Tuesday, March 17, 2015

Towards first submission to journal (2)

I have now added the new version of the "Towards atomistic resolution structure of phosphatidylcholine glycerol backbone and choline headgroup at different ambient conditions" manuscript in the GitHub:

The filenames for this version are HGmodel_ACStemplate.tex and
HGmodel_ACStemplate.pdf. The latter can be found also from the Dropbox link.

The manuscript has been now put in the ACS template and the current idea is to submit it first to the Journal of American Chemical Society (JACS), for the reasons discussed in the Towards first submission to journal post. I have now modified the abstract and conclusions to be more suitable for this journal. The journal for the first submission can be still discussed if there are objections from the authors.

Otherwise, I hope that the current version will become the final version for the first submission once the issues written with red in the manuscript are fixed.

If you want to proofread, or otherwise comment the manuscript, the most convenient way is that you modify directly the HGmodel_ACStemplate.tex file and make a pull request to update the changes also to the GitHub. More traditional options for commenting/modifying can be used, however the changes should be made somehow visible.

We have also started to use the issue tracker in GitHub and it seems to be quite convenient, at least from my point of view:

There are issues related to this version as well, and do not be shy to add more. I think that especially more detailed and technical issues are convenient to deal with the issue tracker.

I am now also writing the draft of the cover letter, and I will add this to the GitHub also in the near future.


  1. I have now added also the first draft of the cover letter into the github:

    You can comment that one as well.

  2. Hi Samuli and all,

    First of all (and again), congratulations for the very nice lipid blog idea, It seems to be working very nicely. Although I did not find the time yet to read your manuscript carefully and completely, for avoiding any possible misinterpretations, I would advice that you change the text concerning the NMR calculation of order parameters S_CH. As it is now, it may induce to calculate wrongly S_CH from dipolar splittings as simply,

    S_CH= (4\pi <(r_CH)^3>) / (h \nu_0 \gamma_H \gamma_C) * splitting,

    when the accurate equation to use crucially depends on the $^1$H--$^{13}$ NMR method used. It is thus important to write the equation as

    S_CH= (4\pi <(r_CH)^3>) / (h \nu_0 \gamma_H \gamma_C) * scaling factor * splitting,

    and clearly state that the scaling factor depends on the $^1$H--$^{13}$ NMR method used.

    I would also additionally suggest two second (but very minor) changes:

    -to replace all expressions "$^{13}$C NMR" by "$^1$H-$^{13}$C NMR"


    -to replace expression " The absolute values of order parameters from the measured quadrupolar splitting [\Delta\nu] ... are calculated using … " by a sentence that explicitly states the correct [\Delta\nu] to be used. Maybe something like " The absolute values of order parameters are calculated using [Equation], where the quadrupolar splitting [\Delta\nu] corresponds to either (i) the distance in Hz between the horns of the powder pattern in a $^2$H spectrum in case of samples with lamellar liquid crystallites randomly oriented, or (ii) the distance in Hz between the two peaks of the $^2$H spectra measured from samples with uniformly aligned bilayers oriented perpendicularly to the magnetic field”.

    Again, Congratulations for the very nice work!


    1. Thanks for the comments!

      I have now changed the text to this:

      "The absolute values of order parameters from the effective dipolar coupling d_CH (1H-13C NMR) are calculated using [equation], where values between 20.2-22.7 kHz are used for [prefactor], depending on the original authors. The effective dipolar coupling d_CH is related to the measured dipolar splitting through scaling factor which depends on the pulse sequence used in the 1H-13C NMR experiment. "

      So in the equation I have the effective dipolar coupling, not splitting. And then I mention that the connection to the splitting depends on the method.

      I have replaced "$^{13}$C NMR" by "$^1$H-$^{13}$C NMR"

      About the last comment, I am not sure if we need such details here. Or are there some other quadrupolar splittings which someone might mess up with these? How common is it to use uniformly aligned samples to measure order parameters? Would you have some reference in mind?

    2. Indeed it is common in the NMR literature to refer to the 2H quadrupolar splitting as the splitting measured from the bilayers that are oriented with the bilayer normal perpendicular to the external magnetic field. So I do not think it is a major issue to change your text in the manuscript. Still I think that it is always better to explicitly define which splitting one is talking about to avoid any misunderstandings. For instance in


      spectra from different bilayer orientations is shown. So in my opinion, using equation 1 of this paper, explicitly showing the bilayer orientation dependence, is more advisable. The 1H-13C NMR part is now good.

  3. Just before the first submission I received some small comments by Luca Monticelli and I made the suggested modifications, see commit:

    In addition to these small language issues, there was a question regarding this sentence on page 8
    "It is important to note that the order parameters measured with different techniques based on different physical interactions are in good agreement with each other (see Results and Discussion), indicating very high quantitative accuracy of the measurements."

    Luca's question was:
    "Are you sure you mean accuracy and not precision? (low systematic error or low statistical error?)"

    My answer is that, yes I mean accuracy (low systematic error). I am mentioning this here since, as Luca also probably realized, this is strong and non-trivial statement. The reason why we can say that the order parameters are measured with high quantitative accuracy is that the 2H NMR and 13C NMR gives very similar results. Different observable with different connection to order parameter are measured in these experiments, thus also the systematic differences between techniques are different. For more discussion see the post:


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