Unlikely hydrogen bond discovered

Unlikely hydrogen bond discovered
Unlikely bonding in Copenhagen lab. Henrik G. Kjaergaard and his team discovered positive hydrogen bonding to positive Phosphorus

As with magnets and alternating current, positively charged molecules never aim for one another. Indeed, similarly charged poles are repelled. Nevertheless, a team from the University of Copenhagen's Department of Chemistry has managed to become the first to bond positively charged phosphorus atoms with positively charged hydrogen ones. Their insight may prove pivotal to understanding how biologically important molecules such as DNA and proteins form properly.

PhD student Anne Hansen, Post-Doctoral fellow Lin Du and Professor Henrik Kjærgaard discovered the unlikely hydrogen/Phospherous bonds in their shared lab at the University of Copenhagen, section. Their findings were published in the Journal of Physical Chemistry Letters.

Function follows form where proteins are concerned. Whether they serve as signaling agents, catalysts or biological building blocks, proteins are only effective if their molecular structure is spot on. Their composition is largely dependent on in the molecules, and the ability of these to create hydrogen bonds with other elements.

Previously, researchers assumed that positively charged hydrogen could only create with negatively charged elements like oxygen, fluorine and nitrogen. That positive can also be bound to positive phosphorus opens up a world of fresh insight into biological processes. It also provides the basis for an entirely new understanding of how atomic charge works. Thus, it may come as no small surprise that Professor Henrik Kjærgaard is proud of their discovery.

"It was thought that atomic charge was global, that is, as something that was uniform and spherically shaped. But our experiment demonstrates, as clear as day, that charge is asymmetric – that small areas of positive charge exist upon atoms which are in fact negative," explains Kjærgaard.

The discovery was worked on in Professor Kjærgaard's Quantum, Spectra and Dynamics group. The group specializes in combining spectroscopic analyses with theoretical modelling and computational chemistry.


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More information: J. Phys. Chem. Lett., 2014, 5 (23), pp 4225–4231 DOI: 10.1021/jz502150d
Citation: Unlikely hydrogen bond discovered (2015, March 13) retrieved 16 June 2019 from https://phys.org/news/2015-03-hydrogen-bond.html
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Mar 13, 2015
Mind boggling. I suppose some quantum effect will be implicated with further study. Just goes to show you we still have much to learn and discover.

Mar 13, 2015
But our experiment demonstrates, as clear as day, that charge is asymmetric – that small areas of positive charge exist upon atoms which are in fact negative

Not just simple dipoles anymore, I wonder how this will change our understanding of the standard model.

Mar 13, 2015
But our experiment demonstrates, as clear as day, that charge is asymmetric – that small areas of positive charge exist upon atoms which are in fact negative

Not just simple dipoles anymore, I wonder how this will change our understanding of the standard model.

Exactly the claim made in the theory at the link below years ago.
Page 36

http://www.scribd...-Physics

Mar 13, 2015
Deleted double post.

Mar 13, 2015
It is surprising that consideration for the hydrogen bond instead of being an electrostatic bond is in fact a magnetic bond. This manifest from a theoretical approach to quantum gravity: http://www.scienc...cale.pdf

This very interesting article gives further support.

Mar 13, 2015
I wonder how this will change our understanding of the standard model.


From the abstract/image that is linked below the article:
The quantum chemical calculations show that both H and P in the OH···P hydrogen bond have partial positive charges, as expected from their electronegativities. However, the electrostatic potentials show a negative potential area on the electron density surface around P that facilitates formation of hydrogen bonds.


So we're not dealing with a 'positive-positive' connection, but with a regular 'positive-negative' connection. Albeit the 'negative' part is localized on a (mostly) positive element.

Mar 13, 2015
Not a chemist, but I think this implies that no one ever saw an OH-P bond before? Did they have to use a special process to force the combine?

