Naked Science Forum

On the Lighter Side => New Theories => Topic started by: puppypower on 21/04/2021 12:09:17

Title: The similarity of chlorophyl and hemoglobin
Post by: puppypower on 21/04/2021 12:09:17
I pondering the similarity between chlorophyl, used for photosynthesis, and the heme aspect of hemoglobin, that is used for the transport of oxygen in the blood. The chemical structures are shown below. As you can see, these are very similar and differ primarily by the central metal ions. This topic is about how these metal ions differ and how this difference can impart very different properties to similar organic structures.

(https://science2be.files.wordpress.com/2012/05/wheatgrass_hemoglobin_chlorophyll_molecule.gif?w=490)

Chlorophyl is much older and came first in terms of evolution. Chlorophyl is photoactive and uses photons from the sun to generate a high energy electron, that will ultimately be used to store solar energy as reduced sugars. The central metal atom, Magnesium; Mg, has the electron configuration of 1S2, 2S2, 2P6,3S2. It typically loses its two 3S2 electrons to become the Mg+2 ion. Mg is very reactive. If you ever burned Mg ribbon it is very hot and bright. The Mg wants to lose its two extra electrons and becomes the stable 1S2, 2S2, 2P6 configuration used by oxide O-2.

When the Mg+2 ion is placed in the center of the chlorophyl molecule, the four nitrogen atoms share electrons with the Mg+2. The four nitrogen atoms are also part of the larger overall resonance structure, where electrons are delocalized throughout the expansive ring structure, switching double bonds back and forth. The electron sharing by the four nitrogen, with Mg+2, is intermittent depending on the coordinated resonance movement of the ring electrons. While the positive charge on the central Mg, helps to stabilize the resonance structure by accepting electrons from nitrogen, so the four nitrogen can also participate in the resonance.

Another important affect of the election sharing of nitrogen, with Mg+2, is to reduce the Mg+2, more to less, back to the metal atom; Mg, but in a way that is intermittent in terms of its empty 3p orbitals. This sharing creates sort of a covalently bonded metal atom.

A photon that impinges anywhere upon the chlorophyl molecule, will energize the ring structure and thereby energize the central Mg. In this case, the central Mg to force it to have too much electron density; up to Mg-1. This is unstable for Mg, and results in the release of an electron that can then be used further down stream.

The situation with the heme molecule is similar. Iron; Fe, has an electron configuration of 1S2, 2S2, 2P6,3S2, 3P6, 3D6, 4S2. Iron can lose it's two 4S2 electrons plus one of its 3D electrons, to form ferrous and ferric ions; Fe+2 and Fe+3, respectively. This losing of electrons by iron is not as exothermic as with Mg. As, such the four attached nitrogen, and energy tweaks to the resonance structure, do not lead to the exothermic expulsion of an electron in Fe. Instead the iron can share O2 electrons, while also sharing with the nitrogen. The latter is with the d-orbital.

One may also notice chlorophyl has some extra carbon at the bottom right. The chlorophyl has some extra electron releasing groups. Since heme does no have these, its resonance electrons are held slightly tighter against accidental excitement by photons.

Analysis has shown that the central Fe of heme is in the ferric state Fe+3. Photons that could excite the resonance ring structure, have an extra place for an excited electron compared to Mg. It can share iron's empty 3D orbital, until the energy dissipates. Since hemoglobin is usually hidden in the dark, this extra electron space becomes reserved for O2. Fe is able to multitask. The heme works with O2 but it does work with CO2, since the central carbon of CO2 is electron releasing and will excite the heme's Fe+3, and this will kick off the CO2.


Title: Re: The similarity of chlorophyl and hemoglobin
Post by: Bored chemist on 21/04/2021 12:20:05
Considering how much you like to bang on about the importance of water, the fact that you have ignored the proteins here is hilarious.

Analysis has shown that the central Fe of heme is in the ferric state Fe+3.
However, the iron in a haemoglobin molecule is on the +2 state.


Just a quick look at WIKI would have helped you avoid these silly errors.
Even though carbon dioxide is carried by hemoglobin, it does not compete with oxygen for the iron-binding positions but is bound to the amine groups of the protein chains attached to the heme groups.

