Hydrogen Bonding

[HydrogenBond]

Hydrogen bonds are the result of hydrogen becoming covalently bonded to highly electronegative atoms like oxygen, nitrogen, chlorine, etc. Because of the affect of the more electronegative atom, the hydrogen is induced slightly positive and the highly electronegative atom slightly negative. Hydrogen bonds form to lower potential by forming secondary bonds between hydrogen and the unbonded electrons on highly electronegative atoms. The attraction is due to the charge dipole as well as due to partial covalent bonding character.

 

To understanding the causal nature of hydrogen bonds one needs to keep in mind the electronegativity difference between hydrogen and the more electonegative atom it is covalently bonded to. For example, in a perfect ice crystal, every hydrogen is hydrogen bonded to oxygen. But because of the partial covalent character of hydrogen bonds, the electrons are shared between the water molecules. Because of the electronegativity difference, with oxygen being more so than hydrogen, the oxygen will always end up with more electron density than the hydrogen. What that means is that, even though all the hydrogen bonds are formed, the hydrogen protons will still have some potential.

 

In other words, the hydrogen bonds are at zero potential, however this zero potential points reflect the limit of how much electron density the more electronegative is willing to share. Oxygen's higher electron affinity will cause it to always keep extra electron density for itself, with the result being, although the hydrogen bonds may be zero potential the hydrogen proton will always have some residual potential.

 

As a visual example, to be taken figuratively, picture if the oxygen and the two hydrogen of water at sitting at a table playing pocker. Oxygen is always the better player (more electronegative) and in the end will win more the poker chips than hydrogen. If the game ended, hydrogen would go away in deficit, while oxygen will have full pockets.

 

The next day, they get together into a room full of poker tables, with one oxygen and two hydrogen at each table. The oxygen are still going to win since they are the better players. When the hydrogen lose their chips they will go into stress. Oxygen is happy with its winnings. To stay in the game, the hydrogen get desparate and begin to reach behind them and pick the back pocket of a nearby oxygen in an adjacent table. Although oxygen loses some chips to the thief, oxygen is still a better poker player and will continue to rake in the chips for a net win at the end of the night. The hydrogen may recoups some of its losses but will go home with less chips than it started the game with because of its lower electronegativity.

 

In the liquid state of water, the oxygen is no longer tight and looking straight ahead. It is more loose and notices its pocket being picked. So it begins to twist away to avoid being robbed of its winnings. The hydrogen now have to lean over even further and get closer to the oxygen to be able to pick its pocket. This is why water contracts when it melts.

[Jay-qu]

This isnt the first thread on the topic, actually I think it was you that started the other one, do you mind me asking what it is that makes you so interested in hydrogen bonding? :)

[HydrogenBond]

Hydrogen bonding is fairly well characterized but something subtle is being overlooked. I am trying to point this point.

[Mercedes Benzene]

I take it that you like hydrogen bonds???

...just a guess....

hahhaa. :)

[Jay-qu]

ok, keep pointing, I will be (and have been) listening. :)

[Michaelangelica]

This isnt the first thread on the topic, actually I think it was you that started the other one, do you mind me asking what it is that makes you so interested in hydrogen bonding? :eek_big:

 

 

I was interested in your other post on DNA & hydrogen bonds.

Hydrogen Bonding are very basic structures

 

So how do we engineer (or muck about with!?) hydrogen bonds?

ie

Make oxygen and hydrogen without using a lot of energy, (say in salt water) then maybe recombine the two to make drinkable water?

 

Does this have anything to do with "caton exchange capacity"?

(see Terra preta thread)

[Mercedes Benzene]

I was just reading an article about how the hydrogen bonds in DNA molecules are *trying* to be utilized to create "super batteries".

Pretty interesting if you ask me... They were talking about how they could replace the modern-day Carbon electrodes in batteries!

[HydrogenBond]

My interest in hydrogen bonds is connected to using hydrogen bonding to model cells. When I first looked into the feasibility of this project, I needed a way to explain how the hydrogen bonds interact within the cell. That got me interesting in hydrogen bonding. Existing theory seemed to be lacking what I needed to make the model work. This meant either the model was a figment of my imagination, or something was overlooked and needed to be discovered first.

 

I tend to work on gut feelings, and being a good chemist, I knew there was something there. Initially, I came up with a dummy variable that I called hydrogen potential. This turned out to be right, in essense, but did not jive with the exsiting theory of hydrogen bonding. But I used it in a qualitative way of high and low and worked under the assumption that hydrogen was interacting cell wide. This led to the understanding of how the cell is set up in hydrogen bonding potential gradients.

