Tuesday, November 6, 2018

In praise of "Arabian Journal of Chemistry"

In early October 2017 I submitted a  paper to Royal Society Open Science (RSOS). It took more than four months before I got any update on its status. After conflicting reviews, RSOS contacted an additional reviewer, who took TWO months to write a two line "report" which rejected my paper due to "lack of novelty" in spite of no other study of the subject matter existing in the literature. I decided then to eschew RSOS for ever and looked for another Open Access journal for my submission. 
Since I currently have no funding, absence of author processing charges was an important consideration. I found out about the "Arabian Journal of Chemistry" and looked into it: in spite of its obscurity, they have a decent Impact Factor (which shows that their papers are at least read within the community and solid enough to warrant being cited) and their APCs are borne by the King Saud University. I sent them my paper, which was unfortunately rejected although the reviewer reports were more consistent with a "Major Revisions" decision. The peer-review process, though, was exemplary: in less than two-and-a-half months, they provided me with SIX solid peer-review reports with enough actionable insights that I could incorporate into my paper to eventually get it published in J. Phys. Chem. A.
 I can only commend them for the utter professionalism, speed and quality of the whole process. I wish Arabian Journal of Chemistry all the best, and that its high standards and level of review will soon make it known among chemists as a premium journal. They  sure deserve that!

Saturday, October 27, 2018

A warning to readers of "Computational studies on the regioselectivity of metal-catalyzed synthesis of 1,2,3 triazoles via click reaction: a review" published in J.Mol.Model. (2015) 21,264-291



J. Mol. Model. instructions for authors clearly state, in the section on “Ethical responsibilities of authors” that “Proper acknowledgements to other works must be given (this includes material that is closely copied (near verbatim), summarized and/or paraphrased), quotation marks are used for verbatim copying of material, and permissions are secured for material that is copyrighted”. Unfortunately, the paper "Computational studies on the regioselectivity of metal-catalyzed synthesis of 1,2,3 triazoles via click reaction: a review" , authored by Tayebeh Hosseinnejad, Bahareh Fattah and Majid M. Heravi contains abundant citation deficiencies and apparent breaches of this policy.  To ensure that readers do not misunderstand the origin of some data reviewed in that manuscript and that proper credit is assigned to the original authors, I provide a (possibly incomplete) listing of those:
- a long section (p.278-282) describes  the computations of the reaction mechanism of the Cu-catalyzed addition of azides to 1-iodoalkynes (performed by Lal, Rzepa et al. [1] and published in ACS Catalysis (2014) 4, 2274-2287) without a reference to the original paper . These results are introduced in p.278, 2nd column , 3rd paragraph, line3,  with the text “The calculated result showed by using [CuI(PPh3)3] as the catalyst…” and finish in p.282 (1st column, 2nd line) : “Very similar results have been obtained by using [CuCl(IPr)]”. The lack of citation leads the reader to mistake this whole section for original research by the review’s authors. This perception is reinforced by the lack of attribution of the results of schemes 15-18 to Lam et al.: these schemes are virtually identical to schemes 8, 10, 11 and 12 of the original publication, and should have been captioned by the review’s authors as “adapted from Lal et al.". The only citation in the captions to these schemes refers, instead, to the paper describing the def2-SVP basis set.
- In p.274, second column, first paragraph, the description of the computational study of reaction of a sugar azide with (E)-trifluoromethyl-2-tosylethene[2] consists of a long, detailed paragraph, beginning with “Single-point energy calculations were performed at the M06-L/6-311+G** level of theory (ref. 114) with PCM method in toluene employing the M06-L/6-31+G* optimized geometries.” Ref. 114 refers to Hehre, Radom, Schleyer and Pople’s “Ab initio molecular orbital theory” (incidentally wrong as a reference to either M06-L or the 6-311+G** basis set) and since no other reference is provided it is likely that, as in the first example above, readers will think that this paragraph refers to original work by the review’s authors. Only in the end of the paragraph does the reader find a reference to the original work (their ref. 109) although in a somewhat opaque form, which does not clarify whether the citation refers to a specific finding or to the whole paragraph: “Strictly speaking, M06-L/6-311+G** and M06-L/6-31+G* calculations proposed that TS of 1,5-DTs is energetically preferred by 0.4 kcal mol1 compared to the corresponding 1,4-DTs (Fig. 7), which is in agreement with the experimental result (ref. 115), and the calculated free energy of activation ΔG‡  also predicts that the formation of 1,5-DTs is preferred by 2.48 kcal·mol-1 compared to the corresponding  1, 4-DTs (ref. 109)”. Figures 6-7 in this review are barely reworked un-attributed versions of Figs. 1-2 of ref. 109, with the energies changed from kJ/mol to kcal/mol.

