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Saturday, 1 December 2018

Carbon-Based Hydrogen Bonding

Many chemists will be shocked to discover that carbon-based hydrogens can hydrogen bond. Weakly. But actually.

If you're not a chemist you're probably thinking that doesn't sound like much of a surprise... A hydrogen can hydrogen bond? Who've thunk it? And that is the first condition for hydrogen bonding – having a hydrogen.

However, until the discovery of the carbon-based hydrogen bond between acetone and halogenated hydrocarbons in 1937, it was believed that that the hydrogen could only make these bonds when attached to something very electronegative – electron-loving.

Why is this?

Electronegative atoms are electron-greedy and pull the electrons in a bond towards themselves. The electrons are shared unequally, leaving the electronegative atom a bit negative and whatever it’s bonded to a bit positive. We call this bond polar, because it has two differently charged ends, like a magnet. And, just like with two magnets, when the positive end of one comes near the negative end of the other, they bond. All polar molecules do this; we call it permanent dipole bonding. But hydrogens do it with an aggressive zeal that marks them out as unique.
Hydrogen bonds form between the slightly positive hydrogen atoms and slightly negative oxygen atoms in water molecules. Image via Wikipedia Commons.
There are three elements considered electronegative enough to polarise a hydrogen: fluorine, oxygen and nitrogen. Fluorine is the most electronegative element in the periodic table, given the Pauling electronegativity value (a made up scale we use to compare electronegativity values) 4. Oxygen is just behind it, with an electronegativity value 3.5, and nitrogen is 3. In contrast, hydrogen has an electronegativity value of 2.1, which means the difference between it and fluorine is 1.9 – considered enough to make a bond polar. But carbon is not very electronegative, and the difference between it and hydrogen is 0.4, surely too little to create polar bonds?

Apparently not.

Atomic Force Microscope image of a hydrogen bond. Image A. M. Sweetman et al. via Wikipedia Commons.

Remember, these electronegativity values are just made up. They’re also an average, and it turns out C–H bonds vary wildly and aren’t represented well by averages: bond strengths alone vary by 30%[1]. Some C–H bonds, it seems, are polar enough, and their hydrogens hydrogen bond to nearby oxygen atoms.
Interconnected water molecule network. Image ©TWDK.

These rulebreaking hydrogens might not be directly attached to very electronegative atoms but, it turns out, they are seldom far away: usually the carbon they are on is playing gooseberry in between the hydrogen and an electronegative atom which pulls electrons away across the carbon in a tug of war. Chemists call such a carbon activated, and the hydrogen acidic.

There is already a lot of mystery about the nature of the hydrogen bond. Why is it so much stronger than other polar bonds? How do we identify it? But the discovery of hydrogen bonding from hydrogens on carbon atoms, has thrown bonding classification into a crisis. This isn’t the first time this has happened either. The hydrogen bond, first described in 1939 by Pauling[2] of the Pauling electronegativity scale, has since had its definition broadened[3] and changed. In 1957, a paper called “The Hydrogen Bond” critically reviewed the evidence for hydrogen bonding, and attempted to explain it. Scientists are still trying.

Carbon-based hydrogen bonds, described as a special kinds of weak hydrogen bonds, have now been observed in lots of biomolecules including amino acids, proteins, sugars, and DNA.


How do we identify a hydrogen bond? And why does it matter?[4]

If we’ve missed carbon-based hydrogen bonds, there are probably lots of other intermolecular interactions we’ve missed, and which could be used to explain the structure and solubility of biomolecules, the way that proteins fold, how the body recognises molecules, methyl group, and answer unresolved questions about “weird” interactions seen in biology.

Water is liquid by hydrogen bonding. Image diego_torres via Pixabay.

1. Hitherto, hydrogen bonding has been singled out because of its unique strength, but hydrogen bonds strengths range from 4 to 50 kJ mol-1, and carbon-based hydrogen bonds are weaker than conventional hydrogen bonds, implying some sort of continuum wherein bond classification gets messy and awkward. When is a weak hydrogen bond just a hydrogen-containing polar bond?[5]

2. Bond length has also been used to classify hydrogen bonding: a C–H···O interaction counts as a hydrogen bond when the H···O separation is less than 3.2 Å, or the sum of the atoms’ radii (meaning they must overlap). The problem with this is that bond strength and length are basically the same thing, so we still have the continuum problem.

3. Others have mentioned that bond angle is important. In some interactions, like a classic hydrogen bond, atoms overlap linearly, or face on (180o), whilst in other structures the atoms are forced to overlap at an angle to avoid bumping into other bits of molecule. The C–H···O bond angle has nominally been suggested to fall within 90-180o, but not only have a huge number of different hydrogen geometries already been observed, but this is actually a pretty enormous range anyway.

The C–H···O bond angle has nominally been suggested to fall within 90-180 degrees. Image ©TWDK.

