Crystal Structures of a Series of Hydroxamic Acids

Round 1

Reviewer 1 Report

Sow et al. report the crystal structures of four hydroxamic acids, which are commercially available (1) or were synthesized (3) according to published methods. The molecular structure of the smallest compound is known, albeit in different space groups. All others are new. In addition, crystallizing compunds with long aliphatic chains is decidedly difficult and the reported success a significant achievement. The study is set well into a general context. The manuscript is well written and has a good structure. The experimental foundation appears overall solid. The work is, hence, publishable and Molbank should be a qualitatively matching outlet. The only question which does arise is, whether it is acceptable to not adhere to the journal’s “one compound per report” policy. This is up to the editors to decide, though.

A few issues should be taken care of prior to any acceptance, which need the attention of the authors during a revision. These are:

Line 23/24: supplement “oxalohydroxamic“ with “acid”

Line 36: typo – isomres (isomers)

Line 47/49: shown in Figure 2 are the “chemical structures” not the “molecular structures”. This should also be specified in the caption of the Figure.

Table 1: check the key for theta. Something went wrong.

It is recommended to split Figure 4 into two Figures so that the drawings do not intertwine.

Line 83: check for subject verb agreement (method/were)

Line 85: should be “crystal structures” or “crystals’ structures”

Line 88: it should be “refined” not “elucidated”.

The trend of the unit cell lengths with the compounds chain lengths is notable enough to include this in the conclusion as well.

 

Crystallography:

Compound 1: Oxygen bound hydrogen atoms should be refined freely not fixed. If that is not possible it should be explained/justified in the experimental part.

Compound 2: Oxygen bound hydrogen atoms should be refined freely not fixed. If that is not possible it should be explained/justified in the experimental part.

The structure should not be refined as twin. The R- value does not change if the TWIN command is removed. Refining as twin simply serves circuiting the Flack alerts.

Compound 3: Oxygen bound hydrogen atoms should be refined freely not fixed. If that is not possible it should be explained/justified in the experimental part.

The structure should not be refined as twin. The R- value does not change if the TWIN command is removed. Refining as twin simply serves circuiting the Flack alerts. The structure should be also inverted.

Refinement should be continued up to convergence of the weight parameters.

Compound 4: Oxygen and nitrogen bound hydrogen atoms should be refined freely not fixed. If that is not possible it should be explained/justified in the experimental part.

The structure should not be refined as twin. The R- value does not change if the TWIN command is removed. Refining as twin simply serves circuiting the Flack alerts.

The use of constraints should be explained/justified in the experimental part. For instance, why was ISOR used and SIMU was not? If ISOR is indeed requisite, it might be better to go to an isotropic refinement of the disordered atoms.

Author Response

Sow et al. report the crystal structures of four hydroxamic acids, which are commercially available (1) or were synthesized (3) according to published methods. The molecular structure of the smallest compound is known, albeit in different space groups. All others are new. In addition, crystallizing compunds with long aliphatic chains is decidedly difficult and the reported success a significant achievement. The study is set well into a general context. The manuscript is well written and has a good structure. The experimental foundation appears overall solid. The work is, hence, publishable and Molbank should be a qualitatively matching outlet. The only question which does arise is, whether it is acceptable to not adhere to the journal’s “one compound per report” policy. This is up to the editors to decide, though.

A few issues should be taken care of prior to any acceptance, which need the attention of the authors during a revision. These are:

Line 23/24: supplement “oxalohydroxamic“ with “acid”

• Done

Line 36: typo – isomres (isomers)

• Done

Line 47/49: shown in Figure 2 are the “chemical structures” not the “molecular structures”. This should also be specified in the caption of the Figure.

• Done

Table 1: check the key for theta. Something went wrong.

• Done

It is recommended to split Figure 4 into two Figures so that the drawings do not intertwine.

• A new figure 4 was proposed as per reviewer 3

Line 83: check for subject verb agreement (method/were)

• Done

Line 85: should be “crystal structures” or “crystals’ structures”

• Done, changed to crystal structures

Line 88: it should be “refined” not “elucidated”.

