Only with reducing text size a little (\small) and reasonably shrinking space between columns (\renewcommand{\tabcolsep}{4pt}), both changes are relatively unnoticeable.
\documentclass[12pt]{report}
\usepackage{threeparttable,booktabs,multirow,lscape}
\usepackage[letterpaper,margin=1in]{geometry}
\begin{document}
\renewcommand{\tabcolsep}{4pt}
\begin{landscape}
\begin{table*}[htbp]
\centering\small
\begin{threeparttable}
\caption{My Results}
\begin{tabular}{rrrrrrrrrrrr}
\toprule
\textbf{FF} & \textbf{} & \textbf{} & \textbf{AA} & \textbf{BB} & \textbf{CC} & \textbf{DD} & \textbf{FF} & \textbf{GG} & \textbf{HH} & \textbf{II} & \textbf{JJJJ} \\
\midrule
\textbf{Ccccccccccc} & \multirow{2}[2]{*}{\textbf{aaaaa aaaaa}} & \multirow{2}[2]{*}{\textbf{aa aa aaaaaa}} & \multirow{2}[2]{*}{\textbf{aaa}} & \textbf{aaaa} & \textbf{aa +} & \textbf{aa +} & \multirow{2}[2]{*}{\textbf{aaa}} & \multirow{2}[2]{*}{\textbf{aaaa aaaaa}} & \textbf{aa +} & \textbf{aa +} & \multirow{2}[2]{*}{\textbf{aaa}} \\
\textbf{aaaaaaaaaa} & & & & \textbf{aaaaa} & \textbf{a-aaaaa} & \textbf{a-aaaaa} & & & \textbf{a-aaaaa} & \textbf{a-aaaaa} & \\
\midrule
\textbf{aaaaaaaa} & \textbf{0000} & \textbf{1111} & 22222 & 333333 & 444444 & 5555 & 66666 & 77777 & 88888 & 99999 & 10100 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\\\
\textbf{aaaaaaaa} & \textbf{0000} & \textbf{1111} & 22222 & 333333 & 444444 & 5555 & 66666 & 77777 & 88888 & 99999 & 10100 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
\textbf{aaaaaaaa} & \textbf{0000} & \textbf{1111} & 22222 & 333333 & 444444 & 5555 & 66666 & 77777 & 88888 & 99999 & 10100 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
\textbf{aaaaaaaa} & \textbf{0000} & \textbf{1111} & 22222 & 333333 & 444444 & 5555 & 66666 & 77777 & 88888 & 99999 & 10100 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
& 000 & \textbf{1111} & 22222 & 33333 & 44444 & 55555 & 66666 & 77777 & 88888 & 99999 & 10.10 \\
\midrule
Aaaaaaa & & \textbf{0000} & \textbf{11} & \multicolumn{1}{c}{\textbf{22}} & \multicolumn{1}{c}{\textbf{33}} & \multicolumn{1}{c}{\textbf{44}} & \multicolumn{1}{c}{\textbf{55}} & \multicolumn{1}{c}{\textbf{66}} & \multicolumn{1}{c}{\textbf{77}} & \multicolumn{1}{c}{\textbf{88}} & \multicolumn{1}{c}{\textbf{99}} \\
\bottomrule
\end{tabular}%
\label{tab:addlabel}%
\end{threeparttable}
\end{table*}
\end{landscape}
\end{document}
see if the following make-up of your table is acceptable:
in your mwe i made the following changes:
- since your table is with
\normalsize fotn size to tall for one page, i reduced font size to \footnotesize if this sizew is to small, than the only options is use longtable and split table to two pages
- remove all vertical and the most of horizontal lines.