"The iron ion may be either in the ferrous Fe2+ or in the ferric Fe3+ state, but ferrihemoglobin (methemoglobin) (Fe3+) cannot bind oxygen.[45] In binding, oxygen temporarily and reversibly oxidizes (Fe2+) to (Fe3+) while oxygen temporarily turns into the superoxide ion, thus iron must exist in the +2 oxidation state to bind oxygen. If superoxide ion associated to Fe3+ is protonated, the hemoglobin iron will remain oxidized and incapable of binding oxygen. In such cases, the enzyme methemoglobin reductase will be able to eventually reactivate methemoglobin by reducing the iron center."


https://en.wikipedia.org/wiki/Hemoglobin#:~:text=In%20binding%2C%20oxygen%20temporarily%20and,and%20incapable%20of%20binding%20oxygen.
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: Bored chemist on 21/04/2021 12:21:11
If you ever burned Mg ribbon it is very hot and bright.
Ditto iron.
https://en.wikipedia.org/wiki/Thermal_lance
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: puppypower on 22/04/2021 13:21:13
Actually I was not looking at the entire modern enzyme complexes connected to chlorophyl and heme, I was only concerned with the chunks shown in the pictures presented. I had more of an evolutionary angle in mind. I was visualizing the good ole days, when things were much simpler and we did not yet have all the modern bells and whistles.

I was more concerned with questions like why is Chlorophyl, with its central Mg atom, photoactive, while heme with its central Fe atom is not, since both form using the same ring structures? Single metal atoms appear to make the entire difference. The rest of the enzyme complex is a support group that utilizes these basic differences. I was concerned with the differences, from day one, by looking at these two known cases, side-by-side; all else equal.

The four nitrogen atoms are sharing electrons with the central metal atoms. Both Fe and Mg are not your typical metals or cations under these conditions. Like atoms within the resonance itself, these metal cations will cycle between reduced and oxidized states; relative to the static mineral metals or cations. This situation is more about covalent bonding of metals, in contrast to ionic bonding found in the oxides or metallic bonding found in metals. These particular bonding states  were not addressed in Wiki under these topics. They stuck with the modern bells and whistles. This is the new theory section, so I though I would take a stab at answering these fundamental questions. Life forms many metal complexes.

A covalently bonded metal ion should be close, at times, to its neutral atomic state. As an analogy, the oxygen molecule; O2, allows both oxygen atoms to complete their octets by sharing electrons with each other; double bonding, while not causing any change of charge from neutral. There is still a potential to gain even more electrons and form a charge.

The central metal ions in Chlorophyl and Heme are forced to be electrophiles, that have to accept electrons that it would prefer give up. The metals are a captive audience. This is not their first choice, but under the circumstances of four nitrogen atoms in a resonance structure, this is what has to happen.

The central metal ions are placed in a state somewhere between metal and ion. Since both free metal atoms tend to lose electrons in nature, there is an internal and environmental atomic push in each metal to reverse any forced metal state, that is being imposed by the nitrogen, via the needs of the mobile electrons within the resonance structures. The overall system wide stability comes at the expense of the central metal.

If you look at resonance structures, such as in benzene aldehyde; shown below, this is usually written as four structures, with the double bonds shifting positions, with positive and negative charges moving around, based on where the double bonds appear, and where the electron need to be at that point in time. It four state average to a neutral ring. In the case of the resonance structures of chlorophyl and heme, the metal atoms helps to stabilize the nitrogen atoms in the resonance by accepting electrons. This is important for many resonance diagrams. This also allows the resonance delocalization of the entire ring to expand further, even into the metal. The metal cannot leave because of this.

(https://useruploads.socratic.org/X7R8K8SVTf6Bu93ui1qB_NCERT%20solution_4-11-08_Sonali_11_chemistry_Ch12_40_SJT_LVN_html_164fda8d.jpg)

Iron, when it goes from ferrous to ferric ion, loses a D-electron. The resonance can share electron density and help to fill in the empty D-orbital to get a resonance average based ferrous ion. This is an extra fail safe, that Mg lacks making Mg more photon resonance sensitive. When the nitrogen become electron deficit in some of the resonance configurations, the ferric can return.