Z99
Mar 13, 2015
@h200dr - What?! Quantum effects in chemistry? I thought chemistry was based on the five humours. (Earth, Fire, Water, Earth, and Spirit) When did that change?!
Firstly, the P species in the abstract is Me3P which can be (and often is) written as (Me)3P: with the colon representing a LONE PAIR of ELECTRONS (which, last I heard, are not positively charged). IOW the bonding is RO-H...:P(Me)3 and seems pretty straightforward. Second, H-bonds vary in their amount of 'covalency' (ie 'directedness') as is well known. I'm not sure what it is the paper's authors are claiming, but positive-positive H-bonding is NOT it. IOW, this article (not the Letters paper) is rubbish. The writer is clearly out of his/her depth and this is sophomore or junior year chemistry. The title "Positive charged P as a H-bond acceptor" has to be interpreted knowledgably, since it might seem (to the uninformed) as if it means that two positive charges are attractive.

Mar 13, 2015
Now that science has discovered the "gay particle", watch for the LGBT crowd to come out in full force that this is evidence that homosexuality is attributable to natural forces.

Mar 13, 2015
Now that science has discovered the "gay particle", watch for the LGBT crowd to come out in full force that this is evidence that homosexuality is attributable to natural forces.

it is, but that's for another discussion....

Mar 13, 2015
But our experiment demonstrates, as clear as day, that charge is asymmetric – that small areas of positive charge exist upon atoms which are in fact negative
:
What else would you expect from an element with odd number of electrons? (in an odd number of shells)
Not just simple dipoles anymore, I wonder how this will change our understanding of the standard model.

Still dipolar...

Mar 14, 2015
But our experiment demonstrates, as clear as day, that charge is asymmetric – that small areas of positive charge exist upon atoms which are in fact negative

What else would you expect from an element with odd number of electrons? (in an odd number of shells)


Just an odd number of electrons does not give rise to a localized (and stable) place of opposite charge where a hydrogn atom could attach. The trick is in the other connections this P atom has, which draws the charge into a stable, uneven distribution.

Mar 14, 2015
unlikely hydrogen/Phospherous bond


Very unlikely, considering the spelling...

Mar 14, 2015
It was thought that atomic charge was global, that is, as something that was uniform and spherically shaped. But our experiment demonstrates, as clear as day, that charge is asymmetric
Why the hell the atomic charge should be uniform and spherically shaped? It's not true even for simplest elements..

Whydening Gyre and david_gold are right, it's an effect of odd number of electrons in valence orbitals of phosphorus, similar to those, which is gives the paramagnetism in another elements. But I wouldn't call it a hydrogen bond just because hydrogen gets involved - it's merely a normal Van der Waals bond.

Mar 15, 2015
uniform charge, positive or negative is assumed in classical interpretation. add quantum uncertainty and you have a chance that a negative charge would be available when you expect a positive charge. Given that, I don't think we have a handle on the big picture. Our 'physics and quantum effect' doesn't describe reality well enough yet. I think there is bold new world out there waiting... for the person who...

KBK
Mar 15, 2015
Consider the bonding claims of HHO

Consider that properly made HHO will implode at approx 21 psi

And all the other claims.

Suddenly, we understand that we're dealing with a very bizarre 'gas' in the case of HHO (brown's) gas.

That it is exactly as they claim: Electrically expanded water.

Mar 15, 2015
Huh. Well perhaps there are other new things we can learn about hydrogen.
http://www.blackl...ats-new/

-We may get to see his commercial reactor sometime this year. Or not.

Watch the presentation. It's new.

Mar 15, 2015
Original study is here. Physics-inclined people seem to be impressed with it - but in fact it's quite common steric effect: polarization of atoms with bulky ligands known from organic or inorganic chemistry, which has been extensively studied just with various substituted alkyl-phoshines (1, 2, 3...).

Mar 15, 2015
What is left over after these guys move the electron toward the nucleus?

Sorry, but to see this put forward by others who insist on "proof" of the claims of others is enlightening.

rgw
Mar 15, 2015
Another hydrogen bomb! Can't we just use the time & money to build schools and organize retreats with our Muslim brothers?

Mar 15, 2015
Why the hell the atomic charge should be uniform and spherically shaped? It's not true even for simplest elements.