- Figures 1-4 of this review are, likewise, lightly re-worked versions of figures under copyright with other journals[3] (See Figures 5, 9 10 and 11 of J Org Chem (2012) 77, 75-89), and should be marked as “adapted from Gold et al. (2012)” . Figure 8 is an unattributed lightly re-worked version of Fig. 4 from their ref. 116 (Kumar et al. (2010)[4] ), and table 1 is taken verbatim (again without attribution) from table 2, ref. 116.  Figures 15 and 17 differ from figures 1 and 3 in Luo et al. J. Org. Chem , 79, 11970-11980 [5]  (ref. 169 in the review) only in the coloring of the azide and alkyne moieties, again without attribution or (presumably) permission from the publisher. Figures  16, 19, and 20 are cropped versions of figures 2, 5 and 6 in [5]. Figure 18 in this review is a duplicate of figure 17. Fig. 21 is an unacknowledged adaptation of fig. 7 in [5]
- In page 277, the reference cited  in “The reactants, products, and transition states were optimized at B3LYP/6-31G* level of theory (ref. 123)” refers to an MP2/6-31G*//HF/6-31G* study of an unrelated reaction.
- In page 278, the reference provided to “the optimized electronic structure was obtained by solving the Kohn-Sham equations self-consistently (ref. 141)” is not related to the Kohn-Sham equations, the self-consistency procedure, the algorithm, or software package used, but to the paper describing the def-2 basis sets.
- Scheme 20 describes to an iridium-catalyzed reaction, but its caption refers instead to a ruthenium-catalyzed one.
- Fig. 12 is an unattributed copy of Fig.4 in [6]. This figure is referred in p. 284, second column, and the original citation (ref. 167 in the review) is not mentioned until p. 286.  Fig.14 and  Schemes 21, 22, and 23 are unattributed copies/reworkings of Fig. 5 and Schemes 2, 3, and 4, respectively, in [6]. Table 2 (p. 288) is an unattributed copy of Table 1 in [6].
- in p. 290, second column, the results of computational research on the iridium-catalyzed azide-alkyne coupling are introduced as “Origins of the observed regioselectivity have been studied mechanistically by performing quantum chemistry calculations on the role of the catalyst in reaction mechanism (illustrated in Scheme 25). All molecular structures and energies were calculated at M06 level of DFT method (ref. 82). The effective core potentials (ECPs) of Hay and Wadt with double-ζ valence basis sets (LANL2DZ) (ref. 170) were used for Ir and 6-31G(d) basis set was employed for N, S, Cl, Br, and O as well as the C atoms in the triple bonds of alkynes and double bonds of 1,5- cyclooctadiene (cod) and 6-31G basis set was used for all other atoms.”  The reader has to wait for a reference at the end of the page to learn that the results discussed originate from Luo et al. [5] (ref. 169 in the original).
-in p. 293, the review’s authors state “The calculated energy profiles for the mentioned possible oxidative couplings have been presented in Fig. 16 and the free energy barriers for ligand dissociation/association processes (e.g.,A to B1 and A to B2 in Fig. 16a, b) were obtained through the method proposed by Hall and co-workers (refs. 171, 172) (Fig. 17)”, without mentioning that those computations were performed by Luo et al.[5].

I understand that the labor-saving reuse of previous images enables authors of literature reviews to more fully devote their minds to the important job of making sense of a wide literature instead of futilely re-inventing the wheel. As such, I do not think that authors of a review paper necessarily have a special obligation to re-draw the computed geometries of intermediates and transition states in every image (e.g. using a different molecular viewer or a different viewing angle), or the potential energy surfaces of every mechanism, even though generating such images anew is nowadays very straightforward due to the commendable practice, widely embraced by the computational chemistry community, of providing at least the geometric coordinates in readily-usable formats. Authors should, however, ensure that readers are not unwittingly misled regarding the provenance or authorship of any of the data they show, and that their presentation does not lead future workers to fail to cite the original reports. An exemplary use of proper citation practices in reviews can be found, e.g.,  in Johansson et al.’s recent overview of ruthenium-catalyzed azide alkyne cycloaddition reaction[7], where every scheme is clearly attributed to the original proponents and the supporting information accompanying computational papers is used to generate new views of the relevant molecules.



1.        Lal S, Rzepa HS, Díez-González S (2014) Catalytic and Computational Studies of N-Heterocyclic Carbene or Phosphine-Containing Copper(I) Complexes for the Synthesis of 5-Iodo-1,2,3-Triazoles. ACS Catal 4:2274–2287. doi: 10.1021/cs500326e
2.        Sahu D, Dey S, Pathak T, Ganguly B (2014) Regioselectivity of Vinyl Sulfone Based 1,3-Dipolar Cycloaddition Reactions with Sugar Azides by Computational and Experimental Studies. Org Lett 16:2100–2103. doi: 10.1021/ol500461s
3.        Gold B, Shevchenko NE, Bonus N, et al (2012) Selective transition state stabilization via hyperconjugative and conjugative assistance: stereoelectronic concept for copper-free click chemistry. J Org Chem 77:75–89. doi: 10.1021/jo201434w
4.        Kumar KK, Kumar RM, Subramanian V, Das TM (2010) Expedient synthesis of coumarin-coupled triazoles via “click chemistry” leading to the formation of coumarin–triazole–sugar hybrids. Carbohydr Res 345:2297–2304. doi: 10.1016/j.carres.2010.07.037
5.        Luo Q, Jia G, Sun J, Lin Z (2014) Theoretical studies on the regioselectivity of iridium-catalyzed 1,3-dipolar azide-alkyne cycloaddition reactions. J Org Chem 79:11970–11980. doi: 10.1021/jo5018348
6.        Boz E, Tüzün NŞ (2013) Reaction mechanism of ruthenium-catalyzed azide–alkyne cycloaddition reaction: A DFT study. J Organomet Chem 724:167–176. doi: 10.1016/j.jorganchem.2012.11.011
7.        Johansson JR, Beke-Somfai T, Said Stålsmeden A, Kann N (2016) Ruthenium-Catalyzed Azide Alkyne Cycloaddition Reaction: Scope, Mechanism, and Applications. Chem Rev 116:14726–14768. doi: 10.1021/acs.chemrev.6b00466