An oxygen molecule is O2 and would like to accept electrons. The best source on the ring will be the central iron. This works better in the ferrous state. The oxygen cannot steal the electron but can only share with the resonance. Once the oxygen is attached, this impacts the ability of the resonance to use iron as completely, since a positive charge back to ferric will compete with the oxygen. In practical terms, the ferrous lingers as the final average state. Once the oxygen is gone, then resonance opens up the other options.

The selectivity for O2 is based on oxygen's high affinity for electrons and its ability to compete with sone of the resistant  resonance structures at the iron position. 
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: Bored chemist on 22/04/2021 13:44:27
I was more concerned with questions like why is Chlorophyl, with its central Mg atom, photoactive, while heme with its central Fe atom is not, since both form using the same ring structures?
Heme is photoactive.
https://core.ac.uk/download/pdf/195352762.pdf

So, you can stop wondering now.
Like atoms within the resonance itself, these metal cations will cycle between reduced and oxidized states;
Not really.
The iron doesn't change much and the magnesium doesn't change at all.
The central metal ions in Chlorophyl and Heme are forced to be electrophiles, that have to accept electrons that it would prefer give up. The metals are a captive audience.
You have that completely the wrong way round.
The reason the metal ions stick in the hole in the middle is because they want to "borrow" the electrons from the nitrogens.

The overall system wide stability comes at the expense of the central metal.
If that was true, the metal would "fall out", but it doesn't.
The central metal ions are placed in a state somewhere between metal and ion.
No. They are charged ions.
This also allows the resonance delocalization of the entire ring to expand further, even into the metal. The metal cannot leave because of this.
If you remove the metal ions, the system is still delocalised.

The selectivity for O2 is based on oxygen's high affinity for electrons
The selectivity for things like carbon monoxide is even higher, but it has little electron affinity.


Why not study some science?
That way you can avoid saying silly things.
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: evan_au on 23/04/2021 09:03:15
If we are comparing metal-containing organic compounds, the blue blood of the horseshoe crab contains two copper ions in the hemocyanin molecule (when oxygenated).
- It splits into two separate molecules (with 1 copper each) when no oxygen is present.
 [ Invalid Attachment ]
Image by Chemthulhu - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=39807956

See: https://en.wikipedia.org/wiki/Horseshoe_crab#Harvest_for_blood


Title: Re: The similarity of chlorophyl and hemoglobin
Post by: puppypower on 23/04/2021 13:52:22
Quote from: puppypower on Yesterday at 13:21:13
The central metal ions are placed in a state somewhere between metal and ion.
No. They are charged ions.
Quote from: puppypower on Yesterday at 13:21:13
This also allows the resonance delocalization of the entire ring to expand further, even into the metal. The metal cannot leave because of this.
If you remove the metal ions, the system is still delocalised.

Quote from: puppypower on Yesterday at 13:21:13
The selectivity for O2 is based on oxygen's high affinity for electrons
The selectivity for things like carbon monoxide is even higher, but it has little electron affinity.


Why not study some science?
That way you can avoid saying silly things.

The mistake you are making is to assume ionic bonding and not covalent bonding with the central metal. As I showed with benzene aldehyde, resonance ring structures do no remain one way, as is often written. Rather these shifts double bonding locations with positive and negative charge and election density moving. This allows for selectivity in terms of chemical reactions.

The central metal of Chlorophyl and Heme does not see a uniform electron density, like an ion, but it see electron density this is fluctuating with the resonance. This is not ionic in nature or based on charge, but covalent and based more on magnetism of electrons in larger scale motion. The covalent bonding orbitals with the central metal are all based on fluctuating electron density with charge repulsion, but magnetic attraction. These use the metal orbitals, too, such as the 3s orbitals of Mg for a transient Mg metal state.

