1

2

3

orbitals on the other two corners, water molecules are symmetrically-

With positively-charged protons (the nuclei of hydrogen atoms) in twoelectron orbitals of an oxygen atom and two negatively-charged open-

charged particles which bind to each other in the liquid state by dynamic “dielectric” hydrogen bonds.

coordinated clusters that they dram-

The bonds are weak but they tie the molecules together in such tight

atically increase the boiling temp-

molecules that do not hydrogen erature of liquid water. Methane, with

bond, boils at -257.8 degrees Fahr-

Even ammonia, with molecules that do hydrogen bond, boils 240 degreeslower than water.

WATER AND THE MOLECULES OF LIFE

Did you ever wonder why water is so essential to Life?

Did you ever wonder what properties water must have to have served

Well, some answers to those questions are now available.Although they have not been transcribed into mathematical terms,

they are easy to understand. Here they are in seven pages.

as the medium in which the molecules of life evolved?

are 2.9 Angstroms apart - close enough to form hydrogen bonds but far enough to rotate. The two small peaks on

X-Ray deflection from the surface of liquid water in a 1972 study revealed that most molecules

questioned. It was not until more information was gainedtheir presence was

by more ridged linear

regarding water and ice, that their presence was confirmed.

the right at 4.5 and 6.8 A seemed to be produced

with bonds of 2.76 A trimers and tetramers

but the peaks were so broad and weak that

10 2 3 4 5 6 7 8 9 10A Narten and Levy (1972)

4.5A2.9A1A

6.8A

25 C

o o

o

o

o

o

X-Ray Tube

Water SamplePattern

Di�raction

X-Ray Beam

O

HH

O

H H

C

100

0

-100

-200

212 F

-77.4 F-28.1 F

-257.8 F

Boilin

g Po

ints

(deg

rees

Cen

tigra

de)

O2H N 3H C 4HS2H

O

H H

O

HH

O

H H

H

H H

H

H

H

H

H

H

H H

H

H

HH

H

H

HH

H

C

C

C

C

CO

H H

H

HH

HCN

H H

HS

H H

o

oo

o

O

H H

enheit, 470 degrees lower than water.

In contrast to dielectric hydrogen-bonds which stabilize water molecules

2

ice, in the trimer and in longer linear elements on surfaces are more ridged, less energetic and, usually, unstable above 0 C. In fact, in 1999, the hydrogen

in the liquid state and between other polar molecules, the hydrogen bonds in

bonds in ice were classified as “covalent” with the electron orbitals of adjacent water molecules circling a central proton. Each bond has 4-to-5 kcal/mole less energy than the more dynamic dielectric hydrogen bonds.

For example, at high pressure on the ocean floor, water forms spherical cages

cages approach the surface, the bonds break, methane is released and flammable bubbles rise to the surface. Larger molecules, like chlorine (Cl ),chloroform (CHCl ) and small hydrocarbons form hydration cages under specialized conditions of temperature and pressure.

around methane molecules as they are released from the bottom. As these

In fact, if liquid water is in contact with the solid surface of graphite,

in ice, it forms several layers of covalently-bonded water mole-cules with linear cubic bonding between the layers. Again, bonding in contact layers is not stable - the molecules continually gain energyand move into dielectric bonding as they move away from the surface.

where surface carbon atoms are in hexagonal shapes similar to those

Covalent bonding produces three circular forms. The chairon the far left is the only one present in cubic ice while

Pentagonal forms, although flat, bond with each otherand with the hexagonal boat at angles to produce sphericalcages around molecules.

both the chair and the boat are present in hexagonal ice.

other in linear elements, like the trimer, to form an ice called “cubic”

Next, as water freezes at 0 C, the molecules initially bond to each

7

8

o

9

10

2

11

cubic ice is not stable at 0 C and rapidly isomerizes to the more stable “hexagonal” form in which the hex-agonal rings are over each other.

with bond-length of 2.75A. However,

CUBIC HEXAGONAL

O

H H

OH

H

5

6

O

H

H

O H

HO

H

O

H HO

H molecular orbital calculations forecast that the trimer

only about a million-millionth of a second (10 sec.).water. However, it is extremely unstable and lasts

First, high-speed neutron irradiation of pure liquid water revealed the presence of the trimer. Back in the 70’s,

would be the the most stable ordered unit in liquid

-12

H

O

HH

H

3

4

o

o

charged heads and sodium ions cluster water around them to form micro-droplets in emulsion. By emulsifying the oil,

acids surround the oil molecules while their negatively- acids) is added to oil on water, the hydrocarbon tails of the If an old-fashion soap (composed of the sodium salts of fatty

soap increases the freedom (the entropy) of both water and oil molecules.

surface water forms covalent linear elements adjacent to peptides with hydrocarbon side chains and dynamic dielectric hydrogen bonds with small peptides like glycine and serine.

