Molecular Creation (logo) A Story of Natural Molecular Evolution from Atoms and Water to the living Cell



Liquid Water

Classically, the term ”Hydrogen Bond” has been used to explain why water has such high melting and boiling points relative to other liquids.5 In the liquid state, water molecules are considered to be dynamically hydrogen-bonded by point-charges on their surfaces to three or four other water molecules while Methane Molecules, CH4, with about the same size and mass (or weight), have very little surface charge and no hydrogen-bonding between them – they move and rotate more freely.

The extremely high boiling point of liquid water, 212oF, relative to -257.8oF for liquid methane is due to the fact that water forms hydrogen bonds while methane does not.

The difference in boiling temperatures between water and methane at atmospheric pressure, as displayed above, is a spectacular 470 degrees F (243 degrees C). Although point-charge hydrogen bonds are weak (1.3 to 2.8 kcal/mole) and form at a variety of angles and distances, they hold water molecules together in dynamic coordinated clusters.5 However, recent studies at the Stanford Linear Accelerator Center provided evidence that the molecules in pure liquid water spontaneously hydrogen-bond together to form a more ridged dipolar Trimer with covalent hydrogen-bonding similar to that in ice.6,12

Recent X-Ray studies indicate that hydrogen bonds between water molecules in ice are more ridged with lower-energy by 4- to 5-kcal/mole than most bonds in liquid water

Molecular orbital calculations performed back in the 70’s support the view that a maximum of three water molecules hydrogen-bond together at any instant with a distance of about 2.76 Angstroms between the oxygen atoms12 and high-speed infrared spectroscopy indicates that trimers last only about 10-12 seconds, a million millionth of a second.13 Since trimers are more ridged, they occupy slightly more space and generate ice-like regions of hydrogen-bonding and lower density.6,12

However, there is another property of liquid water which may change our concept of its role in living cells in years to come. In 2003, Professor Chatzidimitriou-Dreismann and his group in Germany reported that irradiation of pure liquid water with ultra-high-speed neutrons at 10-18 seconds, ejected only 1.5 protons per water molecule rather 2.19 The result provided evidence that protons in water molecules have the same sub-atomic Quantum Mechanical Particle/Wave Property as electrons in metals. Irradiation with neutrons was fast enough to reveal only the particle property - the wave property was invisible.20 Like electrons in a wire, the spin of protons in distant water molecules couple them together to produce a quantum mechanical property called Entanglement.19,20 Nuclear magnetic resonance, which is produced by the spin-coupling of protons in close proximity, is used to image water in living tissues - entanglement involves coupling of spins of multiple protons at extremely high frequencies. Waves last only about 10-15 seconds, a thousand times more briefly than hydrogen bonding in liquid water, with the almost instantaneous interchange of quantized units of energy from one location to another. Based on present information, it seems possible that consciousness and thought may be integrated waves of proton entanglement between different regions of the brain.

The Solid State

As the temperature of liquid water is lowered to 4oC, distances between water molecules decrease and density increases. However, as the temperature approaches 0oC, distances increase and density decreases.5 While covalent trimer-formation and ice-like hydrogen bonding around them may increase as the temperature moves toward 0oC, the two- and three-dimensional forms present in ice cannot be present because pure liquid water in a clean glass container can be cooled to as much as -30oC without crystallizing.26 Glass is a solid liquid with no regular hexagonal surface patterning of atoms to seed ice-formation.5 However, surfaces with hexagonal patterning, like those on iodine crystals and ice, induce immediate crystallization at 0oC.5 If the temperature is lowered on down to -40oC, crystallization occurs immediately.26 However, the crystalline form produced at that temperature is not normal ice, it is cubic ice, the same as that which forms in space as snowflakes. As illustrated on page 2, cubic ice is composed entirely of linear elements, 2.75A between the water molecules.27 Since cubic ice is unstable, as water freezes at 0oC, it immediately isomerizes into normal hexagonal ice in which some of the molecules are not in linear elements and distances between water molecules are 2.75A to 2.84A.27

It is important to realize that X-ray studies, performed by Isaacs at Bell Labs in 1999, provided evidence that hydrogen bonds in both forms of ice are not like the point-charge bonds in liquid water or in stable proteins, they are covalent similar to the bonding between carbon atoms with electron orbital clouds of adjacent water molecules around a central proton.6 At 0oC, covalent hydrogen bonds are stable in hexagonal ice, but not in cubic ice, in trimers or in ordered elements on surfaces above 0oC.12

The Air /Water Interface

Of course, as water molecules approach a surface, motion is arrested and they assume less dynamic more ordered bonding relationships than those in bulk liquid water.