4. Hydrogen bonds leave spectroscopic signatures. Nuclear magnetic resonance spectroscopy (NMR) can pick up hydrogen bonds as a downfield [left] chemical shift in a hydrogen NMR spectrum, whilst infrared spectroscopy (IR) detects a decrease in wavenumber, characteristic of the C–H bond lengthening and weakening as the hydrogen is tugged off to do some other bonding elsewhere. But whilst a downfield chemical shift is seen for NMR in carbon-based hydrogen bonding, something different is seen for IR: an increase in wavenumber, or sign of C–H bond shortening and strengthening. Which is right? Is it a hydrogen bond, or isn’t it? And what’s happening to the C–H bond?

DNA. Image ©ynse (CC BY-SA 2.0).
We still don’t know enough about carbon-based hydrogen bonds to predict them – they just pop up here and there unexpectedly. For example, the base pair thymine and cytosine form C–H···O hydrogen bonds, but apparently the thymine methyl group is the most frequent supplier of the hydrogens that do this, even though it’s not very activated and there are better options available. Scientists aren’t even sure whether what the base pairs do counts as bona fide hydrogen bonding and, as such, our understanding of the structure of DNA is in turmoil.

To make things even weirder, other kinds of hydrogen bonds have also been noticed too – including carbon-based hydrogen bonding to nitrogen (which, you’ll remember, is less electronegative than oxygen), and even sulfur (which, at 2.6, is almost as pathetic as carbon!)[6], and, even weirder, hydrogen bonding onto carbon atoms in O-H···C and N-H···C interactions[7]. These discoveries could be just the beginning of a whole new field of molecular interplay.  

why don't all references have links?

[1] Bond Energies. Organic Chemistry, Michigan State University.
[2] Steiner, Thomas. The hydrogen bond in the solid state. Angewandte Chemie International Edition 41.1 (2002): 48-76.
[3] Smith, Douglas A. A brief history of the hydrogen bond. ACS Symposium Series. Vol. 569. Washington, DC: American Chemical Society, [1974], 1994.
[4] Horowitz, Scott, and Raymond C. Trievel. Carbon-oxygen hydrogen bonding in biological structure and function. Journal of Biological Chemistry (2012): jbc-R112.
[5] Desiraju, GautamáR. Distinction between the weak hydrogen bond and the van der Waals interaction. Chemical Communications 8 (1998): 891-892.
[6] Westler, William M., et al. Hyperfine-Shifted 13C Resonance Assignments in an Iron− Sulfur Protein with Quantum Chemical Verification: Aliphatic C− H··· S 3-Center− 4-Electron Interactions. Journal of the American Chemical Society 133.5 (2011): 1310-1316.
[7] M.A. Viswamitra, R. Radhakrishnan, J. Bandekar, G. R. Desiraju, Evidence for O-H···C and N-H···C hydrogen bonding in crystalline alkynes, alkenes, and aromatics, J. Am. Chem. Soc. 1993, 115, 4868-4869. doi: 10.1021/ja00064a055

Thursday, 15 November 2018

Mysterious Mo

Why is stainless steel stainless?

Iron vs Steel

Steel is made from iron, but it’s not the same thing: steel is an alloy - iron doped with other elements to engineer new, useful properties. Some of these elements have been especially selected to provide certain properties, but not all metallurgy is that well understood: some elements have simply been stuck in and performed well - and we don’t know why.

Saturday, 26 November 2016

TWDK - The New Social Media Platform for Science

A number of astute observers have already noticed (and clicked on) two mysterious links that have appeared on the Things We Don’t Know homepage, along with some other tweaks to our layout and styling. But why register? Why login? It's all part of our upcoming changes, a kind of scientific advent calendar for you all.

Thursday, 22 September 2016

Is there a ninth planet in our Solar System?

By now, you’ve probably heard the hubbub in the news about the hypothetical “Ninth Planet” in our Solar System, and, unfortunately for those of us who studied astronomy before 2006, no, it’s not Pluto. There’s a new Planet Nine on the block, although no-one has ever seen it and we don’t actually know if it exists.

Yes, some scientists think there may be another, unseen planet in our Solar System. How can they think that?

Why haven’t scientists seen Planet Nine yet?

In our solar system, planets are generally considered to be visible things - get yourself a 12-inch telescope and you can see Pluto, and that’s not even a planet any more! So yes, it sounds daft to say that there’s a whole other planet in our Solar System that we haven’t seen yet, but, in our defence, it’s very far away.

Planet Nine is thought to be a trans-Neptunian object - a minor planet that orbits the Sun at a distance further out than Neptune. Both the Kuiper belt and the Oort cloud are included in this region, and Planet Nine is thought to orbit somewhere between the two.

An artist’s rendering of the relationship between the Kuiper belt and the Oort cloud
The Oort cloud is a spherical region of icy debris thought to surround the Solar System. Although it was thought to extend from 5,000 to 100,000 Earth-Sun distances, it may start much closer to the Sun. Image credit: NASA and A. Feild (Space Telescope Science Institute)

Why do scientists think Planet Nine exists?

Monday, 15 August 2016

The Search for the Graviton

What holds the world together? It sounds like a simple question - but it isn’t.We know of four fundamental forces of nature that seem to be doing the job, but have only found three exchange carrier particles (particles which give rise to the forces between other particles). Physicists like symmetry, and we like to think that the universe does too. Faced with the scenario of more forces than carriers, it is natural for a physicist to assume we’re missing one.

