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Abstract: The excited-state calculations for the real green fluorescent protein (GFP) and its mutants, including the wild-type GFP, Y66F, blue fluorescent protein, and cyan fluorescent protein, were carried out at the INDO/S-CIS//ONIOM (B3LYP/6-31G∗∗:AMBER) level. The numbers of singly excited configuration state functions at INDO/S-CIS were over 20 million. The calculated absorption maxima were in good agreement with the experimental data with a computational error of ⩽15nm. For the wild-type GFP, INDO/S-CIS yielded a bathochromic shift of 38nm with respect to its model chromophore in vacuo, which was also in good agreement with the extrapolated experimental shift of 45nm. [Copyright &y& Elsevier]

Abstract: The absorption maxima, , of various organic dyes such as indigo, azobenzene, phenylamine, hydrazone, anthraquinone, naphthoquinone, and malachite green were calculated using the AM1, PM3, and PM5 semiempirical molecular orbital theories with the configuration interaction singles (CIS) and random phase approximation (RPA) approaches. The calculated were then compared with the values obtained by CNDO/S, INDO/S, ab initio CIS, and time-dependent density functional theory (TD-DFT). We found that the values calculated by AM1, PM3, and PM5 were in good correlation with the observed values. When B3LYP/cc-pVDZ optimized geometries were used, the square of the correlation coefficients between the calculated and observed , , at the AM1-RPA, PM3-RPA, and PM5-RPA levels were 0.891, 0.897, and 0.927, respectively. In particular, at PM5-RPA//B3LYP/cc-pVDZ was the largest among those obtained from all the other calculations including TD/B3LYP/cc-pVDZ//B3LYP/cc-pVDZ . Accordingly, the standard deviation of the difference between observed and calculated by the linear regression function at PM5-RPA//B3LYP/cc-pVDZ was the smallest. It was therefore concluded that this method was the most promising for the prediction of of various dyes among the computational methods studied here. When AM1 optimized geometries were used, at the AM1-RPA, PM3-RPA, and PM5-RPA levels were 0.822, 0.841, and 0.901, respectively, and they were also comparable to that at TD/B3LYP/cc-pVDZ//B3LYP/cc-pVDZ. Therefore, although some calibration efforts may be needed for AM1 geometries, PM5-RPA(CIS)//AM1 may be a second candidate available for the prediction of the absorption maxima of dyes, especially in the case of emphasizing computational cost. [Copyright &y& Elsevier]