Because if it weren't the we would get a lot of elements bonding with each other which ordinarily don't (i.e. if the world were as you envision it it wouldd be one HELL of a lot different from what we observe).
The trick why it works in the instance described in the article is that there is a _stable_ place of uneven charge distribution.


Mar 15, 2015
The trick why it works in the instance described in the article is that there is a _stable_ place of uneven charge distribution
At first, the hydrogen bond doesn't require a "stable place of uneven charge distribution". At second, most of molecules have nonsymmetric shape just because of "stable place of uneven charge distribution". At third, you're not describing a trick, it's explanation the less - only your naive interpretation of hydrogen bond in alkylphosphine. Yes, some asymmetry is here - but why it is here? This is the actual trick. So you're triply illogical with your comment.

Mar 15, 2015
Exactly how does this "new" result vary from any metal hydride or even a hydrogen H2 molecule? It sounds just like a covalent bond to me.

Mar 16, 2015
But our experiment demonstrates, as clear as day, that charge is asymmetric – that small areas of positive charge exist upon atoms which are in fact negative

Not just simple dipoles anymore, I wonder how this will change our understanding of the standard model.


Nothing there will change. Chemistry is mainly behavior of atoms, ions and electrons.

JVK
Mar 16, 2015
Chemistry is mainly behavior of atoms, ions and electrons.


Biology requires a link from the sun's energy to the chemistry of RNA-mediated nutrient-dependent protein folding.

"...while sending satellites into orbit and building multi-billion dollar colliders are promising ways to search for new physics, they are not the only ways. New physics can also hide in high precision measurements in your university lab, just ask the theorists. Who knows, there might be a chameleon hidden in your vacuum chamber." http://backreacti...rce.html

If I were an astrophysicist, I would try to place this new result into the context of the fact that "Life is physics and chemistry and communication"

If I were a "big bang" cosmologist, I might try to place the result into the context of the origin of life.

As a medical laboratory scientist I am left to wonder if this is evidence of a "fifth force" (electrostatic?)

Mar 16, 2015
Nope, IMO it's a result of the fact, that the phosphorus is surrounded with three methyl groups in trimethyl-phoshine. This still looks like the symmetric situation, but these methyl groups are rather bulky and not quite spherical, so that they cannot be always arranged into pure plane. Instead of it, they're deformed into flat cone, which leads into polarization of central phosphorus atom..

JVK
Mar 16, 2015
... consideration for the hydrogen bond instead of being an electrostatic bond is in fact a magnetic bond.


Is one of these two bonds more important than the other to link the sun's biological energy to light-induced amino acid substitutions that differentiate the cell types of plants and of animals via their physiology of reproduction?

Chemistry is mainly behavior of atoms, ions and electrons.


Is he claiming that nothing further is needed to explain the link from physics to chemistry and the conserved molecular mechanisms of nutrient-dependent biodiversity?

Are physicists capable of making sense when it comes to the role of their theories when placed into the context of biological facts?

JVK
Mar 16, 2015
the phosphorus is surrounded with three methyl groups in trimethyl-phoshine. This still looks like the symmetric situation, but these methyl groups are rather bulky and not quite spherical, so that they cannot be always arranged into pure plane. Instead of it, they're deformed into flat cone, which leads into polarization of central phosphorus atom..


I asked "Are physicists capable of making sense when it comes to the role of their theories when placed into the context of biological facts?"

Thanks for answering in the most confusing jargon possible: NO, that it not possible because theoretical physicists ignore the role of the sun's biological energy. Apologies if you're not ignoring the sun's biological energy -- but who would know if you are not? And, when only discussing ridiculous theories with other physicists, who cares whether the sun's biological energy is ignored?

Mar 16, 2015
As a medical laboratory scientist I am left to wonder if this is evidence of a "fifth force" (electrostatic?)


Electromagnetism is already one of the four fundamental forces.

Thanks for answering in the most confusing jargon possible


What? Dethe is talking about basic chemistry. There's nothing jargon-y about that comment.

Mar 16, 2015
Also, note the irony in Kohl being confused by chemistry 101 terms (bond geometry is one of the first things you learn about) when he throws around unrelated biology word salad all the time.

