The importance of low-barrier hydrogen bonds (LBHBs) in enzyme catalysis has remained a controversial topic. LBHBs are defined as protons that are delocalized between two heavy atoms. Since the 1990s LBHBs have been proposed to play a crucial role in several enzyme-catalytic pathways by stabilizing transition states or reaction intermediates.[1–3] However, more recently, with the development of improved theoretical tools for enzymatic studies, such as the hybrid quantum-mechanic/molecular-mechanic (QM/MM) method,[4] several theoretical studies have investigated such systems from a quantum-chemical point of view. It appears that the existence of the LBHB is not that clear and several enzymes, such as ketosteroid isomerase,[5] triosephosphate isomerase,[6, 7] and citrate synthase [8–10] have been proven to use short and strong hydrogen bonds (SSHBs), but not LBHBs. This controversy arises from the lack of tools to clearly identify a LBHB. Indeed, the existence of a LBHB is usually invoked when a SSHB is localized between two residues with matching pKa values; this differs from the initial LBHB definition. QM calculations may help to provide the answer. However, those calculations are very expensive in enzymes due to the large size of the systems. Herein, we aim to present a simple procedure to visually assess the presence of such a peculiar type of hydrogen bond (HB) by using the electron localization function (ELF). First we will define and compare the usual LBHB characteristics to other strong HBs, namely, the single-well HBs (SWHBs) and SSHBs. We will then describe the methodology used on a small homonuclear hydrogen-bond system, the [H5O2]+-protonated water dimer, which enables us to discuss the different types of hydrogen bonding. The last part is devoted to larger systems, namely, the heteronuclear trichloroacetate (Tca)–4-methyl-1H-imidazole (HMim) system,[11] the carboxylic acid/carboxylate anionic system,[12] the [N2H7]+ cation,[13] the proton sponge of intra-bridgeheads,[12, 13] the phenol/phenolate anionic system,[12] the hydrogen maleate [12, 14–16] and the hydrogen difluoride anions,[17] which are treated purely by QM methods, and the complete phosphorescent yellow protein (PYP)[18] analyzed by ab initio QM/MM methods.

The proton-transfer reaction between two electronegative atoms (X and Y) can be described by Marcus theory. Let us consider a proton-transfer reaction between two electronegative atoms (X and Y). The distance between H and (for example) X may be used as a reaction coordinate (RC) for this system. The HÀX or HÀY bonds can be modeled by considering the proton as being harmonically bonded to X or Y. The usual representation of a HB is shown in Figure 1a. It is a double-well profile in which the barrier is high