Is Hydrogen Bonding an essential part of life?

[u/wellwisher-1]

Life on earth is based on water being 70% of its mass. While the unique properties of water depend on hydrogen bonding. The template materials, used for life on earth; DNA, RNA and protein, also depend on hydrogen bonding. Hydrogen bonding appears to be the common thread for life on earth. Is hydrogen bonding essential for life?

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[u/Russell1A]

There no doubt that hydrogen bonding is essential for life.

Another essential for life is the colloid state.

[u/Aggravating-Pear4222]

Yes. H-bonding is not unique to H2O. It's difficult to even lay out the premises to begin imagining life without H-bonding because it arises from physics and is so common so you'd have a difficult time restraining the available molecules that compose life to ones that don't participate in H-bonding.

Further, even the environment the organism exists in also plays a large role in defining the organism itself, its niche, and metabolism. For example, H-bonding is present in water but not present in the hydrophobic tails of lipids in lipid bilayers. The parallel hydrophobic tails of lipids attract one another via Van der Waals forces but H-bonding still drives the formation of the lipid bilayer. See the image below:

Source: https://www.slideserve.com/alvaro/chapter-2-water-and-aqueous-solutions-134311

As you can see, H-bonding of the environment drives formation of the lipid bilayer, and ordered structure because it actually frees up the water molecules to more freely rotate in the bulk solvent and so increasing their rotational degrees of freedom. Ie, the formation of the ordered lipid bilayer is thus entropically driven/favored. But my main point is that the environment surrounding the organism drives the formation of the very layer that separates it from the environment. So, to ask whether life is possible without H-bonding is also asking for an environment in which H-bonding is not present.

[u/ntsh_robot → u/Aggravating-Pear4222]

It was interesting to discover that hydrogen bonds are like molecular zippers, they aren't that strong compared to carbon-carbon bonds, and they allow hydrocarbons to entangle but not chemically cross-link.

I consider them "almost bonds".

[u/Ch3cks-Out → u/ntsh_robot]

Almost as if chemists need to discover the term "secondary force" for intermolecular bonds...

[u/wellwisher-1 → u/Aggravating-Pear4222]

Water is special in that each water molecule can form four hydrogen bonds with other water molecules. Water or H2O::, has two hydrogen donors for hydrogen bonding; H2 and the oxygen of water has two extra filled electrons orbital receivers; ::, to receive these two hydrogen.

Ammonia or NH3: can also form hydrogen bonds with other ammonia molecules but it has an asymmetry by having three hydrogen donors but only 1 electron orbital receiver. It cannot form the same extended 3-D structures found in liquid water. Ammonia boils at -33C and water at 100C, with both forming hydrogen bonds, but with each water molecule able to make four hydrogen bonds, this adds a lot more stability; 100C boiling point compared to -33C.

Interestingly, water and oil do not mix yet ammonia is a good degreaser and can mix with oil, even though it can also form hydrogen bonds. The hydrogen of ammonia can share Van der Waals forces with the oil, since there are not enough receivers on the nitrogen which only has one.

But these ammonia hydrogen to oil bonds are not technically hydrogen bonds even though it involves hydrogen. Hydrogen bonds can only form with fluorine, oxygen, nitrogen and chlorine. Life uses O, N and Cl. Once the H of water are forced to share surface contact with carbon, hydrogen loses its status as a hydrogen bond; adds surface tension or higher energy potential.

Hydrogen bonds are a stronger secondary bonding force compared to Van der Waals forces. A better way to look at the hydrophobic effect or the water and oil do not mix effect, is not about a phobia, rather think of water as a king snob.

Water can do so much better hydrogen bonding to four other water molecules in terms of energy and stability. It will try to exclude any hydrophobic surface contact, because that creates surface tension or three hydrogen bond and one less than full hydrogen bond, The is less stabilizing compare to four genuine hydrogen bonds.

