giovedì 2 luglio 2015

THE ORIGINS OF PROTEINS: 1) The molecular asymmetry problem (part five)

Post n. 23 English  

So the question is: how does the water asymmetry determine the asymmetry of the colloidal silica?
The colloidal systems are influenced by several independent factors, and today we still cannot define a complete theory of colloid stability. In order to study the colloidal systems it is therefore necessary, as suggested by various researchers, to standardize the technique and predefine a certain interval before the observation. For several colloids such as silica, H2O gives a considerable contribution to their stability.
It is known that the water molecule has a polar covalent bond, due to the strong electronegativity of oxygen and is therefore a dipole;

As a result of this bond, the water molecules are oriented in all directions, with the hydrogen to oxygen forming larger molecular aggregations (clusters);

The study of ice, through X-rays, has shown that these molecular aggregates give rise to crystals formed by tetrahedral structural units, at the center one oxygen atom and at the four vertices other oxygen atoms. Each oxygen is bonded to four atoms of hydrogen, and then presents a coordination number equals to four. Each molecule is then linked by means of the hydrogen bonds with four other molecules forming a more expanded structure. The directions along which the 4 links are located depart from the center of the atom of oxygen and go towards the vertices of a tetrahedron.
Interestingly Bernal and Flower (JD Bernal and Fowler RH 1933 J. Chem. Phys. 1515,from Iopscience) believed that the transition from ice to water was similar to thetransition from tridymite to quartz and that this same quartzouse structure was responsible for increasing the density of water. However, it is a shared the hypothesisthat liquid water has an almost crystalline structure which forms clusters. It retains tetrahedral structural units, even though the water molecules are continuously exchanged due to the thermal agitation effect. As the temperature increases, while still remaining with a coordination number four, every hydrogen atom is bonded to three oxygen atoms and then to two oxygen atoms.
It is likely that this almost crystalline structure is present even at ordinary temperature and up to 37°C and that this structure is the responsible for the high specific heat of water at these temperatures. Above 37°C the specific heat of water has in fact its minimum value. The most likely hypothesis is that over this temperature, the coordination number is two and the tendency to coordination number four is lost and the almost crystalline structures collapse definitively.
It is important to make it clear that measurements of silica solutions at the polarimeter have also been made at various concentrations and temperatures. For experimental data (see: Prebiotic Chemistry and origin of life) indicate that by increasing the temperature up to 34 ° C the deviation of the polarized light is constant. Beyond 34 ° C, the deviation decreases drastically to zero between 38-40 ° C, the asymmetry of the silica has therefore disappeared.
As already said, the most likely hypothesis is that at the temperature of 37 ° C the almost crystalline structures of H2O collapse definitively. The experimental data shows that around the same temperature the colloidal silica does not deviate any more polarized light. It seems clear, however, there’s a direct relationship between the clusters of H2O and the structure of the colloidal silica (often referred to as silica Sol or simply Sol); once the Cluster is destroyed, finally the asymmetry of silica disappears.
So in addition to the asymmetry of water where, as we have seen, dominated by ortho molecules in

parallel spins, also clusters seem to contribute to determining the asymmetry of the colloidal silica.
Moreover, it is remarkable that molecules and structures connected to life have the same structural units: the quartz consists of tetrahedral structural units, but as we have seen elsewhere, also the amino acids have tetrahedral structural units. We later discovered that the silica and then the water present tetrahedral structural units. Now, if the first clue is by chance and the second one is coincidence then the third clue usually indicates a pattern. The tetrahedral structural unit, energetically very stable, must somehow also have a role in the guidance to the final geometry of the colloidal silica.
We can conclude that there are three contributing factors that tend to help determine the asymmetry of colloidal silica: water asymmetry, clusters and the tetrahedral structural unit.
As already said, the tetrahedral structural unit of the silica is at the center of the silicon atom and the oxygen at the top. Through the binding of these structural units, we have the following the reaction:

From the first of colloidal silica formation where, as seen in Fig.1, many of the oxygens are still linked to a hydrogen atom. Because of the different electronegativity between oxygen and hydrogen, there is the formation of a dipole, and on it water with its characteristic bond orients itself and binds.

Fig. 2
The silica is then wound by a large number of H2O molecules, being in a colloid state gives it a certain stability; in fact most of the H2O molecules around the colloidal silica are oriented in the same way that is with the positive charge on the outside.

