## 3 Results and Discussion
For each of the six QM/MM optimized structures, vibrational frequencies and IR intensities were computed; the results for Fe\({}^{2+}\) and Fe\({}^{3+}\) are listed in Table 3, respectively, and the spectra are shown in Figures 6 and 7, respectively. The results are compared with the FTIR spectra obtained from the oxidized form of native, wild-type (WT) [NiFeSe] hydrogenase as-isolated from _D. vulgaris_[10]. In their experiment, [PERSON] et al. observed two sets of CO bands for different batches of purified enzymes [10]. These two bands were assigned to two different conformations, or isomers (IS), of the active site and termed Ni-IS\({}_{\rm I}\) and Ni-IS\({}_{\rm II}\); Ni-IS\({}_{\rm I}\) is the conformer that shows a more intense CO band at 1904 cm\({}^{-1}\)[10]. For sake of reference, the frequencies obtained from the [NiFeSe] species from the recombinant enzyme (r[NiFeSe]) of [PERSON] et al., as-isolated (as is) and reduced (red) with H\({}_{2}\), are listed as well. An important note: the experimental values of [PERSON] et al. listed in Table 3 were obtained from experiments that are not based on the same crystallized protein that is the basis of our computational study [1]. Nonetheless, as these experimental frequencies are for the native WT [NiFeSe] hydrogenase isolated from _D. vulgaris_ under non-reducing conditions, we will refer to them as a reference with which to compare our calculated frequencies based on the oxidized, recombinant enzyme in Ref. [1]. \begin{table}
\begin{tabular}{c c c c c c c c c c c c c} \hline \hline  & & & & & & & & & & & & & \\ \hline \multicolumn{1}{c}{**Ni-5**} & **Ni-5** & **Ni-Se** & **S-Se** & **Ni-S-Cys492** & **Ni-S-Cys78** & **Ni-S-Cys75** & **Fe-CN1** & **Fe-CN2** & **Fe-CO** & **Fe-S-Cys492** & **Fe-S-Cys78** \\ \hline
1 & 2.52 & 2.21 & 2.37 & 2.17 & 2.19 & 2.25 & 2.22 & 1.85 & 1.87 & 1.74 & 2.28 & 2.26 \\ \hline
**2.41** & **1.98** & **2.34** & **2.20** & **2.22** & **2.31** & **2.19** & **1.82** & **1.82** & **1.82** & **2.34** & **2.26** \\ \hline
**II** & 2.55 & 2.10 & 3.60 & 2.19 & 2.23 & 2.27 & 2.14 & 1.86 & 1.88 & 1.72 & 2.31 & 2.25 \\ \hline
**2.41** & **1.98** & **3.07** & **1.99** & **2.22** & **2.31** & **2.19** & **1.82** & **1.82** & **1.82** & **2.34** & **2.26** \\ \hline
**III** & 2.61 & - & 2.24 & - & 2.24 & 2.27 & 2.18 & 1.85 & 1.88 & 1.73 & 2.20 & 2.32 \\ \hline
**2.41** & **-** & **2.39** & **-** & **2.22** & **2.31** & **2.19** & **1.82** & **1.82** & **1.82** & **2.34** & **2.26** \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Bond lengths (Å) from QM/MM-optimized geometries are listed for each of the three conformers I, II, and III for [Ni\({}^{2+}\)Fe\({}^{2+}\)Se] hydrogenase. For comparison, the bond lengths obtained from the crystal structure (PDB ID: 5]SH [1]) are listed in bold print. \begin{table}
\begin{tabular}{c c c c c c c c c c c c c} \hline \hline  & & & & & & & & & & & & \\ \hline \multicolumn{1}{c}{**Ni-5**} & **Ni-5** & **Ni-Se** & **S-Se** & **Ni-S-Cys492** & **Ni-S-Cys78** & **Ni-S-Cys75** & **Fe-CN1** & **Fe-CN2** & **Fe-CO** & **Fe-S-Cys492** & **Fe-S-Cys78** \\ \hline
1 & 2.54 & 2.17 & 2.38 & 2.17 & 2.21 & 2.25 & 2.21 & 1.85 & 1.88 & 1.72 & 2.27 & 2.27 \\ \hline
**2.41** & **1.98** & **2.34** & **2.20** & **2.22** & **2.31** & **2.19** & **1.82** & **1.82** & **1.82** & **2.34** & **2.26** \\ \hline II & 2.45 & 2.10 & 3.52 & 2.18 & 2.19 & 2.30 & 2.10 & 1.86 & 1.88 & 1.75 & 2.39 & 2.31 \\ \hline
**2.41** & **1.98** & **3.07** & **1.99** & **2.22** & **2.31** & **2.19** & **1.82** & **1.82** & **1.82** & **2.34** & **2.26** \\ \hline
**III** & 2.76 & - & 2.24 & - & 2.25 & 2.32 & 2.15 & 1.85 & 1.88 & 1.72 & 2.29 & 2.20 \\ \hline
**2.41** & **-** & **2.39** & **-** & **2.22** & **2.31** & **2.19** & **1.82** & **1.82** & **1.82** & **2.34** & **2.26** \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Bond lengths (Å) from QM/MM-optimized geometries are listed for each of the three conformers I, II, and III for [Ni\({}^{2+}\)Fe\({}^{3+}\)Se] hydrogenase.