- for remain horizontal line i used rule from
booktabs package
- remove empšty rows and istead of them use
\addlinespaces from booltabs package
- for column type i select
S columns from siunitx package
\documentclass[12pt,twoside
%,draft
]{report}
\usepackage[showframe,
a4paper,
headheight=18pt, width=150mm, top=25mm, bottom=25mm, bindingoffset=6mm, headsep=18pt]{geometry}
\usepackage[spanish,es-noquoting]{babel}
%interprete de idioma castellano
\usepackage[utf8]{inputenc} %relacionado al input
\usepackage[T1]{fontenc}
\usepackage{enumitem}
\usepackage{adjustbox}
\usepackage[flushleft]{threeparttable}
%\floatstyle{plaintop}
\usepackage[justification=centering]{caption}
%\usepackage[hypcap=false]{caption}
%para que funcionen bien las tildes
\usepackage[activate={true,nocompatibility},
final,tracking=true,kerning=true,
spacing=true,factor=1100,
stretch=10,shrink=10]{microtype}
\usepackage{csquotes} %"para citar bien"
\emergencystretch=2em
\decimalpoint
\usepackage{booktabs} % added
\usepackage{siunitx} % added
\usepackage{caption} % added
\begin{document}
\begin{table}[hp]
\centering
\footnotesize
\renewcommand\arraystretch{0.9}
\captionsetup{skip=1ex}
\begin{threeparttable}
\caption{Cálculo de \textit{pKa} extendido}
\label{table:estimación_pka_extendido}
\begin{tabular}{ l
*{5}{S[table-format=2.2]}
}
\toprule
& & \multicolumn{4}{c}{\textbf{RM1}} \\
\cmidrule{2-6}
& & \multicolumn{2}{c}{\textbf{COSMO}}
& \multicolumn{2}{c}{\textbf{SS-COSMO}} \\
\cmidrule(lr){3-4}\cmidrule(lr){5-6}
& {$\mathit{pKa}_{\exp}(298$K)}
& {$\mathit{pKa}_{\textrm{calc}}$}
& {$\Delta\mathit{pKa}$}
& {$\mathit{pKa}_{\textrm{calc}}$}
& {$\Delta\mathit{pKa}$} \\
\midrule
\textbf{Ácidos}
& & & & & \\
\midrule
cloroacético
& 2.85 & 0.5 & 2.4 & 1.4 & 1.5 \\
4-clorobutírico
& 4.52 & 5.0 & -0.5 & 4.7 & -0.2 \\
2-cloropentanoico\tnote{b}
& & -2.3 & & 1.0 & \\
2-clorobutírico
& 2.86 & 0.6 & 2.2 & 0.4 & 2.5 \\
3-clorobutírico
& 4.05 & 3.7 & 0.4 & 3.8 & 0.3 \\
acetoacético
& 3.6 & 3.4 & 0.2 & 2.0 & 1.6 \\
bromoacético
& 2.69 & 1.2 & 1.5 & 1.1 & 1.6 \\
dicloro-acético
& 1.41 & -3.2 & 4.6 & -2.5 & 3.9 \\
iodoacético
& 3.12 & 2.1 & 1.1 & 2.8 & 0.3 \\
L-valina
& 2.29 & -1.9 & 4.2 & 2.6 & -0.3 \\
L-alanina
& 2.34 & -1.6 & 3.9 & 2.3 & 0.0 \\
trichloroacético
& 0.7 & -7.0 & 7.7 & -4.7 & 5.4 \\
2-chloropropanoico
& 2.83 & 0.8 & 2.0 & 0.2 & 2.6 \\
3-chloropropanoico
& 3.98 & 3.4 & 0.6 & 5.2 & -1.3 \\
3-hidroxipropanoico
& 4.51 & 3.8 & 0.8 & 3.5 & 1.0 \\
acético\tnote{a}
& 4.75 & {ref} & {ref} & {ref} & {ref} \\
fluoroacético
& 2.59 & 1.9 & 0.7 & -0.3 & 2.9 \\
fórmico
& 3.75 & 6.4 & -2.6 & 4.3 & -0.6 \\
pirúvico
& 2.39 & -0.3 & 2.7 & 1.3 & 1.1 \\
glioxílico
& 3.18 & 0.3 & 2.9 & 1.0 & 2.2 \\
propanoico
& 4.86 & 4.9 & -0.1 & 4.5 & 0.3 \\
