(The question has currently no tag indicating it is MathJax/Tex/.. related, so let me be more general...)
Smallcaps support in general SE syntax, not (only) in MathJax, is essential for correct typesetting of the D/L- stereochemical prefixes (e.g. in β-D-glucopyranose or L-alanine).*
Citing from the ACS style guide – Conventions in chemistry:
Use small capital letters D and L for absolute configuration with amino acids and carbohydrates.*
or from the Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013:
P-102.3.2 The stereodescriptors ‘D’ and ‘L’ *
(…) The configurational stereodescriptors ‘D’ and ‘L’ must be written in small capital letters and linked by a hyphen to the name of a sugar.*
There's a feature request in meta.SE to allow the <small> tag, which is a usual realization of this typography e.g. at the Wikipedia.
Another possible solution is to use Unicode small capital letters (preview: β-ᴅ-glucopyranose or ʟ-alanine), however these are meant to have IPA/phonetic meaning.
*) The D/L notation is here incorrectly presented in capital letters, because of missing smallcaps support