If we are comparing metal-containing organic compounds, the blue blood of the horseshoe crab contains two copper ions in the hemocyanin molecule (when oxygenated).
- It splits into two separate molecules (with 1 copper each) when no oxygen is present.

* Oxyhemocyanin_full.png (8.59 kB . 316x239 - viewed 918 times)
Image by Chemthulhu - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=39807956

See: https://en.wikipedia.org/wiki/Horseshoe_crab#Harvest_for_blood

This is quite interesting. The trend that I now notice is this is another case of nitrogen atoms binding to the central metal, in all three coordination complexes; Mg, Fe, Co.

Yesterday I was reading about a cancer drug cisplatin, that was based on a central platinum metal atom. It has two attached nitrogen and two attached chloride ions. What this coordination complex does is bind to two very specific nitrogen atoms, one each on two similar resonance bases of DNA. This cross links the DNA making it hard for the cancer to replicate. In this case the two chloride ligands are replaced by the two resonance nitrogen ligands . Once again there is nitrogen up close and personal with metals. I need to ponder why this is the case. What do these metals like about nitrogen and nitrogen within resonance structures?

(https://media.springernature.com/original/springer-static/image/prt%3A978-3-642-16483-5%2F3/MediaObjects/978-3-642-16483-5_3_Part_Fig1-1189_HTML.gif)
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: Bored chemist on 23/04/2021 14:26:28
The mistake you are making is to assume ionic bonding and not covalent bonding with the central metal.
The mistake you are making is not recognising that it is dative bonding.
But that's probably because you refuse to learn science.
As I showed with benzene aldehyde
The stuff is called benzaldehyde.
Making mistakes like that shows that you don't really know what you are talking about.

... resonance ring structures do no remain one way, as is often written.
Actually, they do, but with (about) one and a half bonds each rather than alternating pairs of single and double bonds.

You seem to have believed the "lies we tell to children" version.


The central metal of Chlorophyl and Heme does not see a uniform electron density, like an ion,
Do you imagine that the sodium ion in salt sees a uniform electron density?
Because, in reality, it doesn't.

but it see electron density this is fluctuating with the resonance.
No
Again, you are looking at the nursery school version.
The bonds don't "flip back and to".

but covalent and based more on magnetism of electrons in larger scale motion.
No, chlorophyll and haem are not magnetic.
Your determination to call everything "magnetic" just makes your viewpoint look silly.

I need to ponder why this is the case. What do these metals like about nitrogen
They like the electrons.
This is no shock. The metal ions are positively charged, the lone pair electrons are negative.
It's simple electrostatics.

It's also the reason why this is completely wrong.
The central metal ions in Chlorophyl and Heme are forced to be electrophiles, that have to accept electrons that it would prefer give up.

Why not learn some science?

The nitrogens don't need to be in a resonant system.
You can tell that by thinking about the structures you have drawn in front of you, but you need to stop and think, rather than post tosh.
If you think about it, you will realise that the other nitrogen- platinum bonds are stable. They stay in place while the cisplatin  cross links the DNA. But in thus cases, the link is to ammonia which isn't a resonance structure.
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: puppypower on 25/04/2021 13:01:16
The mistake you are making is to assume ionic bonding and not covalent bonding with the central metal.
The mistake you are making is not recognising that it is dative bonding.
But that's probably because you refuse to learn science.
As I showed with benzene aldehyde
The stuff is called benzaldehyde.
Making mistakes like that shows that you don't really know what you are talking about.

... resonance ring structures do no remain one way, as is often written.
Actually, they do, but with (about) one and a half bonds each rather than alternating pairs of single and double bonds.

You seem to have believed the "lies we tell to children" version.


The central metal of Chlorophyl and Heme does not see a uniform electron density, like an ion,
Do you imagine that the sodium ion in salt sees a uniform electron density?
Because, in reality, it doesn't.

but it see electron density this is fluctuating with the resonance.
No
Again, you are looking at the nursery school version.
The bonds don't "flip back and to".

but covalent and based more on magnetism of electrons in larger scale motion.
No, chlorophyll and haem are not magnetic.
Your determination to call everything "magnetic" just makes your viewpoint look silly.