So far, we have found photons, which carry the electromagnetic force (which describes the interactions between charged particles); W and Z bosons, which carry the weak nuclear force (responsible for radioactive decay); and gluons, which carry the strong nuclear force (which holds the nuclei of atoms together). But what about gravity?

A diagram outlining the interactions between fundamental particles according to the Standard Model.
Not all types of elementary particles interact with all other types, and only some fundamental particles interact with particles of the same type. For example, photons do not (directly) interact with other photons, or with gluons. Image credit: Public domain

This idea is summarised nicely in an article by science writer Brian Koberlein: in quantum field theory … [you] start with a wave form and then ‘quantize’ it, you break the wave down into the smallest amounts of it that can exist (for example, photons are quanta of light). This has been used with photons, and doing so with gravitational waves leads to the idea of gravitons.

However, this approach encounters some problems when tackling gravity. General relativity tells us that that gravity and the curvature of spacetime are intricately linked. As matter travels through spacetime it causes spacetime to curve around it, and as spacetime curves, this tells matter where to move. It is this motion, caused by the curvature of spacetime, that can be considered ‘gravitation’ [8].

Friday, 1 July 2016

How were Mars’ moons formed?

The formation of Deimos and Phobos, the moons of Mars, is still somewhat of a mystery. They were discovered by Asaph Hall in 1877, and observed in 1971 by Mariner 9, a NASA spacecraft orbiting Mars[1]. Although not the smallest moons, they are much smaller in comparison to Mars than Earth’s moon is to Earth.

Color composite of Phobos and Deimos
Deimos and Phobos have mean diameters 280 and 154 times smaller than Earth’s moon respectively. Images courtesy NASA (Phobos) and NASA/JPL-Caltech/University of Arizona (Deimos), composite by TWDK

Possible Theories of Formation: Asteroid Capture

Despite being known for so long, there is no accepted theory regarding their creation. They appear to be made of “...carbon-rich rock mixed with ice”[1], and are oddly shaped, which led to the idea that they are captured asteroids. This would also explain their heavy cratering and small size.

An asteroid is captured when it passes a larger mass (in this case, a planet), and is “caught” by the planet’s gravitational field and is forced into orbit. This means that the orbits of captured asteroids are expected to be very eccentric ellipses, meaning that the asteroids pass close by before swinging out further away. The orbits of Phobos and Deimos, however, are almost circular. Because of this, we can’t consider asteroid capture to be the definitive theory of the formation of Mars’ moons.

Monday, 20 June 2016

Introducing Alice

Hello all, I’m Alice and I’m the new SEPnet intern at Things We Don’t Know. I’ve just finished my third year studying physics at Royal Holloway, University of London, so I’ve just got my masters year left to go.

photograph of Alice Wayne

My interest in physics started in secondary school when I was taught about fundamental particles and forces. At that time, science had found neither the Higgs boson nor the Graviton, and I decided then that I would study physics and contribute toward the search. We’ve now found the Higgs boson, but as the Graviton still eludes us, I am writing my Research Review on the work that has been done so far at CERN to find it, or at least, to find where it isn’t.

Saturday, 18 June 2016

The Case of the Jumping Carbons

Imagine you are inside a nuclear reactor, a UK design. Not only are you inside it, but you are part of it; a carbon atom inside the graphite core which houses the control rods and fuel rods (the ‘moderator’). Around you the environment is glowing with heat and radiation, all given off in the splitting (fission) of uranium-235 nuclei. The temperature of 450°C is no problem, and you remain tightly bound in a lattice arrangement with your fellow carbons.

However, when the uranium nuclei split, they spit out more neutrons which pelt towards you at high speeds. One slams into you, and you slow it down, as is your job, so it travels at a suitable speed to cause more fission events. In this process you absorb the neutron’s energy, and get knocked out of your slot in the lattice. You whiz towards your fellow carbon atoms, knocking more out of their spaces like a billiard ball, wreaking havoc in the strict order of the graphite crystal. Eventually you transfer all of your extra energy to your neighbours and come to rest, filling a vacancy left by another displaced carbon or squeezing in between the orderly lattice layers (as an ‘interstitial’). Here you wait, ready to absorb the excess energy of the next neutron. The upheaval is routine to you, as during your life in the reactor you may switch places up to 30 times.

A finite element model of a graphite sample and how the model behaves when irradiated or heated. Image credit: Dr Graham Hall. Manchester University

This is just one atom, but what are the consequences of millions jumping around like this?

Well, the effects are unpredictable. The radiation barrage that the graphite endures can cause it to change its material properties; its thermal expansion, strength and even its dimensions, in strange ways. Even to the human eye, these changes would be noticeable. The moderator can change shape by up to 2%, depending on the grade of graphite; a surface that started smooth may finish rough. The dimensions may warp so that the control rods used to restrain the nuclear reaction may no longer fit into their channels. It is clearly important to completely understand how the graphite will change when designing new reactors or maintaining the existing ones. The problem is that we don’t.