.
A: The question of the phase transitions presented by the amino acids is studied, at least, since the 70’s. So, it is well stablished that L-alanine – the most studied amino acid crystal investigated up to now – does not presente any phase transition at low temperatures (C.H. Wang, R.D. Storms, J. Chem. Phys. 55 (1971) 3291; H.J. Simpson, Jr., R.E. March, Acta Crystallogr. 20 (1966) 550; R. Destro, R.E. Marsh, R. Bianchi, J. Phys. Chem. 92 (1988) 966; M.S. Lehman, T.F. Koetzle, W.C. Hamilton, J. Am. Chem. Soc. 94 (1972) 2657; C.C. Wilson, D. Myles, M. Ghosh, L.N. Johnson, W. Wang, New J. Chem. 29 (2005) 1318, etc).
Regardind specifically the amino acids discussed in the present study, the following references furnish important informations (at low temperatures) obtained through Raman spectroscopy:
L-valine: indication of the occurrence of a phase transition at ~ 120 K (J.A. Lima Jr. et al., J. Raman Spectrosc. 36 (2005) 1076).
L-isoleucine: stablishment that the crystal structure is stable at low temperatures (F.M. Almeida et al., J. Raman Spectrosc. 37 (2006) 1296).
L-arginine hydrochloride monohydrate: indication of the occurrence of a phase transition at ~ 100 K (R.J.C. Lima et al., J. Raman Spectrosc. 33 (2002) 625).
Taurine: demonstration (also with the help of DSC measurements, beyond Raman spectroscopy) of the occurrence of a phase transition at ~ 251 K (R.J.C. Lima et al., J. Raman Spectrosc. 31 (2002) 751).
Again, the main point discussed in our manuscript is the understanding of the dynamics of hydrogen bonds in materials with biological interest in a large range of temperature, not at particular temperatures (room temperature or liquid nitrogen temperature). As a consequence, even though the crystal structures were determined several years ago, it represents only a secundary aspect of our discussion.
3) Why are the spectra in Figure 1 presented at different temperatures?
A: The spectra presented in Fig. 1 were those obtained at the lowest temperature in four diferent experiments; in the experiments on L-valine and L-isoleucine the lowest temperature obtained was 17 K, on L-arginine.HCl.H2O was 15 K and on taurine was 7 K.
Finally, I am recommending extending the list of experimental techniques at least to liquid nitrogen temperature to obtain more relevant data for discussion of the spectroscopic results.
A: As we have already discussed (answer 2), informations about the low temperature behavior of the crystal were previously published in the literature, so we think other experimental techniques are not relevant for the present discussion, which is focused on vibrational characteristics of the amino acid crystals.
Reviewer 2 Report
The authors found anomalous relationship between H-bond strengths and temperature, based on Raman spectroscopy on a crystal of L-isoleucine. The present manuscript demonstrates that the methodology can quantitatively evaluate changes of H-bonding and structural stability upon temperature. So, the manuscript can be acceptable for Crystals as it is.
Very trivial comments:
For abbreviation of hydrogen-bond, both H-bond and HB are used. It's better to use either of them.
Author Response
Reviewer #2
The authors found anomalous relationship between H-bond strengths and temperature, based on Raman spectroscopy on a crystal of L-isoleucine. The present manuscript demonstrates that the methodology can quantitatively evaluate changes of H-bonding and structural stability upon temperature. So, the manuscript can be acceptable for Crystals as it is.
Thank You for the comments.
Very trivial comments:
For abbreviation of hydrogen-bond, both H-bond and HB are used. It's better to use either of them.
For all hydrogen-bond abbreviation, “HB” was used.
Reviewer 3 Report
The manuscript can be accepted for publication as it is.
Author Response
Reviewer #3
The manuscript can be accepted for publication as it is.
A: Thank You for the comment.
Reviewer 4 Report
The manuscript titled " The behavior of NH3+ torsional vibration ..." by Cavaignac et al reports on the changes of geometric
parameters of the hydrogen bonds in amino acids crystals via the temperature or pressure. The Raman specroscopy was used to show that changes in geometric parameters of the hydrogen bonds is correlated with the temperature behavior of the Raman wavenumber of NH3+ torsional band. This observation is explained by analysis of the torsional vibration of ammonium group in junction with the H-bond associated with amino acid crystals. I can recommend publication
of this manuscript in Crystals after some improvements of the manuscript.
The powerful method of light scattering spectroscopy is described in the introduction
and the micro-Raman system was used as one major method of investigation,
therefore the some links regarding the wavenumber resolved Brillouin light scattering method, which
is actively used nowadays, should be mention.
It will be more instructive if Phys. Rev. B 99, 054424 (2019),
Phys. Rev. Lett. 120, 257203 (2018) are contained in the reference list along with Refs. 3-7.
The influence of the crystallographic orientation of studied crystals on the the wavenumber of the Raman bands
should be mentioned in the manuscript for the convenience of the general Reader.
The authors are asked to address this issues and I hope these corrections will improve the manuscript.