I need to ponder why this is the case. What do these metals like about nitrogen
They like the electrons.
This is no shock. The metal ions are positively charged, the lone pair electrons are negative.
It's simple electrostatics.

It's also the reason why this is completely wrong.
The central metal ions in Chlorophyl and Heme are forced to be electrophiles, that have to accept electrons that it would prefer give up.

Why not learn some science?

The nitrogens don't need to be in a resonant system.
You can tell that by thinking about the structures you have drawn in front of you, but you need to stop and think, rather than post tosh.
If you think about it, you will realise that the other nitrogen- platinum bonds are stable. They stay in place while the cisplatin  cross links the DNA. But in thus cases, the link is to ammonia which isn't a resonance structure.


The mistake that you are making is misunderstanding what oxidation states are. The term oxidation state or oxidation number is an applied chemistry tool that is used to help students and practitioners predict the election flow in redox reactions. The elements are assigned oxidation numbers based on a standard. This standard is a tool. It does not reflect what is actually going on in a pure chemistry sense.

For example in H2O, the oxidation states are,  -2 for oxygen and +1 for hydrogen. If we assume that applied science convention is a statement of pure science, one would expect oxygen to have all the shared elections and the two hydrogen protons to have none. This would suggest that  water is held together by ionic charge. This is useful for predicting this reaction of water going from the oxygen and hydrogen gases; both have oxidation states of 0, but it does not tell use how the electron flow and share with hydrogen being more like, +0.7 and oxygen more like, -1.3. This tells us covalent bond since you cannot split an electron.

In a pure chemistry sense, what is observed is that the electrons are being shared and oxygen never has two full electrons, i.e., -2, within water, when hydrogen are attached, nor does the hydrogen of water always go without any electrons having only a positive charge. Oxidation numbers are an applied science tool and not a statement of pure reality; rookie mistake.

When you look at chemical reaction equations and use oxidation numbers to help predict possible products, the reactions also do not move forward, based on quantum jumps from reactants to products, as is often written on paper. That is also an applied science tool to make it easier to learn. There is a time lag, going from reactants to products. The reactants also need to move between intermediate states, since an energy hill needs to be climbed for activation energy. You appear to be thinking in applied chemistry terms and quantum jumps, while I am thinking in terms of the intermediate states which are a purer form of chemistry.

When you have resonance structures, like within Chlorophyl, Heme and Oxyhemocyanin, the attached nitrogen to the central metal are not static, but rather the situation involves intermediate states based on the movement of the resonance electrons.  Metals share the nitrogen electrons based on trips up and down the energy hill of the resonance rings. As written on paper never exists unless we stop time, but this is not a quantum jump in space without time.

Title: Re: The similarity of chlorophyl and hemoglobin
Post by: Bored chemist on 25/04/2021 13:49:41
The mistake that you are making is misunderstanding what oxidation states are.
I know that oxidation states are just an accounting tool.
That's why the only time I used them was to point out where you were getting them wrong.
You said this:
Analysis has shown that the central Fe of heme is in the ferric state Fe+3.
And I cited the Wiki page which shows that, if the iron in your blood is ferric, you have a problem.

You seem to forget that only one of us is actually a chemist, and you are the one making the mistakes you accuse me of.

Why not learn some science?

Title: Re: The similarity of chlorophyl and hemoglobin
Post by: puppypower on 25/04/2021 13:53:21
In terms of nitrogen being a common link in the four central metals that were discussed, I was looking for what made nitrogen unique. The applied chemistry tool that I began with was oxidation number and oxidation state. This tool was too expansion when applied to all of chemistry including unique manufacturers molecules. So, I narrowed this down further and only used the oxidation numbers for the main atoms within organic chemistry reactions.

For example, oxygen in life is -2, -1 and 0. It can also be +1 in compounds like F2O. The +1 state of oxygen is ignored in organic chemistry since this compound is not found in nature being connected to life. In organic chemistry, Nitrogen has the oxidation states of -3, -2,-1,0, +1, +3. It can also be +5 as nitric acid and nitrates, which plants do use. I did include that. In the ring bases of DNA, the nitrogen are connected amines and imines based on single and double bonded carbon atoms to the nitrogen, respectively.  These all have an oxidation state of -3. The nitrogen of ammonia is also defined as -3, since nitrogen is more electronegative than hydrogen.