As polypeptides are released from ribosomes where they are produced from aminoacids,

S

S

o

S

S

S

14

12

15

If gasoline or oil are on the surface of water, water molecules

circular covalent elements of five to six water molecules.This increased ordering in water not only smooths the surface

cluster more tightly together and, periodically, form linear and

but, as covalent bonds break and convert into dielectric bonds,energy is absorbed from the hydrocarbon molecules - they straighten, align next to each other in layers and produce a rainbow of colors depending on the width of the layers.Water, by moving spontaneously from order toward disorder, moves hydrocarbon molecules from randomness toward order.

3

13

the left above) tend to keep the chain straight while those which form on both sides (like those on the right) introduce so much hydration order to the chain that it twists and turns into a coil to reduce hydration order. At the same time, small peptides which hydrogen-bond directly with water provide flexibility to the chain; to bend and turn and bring complimentary ordering regions together to fill voids and release ordered water.

Extended linear elements which form on one side of the chain and not the other (like that circled on

16

4

to bring one of the regions of hydration order adjacent to aromatic rings to the back side of the coil and release water. Then, as shown below, the chain flips over to bring the other ordering surface to the back side and spontaneously release even more ordered water.

Accordingly, the B-chain spontaneously bends at two regions of hydration disorder to

However, the B chain is only one part of the insulin molecule - there are regions behind and in front of the coil where linear hydration elements still form and must be released to improve stability.

Although coil-formation reduces a major portion of hydration order, transient linear elements stillform in front, below and in back of the coil, as well as adjacent to the three aromatic rings on the right.It is those regions where the order in surface water continues to contribute instability to the chain. It is those regions which induce chains to adopt alternate conformations and combine ordering regions to release water.

which dielectrically cluster water molecules around them as well as a series of ten peptides in the middle of the chain which induce extended covalent bonding on both sides and produce the coil.

For example, the B-chain of the insulin protein, which is shown below, has numerous circled regions

SS

SS

S S

11

17

16

5

random polypeptide sequences most likely were being produced. Sequences which could spon-taneaously fold into stable structures survived - those that could not were torn apart by lytic enzymes into the aminoacids from which they were formed. The B segment of insulin is a good example of a proteinwhich might never have survived if an A unit and a connecting C unit had not been produced at the same time.

When the insulin protein formed in the early stages of biomolecular evolution, a multitude of

17

10

wrap spontaneously into a tight dehydrated unit of two coils with polar groups on the left side and ordering hydrocarbons on the right. The C unit, on the other hand, contains 14 glycines and 9 glutamic acids to cluster water and ions around it and keep it mobile. By moving the A unit (one step at a time) down the Cchain, it is positioned precisely in B. C is removed enzymatically to produce the final stable insulin protein.

The A-unit above, like the B described before, contains the precise order/disorder regions to

above, it has a conical shape with a flat, primarily hydrocarbon, lower right-hand face which studies indicate is the flat ordering surface which binds to a receptor site in membrane to increase the uptake of glucose into cells. It is interesting that the conical shape of the molecule seems to be mimickinga cubic space in the receptor site which may be occupied by water as the insulin molecule enters and leaves.

oIn the assembly view, the molecule has a rectangular shape, but rotated 30 clockwise as shown

S

S

SSS

S

A

B

C

-

-

-

-

S

11

S

-

---

-

SS

S

S SS

S

S

11

SSS

S

S SS

S

S

11

S

SS

SS

S

S

S

18

6

molecules, which bind to ribosomes in multiple orientations and tie triplet nucleotide codes to amino-acids on enzymes of the type shown below, all mimic the spatial shapes of cubic water.