Author Response
Reviewer #4
The manuscript titled " The behavior of NH3+ torsional vibration ..." by Cavaignac et al reports on the changes of geometric parameters of the hydrogen bonds in amino acids crystals via the temperature or pressure. The Raman specroscopy was used to show that changes in geometric parameters of the hydrogen bonds is correlated with the temperature behavior of the Raman wavenumber of NH3+ torsional band. This observation is explained by analysis of the torsional vibration of ammonium group in junction with the H-bond associated with amino acid crystals. I can recommend publication of this manuscript in Crystals after some improvements of the manuscript.
The powerful method of light scattering spectroscopy is described in the introduction and the micro-Raman system was used as one major method of investigation, therefore the some links regarding the wavenumber resolved Brillouin light scattering method, which is actively used nowadays, should be mention. It will be more instructive if Phys. Rev. B 99, 054424 (2019), Phys. Rev. Lett. 120, 257203 (2018) are contained in the reference list along with Refs. 3-7.
The influence of the crystallographic orientation of studied crystals on the the wavenumber of the Raman bands should be mentioned in the manuscript for the convenience of the general Reader.
The authors are asked to address this issues and I hope these corrections will improve the manuscript.
A: We acknowledge the comments of the referee and the suggestions. We have discussed about the crystallographic orientation and we have also introduced these new references in our manuscript:
Sadovnikov, A. V., Grachev, A. A., Sheshukova, S. E., Sharaevskii, Y. P., Serdobintsev, A. A., Mitin, D. M., & Nikitov, S. A. (2018). Magnon straintronics: reconfigurable spin-wave routing in strain-controlled bilateral magnetic stripes. Physical review letters, 120(25), 257203.
Sadovnikov, A. V., Beginin, E. N., Sheshukova, S. E., Sharaevskii, Y. P., Stognij, A. I., Novitski, N. N., ... & Nikitov, S. A. (2019). Route toward semiconductor magnonics: Light-induced spin-wave nonreciprocity in a YIG/GaAs structure. Physical Review B, 99(5), 054424.
Round 2
Reviewer 1 Report
Revised manuscript unfortunately doesn’t contain any corrections concerning my comments and suggestions. Only minimal changes were made in Chapter 3 in the text concerning geometry of Raman spectra recording – unfortunately this extension contains only textbook knowledge associated with Raman study of oriented single crystals.
I do appreciate author’s response to all my comment especially concerning phase transitions – unfortunately this information should be present in the text of the manuscript not only as answer to reviewer. The discussion based on previously obtained results concerning latest crystallographic and spectroscopic studies is necessary for the understanding of the observed temperature behaviour of NH3+ torsional vibration. Especially low-temperature phase transformations, which are almost always associated with the changes of hydrogen bonding in the studied crystal, should be considered in the discussion concerning hydrogen bonds strengths.
Also the explanation concerning slightly different temperature range studied for particular samples should be included in the text of the manuscript.
Finally, I still recommend major revision of the manuscript to improve the relevance of the presented conclusions, which can be accomplished by the incorporation of previous spectroscopic and crystallographic results focused on studied amino acids to overall discussion.
Author Response
Dear editor,
The "answers to referees", with point-by-point discussion are below.
Revised manuscript unfortunately doesn’t contain any corrections concerning my comments and suggestions. Only minimal changes were made in Chapter 3 in the text concerning geometry of Raman spectra recording – unfortunately this extension contains only textbook knowledge associated with Raman study of oriented single crystals.
A: In the present version we have introduced a series of modifications as suggested by the referee [all modifications are marked by red letters]. Regarding specifically the geometry of the Raman spectra the explanation is done – as suggested by one of the previous referees – “for the convenience of the general reader”.
I do appreciate author’s response to all my comment especially concerning phase transitions – unfortunately this information should be present in the text of the manuscript not only as answer to reviewer. The discussion based on previously obtained results concerning latest crystallographic and spectroscopic studies is necessary for the understanding of the observed temperature behaviour of NH3+ torsional vibration. Especially low-temperature phase transformations, which are almost always associated with the changes of hydrogen bonding in the studied crystal, should be considered in the discussion concerning hydrogen bonds strengths.
A: We acknowledge the suggestions and the comments of the referee and included the discussion about phase transition at low temperatures taken from "answer to reviewers" into the manuscript text in "Results". We have included the references presented in “answer to reviewers" too. The new references are added on text between 11 and 19.
Also the explanation concerning slightly different temperature range studied for particular samples should be included in the text of the manuscript.
A: We have introduced this information in the text of the manuscript.
Finally, I still recommend major revision of the manuscript to improve the relevance of the presented conclusions, which can be accomplished by the incorporation of previous spectroscopic and crystallographic results focused on studied amino acids to overall discussion.
A: We have incorporated in the text of the manuscript several informations regarding spectroscopic and crystallographic results on studied amino acids as suggested by the referee.
Round 3
Reviewer 1 Report
Authors have significantly improved discussion concerning previous studies focused on low temperature behaviour of studied amino acids in revised manuscript. I hope that this improvement will help readers to understand better the presented results.