In all coordinated metal complexes above, including the ammonia on the cancer drug cisplatin, all the attached nitrogen are in the -3 state. Cisplatin begins with two ammonia and two chloride. Upon injection into the body, the cisplatin will be hydrolyzed by the body's water, with H20 replacing one or two chloride-1. This is the intermediate state that is then followed by the nitrogen -3, on the base ring structure of DNA, replacing the water. The nitrogen -3 is the most stable ligand, meaning it offers the most electron density to the Pt.  This forms a cross link on the DNA, that the repair apparatus of the cancer cell cannot overcome, even in water. This is not an ionic bond, that enzymes and/or water can reverse like the chloride and water equilibrium.

Once again the -3 state of the nitrogen atom is an assigned convention. The higher electronegativity of the nitrogen, versus any of these metals, will favor the nitrogen holding the majority of the shared electrons. In the case of chlorophyl and magnesium we have four nitrogen with -3 oxidation numbers, which totals twelve electrons on paper. Magnesium is only +2. All it can accept is an average of 1/2 electron from each nitrogen. This can form the metal or a transient or transitional facsimile there of. The resonance delocalization makes this more complicated, cycling in and out of the pseudo-metal state. Photons can exceed the stability of the metal to deal with 4 times -3 electrons, in resonance, and allow a one election current.

Nitrogen is very electronegative and can accommodate the electrons better than any of the central metals. It willingly shares a fraction of an electron density; probability function. A photon impinging on the chlorophyl can change the odds and overwhelm the Mg.
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: puppypower on 25/04/2021 14:35:31
The mistake that you are making is misunderstanding what oxidation states are.
I know that oxidation states are just an accounting tool.
That's why the only time I used them was to point out where you were getting them wrong.
You said this:
Analysis has shown that the central Fe of heme is in the ferric state Fe+3.
And I cited the Wiki page which shows that, if the iron in your blood is ferric, you have a problem.

You seem to forget that only one of us is actually a chemist, and you are the one making the mistakes you accuse me of.

Why not learn some science?

I am/was a chemical engineer. I was inducted into an Honorary Chemistry Society as a junior, even with my heavy engineering course load. I aced all the chemistry final exams. As a professional I had to deal with both applied and pure chemistry in the context of lab tests, leading to the scaling and inventing of chemistry for chemical processes.

Engineering can only use the most solid of science theory. Not all theory can be scaled, since scaling involves other things such as the impact of mass and heat transfer, for example. These variables can impact reaction thermodynamics. These things may have to be dealt with. Sometimes you need to reinvent the wheel, if the base theory will not scale outside the orchid greenhouse. Scaling is less of a problem in the test tube. But in process development, one learns to think in terms of extra variables not part of the base theory.

Statistical modeling, common to the life sciences, is an applied science tool that has been mistaken for pure science, for decades. Statistics is not a statement of reality, but it is an applied science tool used to approximate reality for fun and profit. This misunderstanding has been an uphill battle, since the brain wash is so deep through education and applied science jobs that require the tool. Any excuse to black box the details should raise a yellow flag.

I could have used statistics, so I could black box things and ignore the details. But this was not very challenging nor did it require my education. I was more about finding rational pure science solutions that could fill in the blanks and also scale. From the POV of scaling, a better water analysis is needed for life and metal coordination complexes are an expected part of life.

My problem is I still like to practice these skills by looking at situations, and figuring them out from scratch, even if this requires reinventing the wheel. My take on metal coordination complexes uses the same approach. I only need the chemical structure and the rest can be translated down to the tiny details. I get ahead of the applied tools, like statistics, which incites a taboo.
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: Bored chemist on 25/04/2021 14:51:29
. Not all theory can be scaled, since scaling involves other things such as the impact of mass and heat transfer, for example.
So... they can be scaled- you just have to do it properly...
Statistics is not a statement of reality,
In a lot of QM, it is the only statement of reality.