Mar 16, 2015
NO, that it not possible because theoretical physicists ignore the role of the sun's biological energy
What the shielding of methyl groups has to do with "sun's biological energy"? IMO you're a victim of schizophrenia delusions. It's curable, you just must cooperate with your doctor responsibly.

JVK
Mar 16, 2015
Quantum Criticality at the Origin of Life http://arxiv.org/...02.06880

"Our results also suggest that quantum transport played a distinguished role in evolution and selection. Both the number of known small molecules and proteins is about 108 and the number of chemically feasible small (< 500Da) organic compounds is astronomical, estimated[52] to be 10~60. The number of proteins grows exponentially with the number n of amino acids as 20n, and the largest known has about n 26000. This shows that chemical and biological evolution selected only a tiny fraction p 10"

Correct me if I am wrong. I think what the comments here show is that not one of the theoretical physicists has considered the fact that their ridiculous theories are useless if they cannot be connected to cell type differentiation by what is known about the conserved molecular mechanisms that establish the links from RNA-mediated amino acid substitutions to biodiversity.

JVK
Mar 16, 2015
Electromagnetism is already one of the four fundamental forces.


Great. How does that answer questions about electrostatic interactions?

What the shielding of methyl groups has to do with "sun's biological energy"?


RNA-directed DNA methylation links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man.

Other than that, the sun's biological energy has nothing to do with anything concerning life on this planet.

It could have arrived here from "deep space," for example. Anything is possible, in theory.

That's why serious scientists complain about the pseudoscientific nonsense touted by the folks here.

Scientific method: Defend the integrity of physics http://www.nature...-1.16535

IMO you're a victim of schizophrenia delusions.
You are a science idiot. Your opinion does not count. George Ellis confirmed that.

Mar 16, 2015
How does that answer questions about electrostatic interactions?


Such as?

Mar 16, 2015
What the shielding of methyl groups has to do with "sun's biological energy"? RNA-directed DNA methylation links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man
You've fixed idea and you're pushing it everywhere in a pathological way. The shielding of methyl groups is steric effect, independent of solar activity. You could justify whatever crime for yourself with your way of "reasoning", it's not quite safe condition for you. Just seek medical help, I mean it seriously - normal people don't combine apparently unrelated things in this way.

Mar 16, 2015
This could also have implications for gravitational attraction.

Mar 16, 2015
normal people don't combine apparently unrelated things in this way.


Look at any of his blog posts and you'll see the same pattern. Take this gem, for example:

Population geneticist ignore the need for anti-entropic epigenetic traps that link entropic elasticity to epistasis.


Epigenetic traps are feedback loops that ensure transcription of one allele, explained here:

http://www.scienc...13007782

Entropic elasticity refers to the stretching and rebounding properties of molecules.

Epistasis is the interaction of two or more genes contributing to a single trait.

Now, with that in mind, there is a link between DNA elasticity and epistasis due to how DNA topology affects transcription. Altered supercoiling could change transcription levels, which could change epistatic interactions.

As for epigenetic traps? Those are, at best, tenuously connected to DNA elasticity and epistasis.

JVK
Mar 16, 2015
Epigenetic traps link the speed of light on contact with H2O to the spectral energy measured as differences in levels of glucose and CSF in mammals via light-induced amino acid substitutions in plants that control the chemistry of their nutrient-dependent physiology of reproduction.

This cause and effect relationship extends to species from microbes to man via what is currently known about the biophysically constrained chemistry of RNA-mediated protein folding and their nutrient-dependent pheromone-controlled behaviors.

Nutrient-dependent metabolic networks link genetic networks to pheromone-controlled behaviors via the fixation of amino acid substitutions in the organized genomes of all animals. The fact that the molecular mechanisms of cell type differentiation are first recognizable to serious scientists who study plants, should only continue to bother pseudoscientists who know nothing about physics, chemistry, or biology.

http://rna-mediated.com/

JVK
Mar 16, 2015
Epigenetic traps are feedback loops that ensure transcription of one allele, explained here:


The feedback loops are explained here: Feedback loops link odor and pheromone signaling with reproduction http://www.scienc...05009815

They were first detailed here: http://www.hawaii...ion.html From Fertilization to Adult Sexual Behavior

They are RNA-mediated in species from microbes to man via amino acid substitutions that link cell type differentiation to the light-induced amino acid substitutions in plants.

