No abstract

The enzyme protochlorophyllide oxidoreductase (LPOR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), a crucial step in chlorophyll biosynthesis. Molecular understanding of the photocatalytic mechanism of LPOR is essential for harnessing light energy to mediate enzymatic reactions. The absence of X-ray crystal structure has promoted the development of LPOR homology models that lack a catalytically competent active site and could not explain the variously reported spectroscopic evidence, including time-resolved optical spectroscopy data. We have refined previous structural models to account for the catalytic active site and the characteristic experimental spectral features of Pchlide binding, including the 26 cm red shift of the C carbonyl stretch vibration in the mid-infrared (IR) and the 12 nm red shift of the Q electronic band. A hierarchy of theoretical methods, including homology modeling, molecular dynamics simulations, hybrid quantum mechanics [(TD-)DFT]/molecular mechanics [AMBER] calculations, and computational vibrational and electronic spectroscopies, have been combined in an iterative protocol to reproduce experimental evidence and to predict ultrafast transient IR spectroscopic fingerprints associated with the catalytic process. The successful application to the LPOR enzyme indicates that the presented hierarchical protocol provides a general workflow to protein structure refinement.

The ωB97-XD/6-311++G(d,p) calculations were carried out on dimers and monomers of salicylic acid and salicylamide as well as on their thiol counterparts; different conformations of these species were considered. The searches through the Cambridge Structural Database were performed to find related structures; thus the analysis of results of these searches is presented. Various approaches were applied to analyze inter- and intramolecular hydrogen bonds occurring in the above-mentioned species: natural bond orbital (NBO) method, symmetry-adapted perturbation theory (SAPT) approach, the quantum theory of atoms in molecules (QTAIM), and the electron localization function (ELF) method. The results of calculations indicate a slight mutual influence of inter- and intramolecular hydrogen bonds. However, the frequent occurrence of both interactions in crystal structures indicates the importance of their coexistence. The occurrence of intramolecular chalcogen bonds for trans conformations of species analyzed is also discussed.

MP2/aug-cc-pVTZ calculations were carried out on complexes wherein the proton or the lithium cation is located between π-electron systems, or between π-electron and σ-electron units. The acetylene or its fluorine and lithium derivatives act as the Lewis base π-electron species similarly to molecular hydrogen, which acts as the electron donor via its σ-electrons. These complexes may be classified as linked by π-H∙∙∙π/σ hydrogen bonds and π-Li∙∙∙π/σ lithium bonds. The properties of these interactions are discussed, and particularly the Lewis acid units are analyzed, because multi-center π-H or π-Li covalent bonds may occur in these systems. Various theoretical approaches were applied here to analyze the above-mentioned interactions—the Quantum Theory of Atoms in Molecules (QTAIM), the Symmetry-Adapted Perturbation Theory (SAPT) and the Non-Covalent Interaction (NCI) method.