I could have used statistics
Well, yes; or you could have used flower arranging. But neither of them apply to this thread very well.

About th only time you could use it, you did:

. It willingly shares a fraction of an electron density; probability function.


From the POV of scaling, a better water analysis is needed for life and metal coordination complexes are an expected part of life.

Most of that makes no real sense.

I aced all the chemistry final exams.
So, when did you forget about it?
Because it's pretty plain from things like this,
Once again there is nitrogen up close and personal with metals. I need to ponder why this is the case. What do these metals like about nitrogen and nitrogen within resonance structures?

and that you get the wrong oxidation state for the iron in blood,  that you don't know it now.
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: Bored chemist on 25/04/2021 14:53:28
This tool was too expansion when applied to all of chemistry including unique manufacturers molecules.
Did you think that meant something, if so, what?
Photons can exceed the stability of the metal to deal with 4 times -3 electrons, in resonance, and allow a one election current.

ditto.
This is not an ionic bond,
Nobody said it was.
On the other hand, I did point out that it''s a dative bond.
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: puppypower on 28/04/2021 12:19:16
This tool was too expansion when applied to all of chemistry including unique manufacturers molecules.
Did you think that meant something, if so, what?
Photons can exceed the stability of the metal to deal with 4 times -3 electrons, in resonance, and allow a one election current.

ditto.
This is not an ionic bond,
Nobody said it was.
On the other hand, I did point out that it''s a dative bond.

From years of observing your negativity and cynicism to everyone not mainstream, I have come to the conclusion that you memorize, but are not able to think on your own. You take the safe path, by attaching you wagon to consensus thinking and then become self righteous, criticizing anything not with the program. You are in the wrong section. This section is for thinkers, not parrots.

I will try to help you think, since outside the box might be scary for you. If you apply oxidation states to the Heme molecule and assume iron +2, the four nitrogen are assigned oxidation numbers -3, each.

Explain to us how iron remains at +2, while accommodating up to 12 electrons stemming from there four nitrogen-3, yet still remain +2.  Maybe math was your worse subject since this is often problem solving.

What is the point of having the iron in the middle of the resonance ring, always confined to +2, if this state cannot  accommodate any of the electrons of nitrogen? Thinking is important in applied science, but may not be needed in pretentious memory science.

One possible answer is the iron is +3, so it can accommodate the equivalent of 1 electron, from the four nitrogen, so it appears to be +2 at steady state. If it always remains at +2, it is not sharing any electrons and is therefore useless and should not remain there. 
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: Bored chemist on 28/04/2021 13:24:43
From years of observing your negativity and cynicism to everyone not mainstream, I have come to the conclusion that you memorize, but are not able to think on your own. You take the safe path, by attaching you wagon to consensus thinking and then become self righteous, criticizing anything not with the program. You are in the wrong section.

It's not that I don't, or can't think.
It's that I don't need to.
You post stuff that is clearly wrong.
It's at odds with observations.
What you seem to want to write off as "mainstream" is the collected experience of millions of person years of research.
The degree of conceit needed to imagine that you somehow know better than all that is bordering on insanity- all the more so since you haven't apparently bothered to learn what the collective knowledge actually is.


I will try to help you think,
You don't seem qualified.
outside the box might be scary for you.
You need to understand what's in the box first.

Here's some out of the box thinking for you.
It is impossible to paint an electron purple.

It isn't possible to label an electron as being "from the iron" or "on the heme".


Your question is meaningless because, in fact, the iron in blood is coordinated by 5 nitrogens not 4. You have, as I pointed out in my first post here, ignored the environment in which that nice pretty ring system finds itself.

That's what I mean by needing to understand what's in the box first.


What is the point of having the iron in the middle of the resonance ring, always confined to +2,
I'm not sure anyone said it was.

It seems you forgot that haemoglobin (where  the pointless bookkeeping says that the iron is Fe(II) ) is not the same as oxyhaemoglobin where the iron is, according to the bean counters, Fe(III).

And the oxygen (for those who like doing impersonations of  "The Count" from Sesame Street)  has an oxidation number of minus a half.

