a bonobo humanity?

orbitals – one day we may understand

Jacinta: Well, in ‘researching’ – I have to put it in quotes cause what I do is so shallow it barely counts as research – the last piece, I came across a reference to Philip Ball’s choice of the top ten unsolved mysteries in science, at least chemical science.

Canto: Philip Ball, author of Curiosity…

Jacinta: Among other things. His list was published in Scientific American in 2011, the official ‘Year of Chemistry’ – which passed unnoticed by supposedly scientific moi. The actual article is largely unavailable to the impoverished, but at least I’ve been able to access the list here. So I thought we might have fun discussing it in our quest to self-educate autant que possible before we die.

Canto: Yes I don’t know enough about chemistry to say whether this is a bog-standard list or an eccentric one, but there are no quibbles about the first mystery – the origin of life. But have we already covered that?

Jacinta: Not really. Ball’s mystery number 1, to be exact, is ‘How did life begin?’ – by which he presumably means life as we know it. And, as Jack Szostak puts it, the answer lies with ‘chemistry plus details’. Putting the right chemistry together in the right order under the right conditions, which they’ve managed to do in a ‘small way’ in the lab, synthesising a pyrimidine nucleotide, as noted in our last post.

Canto: Yes it seems to me we’re never going to solve this mystery by somehow stumbling upon the first life on Earth, or even a trace of it. How will we ever know it’s the first? Then again creating different kinds of conditions – gases and pressures and molecular bits and pieces – and mixing and shaking and cooking, that may not solve the mystery either, because we’ll never know if it happened like that, but it might show how life can begin, and that would be pretty awesome, if I may use that word correctly for once.

Jacinta: Usage changes mate, live with it. So what’s Ball’s second mystery?

Canto: ‘How do molecules form?’ Now we’re really getting into basic chemistry.

Jacinta: But isn’t that a known known? Bonding isn’t it? Like O² is an oxygen atom bonding with another to create a more stable configuration… I don’t know.

Canto: Well let’s look into it. What exactly is a chemical bond and why do they form? Molecular oxygen is common and stable, but what about ozone, isn’t that just oxygen in a different molecular form, O³? Yet in different molecular form, oxygen has different qualities. Ozone’s a pungent-smelling gas, whereas standard oxygen’s odourless. So why does it have different molecular forms? Why does it have any molecular form, why doesn’t it just exist as single atoms?

Jacinta: But then you could ask why do atoms exist, and why in different configurations of protons and neutrons, etc? Best to stick to how questions.

Canto: Okay, I’d like to know how, under what conditions, oxygen exists as O³ rather than O².

Jacinta: So we have to go to bonding. This occurs between electrons in the ‘outer shell’ of atoms. In molecular oxygen, O2, the two oxygen atoms form a covalent bond, sharing four electrons, two from each atom. The water and carbon dioxide molecules are also covalently bonded. Covalently bonded molecules are usually in liquid or gas form.

Canto: What causes the atoms to form these bonds though?

Jacinta: There are two other types of bonds, ionic and metallic. As to causes, there are simple and increasingly complex explanations. I’m sure Ball was after the most complex and comprehensive explanation possible, which I believe involves quantum mechanics. For a very introductory explanation to the types of bonds, this website is useful, but this much more complex, albeit brief, explanation of the O2 bond in particular will leave you scratching your head. So I think we should do a sort of explication de texte of this response, which comes from organic chemist David Shobe:

If you mean the molecule O2, that is actually a complicated question.  It is a double bond, but not a typical double bond such as in ethylene, CH2=CH2.  In ethylene, each carbon atom has a sigma orbital and a pi orbital for bonding, and there are 4 electrons available (after forming the C-H bonds), so each bonding orbital (sigma and pi) has 2 electrons, which is optimal for bonding.  Also, since each orbital has a pair of electrons, one gets a singlet ground state: all electrons are in pairs.

In O2, there are 1 sigma orbital and 2 pi orbitals for bonding, but 12 valence electrons.  Four electrons, 2 on each oxygen atom, are in lone pairs, away from the bonding area.  This leaves 8 electrons for 3 bonding orbitals.  Since each orbital can only hold 2 electrons, there are 2 electrons forced into antibonding orbitals.  This is just what it sounds like: these electrons count negatively in determining the type of bond (technical term is bond order), so 2 sigma bonding electrons + 4 pi bonding electrons – 2 pi antibonding electrons, divided by 2 since an orbital holds 2 electrons, equals a bond order of 2: a double bond.