 

Many years ago I was ready to run with it. All I needed was expert affiliation to make sure I was consistent with fine structure data. But nobody seemed to be able to get past the hydrogen variable. That made it dead in the water. I got burnt out and shelled shocked for trying and finally had to stop for many years to clear my head.

 

About a year ago or so, I started to exercise my imagination and creativity through forums, like this one. I am often way out there because I like to brain storm off the top of my head, trying to generate new ideas and new ways of looking at things. I am starting to shift through all my brain storming ideas, separating the garbage from the reasonable and good. The hydrogen bonding model of the cell didn't go away. So I continue to brain storm the hydrogen bonding variable from many angles hoping something will click within others. The rest of cell model is real easy to do, once the foundation variable is clarified.

 

It comes down to hydrogen proton potential. Because of electronegativity differences, no matter whether hydrogen bonds form or not, minimize the hydrogen bond potential or not, hydrogen protons will have some residual potential. It is not the bond that is key, but the hydrogen proton itself. This proton potential means electron deficient or electrophilic potential.

 

In the living state there are different hydrogen bonding situations. Some will increase the innate hydrogen potential and some will lower it. By looking at different materials in the cell one can determine high and low. For example, proteins wind in helixes created by hydrogen bonding. These hydrogen bonds are often at odd angles, implying less than minimum potential hydrogen bonds. If we add this throughout the whole protein, the whole protein will become electrophilic. This is an important part of the catalytic potential of proteins. The strucutural hydrogen bonding need for electrons will help excite the electrons of the attached reactant. The active site is selective to a particular reactant-structural interaction.

 

The electrophilic structural potential has a second use. It defines where in the cell a particular material will call home. For example, it is not coincidence that ion pumps end in the cell membrane. The reason this occurs is that an aquoeus hydrogen bonding potential gradient exists between the DNA and the inside of the cell membrane (ion pumping). Things know where to go, not because of magic or intellegence, they are merely dmoving toward an equilibrium zone in the gradient.

 

Much of the mystery stuff in the cell isn't a mystery at all if one takes into consideration hydrogen proton potentials, gradients and equilibrium.

[Isana Kadeb]

Just a question, hydrogen bonding seems to occur with carbonyl groups as well (eg. C=O --- H-O-R). I thought it only occured in molecules where hydrogen was bonded to Nitrogen, oxygen or fluorine (eg. Ammonia, water etc)?

[Mercedes Benzene]

Hydrogen bonds must be attached to Nitrogen, Fluorine, or Oxygen. That is for intramolecular hydrogen bonds.

Otherwise, hydrogen bonds can occur between molecules....

 

....at least I think that is the way it works.

[Isana Kadeb]

Hydrogen bonds must be attached to Nitrogen, Fluorine, or Oxygen. That is for intramolecular hydrogen bonds.

Otherwise, hydrogen bonds can occur between molecules....

 

....at least I think that is the way it works.

 

Thanks, that makes sense.

[HydrogenBond]

That is essentially correct Mercedes. When modelling the cell, this is the criteria that is used.

 

The integrating substance for cellular modelling is the hydrogen bonding within the cellular water. Water accounts for 80-90 percent of the cell and is essentially everywhere in the cell. Water, being so dominant and being a polar solvent, will orientate cellular materials with their hydrophilic groups of the surface. It will also push hydrophobic materials, because of surface tension, into minimum potential van der Waals states.

 

If we look at liquid water, it is more complicated than most liquids. Not only is there the random movement of individual water molecules, but liquid water also shows considerable hydrogen bonding structure. What this range of hydrogen bonding states indicate is that liquid water expresses a range of hydrogen bonding states, from minimum potential bonds, in various sized clusters, to individual molecules that have only marginal hydrogen bonding. To add to this range of hydrogen bonding, water also shows what we call pH. This is where a covalent bond of a water molecule breaks, resulting in water becoming -OH and H+ (H3O+), or acidic and basic at the same time.

 

Because of this spectrum of hydrogen bonding potentials within liquid water, water can assume a hydrogen bonding expression that can parallel or be in equilbirum with any local hydrogen bonding environment within the cell. For example, if a protein has plenty of electron density to share with the water, this will help the water define a local zone of low hydrogen bonding potential. On the other hand, if a protein has no electron density to share, the local aqueous hydrogen bonding potential will stay higher.

