How to improve chances of acceptance of a paper with an atypical structure?
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.