As already noted in the comments the “problem” is that you don't use a font with bold sans serif small caps. Indeed, your example produces in the log file
LaTeX Font Warning: Font shape `OT1/cmss/bx/sc' undefined
You have a few choices to circumvent the issue:
use a font that has bold face sans serif small caps (such as Linux Biolinum, the accompanying sans serif to Linux Libertine, for example)
\documentclass[a4paper]{scrreprt}
\usepackage[T1]{fontenc}
\usepackage{libertine} % <<<<
\usepackage{chemmacros}
\begin{document}
\paragraph{\iupac{\D-Proline}}
\end{document}
use standard fonts but change the headings fonts from sans serif to serif
\documentclass[a4paper]{scrreprt}
\usepackage[T1]{fontenc}
\setkomafont{sectioning}{\bfseries} % <<<<
\usepackage{chemmacros}
\begin{document}
\paragraph{\iupac{\D-Proline}}
\end{document}
change the definitions of \D to \L so they don't use small caps any more, e.g. with the relsize package:
\documentclass[a4paper]{scrreprt}
\usepackage[T1]{fontenc}
\usepackage{relsize} % <<<<
\usepackage{chemmacros}
\RenewChemIUPAC\D{\textsmaller{D}} % <<<<
\RenewChemIUPAC\L{\textsmaller{L}} % <<<<
\begin{document}
\paragraph{\iupac{\D-Proline}}
\end{document}
libertineand test again. – Johannes_B Mar 09 '14 at 08:46\Dorchemmacrosper se, but the fact that your document class is picking a font which doesn't have sanserif bold small caps. The question then is what you want to change: the font, the use of sanserif, ... – Joseph Wright Mar 09 '14 at 11:53\paragraphis (a) a command, not an environment and (b) a sectioning command like\sectionor\chapter, yes? – Joseph Wright Mar 09 '14 at 11:58