However, there are *two* pi antibonding orbitals with the same energy.  As  a result, one electron goes into each pi antibonding orbital.  This results in a triplet ground state: one in which there are two unpaired electrons.

That may be more answer than you wanted, but it’s what chemists believe.

Canto: Wow, a tough but interesting task. So a very good place to start is the beginning. By double bond, does he mean covalent bond?

Jacinta: Well according to this clearly reliable site, ethylene, aka ethene (C2H4) is the simplest alkene, that is an unsaturated (??)  hydrocarbon with double bonds – covalent bonds – between the carbons. So I think the answer to your question is yes… or no, there are triple covalent bonds too.

Canto: Okay so I’d like to know more about what a covalent bond is, and what valence electrons are, and then we need to know more about orbitals – pi and sigma and maybe others.

Jacinta: Well guess what, the more you dive into molecular bonding, the murkier stuff gets – until you familiarise yourself I suppose. There are different types of orbitals which lead to different types of covalent bonds, single, double and triple. The term ‘covalent’ means joint ownership, sharing, partnering, as we know, of valence. So how to describe valence? With great difficulty.

Canto: Just watched a video that tells me that covalent compounds or molecular compounds only exist between non-metallic elements, whereas ionic compounds are made up of non-metallic and metallic elements, and ionic bonds are quite different from covalent bonds. And presumably metallic bonds join only metallic elements. Don’t know if that helps any.

Jacinta: Well yes it does in that it tells us we really need to start from scratch with basic chemistry before we can get a handle on the molecule problem.

Canto: Okay, time to go back to the Khan academy.

Jacinta: Yes and we’ll do so always bearing in mind that fundamental question about the formation of molecules. So our chemistry lesson begins with elements made up of atoms so tiny that, for example, the width of a human hair, which is essentially carbon, can fit a million of them.

Canto: And the elements are distinguished from each other by their atomic numbers, which is the number of protons in their nuclei. They can have different numbers of neutrons, but for example, carbon must always have six protons.

Jacinta: And neutral-charge carbon will have six electrons buzzing about the nucleus, sort of. They keep close to the nucleus because they’re negatively charged, we don’t know why (or at least I don’t), and so they’re attracted to the positively charged protons in the nucleus.

Canto: More fundamental questions. Why are electrons negatively charged? Why are positively charged particles attracted to negatively charged ones? And if they’re so attracted why don’t electrons just fall into the nucleus and kiss their attractive protons, and live in wedded bliss with them?

Jacinta: Let’s stick to how questions for now. Electrons don’t fall into the nucleus but they can be lost to other atoms, in which case the atom will have a positive charge, having more protons than electrons. So with the losing and the stealing and the sharing of electrons between atoms, elements will have changed properties. Remember oxygen and ozone.

Canto: So it’s interesting that, right from the get-go, we’re looking at that ancient philosophical question of the constituents of matter. And though we now know that atoms aren’t indivisible, they do represent the smallest constituents of any particular element.

Jacinta: But as you know, that smallest constituent gets weird and mathematical and quantum mechanical, with electrons being waves or particles or probability distributions, with the probability of finding them or ‘fixing’ them being higher the closer you get to the nucleus. So this mathematical probability function of an electron is what we call its orbital. Remember that word?

Canto: Right, that’s a beginning, and it gives me an inkling into types of orbitals, such as antibonding orbitals. Continue.

Jacinta: We’ll continue next time. We’ve only just entered the darkness before the dawn.

http://solarfuel.clas.asu.edu/10-unsolved-mysteries-chemistry

https://www.factmonster.com/dk/encyclopedia/science/molecules

https://www.quora.com/What-type-of-bond-do-2-oxygen-atoms-have

https://chem.libretexts.org/Core/Organic_Chemistry/Alkenes/Properties_of_Alkenes/Structure_and_Bonding_in_Ethene-The_Pi_Bond

https://en.wikipedia.org/wiki/Unsaturated_hydrocarbon