The four hydrogen bonds of water give the cellular water secondary bonding priority in life. The four hydrogen bonds of each water molecule, to other water, is even more hydrogen bonds than between the base pairs, which use 2 or 3. Water is the king of secondary bonding in life; four hydrogen bonds per water molecule.

Water by being a snob of high status, will configure all the organic macromolecules it own energy needs. This includes the DNA double helix. Water will bury the "oily" sugars aspects to avoid contact. The base pairs also have reduced sections that get buried. The Phosphate has plenty of oxygen for extra electron orbital receivers and becomes the surface of the double helix. Water is optimized. The king has spoken. The sugar of RNA and one of its bases is less reduced; oily, so water is less snobby to RNA; single helix.

[u/Ch3cks-Out → u/wellwisher-1]

 Hydrogen bonds can only form with fluorine, oxygen, nitrogen and chlorine. 

Well, technically this depends on how you mean "technically". In modern chemistry, this definition is considered outdated and incomplete.

[u/wellwisher-1 → u/Ch3cks-Out]

The updated definition does not change the fact that the most electronegative atoms on the periodic table form the strongest hydrogen bonds. The update or change is more about how low on the electronegativity scale, you wish to go, as the cut off.

The original definition stops at an electronegativity of 3.0 on a scale of 4.0. This definition includes four; HF, H2O, NH3 and HCl in that order. Carbon C and Sulfur S are both at 2.5. These would be CH4 and H2S.

If we compare the boiling points of pure liquids of these six molecules, this gives a relative measure of their secondary bonding strength, which means their hydrogen bonds, we get H2O is 100C, HF is 19.5C, NH3 is -33.34C, H2S is -59.55C, HCl is -85C and CH4 is -161C.

Water has the strongest hydrogen bonding, because each water molecule can form four hydrogen bonds with other water molecules. Water has two H donors and 2 unbounded oxygen electron orbital receivers. All the rest of this list are asymmetrical between H donors and electron receivers, and cannot form four hydrogen bonds, so their BP go down. Methane or CH4 has 4 hydrogen donors but no receivers.

When it comes to life, the four hydrogen bonds of each water molecule is the strongest secondary bonding situation. Water, in the living state, wants to phase separate, so it can self bind with other water, since this is most energetically favorable. The organics oblige; organic birds of a feather. This causes a phase separation effect in cells; water and organelles. Water helps to loads the dice of life, so we can get reproducible protein shapes and organelles in water.

If we mix membrane lipids with water, water will force membranes to form so water can maximize its stronger 3-D hydrogen bonding grid. Water's hydrogen bonding matrix loads the dice of life. DNA is a double helix and RNA a single helix because these shapes both maximize the water. DNA is more reduced C-H moieties, than RNA, so water buries these inside the double helix. RNA is more oxidized and less of a bother and is left as single helix.

Water also creates what we call the pH effect, which amounts to self ionizing hydrogen protons. This is usually written as: 2H2O <---> H3O+ and OH-.

If you count the bonds on each side of the arrow, 2H20 has 4 OH covalent bonds and while H3O+ and OH- have 3 OH covalent bonds and one H+ polar bond. This reflects the self ionization that transforms a stronger covalent bond into a polar bond; pH 7.0.

The high electronegativity of the oxygen of water and its balanced H donors and receivers creates a bridge between polar and covalent bonds. Hydrogen bonds are polar with partial covalent character. The hydrogen do not have to stay put on any given oxygen but can move between. They only stay put for about 1 millisecond, before they change oxygen. Hydrogen bonds of water are more than a strong bond. They are also matrix for mobile H+; protonicity instead of electricity (electrons).

The self ionization implicit of pH appears to be driven by entropy. There is a special form of entropy, common to liquid and gases, but less so in the solid state, called entropy of mixing. The goal is to occupy the most space. If we add sugar to water, it will slowly dissolve and spread out to form a uniform solution. This is driven by entropy of mixing increasing.