X-ray deflection from the surface of liquid water produces a major peak at 2.9 Angstroms for weakly hydrogen-bonded molecules and at 4.5 and 6.8A for trimers and tetramers.

In 1972, Narten and Levy deflected X-rays from the surface of pure liquid water at 25oC (77oF) and used the diffraction pattern to determine the structural character of water molecules at the interface.14 As illustrated, most water molecules on the surface are about 2.9 Angstroms apart, far enough to permit point-charge hydrogen bonding and coordinated motion, but close enough to permit periodic covalent hydrogen-bonding between three and four molecules at 4.5 and 6.8 Angstroms with mean distances between oxygen atoms of 2.76A.

 Since a significantly smaller number of these ordered units exist at any instant and distances between oxygen atoms can vary as much as 10%, the peaks are shorter and broader than those involved in more dynamic point-charge bonding. However, covalent linear elements, by forming and decaying extremely rapidly and continually propagating the formation of additional linear elements, smooth the surface and increase the surface tension. However, as mentioned before, no two-dimensional hexagonal forms appear to be present at the interface between air and water because crystallization does not occur at 0oC unless seeded by an hexagonal pattern of atoms.5

The Hydrocarbon/Water Interface

It is important to realize that covalent linear elements, containing five and six water molecules, are calculated to form in particular orientations on non-hydrogen-bonding hydrocarbon surfaces.7 However, hydration order on surfaces of hydrocarbons, like gasoline and oil, is substantially different from that adjacent to air. At the interface with air, covalent bonding between water molecules produces only one-dimensional linear elements. However, adjacent to hydrocarbons, the ends of the hydrocarbon molecules, by forming two-dimensional hexagonal patterning at the interface,16 draw water molecules into that pattern and induce immediate ice-formation at 0oC.5

At the interface between non-hydrogen-bonding hydrocarbons and water, water continually moves from strong to weak bonding and removes energy from hydrocarbons.

In the liquid state, hydrocarbon molecules have the freedom to move and rotate in all orientations, but, in contact with water, they are forced to assemble side-by-side - they can exchange positions but are restricted from rotating end-over-end.16 At the same time, water molecules, which continually form covalent linear elements on the surface, are drawn into regular hexagonal patterns which seed ice formation.5

 Adjacent to non-hydrogen-bonding hydrocarbons, it is critically-important to realize that it is the unidirectional movement of energy from the hydrocarbon molecules into water which drives them from randomness toward order. As small water molecules move from point-charge bonding in bulk liquid water into covalent water-to-water bonding on surfaces of hydrocarbons, 4 to 5 kcal/mole of energy is transferred to adjacent water molecules.5 But, as the covalent hydrogen bonds break and water molecules move spontaneously into point-charge bonding, from order toward disorder, similar quantized units of energy are removed from more massive slower-moving hydrocarbon molecules and they spontaneously move from randomness toward order.16,17 In fact, recent studies by the late Professor Zewail and his group at CIT, employing ultra-high-speed crystallography, have revealed that water on the hydrophobic surface of solid graphite forms ordered layers of hexagonally-patterned linear elements with crystallites of cubic ice.28 Other studies indicate that motions of water molecules adjacent to large ions and ordering surfaces conform to Quantum Mechanics, not Newtonian Physics they “jump” from one bonding relationship to another with the exchange of quantized units of energy.10

 Thus, water, adjacent to non-hydrogen-bonding liquid and solid surfaces, exhibits significantly more elements of transient structural order than in the bulk liquid state or at the interface with air.8 However, water molecules have too much energy to be held in ordered forms for long - high thermal energy drives them toward freedom.5 Ordered water on surfaces lasts no more than 10-12 to 10-10 seconds - molecules then rotate and return to their more dynamic point-charge state and others take their place as transiently-ordered units. In fact, hydrocarbon and water molecules spontaneously move away from each other to minimize contact and increase freedom. Hydration Entropy increases as they move and spin more freely. Two simple experiments demonstrate this Second Law of Thermodynamics.

If oil and water are mixed rapidly, the small droplets which form rapidly coalesce to reduce ordering contact. On wax, water forms balls to minimize ordering contact.