But insulin is not the only vital molecule which mimics the cubic lattice of water. Transfer RNA

Cholesterol, which is a major stabilizing molecule in nerve membrane, not only mimics an ordered linearelement of water, but, by enzymatically removing the tail, the body produces a variety of hormones whichmimic linear elements of 6 or 7 water molecules.

19

10

15

Since binding sites are open for only about 10 seconds and are surrounded by dynamically-bonded waterto provide flexibility, it will be difficult to provide experimental evidence for the presence of ordered water but most likely it is there and most likely it played a vital role in the selection of molecules as regulators.

-10

Since neurotransmitters and hormones of the types shown below all mimic ordered units of water molecules and all bind to specific sites to regulate functions, it is likely that ordered water occupies those receptor sites as they open and close to admit and release the regulator molecules.

Acetylcholine

Prostaglandin-PGE

Glycine

Histamine

++

-

+

Gama-aminoButyric Acid

Serotonin

+

+

+

Dopamine

--

-

-

2

Adrenaline

+--

Aminoacid+ATP

t-RNA /ENZYMECOMPLEX

Transfer RNA

t-RNA ENZYME

Testosterone

Estradiol Progesterone

Cholesterol

Steroidal Hormones

Androstendione

10

7

hexagonal water (H O ) and binds to a multitude of sites in living cells, has a molecular structure with four of its oxygens in the same spatial positions as four water molecules in hexagonal water.

Today, glucose is formed in plants by photosynthesis by reducing carbon dioxide , CO , to formaldehyde,CH O, with active hydrogen and condensing 6 formaldehyde molecules together to form glucose. However, glucose, as well as most other natural sugars are produced spontaneously if formaldehyde is in contact with cyanide and calcium ions in aqueous solution. Thus, it is likely that glucose, as the most abundant natural molecule on earth today might well have been one of the first produced when biomolecular evolution began.

In fact, glucose (C H O ), which is the carbon analog of

scientists, is that it is covalent hydrogen bonding in surface water, which, by spontaneously converting to more stable dielectric hydrogen bonding, not only provides the energy to drive the assembly of polypeptides and nucleic acids from randomness toward order but, by forming tran-sient linear elements between charges on their surfaces, directs them into unique functional associations. By mimicking the energetic and spatial properties of the environment in which they evolved, natural molecules assemble spontaneously and function harmoniously to produce “life.”

If you enjoyed the above pages, you might also enjoy www.molecularcreation.com and www.linearwater.com.

References:1.

Thank you for taking the time to read this web site.J. C. Collins, PhDjcbjh2o@aol.com

We all know that water is critical to life - what is not known and not yet accepted, even by most

the scientific profession are unaware of the extreme Importance of the order in surface water in regulating the structures and interactions of molecules in the living cell.For example, DNA, which is the symbol of modern molecular biology, is never pictured with water around it while at least 13 water molecules per base pair are required to stabilize it in its natural helical form. Numerous spectroscopic studiesindicate that the surface water is “ice-like” and sodium ions, which orient water in circular forms around them, are kept outaway from the double helix by the linear elements which con-tinually form and interact with each other in an “ice-like” manner.

Indeed, it is unfortunate that the public and most of

Hexagonal

Water

TG

T

C

C

AG

T A

T A

A

G

A

C

C

T

G

G

C

C

Na

Na

Na

Na

-D-Glucose

6 6

2

15

2

6

12

12

20

21

A Comprehensive Treatise. (Plenum, 1972). Also, D. P. Stevenson, Structural Chemistry 2.. H. S. Frank, Science 169: 635 (1970). The Structure of Ordinary Water. See also, F. Franks(Ed.) Water -

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6. A. Tokmakoff, Science 317: 54-55 (2007). Shining light on the rapidly-evolving structure of water.

10 J. C. Collins, The Matrix of Life (Molecular Presentations, 1991).

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9. D-S. Yang and A. H. Zewail, Proc. Natl. Acad. Sci. USA 106(11): 4122-4126 (2009). Ordered water structure at hydrophobic graphite interfaces observed by 4D ultrafast electron crystal-lography. See also, C-Y. Ruan, V. A. Lobastov, F. Vigliotti, S. Chen and A. H. Zewail, Science 304:

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