I can do the silly counting bit, but the reality is that it is meaningless.

Just as meaningless as the "flipping" or "alternating" bonds in benzene.


On a related note, what would be the point of the magnesium in the chlorophyll, given that it really can't change its oxidation state?

The answer is that it's largely structural.

The role of the iron is much more complicated than you seem to think.
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: puppypower on 29/04/2021 14:29:32
I am more interesting in developing new ideas than fighting to shine or defend the ego. I think I have figured out how to explain this, so it is easier for everyone to see. I like to derive things from scratch and compare later. This is how you practice ingenuity. Sometimes a better mouse trap appears.

A Fe+2 or ferrous ion, in isolation, will react with O2; oxygen, through a series of 5-6 steps to form Fe+3. This reaction speeds up higher temperature. In practical terms, the Heme molecule would be of limited usefulness if the central iron, as ferrous+2 was oxidized to Fe+3, in the process of attaching and carrying oxygen. It would stop being useful and affective as soon as the Fe+3 appears. This is not observed, so there has to be trick that nature has evolved to prevent the oxidation of the central Fe. 

The trick has to do with the attached ring structure; Heme, via the four nitrogen atoms, with oxidation numbers; -3, are attached to the central Fe. This arrangement is not electrostatic, but covalent in nature. The central iron atom shares electrons with the ring, via the nitrogen, allowing the central Fe, to sustain the ferrous state.The oxygen will take the bait, attach and then try to oxidize it to Fe+3, but it cannot, due to the trick.

The trick is the central iron atom is already in the Fe+3 state. However, the covalent sharing of elections by the resonance ring structure, with the central iron, creates the equivalent of Fe+2*; Fe+3 plus one shared electron equivalent. Shared electrons are not the same as owning the electron. With sharing other atoms also need to share it and they may not want to give it up. This is the bait and switch, to get the oxygen to attach.

As a loose analogy, your neighbor borrows your lawn mower to mow his yard. He does a good job. A passerby sees his nicely trimmed yard and offers to buy the mower at a good price. The price is good but the neighbor cannot sell the mower, because it does to belong to him. He can use it and that makes it looks like he owns it, but it is still not his to sell.

In the case of the Heme, the shared resonance electron density with the Fe+3 creates the impression of Fe+2. We will measure this as the average state. The oxygen sees this as free electron food. This will cause the oxygen will stop, look and attached for the extra electron. However, this Fe+2* electron density is borrowed, and really belongs to more than dozen atoms in the huge resonance ring structure, with Fe+2* not having the authority to release it. The oxygen lingers, tries to sell the deal, until it needs to leave; O2 is released.

In the case of Chlorophyl, the Mg is also sharing with the ring. It is borrowing the hedge trimmer for a couple of days. This sharing the hedge trimmer fills up its orbital garage, where all the tools are stored. Any further tools become overflow.

When photons impinge on the Chlorophyl resonance, there is electron excitement that is focused at the Mg atom, since this has the least stable atomic state in the resonance ring. The Mg is being slightly reduced by sharing electrons with the nitrogen. Photons will add energy. Unlike Fe which has Fe+2 and Fe+3, Mg+2 has no extra buffer for the electron, so it overflows. Mg+2 by itself will not do this since will not be able to covalently share with ions such as oxide; O-2.

Coordination complexes are a primitive form of enzyme. I was interested in this since I was looking for ways to get past the key bottlenecks within Abiogenesis.  I am heading back to the topic Water and Life to discuss Abiogenesis and water.
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: Bored chemist on 29/04/2021 15:34:24
I am more interesting in developing new ideas
I'm more interested in ideas that are not demonstrably wrong.
It doesn't matter if they are new or not.

Your ideas are demonstrably wrong.
So they are useless- at least to science; they may make great poetry.
Title: Re: The similarity of chlorophyl and hemoglobin
Post by: Bored chemist on 29/04/2021 17:31:33
Sometimes a better mouse trap appears.
Often you starve to death because a mouse eats all your cheese in much less time that it takes you to reinvent the wheel.