If oil and water are mixed rapidly, small droplets form. However, if the mixture is allowed to stand, the droplets spontaneously coalesce into a single layer - the liquids move spontaneously to minimize contact between each other. If water is placed on a wax surface, it forms balls to minimize Multi-dimensional Ordering in contact with wax in favor of One-dimensional Ordering in contact with air.

Spontaneous Assembly

Paradoxically, it was this spontaneous movement of water molecules away from each other to reduce order and increase freedom which drove the development of natural molecules to ever-increasing levels of higher order.3,8,17,18

As you will see when we view the spatial structures of natural molecules, it is the distribution and nature of atoms on each surface which define the degree and orientation of Transient (Covalent) Linear Hydration on surfaces and Quantized (Cubic) Hydration Patterning around the molecules.11,29 Just as hydrocarbon molecules in oil spontaneously move away from contact with ordering water in favor of associations with their own kind, non-hydrogen-bonding hydrophobic surfaces on natural molecules, such as polypeptides, spontaneously form coils or assemble side-by-side to permit covalently-ordered water to leave. As hydration-ordering regions of polypeptides assemble to produce dehydrated central regions of proteins, small hydration-ordering regions, which are left on outer surfaces, regulate the orientation of surface water to integrate motions and interactions with other proteins and vital molecules.8,17

Polypeptides, like that of insulin, spontaneously assemble by bringing hydrocarbon regions together to reduce contact with and release ordered water.

The Insulin Molecule is an excellent example of how surface water drives and directs the folding and assembly of a polypeptide with a specific sequence of peptides to spontaneously produce a natural protein.30 As the linear insulin polypeptide emerges from the ribosome where it is assembled, water must surround it on all sides. Covalent ordering of water is at a maximum adjacent to hydrocarbon regions - hydration freedom (entropy) is at a minimum. Three regions of the segment containing peptides with hydrocarbon side chains wrap rapidly into Coilsto permit water to move from order toward disorder; three regions with ordering peptides on about every-other position remain as Linear Segmentsand two, at C and D, are Mobile they are composed of small peptides which, by continually forming point-charge bonding with surface water, prevent covalent linear-element formation. Mobility in C permits it to guide residual hydration-ordering regions on A and B together to form a dehydrated central core. At each stage of assembly, ordered water molecules are released until, finally, a thermodynamically-stable water-soluble protein is produced with no water inside and predominantly hydration-disordering point-charge hydrogen-bonding peptides on the outer surface.30

By spontaneously bringing opposite charges and hydration-ordering regions together, a protein is produced with no internal water and high internal order. Most of the peptides which hydrogen-bond directly with water are left on the surface increasing hydration disorder, stability and solubility. However, insulin differs from most water-soluble proteins in that its outer surface retains the external cubic geometry which directed its formation. Its conical shape continues to permit water to form transient linear elements of covalent bonding on some of its surfaces, particularly the lower right-hand face next to the linear element and coil. It is that flat planar surface which has been shown to bind to a complimentary surface on a Receptor Protein which regulates the uptake of glucose into cells.31 Although no hydration studies have been reported for the binding site of that receptor protein, it is likely that it also induces the formation of transient linear elements of hydration when the site is open and not occupied by the insulin molecule.

However, covalent linear elements of hydration are extremely unstable. Nuclear magnetic resonance displays them on surfaces as doublets, like those in ice, rather than as singlets, like those in liquid water,7, 15 but they form and decay so rapidly and present such a small proportion of the surface water, that they are similar to the electrons around atoms – they may be viewed only as Quantum Mechanical Entities which occupy space and regulate interactions but, like electrons, are only in probability locations.20

Thus, as molecules were produced at random during the early phases of natural molecule formation, surface water spontaneously assembled them into sets with uniquely coordinated functions. A molecular world was produced in which surface water provided the principles of spatial control in which the movement of each molecule was communicated to others by transient linear elements of hydration and proton entanglement. It was a world in which many of the rules for molecular selection and assembly were established by the aqueous environment. Spontaneity, from order toward disorder, with which we are familiar in air, was reversed. Energy from the sun powered the conversion of small molecules into an almost infinite variety of complex molecules while linearizing surface water functioned symbiotically to select and direct spatial forms into complex assemblies which could function spontaneously to produce he Miracle of Cellular Life.25

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