 

If these two proteins where brought close together, the local water would form a gradient of hydrogen bonding states between the two different surface potentials. If we saturate this local zone with a lot of electron sharing proteins, the global water potential will lower and will have a low hydrogen bonding potential impact on the protein that does not share.

 

One of the main global affects within the cell water potential are all the membrane materials that exist throughout the cell. These are not just on the outer surface but extend throughout the cytoplasm. These materials do not like to share electron density because they are hydrophobic. However, their massive presence in the cellular water causes aqueous hydrogen bonding hydrogen to be put in position, at these membrane surfaces, where hydrogen bonding potential stays high, due to the lack of lelectron density to share.The net affect for the cell is an increase in the average aquoeus hydrogen bonding potential, relative to pure water.

 

The second important global affect is connected to cation pumping. The sodium/potassium cation pumps use the lions share of a cells energy. What they do is pump out three sodium cations and let two potassium cations in. The net affect is a slight negative charge on the inside of the cell membrane. This will have the opposite impact compared to the cytoplasm membrane material. The key difference is, this charge is fixed at the inside surface of the exterior membrane The affect is a aqueous hydrogen bonding potential cellular gradient with the inside of the exterior membrane being at lowest potential.

 

If we come back to one of the little proteins, in pure water it will create a certain water shroud around it to reflect its impact on the aqueous hydrogen bonding potential. If we stick it in the gradient, it will define nonequilibrium unless it migrates to a place in the gradient that reflects the type of water shroud that is in equilibrium with it. The gradient is like the traffic cop that defines where the proteins need to be.

 

The cell and proteins have a trick up its sleave. This is connected to structural proteins. The structural proteins can anchor down proteins in the grid in places where they would not be if they were free floating. The cell will often use ATP energy to move them against the gradient. This slight potential can be used to add extra reaction potential to enzymes.

 

The DNA plays a very important role in the cellular grid. It defines the higher aqueous hydrogen bonding potential pole of the celluar gradient. So when something enters the cell, it usually defines nonequilibrium. This slight alteration in the gradient potential will impact the DNA, priming the DNA for an equilibrium adaptation.

[HydrogenBond]

I would like to add a third global hydrogen bonding potential affect within the cell. This is connected to ATP. The main place of interest, with respect to the global aqueous hydrogen potential, are the three phosphate groups at the end of the molecule. Phosphate is a relatively strong acid with a relatively weak conjugate base. This means that the tri-phosphate end is not going to extract hydrogen protons, but will nevertheless provide lower value electron density for the hydrogen bonding to share, via the large number of oxygen atoms on the three phosphates groups.

 

This electron density will cause ATP to migrate to zones of high aqueous hydrogen bonding potential, like enzymes. While ATP's bulk presence within the cell will help lower the aqueous hydrogen bonding potential.

 

When ATP forms from ADP and phosphate, this reaction is endothermic. The energy requirement is about 7kcal/mole. This is at the top end of hydrogen bonding energy. The ATP being a source of electron density for hydrogen bonding will flow toward zones of high aqueous hydrogen bonding potential. These hydrogen share with the oxygen of ATP causing the phosphoros atoms to become slightly more positive. The ATP will react with an -OH group that is made slightly more nucleophilc also due to the affect of the ATP in the local water. In other words, the aqueous hydrogen bonds onto the -OH group will jump ship to ATP when ATP is nearby due to its many negative charges, temporarily allowing the -OH define slightly higher electron density.

 

The ATP is produced at the mitochondria. These little buggers are a mobile source of gradient potential within the cell. They generate low aqueous hydrogen bonding potential value. They position themselves so they can lower the local and global potential within many zone of the cell. They are here and there and will set up interior sub-gradient potentials with various cellular structures.

 

If we look at one mitochondrion and place it in an imaginatary bubble and do a rough mass balance on its primary materials, what is going in are glucose, oxygen, ADP and phosphate. What is coming out is bicarbonate ionsand ATP. One may notice the amount of negative charge is quite high. This makes the outer surface of the mitochondria define a low aqueous hydrogen bonding potential.

 

If we go below the outer membrane, we have a high concentration of high potential hydrogen protons on the inner mitochondrial membrane. These high potential hydrogen protons are generated by the mitochondria, via proton pumps. These proton pumps are the forefathers of sodium pumps. Besides being used to provide potential to produce ATP, they also help balance off the negative charge, allowing ADP and phosphate to migrate into the mitochondria against the negative charge potential.

