Whether a hydrogen bond is formed or not depends on the electronegativity of an atom, as electronegativity is the power of an atom to attract electrons to itself. As a consequence and due to the historical focus on nitrogen and oxygen, the definition of a H-bond is primary based on the characteristics of oxygen and nitrogen 2. Most hydrogen bonds (H-bonds) focus on oxygen and nitrogen atoms as both acceptors and donors, with less attention devoted to sulfur, which is also known to form H-bonds and whose nucleophilic character is essential for numerous enzymatic reactions 1. In general, current methods to determine H-bonds will need to be reevaluated, thereby leading to better understanding of the catalytic mechanisms in which sulfur chemistry is involved. Furthermore, based on the identification of the weakest sulfur-water H-bond, the location of hydrogen peroxide for the nucleophilic attack by the cysteine sulfur can be predicted. This new algorithm will be implemented in the next release of the widely-used CHARMM program (version 41b) and will be particularly useful for analyzing water molecule-mediated H-bonds involving different atom types. We found a different sulfur hydrogen-bonding network to that typically found by established methods and we propose a more accurate equation for determining sulfur H-bonds based on geometrical criteria. We applied the NCI index on the active site of a single-cysteine peroxiredoxin.
A more accurate method is the non-covalent interaction index, which determines the strength of the H-bonds based on the associated electron density and its gradient. These methods often give rise to systematic errors when sulfur is involved. In many established methods, identification of hydrogen bonds (H-bonds) is primarily based on pairwise comparison of distances between atoms.
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