• Replaced instead to solved as shelxt is not a refinement program

The trend of the unit cell lengths with the compounds chain lengths is notable enough to include this in the conclusion as well.

• Added to the conclusions: ... in which a remarkable linear correlation is noticeable between the variation of the c-axis and the number of carbon atoms in the alkyl chain.

 

 

Crystallography:

 

1. Compound 1: Oxygen bound hydrogen atoms should be refined freely not fixed. If that is not possible it should be explained/justified in the experimental part.

 

• All N/O hydrogens now freely refined.

 

1. Compound 2: Oxygen bound hydrogen atoms should be refined freely not fixed. If that is not possible it should be explained/justified in the experimental part.

 

• All N/O hydrogens now freely refined.

 

The structure should not be refined as twin. The R- value does not change if the TWIN command is removed. Refining as twin simply serves circuiting the Flack alerts.

 

• No longer refined as a TWIN

 

1. Compound 3: Oxygen bound hydrogen atoms should be refined freely not fixed. If that is not possible it should be explained/justified in the experimental part.

 

• The H on the oxygen was not refined freely as the H was placed disordered over 2 sites. This was added to the experimental part.

 

The structure should not be refined as twin. The R- value does not change if the TWIN command is removed. Refining as twin simply serves circuiting the Flack alerts. The structure should be also inverted.

 

• No longer refined as a TWIN

 

Refinement should be continued up to convergence of the weight parameters.

 

• In fact, it should not, according to the manual and personal communication with G Sheldrick.
• The wght scheme was manually optimized to give the best combination of R/wR2 and S while taking care not to introduce systematic trends in the analysis of variance. In any way the suggested wght is flawed in not taking into account the resolution dependence.

 

1. Compound 4: Oxygen and nitrogen bound hydrogen atoms should be refined freely not fixed. If that is not possible it should be explained/justified in the experimental part.

 

• All N/O hydrogens now freely refined.

 

The structure should not be refined as twin. The R- value does not change if the TWIN command is removed. Refining as twin simply serves circuiting the Flack alerts.

 

• No longer refined as a TWIN

 

The use of constraints should be explained/justified in the experimental part. For instance, why was ISOR used and SIMU was not? If ISOR is indeed requisite, it might be better to go to an isotropic refinement of the disordered atoms.

 

• My instance it's never a good idea to refine parts of a structure only isotropically (even when disorder is in play).
• SIMU should in general be used for large low-resolution structures, while DELU hold accurate for covalently bond atoms.
• I typically refine such disorder with a combination of DELU and ISOR to prevent the thermal ellipsoids from becoming cigar shaped, in this case the use of ISOR showed no virtual difference. The ISOR restraint was thus omitted.

 

All cif files were redeposited in the CCDC database

Reviewer 2 Report

I have something to make sure of you.

The space group of the crystal in HA2 is P21/c. However, the space groups of other crystals are P21, which has no inversion center. You said, " The alkyl chains themselves are set off about 40° from the N-hydroxyacetamide plane." In this packing, the bending of a long alkyl chain was oriented in the same direction. It causes acentric packing in the crystals of N-hydroxyacetamide with a long alkyl chain. Is this interpretation right?

Author Response

I have something to make sure of you.

1. The space group of the crystal in HA2 is P21/c. However, the space groups of other crystals are P21, which has no inversion center. You said, " The alkyl chains themselves are set off about 40° from the N-hydroxyacetamide plane." In this packing, the bending of a long alkyl chain was oriented in the same direction. It causes acentric packing in the crystals of N-hydroxyacetamide with a long alkyl chain. Is this interpretation right?

• Not necessarily, molecules could equally be connected by an inversion centre (instead of the 2-fold helical axis). As the molecules are not chiral, there is no need to crystallize in a chiral space group. The obtained packing will be a combination of molecular interactions, both from the N-hydroxyacetamide plane as well as from the hydrophobic alkyl chain.