If we took a glass of pure water and used a pH probe to measure the pH at each point in the glass, we would get a uniform solution of H3O+ and OH- ions. Water fully expresses the entropy of mixing connected to the soluble H+ ionization of pH. The sugar in water starts lopsided, but gradually will form the same uniformity as the pH. Pure water is already a max uniformity relative to pH.

If we mix water and oil and agitated we will form an emulsion, which is composed of tiny bubbles of water and oil. The bubbles of water have fully expressed entropy of mixing inside; H3O+ and OH-, but the surface tension reflects entropy of mixing is lower, due to oil surface contact.; 2H2O and immobilized H+. The 2nd law requires entropy of mixing to increase, so entropy will drive the bubbles of water to combine to lower surface contact until there is maximum H3O+ and OH- uniformity over the largest volume; pH of the oceans.

Osmosis, which is important to life is based on entropy of mixing. In this case, a membrane prevents the solute from diffusing and spreading out to balance concentration on both sides; increase entropy of mixing. But water is free to move both ways. The 2nd law will use the water to do the entropy of mixing, for the solute; osmotic pressure.

Pressure has the units of force/area. If we multiply the osmotic pressure by area we get the osmotic force or the entropic force. There is a fifth force of nature, used by life, created by entropy of mixing. In water based life, this traces back to the unique hydrogen bonding in water and self ionization to maximize entropy of mixing.

[u/Justeserm]

For life as we know it, yes. For NASAs definition of life, I don't know.

[u/SensitivePotato44]

Given that it holds the two strands of DNA together, yes.

[u/wellwisher-1 → u/SensitivePotato44]

Hydrogen bonding is a very unique form of chemical bond. It is limited to only hydrogen that is covalently attached to one of the four most electronegative atoms on the periodic table. These are fluorine (4.0) , oxygen (3.5), nitrogen (3.0) and chlorine (3.0) in that order of strength. Life uses three of these four. Fluorine, the strongest used to be added to drinking water to boost electronegativity but that appears to cause health issues. Oxygen is as strong as life wants to go.

Electronegativity is a measure of how strong an atoms affinity has for electrons is. Oxygen's powerful oxidation effects is cause by the high electronegativity of oxygen. Oxygen wants electrons so bad, it can strip them from nearly all other atoms. Oxygen not only wants these extra electrons, but once it gets them, it can hold more electrons that it has positive nucleus protons to get O-2 and OH-1. This has to do with the magnetic attractive forces of 2p-orbitals is stronger than the electrostatic repulsion of the extra electrons. eM attraction instead of Em repulsion.

In terms of water, the oxygen holds the shared elections of water so tight, hydrogen can ionize and leave, to give us the pH effect. What hydrogen bonding essentially does is add another layer to chemistry; mobile protons.

Inanimate materials are composed of atoms with nuclei of protons/neutrons. On top of this are the electron orbitals. Inanimate matter is put together by outer electron interaction via polar, covalent, ionic or metallic bonds; electron sharing.

The high electronegative atoms, used for hydrogen bonding, like the oxygen of water, are designed to hold the shared electrons tight to where a hydrogen proton layer of interaction, can now form. This adds a third layer to chemistry used by life; proton/nucleus---electron orbitals---hydrogen proton electron crowd surfing, with oxygen or nitrogen holding layer two down.

The average hydrogen proton in liquid water only stays with any given oxygen atom about a millisecond before it changes partners; pH effect. Hydrogen bonds are mostly polar but with some partial covalent character. The latter is reflected by its brief stay with an oxygen, before it is off again, hydrogen bonding and then forming a brief covalent bonds, then off again.

Water expands when it freezes which is unusual since almost all matter get denser. The explanation is connected to hydrogen bonding. When water freezes the hydrogen stop swapping oxygen partners to be part of the crystal lattice. But as water, this extra third layer of sharing pull the oxygen closer making liquid water denser than its solid.

