Not so different from samcarter's answer, but with some valuable tricks.
The symbol “pKa” should not appear in italics, so I defined a couple of macros to deal with this and to simplify input.
The notes should not be in \scriptsize, which is way too small.
Avoid scaling tables and also special characters in \label.
\documentclass[a4paper]{article}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage[spanish]{babel}
\usepackage{threeparttable}
\usepackage{siunitx} % for numeric tables
\usepackage{booktabs} % for better tables
\newcommand{\pKa}[1]{%
\textnormal{pKa}%
\if\relax\detokenize{#1}\relax
\else
\ensuremath{_{\mathrm{#1}}}%
\fi
}
\newcommand{\DpKa}{\ensuremath{\Delta}\pKa{}}
\begin{document}
\begin{table}[htp]
\begin{threeparttable}
\caption{Estimación de \pKa{} para ácidos, alcoholes y aminoácidos}
\label{table:estimacion_pka_RM1_con_aminoacidos}% <-- avoid accents in labels
\centering
\begin{tabular}{
l
S[table-format=1.2]
S[table-format=-1.1]
S[table-format=1.1]
S[table-format=-1.1]
S[table-format=-1.1]
}
\toprule
& & \multicolumn{4}{c}{RM1} \\
\cmidrule(lr){3-6}
& & \multicolumn{2}{c}{COSMO} & \multicolumn{2}{c}{SS-COSMO} \\
\cmidrule(lr){3-4} \cmidrule(lr){5-6}
& {\pKa{exp} (\SI{298}{K})}
& {\pKa{calc}}
& {\DpKa}
& {\pKa{calc}}
& {\DpKa}
\\
\midrule
\textit{Ácidos} \\
acético & 4.75 & 2.1 & 2.6 & 4.2 & 0.6 \\
fluoroacético & 2.59 & -0.8 & 3.3 & -0.8 & 3.4 \\
fórmico\tnote{a} & 3.75 & {ref} & {ref} & {ref} & {ref} \\
pirúvico & 2.39 & -3.0 & 5.4 & 0.7 & 1.7 \\
glioxílico & 3.18 & -2.3 & 5.5 & 0.4 & 2.8 \\
propanoico & 4.86 & 2.3 & 2.5 & 3.9 & 0.9 \\
butanoico & 4.83 & 2.6 & 2.3 & 4.2 & 0.7 \\
acrílico & 4.25 & 2.0 & 2.3 & 1.0 & 3.3 \\
láctico & 3.86 & 0.7 & 3.2 & 5.0 & -1.2 \\
benzoico & 4.2 & 1.1 & 3.1 & 1.6 & 2.6 \\
\midrule
MAE & & & 3.1 & & 1.6 \\
\bottomrule
\end{tabular}
\begin{tablenotes}
\footnotesize
\item[a] Desprotonación de referencia
\item[b] Sin valor experimental
\item Estimación y comparación de \pKa{} calculados con RM1 y dos estrategias
de solvatación: implícita (COSMO) y explícita-implícita(Solvateshell-COSMO).
El \DpKa{} se realizó como $\DpKa=\pKa{exp}-\pKa{calc}$. La sigla SS significa
Solvateshell.
\end{tablenotes}
\end{threeparttable}
\end{table}
\end{document}
