How to improve chances of acceptance of a paper with an atypical structure? 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.
I struggled with this very issue for my first couple of papers. I'll bet it's the middle part (Methods, Results, Discussion) that you feel doesn't fit the paper you're trying to write. That may because your view of the type of thing that goes into those sections is too narrow.

First, it may help to approach the writing a bit differently. Forget about the sectioning for the moment, and just write, in any order. Make the points you want to make. Add in the arguments or experimental results that you need to support those points. As you're writing, you realise that there are things your reader needs to know in order to understand your paper, so write that as well.

Now you can start to think about the order that the information should be presented in. So rearrange what you've written into logical paragraphs, and put them in a sensible order.

As you're doing this, a natural structure for your paper should emerge. There's stuff that the reader needs to know in order to understand your paper. That goes at the beginning, in the introduction. You'll also want a short summary of your main points. This will go in the conclusion. You might want to suggest areas for future research. 

You may not need any acknowledgements in your paper. Ask your supervisor. You obviously need references.

The abstract is a summary of what the paper is about. I tend to write the abstract last, because it's only then that I know exactly what the "story" the paper is trying to tell is!

But it's the middle part (Methods, Results, Discussion) where the structure can be a bit confusing, especially if your paper isn't about a typical chemistry experiment. This seems to be the area where there's the most difference in structure between papers. For example, the results and discussion of those results might be combined into a single section, typically called "Results" or "Results and discussion".

So let's think of those sections a little more generally. You need to explain how you approached the problem. If your paper is an argument for something, then you need to explain your underlying assumptions, and how you reached the conclusions you reached. This is the sort of thing that goes into the "Methods" section -- although you may want to give this section a different title.

For an argument paper, it might be difficult to separate the "Results" from the "Discussion". So perhaps those sections could be combined into one section that presents your argument. Look for some papers that present arguments, you'll get ideas on structure.