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

Wednesday, October 18, 2017

Some common-sense advice regarding responding to peer-reviewers

Editing and (especially) reviewing are mostly thankless jobs which take time and attention from the busy schedules of reviewers. Facilitating their work (or at least not making it harder than absolutely necessary) is therefore a very important way to improve the odds of a favourable decision. As such, it is absolutely crucial that every reviewer/editor comment be acknowledged and addressed. Authors may always decline to make a requested change by presenting their reasons, but failing to mention any one of the reviewer's comments (even if to reject their pertinence) may come across as evasive and less than fully transparent. Moreover, it is one of the worst things an author can do to their chances of a favourable outcome: at best, it can be taken as a passive-agressive way to signal discontent with "dreaded reviewer#3". At worst, it can be mis-interpreted as an attempt to hoodwink editors.  In any case, it increases the probability of tipping the editor's judgment away from a positive decision.

A few hints to help reviewers appreciate your response:

  • When you prepare your rebuttal,  provide the full text of all of the reviewers' comments to the initial version of this submission, interspersed with your detailed replies to each point (preferably in a different font, for ease of reading).
  • Some journals request re-submissions to be accompanied by a copy of the manuscript file with highlighted changes. In that case, do not highlight those changes manually: use your word-processor built-in "track changes feature" instead, to compare the initial submission to your modified manuscript.

Friday, July 7, 2017

Today I became dreaded reviewer #3

I am now writing a referee report. I usually frame my comments diplomatically and try to be constructive (you will have to take my word for it...). Unfortunately, my first comment to these authors is uncharacteristically harsh, and I wish I had not needed to write it:
"I do understand that productivity and impact metrics like the number of citations, h-index, etc. are wrongly used by intitutions and funding agencies to measure research productivity, and that scientists are implicitly (or explicitly) pressured to inflate them. I cannot, in good conscience, agree with that practice but would have kept silent if a manuscript cited a couple of papers by the authors in the introduction. However, in this manuscript 46 references are cited, of which 23 (number 8-11, 15-19 , 21-23 , 34-42 , 44-45) are from the current authors. None of these 23 citations refers to specific results from those papers: they are rather cited as examples of well-known facts which either require no citation or should cite seminal papers/reviews in the area. I will not accept this paper in any form, for publication in this or any other journal, if those references remain."

I am afraid such comments to authors and editords must become much more common to stop the continuous gaming of the system. As long as metrics are used for ends they were not designed to, authors will (more or less grudgingly) try to game them, if only to ensure that they do not "fall behind" in comparisons with colleagues who feel even less compunction to game. Race to the bottom, and all that...

Thursday, April 28, 2016

New scientific biographies wanted....

Biographies fulfill several different roles: they may simply satisfy one's curiosity over the lives/achievements of the biographees, provide tasty morsels of gossip or interesting stories, or play an "educational" role. Traditionally, the "educational role" of biographies has focused on their presentation of "role models" - whether moral, political or social - or the conditions/life experiences which led to the special significance of the biographee. Scientific biographies follow the same pattern. Like traditional biographies, they are usually limited to people of special significance: trailblazers, mavericks, geniuses, and people who left a mark on their scientific discipline or on the public perception of the worth of their subject.

I wish there were also another kind of biography, devoted to the intelectual careers of "normal" researchers: people who simply follow their intelectual curiosity, who are constrained by the amount of funding they can get and who pass away in obscurity after adding their small contributions to our colective knowledge. I do not want "human interest stories" played by researchers: I rather long for a description of their intelectual journeys, why they decided to study a specific problem, what kinds of mental connections they made (and why), in what measure their interpretation of their results was "commonplace" or (in contrast) specifically triggered by insights coming from seemingly unrelated work they had performed earlier, etc.

I want to read stories that show how each of these normal people, in their own way, made work which seems ordinary but is, in contrast, highly personal: work that would not have been done, or which would not have yielded the same insights, if that scientific question had been tackled by someone with a different research history. I am reasonably confident that most rank-and-file scientists would be fitting subjects for this style of biography, and that the study of these stories would teach us a lot about the roles that creativity, personality, luck and culture play in the fostering of a thriving research environment. 

Friday, December 11, 2015

On the difficulty of finding peer-reviewers

I have recently become an Associate Editor at PeerJ. I had several motivations for this:
  • I strongly believe in their mission, and am very happy with my three publishing experiences with them.
  • I mostly work alone and therefore my papers, in the long run, will not be a profitable for them. I felt that I should give them some extra support in exchange for their extremely low number-of-authors-based APC.
  • As a mid-career researcher at a little-known teaching-based institution, I reasoned that this opportunity might increase my visibility and improve my CV.

I am enjoying my run as an editor. So far, I have shepherded seven papers through the publishing process: one of them was published a week ago, I rejected one "on arrival",  and five of them are undergoing review.  I target my peer-review invitations to people who have recently published work using the same methods, or studied the same question, both for the obvious expertise and hoping that they will find the paper interesting. Still, I was quite surprised with how hard it is to get people to accept reviewing papers: for two papers, I managed to get two reviewers with around 6-8 invitations, but my latest assignments required more than 15 invitations each!  I understand that everybody is busy researching, writing papers, applying for funding, etc., but I never thought that the acceptance rate for peer-review requests would be < 15%. I do not get many peer-review request myself, but I do believe I have an obligation of accepting as many requests as possible (and reviewing them promptly), and I thought this was the "common" mindset... Maybe the people I target for my invitations are simply too senior and are therefore swamped with review requests, but the emails of "non-senior" members of a Lab are too often hard to find, due to the common practice of including only the the lab leader "corresponding author".

Any thoughts/suggestions/gripes?

Wednesday, July 8, 2015

Gamess (US) frequently asked questions. Part 7: How to distinguish alpha from beta orbitals in the $VEC deck

Each line in a $VEC group contains the coefficients of five basis functions for a given orbital. These are formatted in a special way, with seven numbers in each line. These numbers are:

1st) the number of the orbital to which the coefficients belong (written with at most two characters, so that 1 means orbital 1, .. , 99 means orbital 99, 00 means orbital 100) . This number is repeated in the beginning of every line, until all coefficients for that orbital have been written

2nd) this number tells the program how to assign the coefficients to the basis functions. "1" means that the coefficients are for basis functions 1-5, "2" means that the coefficients are for basis functions 5-10, etc. In general , that number "n" directs the program to assign the five coefficients present in the line to basis functions 5*(n-1)+1 to 5*n.

3rd to 7th) coefficients of five basis functions

BETA orbitals are punched as a group immediately after all ALPHA orbitals.

This format entails that in molecules with more than 100 orbitals the $VEC group contains several blocks with the same 1st number. For example, in a molecule with 200 orbitals, alpha orbital 27 is described by the first block of lines beginning with "27", and alpha orbital 127 is described by the SECOND block of lines beginning with "27".

I usually find the beginning of the BETA orbitals by repeating a search for the string " 1 1" : if that string is preceded by a block beginning with "00 1", it usually refers to orbitals 101, or 201, etc. (the exception being those systems with exactly 100, 200, etc. orbitals). If string " 1 1" is NOT preceded by a block beginning with "00 1", you are sure to have found the beginnning of the BETA orbitals