[HydrogenBond]

Many well-documented biochemical processes lack a molecular mechanism. Examples are: how ATP hydrolysis and an enzyme contrive to perform work, such as active transport; how peptides are formed from amino acids and DNA from nucleotides; how proteases cleave peptide bonds, how bone mineralises; how enzymes distinguish between sodium and
potassium; how chirality of biopolymers was established prebiotically. Methodology/Principal Findings. It is shown that involvement of water in all these processes is mandatory,

Citation: Wiggins P (2008) Life Depends upon Two Kinds of Water. PLoS ONE 3(1): e1406. doi:10.1371/journal.pone.0001406

This article discusses how many of the established mechanisms of basic biochemical processes, although well defined at the level of biochemistry and even part of text books, do not add up in terms of the energy requirements of physical chemistry. What the authors tried to do is add the difference in needed potential using high and low density water domains. The difference in aqueous hydrogen bonding creates a potential difference that is essential to life processes. It took a while for the science to catch up. Unfortunately for the researchers, there is a dogmatic insistence protecting the status quo. Right now we can work around this with a fudge tool. I have no problem with that, from a practical point of view, just that it is leading to a philosophical bias as though this is real.

For example, if water is needed to form DNA from nucleotides, mutations on genes are also dependant on the local water since the very reaction will not occur without water. The local water, in turn, should be dependant on the potentials in the surrounding water. Random is needed when you ignore variables as part of the philosophy. Its is a good first approximation.

The authors could take it one step further, but this would be confronted by a bias in physical chemistry. This bias is connected to the practical difficulties in observing small dynamic systems of hydrogen bonds. One can't go too far too fast until the experimental capability is able to catch up. This may take physics getting more involved to push this understanding theoretically. There are already some quantum modeling such as proton tunneling affects. It is boring waiting around. We should have been at this point twenty years ago. I have a lot of disappointment with the care takers of the science traditions. Maybe that is why I fight against it.

[HydrogenBond]

If the DNA needs the surrounding water to form from nucleotides and the enzymes need the surrounding water to do useful work from ATP, then we need to look at the DNA differently. This extra layer of unaccounted for water potential, is why there has been a push toward random. If we leave out one the variables, which in this case is one of the critical variables, then we have to resort to fudge factors. Anything that extrapolates from there may still have practical value, but should not be confused with reality. We need to start looking at the old approach as a good first approximation. This is helpful since it opens the mind allowing one to think outside this little box.

[HydrogenBond]

I will try to be more constructive. Below is a qualitative energy diagram for high and low density water. The (a) is the high density and the (b) is low density. The difference is the high density (a) has a higher degree of nondirectional van der Waals and electrostatic interaction, while the low density (b) has a higher degree of directionality due to more directional partial covalent bonding character. The partial covalent bond separates the water molecules for better orbital overlap and reduces the number of water molecules that are in contact to a maximum of four, although it can also be less. The small potential energy barrier allows normal thermal affects to shift between the two easily so both zones will be found in water.



Here is my theory. The way I explain this is due to a tug of war between oxygen and hydrogen. An isolated water molecule has hydrogen attached to a highly electronegative atom. The electron density sharing stabilizes the oxygen but also creates a dipole. As we start the process the net burden of potential is on the hydrogen. At (a) the hydrogen is able to lower its potential better by sneaking around the oxygen, sharing as much electron density as possible by increasing density. Although this is great for hydrogen it will increase the potential of the oxygen. In (b) the oxygen does not take this lying down. Instead, it asserts its higher electronegativity forcing the hydrogen into more directed partial covalent bonds. This is energetically better for the system since the oxygen is more electronegative and gets its rightful share. But this sends some of the burden back to hydrogen. The hydrogen, in turn, with the help of a little thermal energy, tries to go back to (a). There is a constant tug of war.

An interesting tidbit is although we define water as H2O, in the liquid state this molecule will exist for about a milli-second. The covalent bonds are breaking and reforming due to proton-deprotonation type processes sort of mediated by hydrogen bonding. Again, this is the tug of war between oxygen and hydrogen, the oxygen is trying to assert its higher electronegativity and hog the electrons, while little hydrogen is looking for a better deal.
Water molecule structure