I am working on a manuscript for publication in a chemistry journal. I find that my approach to the problem is very different to previous work on the matter. I find very hard to fit its argumentative line into the common scheme: Abstract, Introduction, Methods, Results, Discussion, Conclusion, Acknowledgements, References.
I am scared that my paper will be automatically rejected if it doesn't follow conventional sectioning. Is this an issue?
What should I do to increase chances of acceptance of my paper?
I can only think of the following alternatives, but I am not experienced and I am unsure of which is the best way to go:
Force the standard sectioning at any cost of the argumentative line?
Use many paragraph in the introduction to describe the sectioning?
Just use my criteria and structure the paper in the way I think it is better?
My thesis is that previous work did not consider some peculiarities and because of that their results aren't reliable. I need to prove the existence of these peculiarities and argue that my approach is better in these cases. Only experts in method X itself know that method X fails in some cases, and most researchers just apply method X assuming that its results are very good, so I feel myself in the need to show believers in method X that the method fails in certain cases (I'm not an experienced published author, so maybe my ideas are wrong about the need to convince others).
Finally, as there is not a method Y that works for all cases, I used results of many methods for each case and made a deep analysis considering the strengths and weakness of each method. Due to this, and the particularities of each case, I used a different method for each case. Even if I list methods for each case, I would have trouble fitting this into a Methods section early in the paper.
Due to the peculiarities I mentioned, I analyzed secondary properties as well. This gave rise to a lot of methods and situations that are hard to describe. I performed many calculations with a variety of objectives (first showing the existence of the peculiarities, and then calculating a useful value), and as many of the readers are not experts in the method itself, I think I need to provide a lot of background information before describing the methods themselves.
Note: The reason I chose a journal in which I know that most readers aren't aware of these kinds of situations, is that the properties calculated are of their main/exclusive interest. In other fields these kinds of things are well known and this work does not provide any insight on them. I'm just trying to correct previous values reported in one field, by applying well known facts from another field.