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Kinetic Thinking: Back to the Future
Published in Clive R. Bagshaw, Biomolecular Kinetics, 2017
Regarding the forward direction of Equation 10.4, the calculated collision frequency of 7 × 109 M−1 s−1 ignores charge and tunneling effects, which would favor faster association, but another major factor comes from the anomalous diffusion coefficient of H3O+ compared to similarly sized ions. Grotthus accounted for this behavior in 1806 before water was known to have an H:O stoichiometry of 2:1 [698,699]. The idea then resurfaced 100 years later, when the molecular properties of water were better understood. The Grotthuss mechanism envisages that protons are rapidly exchanged between adjacent water molecules, so cutting down on the distance an individual proton has to move is analogous to a bucket brigade (Figure 10.2). The reaction is formally represented as
Nuclear Magnetic Resonance Spectroscopy of Copper Proteins
Published in René Lontie, Copper Proteins and Copper Enzymes, 1984
Anthony E. G. Cass, H. Allen, O. Hill
Chemical modification studies have revealed the importance of Arg-141 in the enzyme turnover:63 this arginine is approximately 5 Å from the copper. We have incorporated this in our mechanism (Figure 10) where we propose that the superoxide ion, as a hydrate, hydrogen bonds between the arginine and the axial water molecule. All electron transfers are outer-sphere and in the reduction of the superoxide, the arginine serves to neutralize the charge on the substrate and to protonate the developing peroxide dianion: the second proton comes via the copper-bound water molecule so that proton and electron transfer occur in a concerted and rapid process. Reprotonation of the metal bound water and the arginine then occurs from water molecules in the active site and the resulting hydroxide ions are released into the bulk medium by a series of proton transfers by the ordered water in the protein in a mechanism analogous to proton/hydroxide transport in ice (Grotthus mechanism). Anions such as iodide and perchlorate (the so-called chaotropic ions) could therefore also affect the copper site via changes in the water structure.
Calcium ion cyclotron resonance in dissipative water structures
Published in Electromagnetic Biology and Medicine, 2018
The ICR mechanism is addressed by some fundamental theoretical works about the interplay of physics and biology: the thermodynamics of irreversible processes pioneered by Ilya Prigogine (Prigogine, 1969), the quantum field theory (Feynman & Vernon, 2000), and the “Quantum Electro Dynamics of condensed Matter” elaborated by Giuliano Preparata (Del Giudice et al., 1995). According to these considerations, water plays the decisive role for biological EMF effects. This solvent for ions is the universal and indispensible mediator of all biological process and constitutes more than 80% of any living being. According to quantum electrodynamic (QED) theory water exists already at ambient temperatures as a two phase fluid. The first one is the incoherent phase of bulk water in which the water molecules behave gas-like and uncorrelated. The other phase consists of water molecules with a far-reaching structural order favored by their attempt to reach tetrahedral conformation. This will be enabled, because only H3O+-ions can enter such a coherence domain (CD) alleviated by the Grotthuss mechanism, also known as proton-hopping, whereby the protons are not delocalized about the whole water cluster (Agmon, 1995). The CD is characterized by a size of up to 100 nm and shrinks with rising temperature. The molecules are coherently entangled by an electromagnetic (EM) field trapped in the CD, because the water molecules inside the CD should be stronger polarized and the refraction index higher than the commonly known εr of about 80 for water (Del Giudice et al., 2002). About 5.5 × 106 molecules oscillate in phase between the two configurations of the molecular electron cloud: the ground state with an ionization energy of 12.6 eV, and the exited state at 12.06 eV where one electron is quasi-free and can act as an electron-donor for the environment against the outer incoherent phase at ambient temperatures. The domain size of such a coherent region will be given by its diameter lCD, which will amount to ~100 nm at room temperature: