PubMed · 5482619
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P A Bennett, J V Sullivan, A Walsh. 1970. A simple protein meter.. https://doi.org/10.1016/0003-2697(70)90339-8
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A quantum mechanics/molecular mechanics (QM/MM) implementation that uses the Gaussian electrostatic model (GEM) as the MM force field is presented. GEM relies on the reproduction of electronic density by using auxiliary basis sets to calculate each component of the intermolecular interaction. This hybrid method has been used, along with a conventional QM/MM (point charges) method, to determine the polarization on the QM subsystem by the MM environment in QM/MM calculations on 10 individual H(2)O dimers and a Mg(2+)-H(2)O dimer. We observe that GEM gives the correct polarization response in cases when the MM fragment has a small charge, while the point charges produce significant over-polarization of the QM subsystem and in several cases present an opposite sign for the polarization contribution. In the case when a large charge is located in the MM subsystem, for example, the Mg(2+) ion, the opposite is observed at small distances. However, this is overcome by the use of a damped Hermite charge, which provides the correct polarization response.
Semiempirical molecular orbital theory has been used for a systematic scan of the binding positions for a Mg2+ ion with 5a,6-anhydrotetracycline taking both conformational flexibility and possible different tautomeric forms into account. The magnesium ion has been calculated alone and with four or five complexed water molecules in order to simulate the experimental situation more closely. The results are analyzed by comparing the behavior of the title compound with that of tetracycline itself and possible causes for the stronger induction of the Tetracycline Receptor (TetR) by 5a,6-anhydrotetracycline than by tetracycline are considered. Energetically favored 3D-structure of the zwitteranionic 5a,6-anhydrotetracycline magnesium complex in solution.
Infrared frequencies and intensities for the metal-free porphyrin (H2Por), N',N-dideuterio porphyrin (D2Por), and magnesium porphyrin complex (MgPor) have been calculated at density functional B3LYP level using the 6-31G(d) basis set. Detailed assignments of the NH and NM vibrational bands in the IR spectra have been made on the basis of comparison between the calculated data and the experimental results. The previous empirical controversial assignments for the bands at 1224, 1110 and 771 cm(-1) for metal-free porphyrin are also clearly interpreted.