JVK
Mar 16, 2015
... steric effect, independent of solar activity.


What we've just seen detailed is that nothing excerpt the magic of ridiculous theories is independent of solar activity.

Ask yourself this. Why is this being reported more than 3 months after its publication. I think that, at first, journalists were afraid to report it, but now they are afraid not to report it.

Those who have followed the research from other disciplines will understand the initial fear and the change.

Theorists will continue to believe in magic, because that's all they can do. They are incapable of understanding the fact that biologically based cause and effect starts with physics and chemistry, and it includes information that links the epigenetic landscape to the physical landscape of DNA via metabolic and genetic networks -- because it must. Nothing about that fact involves magic or pseudoscientific nonsense.

http://dx.doi.org...as.12570 Life is physics and chemistry and ...

Mar 16, 2015
@Z99 .. your analysis is spot on .. trimethyl phosphine has a long pair on the phosphorous, and of course that is what is acting as an H-bond acceptor in this molecule. I haven't the foggiest idea why the authors didn't realize this, but sadly the do actually claim that there is a partial positive charge on both H and P, then going onto say that the electrostatic potential shows a "negative potential area around the phosphorous" that "facilitates formation" of H-bonds. A word-salad to be sure, but it reveals that they got their partial charges from electronic structure calculations .. according to the paper they used the atomic polar tensor method to derive their atomic charges. That method is problematic, and for example gets the direction of the CO dipole wrong; this is relevant here, because that also involves a diffuse lone pair on an element (C) with low electronegativity. In summary, I think their claimed "partial positive" on phosphorous is likely a computational artifact.

JVK
Mar 16, 2015
...normal people don't combine apparently unrelated things in this way.


"Normal" people are biologically uninformed science idiots. Intelligent serious scientists link things like these to show how biologically uninformed the science idiots are.

Alternative Splicings
RNA Directed
Nutrigenomics
Pharmacogenomics
Neuronal Plasticity
Model Organisms
Human Pheromones
Diseases & Disorders
Ecology
Adaptations
Physics
Light Energy
Variations
Human Brain

Here you will find information that links physics, chemistry, and molecular epigenetics via RNA-mediated events such as the de novo creation of olfactory receptor genes in order to encourage a public discussion of a paradigm shift. http://rna-mediated.com/

JVK
Mar 16, 2015
I think their claimed "partial positive" on phosphorous is likely a computational artifact.


Great. I think that means that phosphorylation cannot be linked from amino acid substitutions to cell type differentiation in all cells of all individuals of all animal species based on what is known about photosynthesis in plants.

That means that all theorists are safe, and that their theoretical nonsense is not going to be fully exposed until later this week, or perhaps next week, or next year.

Mar 16, 2015
Epigenetic traps link the speed of light on contact with H2O to the spectral energy measured as differences in levels of glucose and CSF in mammals via light-induced amino acid substitutions in plants that control the chemistry of their nutrient-dependent physiology of reproduction.


This is a perfect example of what Dethe was talking about.

What do epigenetic traps have to do with the speed of light?

JVK
Mar 16, 2015
That's what I have detailed at RNA-mediated.com

Try to follow the topics from Alternative Splicings to Variations in the Human Brain. They are linked from the balance of viral microRNAs to nutrient-dependent microRNAs and the stability of organized genomes via RNA-directed DNA methylation and RNA-mediated cell type differentiation. This is not something that can be simply explained to biologically uniformed science idiots.

As indicated, you must start with the fact that "Life is physics and chemistry and communication" http://dx.doi.org...as.12570

You want to start with deVries definition of "mutation," which is more than 100 years old and accompanied by 100 years of pseudoscientific nonsense that cannot be removed from the thoughts of those who believe in it. That's the difference between a biologically uniformed science idiot and a serious scientist. Serious scientists provide experimental evidence to support their theories, not just assumptions.

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