Reviewer 3 Report

See attached file

Comments for author File: Comments.pdf

Author Response

This manuscript presents the X-ray crystal structures of 4 different (HA) with pendant aliphatic chains having 2, 6, 10 or 12 carbon atoms. Compounds of this kind may adopt different structures (arising from tautomeric equilibrium and /or the relative orientation of the substituents) depending on the experimental conditions (i.e. solvent, pH, temperature among others) are gaining relevance due to their potential biological activities. The number of crystal structures of hydroxamic acids reported so far is still rather low. Therefore, the X-ray studies presented in this work for 4 members of this family of compounds is not only a valuable contribution in the characterization of this type of compounds in the solid state, but also provides relevant information concerning the effect of the length of the —(C-C)n- chains. In my opinion the studies and results presented in this manuscript, fulfil the requirements for their publication in this journal. However, from my point of view since no additional studies or experiments are required, I tend to recommend a "minor revision" that may contribute to improve its clarity, to ease its reading and understanding and also to make it more attractive to readers.

In the following paragraphs you will find some comments and suggestions to be considered by the authors during the revision of the manuscript

1. Abstract: The last 4 words of this section should be removed, because for the HAs presented in this work, the a and b parameters are quite similar but, as shown in table 1 and also as indicated in the text (see lines 74 and 75), the c parameter varies. [See Table 1: from ca 7.0434 A (for HA2) to ca. 33.448 A (for HAl2)].

• Done

2. Introduction section: This part could also be improved, for instance:
3. a) It is well known that hydroxamic acids (HA) and their derivatives are attracting a great deal of interest in a wide variety of areas, and specially due to their varied and multiple biological activities and their potential interests in Biomedical areas. I would recommend the authors to emphatise this in this section in order to enhance the interest of other readers. If this is done, then I would also recommend to include two additional references, the book published in 2013, and also a recent review

Book: Satya P. Gupta (Ed.) Hydroxamic Acids. A Unique Family of Chemicals with Multiple Biological Activities, Springer, 2013,

Review: Z. Syed, K. Sonu, A. Dongre, G. Sharma, M. Sogani A review on Hydroxamic Acids: Widespectrum Chemotherapeutic Agents, International Journal of Biology and BioMedical Engineering, 2020, 14, 75-88 (DOI: 10.46300/91011.2020.14.12).

• The introduction was rewritten as follows, with both references added

HA constitute one of the most important families of organic bioligands; and one of the first physiological roles of these compounds was associated with their use as siderophores, a class of compound iron-sequestering agents [2]. Desferrioxamine B is effectively used to deal with iron overload in transfusion-dependent patients such as those suffering from thalassemia. Besides being used as siderophores, HA play a number of other biological and pharmacological roles. They act as potent and selective inhibitors of a large number of enzymes, such as matrix metalloproteinases, peroxidases, hydrolases, ureases, lipoxygenases, cyclooxygenases, histone deacetylases, peptide deformylases [2]. HAs are reported to possess anti-inflammatory, anti-tubercular, anti-leukemic, anti-microbial and tumor inhibiting properties [3]. They play a vital role in the manufacturing of various biologically active drugs as anti-depressants, anti-tumor agents, anti-HIV agents and anti-malarial agents and are also used in industries as insecticides, antioxidants, as inhibitors of corrosion and for the extraction of toxic elements [3].

 

 

1. b) Scheme 1 and also Figures 1 and 2: I wonder whether the authors could present the symbols of the N and 0 atoms in the formulae depicted in these plots using the same colors as in the crystal structures (N in blue and 0 in red), obviously then the numbers that appear in the current figure 2 should be shown in a different color). Moreover, I would also suggest the authors to include below the formulae shown in scheme 1, the "keto" / "enol" and "E" and "Z" indicators below the corresponding formula.

• Done, Scheme 1, Figures 1 and 2 were altered as to the reviewer’s suggestions

3. Results and discussion sections: In my opinion these two sections are too short.

 

As already mentioned by the authors in lines 25 and 26, the resolution of crystal structures of HA is not easy at all. Therefore, the study and the results presented in this contribution have an additional value and this is the reason why I consider that these two sections require a more detailed description of the crystal structures and also on the assembly of the units in the crystal. A few specific details are given in the following points:

1. a) First I would suggest to modify Figure 3 in order to show the ORTEP plots including the labels of the majority of atoms (labels of H-atoms could be omitted in order to simplify the plots if necessary). The graph showing the tilt of the alkyl chain could be kept as it is next to the ORTEP of H2A.

