# Binding of Arsenic by Common Functional Groups: An Experimental and Quantum-Mechanical Study
## 2 Materials and Methods
### Quantum-Mechanical Calculations  
Static quantum-mechanical calculations were performed by means of the Gaussian 09 software [20]. This software enables the evaluation of the ground-state structures along with the associated potential energy of selected molecular species. In this work, optimization of all the investigated molecular structures was performed by means of the hybrid B3 LYP [21; 22; 23; 24] Density Functional Theory (DFT) exchange and correlation functional. Geometry optimizations of the molecular structures were executed under implicit solvation employing the 6-311++G(d,p) atomic basis set for all atoms. As far as the simulation of the solvent is concerned, the conductive polarizable continuum model (CPCM) [25] was employed by setting parameters mimicking the water electrostatics. This way, geometrical relaxations at the ground-state of several structures were executed with the aim of quantifying the energetic gain associated with a series of chelation reactions between the investigated functional groups (i.e., thiol, amino, and carboxylic) and typical arsenic-bearing species present in aqueous solutions such as arsenous acid (As(OH)\({}_{3}\)). In particular, the following de-hydration reactions have been considered and energetically characterized:  
\[\text{CH}_{3}\text{CH}_{2}\text{SH}+\text{As(OH)}_{3}=\text{CH}_{3}\text{CH}_{2 }\text{SAs(OH)}_{2}+\text{H}_{2}\text{O} \tag{1}\]  
\[\text{CH}_{3}\text{CH}_{2}\text{COOH}+\text{As(OH)}_{3}=\text{CH}_{3}\text{CH}_{ 2}\text{COOAs(OH)}_{2}+\text{H}_{2}\text{O} \tag{2}\]For the sake of completeness, a series of reactions involving the binding of the amino group toward arsenous acid was also executed. However, because the related reactions contain charged species, the comparison of its energetics with those of reactions (1) and (2) is certainly disputable. In fact, the \(\Delta\)E value emerging from this analysis in the presence of charged entities is biased by the fact that screening effects are only poorly handled by continuum models of water and by the evidence that comparing energy differences between \"neutral\" reactions, such as reactions (1) and (2), with those emerging from \"charged\" processes renders the absolute energetic ground-state (reference) as ill-defined, from which energies are determined and, hence, makes questionable any stability ranking coming out from this specific analysis. With the aim of exploring a series of alternative \"neutral\" reactions involving the complexation of As(III) by the amino group, reactions such as CH\({}_{3}\)CH\({}_{2}\)NH\({}_{2}\) + As(OH)\({}_{3}\) = CH\({}_{3}\)CH\({}_{2}\)NH\({}_{2}\)As(OH)\({}_{3}\) and CH\({}_{3}\)CH\({}_{2}\)NH\({}_{2}\) + As(OH)\({}_{3}\) = CH\({}_{3}\)CH\({}_{2}\)NH\({}_{3}\)OAs(OH)\({}_{2}\) were also investigated. However, products of these reactions appear to be completely unstable since neither local nor global energy minima have been found. Finally, with the aim of evaluating the chelation capabilities of the SH, NH\({}_{2}\), and COOH functional groups toward As(III), structural optimization--conducted at the B3 LYP/6-311++G(d,p) level under implicit water solvation (CPCM)--of cysteine bound to arsenic-bearing species was performed as well. Cysteine was chosen as a prototypical molecule containing all the three functional groups here investigated so as to evaluate eventual competitive effects between them in the complexation process of As(III). In particular, all possible permutations of binding were considered, from the direct one-to-one (1,1) interaction between each functional group and As-bearing species up to the simultaneous threefold coordination (3,1) of As(III) with the thiol, amino, and carboxylic groups, passing through the two-to-one (2,1) interaction involving two groups at a time binding As(III). This way, quantum-mechanical calculations of seven systems constituted of cysteine+As(III)-bearing complexes were conducted in addition to the above-mentioned reactions.