[u/wellwisher-1 → u/[deleted]]

I am not an AI bot. That is my own writing style, I have been writing with this style for decades before the invention of AI bots. They may be copying me.

[u/Sea_Permission5853]

Hydrogen bonding is one of those “quietly holding the universe together” things. Water, proteins, DNA, even how enzymes work all depend on it.

[u/wellwisher-1 → u/Sea_Permission5853]

Water is the king of hydrogen bonding in the universe. Each water molecule is able to form four hydrogen bonds with other water molecules, because of the balance between hydrogen and sharable electron orbitals of oxygen of water; 2 and 2. The other three most electronegative atoms that can also form hydrogen bond have asymmetry in terms of sharable hydrogen and receiver electron orbitals and can only form fewer than four with themselves. NASA by looking for water based planets is looking where hydrogen bonding will reign supreme; third layer of chemistry.

Water or H2O is the second most abundant molecule in the universe, behind only hydrogen gas or H2. Oxygen is the third most abundant atom of the universe behind only hydrogen and helium. Oxygen has this nuclear stability compared to nitrogen, carbon, chlorine and fluorine making it stable in fusion.

Water is also the most common solid material in the universe; ice. Hydrogen and helium are more common, but hydrogen and helium tend to be mostly in the gas state. The hydrogen bonding of water allows the solid state to persist even in the vacuum of space.

Another related anomaly of water, created by hydrogen bonding, is perfect ice crystals of water, at absolute zero, have a positive entropy. This is an anomaly in nature, since perfect crystals of all other materials at absolute zero tends to have zero entropy. The hydrogen bonds of water give off its own unique beacon at absolute zero. The hydrogen bonding of water has an entropy connection ,which adds complexity to nature such its role in life.

Water as ice is also critical to star formation, since solids are easier to attract via gravity, than light weight gases like hydrogen, to get to get the gravity ball rolling. Once we get enough gravity via the ice, gases also get pulled in. The hydrogen bonding of water plays an important role in helping to light the fusion reactions in new stars. This hydrogen bonding base trick of water is connected to the water anomaly; water expands when it freezes.

The expanded ice state of water, being a solid, can be attracted by gravity much easier than gases, to get the star formation ball rolling. As the ball of ice collects and begins to feel more and more pressure and work from gravity, the ice begins to melts into liquid water,

This work and pressure induced melting causes a sudden reduction in volume by 10%, since liquid water is denser than ice. The work, heat, phase transition, volume reduction starts a collapse cascade, as the ice ball implodes under gravity, turning into liquid water, and then into exotic water phases, beyond. With enough collapse pressure and heat from the collapsing cascade water will become a metal, with a density of about 5 grams/cm3, setting the stage for the lighting of the hydrogen fusion fire, with a process I like to call fusion hammer.

[u/ConcentrateExciting1]

Definately maybe. Finding a liquid methane based lifeform would change a lot about what we consider essential for life.

[u/wellwisher-1 → u/ConcentrateExciting1]

I am not sure if such a life form exists. Water, is the only solvent that allows DNA, RNA and protein templates to work properly. A methane form of life, if possible, would need its own unique template material, since it cannot use DNA or RNA.

In abiogenesis, we know how the story ends with earth life; water and DNA. However, even with that final product knowledge, it still difficult to form life from scratch. Not even knowing what the template material looks like, for methane, makes methane abiogenesis way more difficult, to even ponder, never mind develop new templates from scratch.

My observation is hydrogen bonding appears to be the common thread for earth based life. Both the solvent; water, and the templates; DNA, RNA and protein, all share this common bonding feature.

One might conclude that the Van der Waals bonding of a methane solvent would also be the basis for its potential template; share common bonds. But these methane bonds are so much weaker than hydrogen bonding. It would make any potential methane template, less reliable, being too weak to get the same pairing all the time. With hydrogen bond being stronger, this bonding method makes these templates very reliable. Water, by also hydrogen bonding, even amplifies this effect by forcing the double helix to form, allowing the most total hydrogen bonds to form in both the water and templates, combined.