The repulsion between the positive charges delays the aggregation of the colloidal particles and the formation of amorphous silica (silica gel). Water molecules that are found around the colloidal silica are not single molecules, they always belong to the water cluster that preserve tetrahedral structural units.
So, how do the three factors listed above lead to the asymmetry of the colloidal silica?
We try to give an answer, with the risk to making a fool of ourselves.
We know that if current flows in a wire around it generates a magnetic field. If the wire is surrounded by small magnets, placed on a plane, they will be oriented around the wire so as to form a closed circumference.

If, however, no current is flowing in the wire, the small magnets should slowly be arranged so as to minimize the electrical power consumption, as represented in the figure.

But this arrangement is not realistic because all the magnets must be aligned with Earth's magnetic field (indicated by the large arrow).

Now, let us imagine to have a glass of water and we agitate it vigorously with a stirrer so as to destroy all clusters. What happens as soon as you stop stirring the water? The predominant force is the dipole-dipole interaction between the water molecules. Under the effect of this force, the clusters of water with their tetrahedral structures would rebuild.
The tetrahedral structure within the clusters is the most stable structural unit. But this stability is achieved not only because -Hδ+ are geared toward -Oδˉ and also taking into account the effect of the spin, even if that contribution is very small. The direction of rotation of the hydrogen nucleus, which generates a small magnetic field, can rotate clockwise or counterclockwise, this direction is referred to as spin up and spin down. Imagining the tetrahedral structure out of context, there is no doubt that the increased stability is obtained when within it the four hydrogens have 2 spin up and 2 spin down, as indicated by the small arrows in the figure; in this way the very small magnetic fields associated with them cancel each other and the structure is more stable.

The tetrahedral structure in formation is, however, surrounded by Earth's magnetic field. If the barycentre of small magnetic fields were coincident, Earth's magnetic field would not have any influence on them. The nuclei of hydrogen inside the tetrahedral structure, however, are at a distance of approximately 4Å and are more subject to the effect of the Earth's magnetic field than to their mutual attraction. It may be that Earth's magnetic field imposes the formation of structures of ortho water molecules and the hydrogen magnetic fields aligned with them.

Certainly, this is not to say that the Earth's magnetic field shifts the axis of spin as in NMR resonance. The water molecules, due to the thermal agitation effect, are oriented in all directions. Here we only want to emphasize that probably, due to Earth's magnetic field, only the ortho water molecules oriented in the direction of that field, become part of the tetrahedral structure, so as to make the structure slightly more stable.
For simplicity, we’ll indicate using a single arrow above the structure, the small magnetic fields of nuclear spin oriented in the direction of Earth's magnetic field.

Now, we do so in our glass to form the silica sol. The exact composition of the sol is not clear, what we can assume from Fig. 1 is that most of the oxygen atoms at the periphery of the sol are bonded to hydrogen. Around them, with -Oδ- towards -Hδ+, will bind with their tetrahedral structures, with the water molecules.
It is important to highlight that the tetrahedral structures impose bond angles between the atoms, of about 110 °.  Small magnetic fields associated with the hydrogens inside the tetrahedrons cannot be aligned with Earth's magnetic field, since the link between Hδ+ of the colloidal silica structure and Oδ- of water tetrahedrons are predominant, small magnetic fields associated with the hydrogens inside the tetrahedra cannot be aligned with Earth's magnetic field. This provision can be represented with the tetrahedra of the water that, due to the bond angles of the tetrahedral structures, assume a different orientation. Consequently, the magnetic fields associated with the tetrahedra are not aligned any more to Earth's magnetic field and will be subjected to various actions by Earth's magnetic field.

Now, imagine for a moment that the whole structure is rigid except at the point of conjunction between the silica tetrahedrons. As can be seen from the following figure, the bottom of the colloidal silica tetrahedral structure, under the action of Earth's magnetic field, the clusters linked to -OH in position 1 and 3 are subject to a counterclockwise push while those in position 2 will undergo a clockwise push; the counterclockwise prevails.
On the contrary, in the structure of the upper tetrahedral colloidal silica, the clusters in position 4 and 5 will suffer a clockwise push, and the clusters in position 6 on in a counterclockwise direction; in this case, the push in a clockwise direction prevails.

The final result is that the thrust will drag the lower tetrahedral structure of the colloidal silica by rotating it counterclockwise, and drag the upper structure zone rotating it clockwise.
Ultimately the tetrahedral structural units of the silica, when binding to create colloidal particles, could have any orientation, and any contribution, even if very small, may determine a preferred direction. This contribution could be given to the combined effect of Earth's magnetic field and the three factors listed above the asymmetry of water, the formation of clusters and the tetrahedral structural unit.
It is therefore possible that this combined effect impose a preferred direction and are at the base of the origin of the asymmetry of the colloidal silica.

                                                                                                          Giovanni Occhipinti

Translated by: Sydney Isae Lukee