Sunday, January 22, 2006

Hydrogen bond and dark matter

The notion of dark N-H atoms leads to a new view about hydrogen bond. For the necessary context see background ideas see this, this, and this. Indeed, the little discovery of this morning was that the hydrogen atoms associated with hydrogen bonds could be actually λk-H atoms. This hypothesis has interesting implications and predicts the formula H1.5O for water in atto-second time scales suggested by neutron diffraction and electron scattering.

  1. The formation of hydrogen bond would correspond to a fusion of name and conjugate name between N-H-O-H atom and its conjugate Nc-H-O-H atom (the shorthand notation Nc= λk-N will be used. This process would drop one proton to a larger space-time sheet and could transform it to a dark proton. In the original situation water would be chemically like H2O expect that the water molecules would have fractional positive charges N/λk and 1- N/λk meaning that water without hydrogen bonds would be positively charged.

  2. H-O-(λk-H)-O-H pairs obey the chemical formula H3-O2. Hence the darkening of protons in the formation of hydrogen bonds would predict the H1.5O formula suggested by neutron diffraction and electron scattering in atto-second time scale.

  3. The mass of (N-H)-O-H molecule would be by N-1 electron masses higher than ordinary water molecule and it would behave like fractionally charged object. The λk-hydrogen associated with hydrogen bond would in turn have mass mpkme. For λ≈ 211≈ mp/me and k=1, this would mean that the mass would be approximately 2mp instead of mp.

    On the other hand, the hydrogen bonding in TGD framework yields pairs H-O-(λk-H)-O-HH3O2== 2H1.5O rather than pairs H2O-H...OH2== 2H2O. For the favored value λ=211≈ mp/me of λ and k=1 the mass of a pair of hydrogen bonded molecules in TGD Universe would be nearly the same as the mass for ordinary hydrogen bonded H2O molecules in the Universe of standard model. This could explain why chemists would have failed to discover that water is not quite what we believe it to be. Be as it may, these are testable predictions and in principle could allow to check whether the model makes sense and if so, also determine the value of λ and k.

  4. It is quite possible that most of water is ordinary and an interesting question is whether pH could measure the amount of pairs of (N-H)-O-H atom and its conjugate (Nc-H)-O-H. If pH measures the number of pairs of this kind of molecules, the mass density of water would depend slightly on pH.

  5. As discussed in previous posting, the stability of negatively charged DNA strand is poorly understood. The presence of fractionally charged (N-H)-O-H water molecules in the vicinity of DNA would have a stabilizing effect.

  6. The energy needed to cut hydrogen bond is expected to depend on N-Nc pair characterizing the final state and on the molecular environment where the pair exists and would not thus be a property of hydrogen bond. It is not clear whether this energy can be identified as the energy of hydrogen bond (the value of which varies in water). The letters appearing in the names of molecules would be characterized by the energies needed to produce them, and the N-Nc pair with the minimum energy would dominate in a given environment which could be also macromolecule so that name of the molecule would be dictated by the properties of molecule.

  7. Genetic code would reduce at deeper level to the names of DNA nucleotides. It is quite possible that the splitting of DNA double strand gives rise to quantum superposition of N-Nc pairs. This would make possible quantal mechanism of mutations. McFadden has suggested this kind of mechanism but assuming that different DNAs would superpose which to my opinion cannot be the case. Also quantum computations by RNA strands can be imagined if it is possible to achieve the situation that the probabilities of various pairs in superposition are essentially identical.

For more details see for instance the chapters Pre-biotic Evolution in Many-Sheeted Space-Time of "Genes, Memes, Qualia,...".

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