butanoico
& 4.83 & 5.2 & -0.3 & 4.7 & 0.1 \\
acrílico
& 4.25 & 4.6 & -0.3 & 1.5 & 2.7 \\
láctico
& 3.86 & 3.3 & 0.6 & 5.6 & -1.7 \\
benzoico
& 4.2 & 3.7 & 0.5 & 2.2 & 2.0 \\
\midrule
\textbf{MAE}
& & & 1.8 & & 1.7 \\
\addlinespace
\textbf{Alcoholes}
& & & & & \\
\midrule
glicerol(doble hidrato)
& 14.15 & 11.0 & 3.2 & 14.1 & 0.0 \\
fenol
& 9.99 & 1.2 & 8.8 & 5.9 & 4.1 \\
etilenglicol
& 14.8 & 12.4 & 2.4 & 12.9 & 1.9 \\
2-metil-1propanol\tnote{b}
& & 17.6 & & 20.3 & \\
fenilmetanol
& 15.4 & 15.6 & -0.2 & 14.0 & 1.4 \\
butanol
& 16.1 & 16.1 & 0.0 & 15.2 & 0.9 \\
metanol
& 15.5 & 14.7 & 0.8 & 12.5 & 3.0 \\
trifluoroetanol
& 12.47 & 4.6 & 7.8 & 9.8 & 2.7 \\
etanol\tnote{a}
& 15.9 & {ref} & {ref} & {ref} & {ref} \\
n-propanol
& 16 & 16.2 & -0.2 & 16.4 & -0.4 \\
terbutanol
& 19.2 & 17.3 & 1.9 & 16.3 & 2.9 \\
\midrule
\textbf{MAE}
& & & 2.8 & & 1.9 \\
\addlinespace
\textbf{Aminoácidos}
& & & & & \\
\midrule
L-serina
& 2.19 & 1.2 & 1.0 & 0.2 & 2.0 \\
L-isoleucina
& 2.32 & 1.9 & 0.4 & 1.3 & 1.0 \\
glicina\tnote{a}
& 2.35 & {ref} & {ref} & {ref} & {ref} \\
L-valina
& 2.29 & 1.7 & 0.5 & 2.2 & 0.1 \\
L-alanina
& 2.34 & 2.0 & 0.3 & 1.9 & 0.4 \\
L-arginina
& 1.82 & 1.9 & -0.1 & 1.8 & 0.0 \\
L-lisina
& 2.16 & 4.7 & -2.5 & 3.6 & -1.4 \\
\midrule
\textbf{MAE}
& & & 0.8 & & 0.8 \\
\bottomrule
\end{tabular}
\begin{tablenotes}\scriptsize
\item[a] Desprotonación de referencia.
\item[b] Sin valor experimental.
\item Estimación y comparación de p$Ka$ calculados con RM1 y dos estrategias de solvatación: implícita (COSMO) y explícita-implícita(Solvateshell-COSMO). El $\Delta$p$Ka$ se realizó como $\Delta$p$Ka$=p$Ka_{\textrm{exp}}$-p$Ka_{\textrm{calc}}$. La sigla SS significa Solvateshell.
\end{tablenotes}
\end{threeparttable}
\end{table}
\end{document}
addendum:
if you like to have table width the same as is text width you have more options. for example use tabularx or tabular*. use of adjustbox is more or less desperate action of last resort when all other actions fails ...
the simplest way seems to me is use of tabular* in this case you need make only small changes to code in above mwe:
\begin{tabular*}{\linewidth}{%
@{\hspace{\tabcolsep}\extracolsep{\fill}}% this add extra space between columns
% that the table width become equal to text width
l
*{5}{S[table-format=2.2]}
}
...
\end{tabular*}
all others code is the same. in this case the table is looks like this (showed only top part of table):
note: in real document you should remove geometry package option showframe (which now, only for test purposes, show page layout
edit: in code i now consider Bernard comment below.
Best Answer
Two solutions based on
tabularx. The second uses thebooktabspackage, with only $3$ horizontal rules: