Thank you for the question. You are right that when transcribing Chemistry, each capital letter in a chemical formula should be capitalized separately.
You are also right that contractions should not be used in chemical formulas.
Now, how do we convince Duxbury to do that? Good question.
Yes, you can use ExactTranslation to change the font to braille in print and essentially tell the program exactly what cells to use. You could also perhaps use the techniques employed in the attached DOCX file.
Also attached are an image of the print and braille we are talking about and a BRF of the braille.
Again, thank you for the question. Please post again if you have follow-up questions or concerns.