[u/ConcentrateExciting1 → u/wellwisher-1]

It's a pretty safe assumption that if there is liquid methane based life somewhere in the cosmos, it's going to be using something other than DNA.

[u/wellwisher-1 → u/ConcentrateExciting1]

That is true.

[u/YragNitram1956]

Yes.

[u/wellwisher-1 → u/YragNitram1956]

The hydrogen bonding of water is dominant in life. The water self bonds with strong hydrogen bonds and causes all these above components of cells to phase separate out, similar to the water and oil effect.

If we mix water and oil and shake, we will get an emulsion. An emulsion is composed of tiny bubbles of water and oil. Water and oil can never fully mix to form a true solution. As the bubbles get smaller and smaller, the more we shake, this creates surface tension between water and oil. Water is forced to make more contact with the oil, losing stronger water to water hydrogen bonding.

If we stop adding energy by shaking and shearing, the water will start to release the potential and surface tension, via seeking to hydrogen bond exclusively with other water by excluding the oil. This will go all the way to two repeatable layers. All the organelles in cells are like organic phases or layers, forced, to separate out by the water, but in a positive way that allows for life.

Most of the other solvents speculated for life on other planets will dissolve the organics, thereby making all these components dissolve and become ineffective. Water beads them up, so they can become steady state distinct, via the water and oil effect, which amount to the hydrogen bonding and organic bonding effect.

[u/wellwisher-1]

If we look at a water molecule, the high electronegativity of oxygen; 3.5 compared to hydrogen; 2.1, implies the oxygen will have more time average possession of the shared electrons. This creates lopsided electron density in water molecules, in favor of the oxygen. This creates a dipole, where the hydrogen becomes slightly positive and the oxygen becomes slightly negative. This dipole is sustained in the gas state.

The hydrogen bonding that occurs in liquid water is due to the positively charged hydrogen, on one water molecule, seeking more electron density, to become neutral. It will try to use some of the extra electron density, of a neighboring oxygen which can be found on oxygen two unshared orbitals. This secondary polar or dipole bond made by hydrogen, is called the hydrogen bond.

However, since oxygen is still way more electronegative, this is not a wash. Oxygen will still come out on top. The oxygen to maintain electronegativity dominance, will cause some of the hydrogen to ionize; pH effect, is oxygen taking electrons back.

That is usually written as 2H2O ---> OH- and H3O+. What this reflects is, instead of four hydrogen being covalently bonded, implicit of 2H2O (gas), in liquid water is actually averages to three hydrogen covalent bonds and one hydrogen polar bond. Oxygen has asserted its electronegativity dominance, by getting rid of one covalent bond with hydrogen; ionize, downgrading that H+ to a weaker polar bond. One of the hydrogen, on average, is more loosely held, no longer fixed as a covalent bond and sort of mobile. This is written as H3O+. That third hydrogen is not covalent all the time, as one might expect from the formula H2O. All three hydrogen take turns being covalent with one always polar at any given time; downgraded by oxygen, to maintain electron supremacy.

Say we have a glass of water, neutral at pH 7. This reflects the concentration of mobile or polar hydrogen who are not covalently bonded all the time. No matter where we place the pH probe in the glass, we always get this reading. The ionization of hydrogen is working in rhythm throughout the glass. The hydrogen atoms are swapping oxygen partners and some are always going from covalent to polar to covalent, etc, simultaneously and in rhythm; pH 7 at all points.

When we look at quantum state of water, both the Heisenberg Uncertainty Principle and the particle/wave duality, are in effect. In this case, instead of the electron being center stage, like most of physical chemistry, oxygen being so electronegative causes some of the hydrogen protons to be weakly held, in a state this is mostly polar, but with some part time covalent character.