 

This observations suggests that the low aqueous potential defined by mitochrondria is more a function of output products, i.e., ATP and HCO3-, with the imput materials balanced out by the high hydrogen bonding impact of the proton pumps. The bicarbonate migrates to the exterior cell surface where it is pumped out of the cell. It influence on the cell gradient is sort of a steady background of low aquoeus hydrogen bonding potential.

[HydrogenBond]

If we take an enzyme and carefully unravel it, we would get a long chain helical polymer with animo acids residues sticking out along the axis. After stretching it out, we then twist it to remove its helical backbone, creating a more or less flat polymer, that will alter the orientation of the animo acid residues with respect to each other. If place this in water and let it go, the helical backbone will reform. The animo acid residues will also create various potentials in the water and will begin to clump and group to reflect a movement toward minimizing the water potential as well as the potential defined by the protein itself. The final result will be the same enzyme polymer, but its properties will change due to its 3-D configuration being different than what we started with.

 

The reason this is so it connected to the formation of proteins. They undergo polymerization on ribosomes. What that implies, is that in the beginning only a small end piece is dissolved in the water. This will see the global water potential and will behave like it is the whole protein. Its packing will only reflect the water and a small piece of protein. As more and more, protein length is added, the new protein addition is affected by the water but also needs to add to the existing protein structure in a way that minimizes its potential. This process is useful because it allows more efficient packing (if the animo acid order is properly defined on the mRNA) and can add potential zones which would be lost or buried.

 

The reason I bring this up is that bio-structures are not just based on their composition but also on the way this composition is arranged in space. The arrangement in space, in turn, will be influenced by the local water potential within the region where the bio-structure is being formed.

 

For example, the ribosomes where proteins are made, extend from the nuclear membrane well into the cytoplasm. This gradient extension represents a range of slightly different water potential environments. If the same protein formed near the nuclear membrane or at the end of the ribosome train, the different potentials could result in different packing. The way around this is connected to the configurational potential define by the mRNA (messenger RNA). Each mRNA will form equilibrium at certain potentials within the ribosomal gradient. This will also define the aqueous environment which will help induce the protein structure.

[HydrogenBond]

I would like to back track a little bit. When we look at the cell there is actually two layers of potentials at work. One is based on the tradtional biochemistry that populates textbooks and libraries. The second parallel layer is based on equilibrium hydrogen bonding and hydrogen bonding gradients. Both work together, side by side.

 

What the hydrogen bonding analysis brings to the table is the ability to look at the same biochemistry but in an in vitro way. For example, observational data has long understood that rRNA (ribosomal RNA) is formed on the DNA and then collects in the nucleolus aspect of the nucleus. There the rRNA are packed wth proteins. As these packing structures of rRNA and protein mature to form ribosomal subunits, they bud off and will flow out of the nucleus and combined to become the ribosomes within the cytoplasm. These do not cluster in just one place but extend from the nuclear membrane into the cyctoplasm.

 

If we add the hydrogen bonding layer to the biochemical analysis, everything has very simple logical explanations using only equilibrium hydrogen bonding potential and hydrogen bonding potential gradients.

 

Although I have not discussed the DNA and nucleus equilibria, yet, all RNA will define a lower hydrogen bonding potential than DNA. As such, the nucleolus represents the low hydrogen bonding potential pole of the nucleus's hydrogen bonding potential gradient. The packed aspects of the DNA, define the higher potential pole. The active DNA is in the middle.

 

The reason the ribosomes bud off is that they begin to define structural nonequilibrium within the nucleus. These would like to lower the nucleus water potential but the huge DNA is so dominant that its differentiated expression will maintain a certain nucleus water potential. The assembled ribosomal components need to leave the nucleus due to their structural nonequilibrium. These will move into the cytoplasm and seek a place in the rough ER gradient (where the ribosomes can find equilibrium).

 

If I was to paint a picture of how the two layers, i.e., hydrogen bonding and biochemical, are integrate, the easiest way is to picture all the same biochems but with a water wrapper around each biochem. ATP is no longer just plain old ATP but it is ATP plus a water coat. The water coat interfaces all the biochems with the gradient potentials within the cell's water.

[HydrogenBond]

I would like to go back to the basics of hydrogen bonding and hydrogen proton potential. If we look at ice, all the hydrogen bonds of water are essentially formed, with all the hydrogen of each water molecule hydrogen bonded to the free electron pairs of neighboring oxygen atoms. Because hydrogen bonds contain covalent character, the electrons of the hydrogen bonds are being shared by both hydrogen and oxygen.

