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]

Originally Posted by 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?

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.