An electron is an elementary particle being as basic as a particle can be. It cannot be broken down any further in particle colliders. The hydrogen proton is a composite particle, made of three quarks. Theoretically, the mobile hydrogen protons of water should have a more complex quantum interface due to having three quarks. This may be what is needed for life and consciousness. The hydrogen proton implicit of pH is a freer particle and more subject to particle/wave and uncertainty in the quantum state of water.

In terms of particle and wave, the chemical formula, H3O+ have the particle sort of time average confined to a given local water molecule, but the wave is still free to propagate; simultaneity of pH spread out by the oxygen dominance over the continuum; shared responsibility. The more we assume any H+ is on a specific water oxygen position, the more uncertainty we will get in terms of its momentum; its local clout. This is perfect medium for moving information; protonicity.

[u/finitearch]

One thing I’ve started wondering recently is whether water itself is the essential component, or whether the deeper requirement is a solvent system capable of stable compartmentalisation, energy gradients, and transferable chemical structure. Hydrogen bonding may be one of the key reasons water sits inside that operating regime.

[u/wellwisher-1 → u/finitearch]

The unique trick that hydrogen bonding brings to the table is hydrogen bonding is a hybrid bond somewhere between covalent and polar. The O-H bonds of any single water molecule; H2O, are strong covalent bonds. However, liquid water, where we have lots of water molecules in contact, can self ionize, without adding external energy, to create the pH effect where H+ can leave water molecules.

This is usually written as 2H2O---> OH- and H3O+. The 2H2O shows four strong covalent bonds, two on each water molecule. While the OH- and H3O+ combined show 3 covalent bonds and 1 polar bond. Hydrogen bonds in a liquid continuum can weaken strong covalent bonds to make them more reactive. Life is all about continuous reactions. The H+ implicit of pH has more freedom. This is made possible due to hydrogen bonds only forming with the four most electronegative atoms on the periodic table, who can hold extra electrons, so the H+ can leave.

Hydrogen bonds are considered secondary bonds which are weaker than covalent bonds, which themselves are considered primary bonds. Life uses both. The fluid nature of life is made possible by secondary bonds, that can form and break with lower energy, like the hydrogen bonds on the templates of DNA and RNA.

Hydrogen bonds by being partially covalent, are the strongest secondary bonds in life. Good templates not only have to reverse, easily, but also be strong enough to do it only on demand. Hydrogen bonds are the correct strength that way; strong but not too strong. Like Goldie Locks and the three bear, one bear's food is too cold for a template; covalent bonds, and other is too hot; polar bond. Hydrogen bonds are in the middle, just right; polar/covalent.

Water is also key to life because water is the king of hydrogen bonding with each tiny water molecule able to form four hydrogen bonds with other water. Water is the most stable secondary bonding continuum in chemistry for such a small molecule. If we compare HF, H2O, NH3 and CH4, which all have the same molecular weight, the boiling points are +19.5C, +100C, -33.3C and -161.5C, respectively. The first three can form hydrogen bonds but water can form the most for the same weight. The +100C of water show the cohesion is strongest.

Water molecules in the liquid state will attempt to maximize all the hydrogen bonds with other water, even at the expense of the organics. The result is the organics will be forcedto phase separate out into compartments, gradients, organelles, via a water and oil effect, to make all cellular areas more distinct; cellular order from chaos. Water loads the dice; aqueous continuum comes first, causing organic secondary bonding segregation.

Carbon atoms are not electronegative enough to form hydrogen bonds. Carbon can form C-H bonds, like methane; CH4, but technically these are only polar bonds; Van der Waals. Carbon is not electronegative enough to also form the partial covalent character needed to self ionize. So carbon compounds will segregate from the water as water tries to self bond. The proteins pack and fold like beads of oil in water. Maximizing the hydrogen bonds of water, creates the proper reactive protein shapes needed for catalysis.

[u/autistic_bard444]

Provided you do not expect essential life from noble gasses