• The stick representation was changed to ORTEP , labels were not added, as they complicated the view and no reference was made to any labels in the manuscript

1. b) Table 1: 1st column:

-          Row 6: unit cell dimensions, the units for the "b angle " are missing"

• Done

-          Row 10, please check the symbol that appears before "range" it should be a q

• Done

-          Row 15, in "I >2s(I)" please replace the "s" by a "s" (sigma symbol)

• Done

1. c) The discussion section should be rewritten. I would suggest to reorganize this part and to try to show the main findings, similarities and differences between the structures of the HAs under study. For instance, the authors could include a new plot either in the main body of this manuscript or as supplementary materials showing the variations of the cell parameters (a, b and c) or at least the c- parameter versus the number of carbon atoms of the alkylic skeleton. This will allow to show clearly, that the length of the —(C¬C)n- chain does not affect significantly the a and b parameters, but it produces a significant change of the c parameter. Data for compound HA8 [reported previously (see ref. 9) could also be included in the plot: c-value versus number of C-atoms)].

• Done, a plot with the variation of the unit cell parameters in function of the number of carbon atoms is added as Figure 5

In my opinion, Figure 4 is not very clear. The superposition of the structures does not give a "neat view" (I wonder if the resolution of the plots on the middle and left side is too low). Besides, the plot in the right hand side should be improved. Right now, it is really difficult (I will even say "almost impossible") to see which atoms are involved in the intermolecular interactions and how the molecules of HA6 are assembled in the crystal. If the picture cannot be improved, maybe a table containing some data concerning these intermolecular interactions for all the HAs could be added either in the main body of the manuscript or as supplementary materials.

Is there any difference between the relative orientation of the molecules of the HA under study in the crystal? Probably, a more detailed explanation and additional figures (or new ones to replace the current Figure 4) may help to clarify these points.

• The following was added to clarify:

The relative positions and orientation of the HA molecules in the a- and b- direction is idential, with similar hydrogen bond interactions involving the N-hydroxyacetamide. This is also visible by the gradual linear expansion of the c parameter of the unit cell, while a and b remain unchagned (Figure 5).

• A new Figure was proposed to replace figure 4 in which the crystal packing is shown along the a-axis. The 3 reported structures are placed offset, rather than superposed allowing to better distinguish the different interactions.

1. d) I have looked up some recent papers published as communications in this journal and in some of them the two sections "Results" and "Discussion" were unified. Probably it would be worth to combine the two sections of the present manuscript into a new Results and Discussion one in the revised version.

• Done

4. Materials and methods section. I wonder whether the authors could give more details of the method used to grow up the crystals. Since the crystallization of HAs in general is not an easy task, this information could be useful for other researchers interested in this type of compounds and their structures.

• The following was added to the manuscript:

In this study, ethyl acetate (EtOAc) was used as a solvent for recrystallizing the HA. To further purify, the crude product was dissolved in hot EtOAc and filtered. The filtrate was cooled to room temperature to afford pure HA as crystals in period of 72h. The residual solvent was removed by filteration, crystals were washed with water and dried under vacuum at 40 °C.

5. References: Please add the missing doi for refs 6 and 8:

Ref. 6 —> doi.org/10.1002/mrc.1260290109 and Ref. 8 —> doi.org/10.1107/S0567740870004764

• Done

6. Typographic error: Line 36, Legend of Scheme 1: "isomres" please check spelling, it should be "isomers.

• Done

Round 2

Reviewer 1 Report

Sow et al. have submitted a revised version of their original manuscript to Molbank. This reviewer’s concerns were all addressed. Though there remains one disagreement on how to handle X-ray data and the respective response is not really convincing, this is absolutely not critical and it has no impact on the interpretation of the data. The changes to the data treatment and manuscript are sufficient and the manuscript has become fully acceptable for Molbank.