On the Nature of the Hydrogen Bonds to Neutral Ubiquinone in the QABinding Site in Purple Bacterial Photosynthetic Reaction Centers

Abstract

The nature of hydrogen bonding to pigments in protein complexes is currently a topic of some debate. The debate centers on whether hydrogen bonds can be understood on purely electrostatic grounds or whether they need to be considered quantum mechanically. This distinction is of current relevance primarily because of the application of QM/MM computational methods to the study of biological problems. To address this problem we have used QM/MM methods to study the neutral state of the hydrogen bonded ubiquinone molecule termed QA that functions as an electron transfer cofactor in purple bacterial photosynthetic reaction centers. In these calculations we have treated the hydrogen bonding amino acids either quantum mechanically or using molecular mechanics methods. As a specific metric for comparing the different computational methods isotope edited FTIR difference spectra are calculated. The calculated spectra are in remarkable agreement with experimental spectra, and it is found that the calculated spectra are very similar when hydrogen bonding amino acids are treated using either QM or MM methods. The latter result suggests that hydrogen bonding to neutral ubiquinone in purple bacterial reaction centers can be considered in purely electrostatic terms, which is contrary to the widely held belief that the hydrogen bonding amino acids should be treated quantum mechanically. Natural bond orbital analysis is used to further verify that the hydrogen bonds are predominantly electrostatic in nature. Calculated bond lengths and vibrational frequencies of the N-H groups involved in hydrogen bonding are used to estimate the relative strengths of the hydrogen bonds to either ubiquinone carbonyl group.