 

Because oxygen is more electronegative than the hydrogen, the oxygen will still end up with the majority of electron density. The net result is that although the hydrogen bonding potential may be zero throughout the ice, the hydrogen protons remain slightly electron deficient. This causes the hydrogen protons within ice to exist with residual electrophilic potential.

 

The phenomena within liquid water that expresses this residual potential is pH. If we start with two water molecules, 2H2O, and form H3O+ and OH-, the hydrogen of the H30+ will gain some potential. Rather than just sharing unbonded electrons with hydrogen bonding, the extra H+, more tightly bonded makes it harder for the original two hydrogen to see the same electron density they saw in H2O.

 

On the other hand, the OH-, will actually help the single hydrogen that remains to lower its potential beyond what H2O hydrogen bonded to another H2O can provide. The negative charge feeds the electronegativity needs of oxygen allowing the single hydrogen to share the surplus. What is special about this is that this situation lowers the potential of a hydrogen proton of water to below what it can achieve in ice. In other words, its addresses some of the residual hydrogen proton potential that even zero potential hydrogen bonding can not reduce.

 

If we look in liquid water the pH affects forms unformly throughout the aqueous continuum at the concentration of 10-7 moles/liter or pH=7. Picture the pH affect as rocks thrown into a pond. Essentially what is set up is an interference grid of waves, with nodes that depress the waves and nodals that raise the crest of the waves. If we add it all together the pond is flat, but the deep wells and the high wave crests offer intermittant areas where the local hydrogen proton potentials may reach zero or even negative, while the wells allow intermittant zones of amplified proton potential such as the the energy potential needed to break the covalent bond to water so the hydrogen can form H3O+.

 

If we come back to the cell a similar affect is also at work. We not only have a range of hydrogen bonding potentials, but there is also a deeper layer that pertubates the residual hydrogen proton potential above and below the zero point of hydrogen bonds. A major component of the interference grid (rocks in the pond) is connected to ATP energy. For example, ATP drives the ionic impulses at the cell membrane. While the negative charge generated at the inside of the cell membrane provides a zone where the hydrogen proton potentials can exist below that associated with the residual potential below zero potential hydrogen bonding.

[HydrogenBond]

Knowledge of the importance of hydrogen bonding with respect to characterizing biomaterials first appeared my sophomore year at RPI. It was second semester organic chemistry and we were doing a short section on the bio-polymers like protein, DNA, etc.. The authors of the textbook, Mossison and Boyd, commented on hydrogen bonding being an important frontier that needed further investigation. This struck a chord in me. At that time, it was way over my head, so I put it on the back burner.

 

Years later, as an engineer, the hydrogen bonding model came back to me by coincidence. I was given a development project to see if it was feasible to run an in situ bio-denitrification within open waste acid ponds. I never had any training in biology but was a good chemist. I always had this love/hate relationship with biology because it required too much memory work for my tastes. I was more attracted to sciences that were more conducive to applying basic principles to achieve new results. In chemistry one can learn about alcohols and then predict new reactions of unseen alcohols using basic principles and little ingenuity. With biology, it was memorize this, but don't try to extrapolate, since the bio-science have not yet achieved the same level of practical utility. The bio-sciences was more based on observation, correlation and statistics.

 

I felt a little intimidated by the project because of my lack of expertise in both biology and bioreactors. At the same time, I was being asked to do something that exceeded all the parameters of the existing state of the art. The ponds were open, so I could not control oxygen for an anaerobic reaction or the pH with precision. The nitrate levels were two orders of magnitude higher than optimium, and there were plenty of heavy metals and various fluro-chloro solvents within the ponds. It was not suppose to work according to the experts. My ignorance was bliss and my job was to make it work, somehow. To make a long story short, I always had a green thumb, now even with bacteria; the little buggers pushed the state of the art up the ladder of progress.

 

After the process was transferred to production, I overcame my inhibition about biology and began to think about hydrogen bonding again. Thats when I began to speculate about a hydrogen proton variable. What really got me hooked was my ability to correlate the why's of the cell cycle using only equilibrium hydrogen bonding consideration. Biology can answer the hows in amazing details. I was going after the why's.

 

What is interesting about the cell cycle, it is the engine of cancer. Cancer cell often replicate out of control. If one knows the whys of the cell cycle one can also deduce some of the whys of cancer. We continues to find new details of how, but we continue to ignor the whys because existing theory is still ignoring the cause of the why's, i.e., hydrogen bonding. One last note; has anyone considered why 1950's radiation is still the state of the art in many cancer cases? It affects the hydrogen protons.