Wikipedia:Reference desk/Archives/Science/2018 September 22

= September 22 =

Valence Bond theory vs Molecular Orbital theory descriptions of O2
I am reading this paper on the use of VBT and MOT in teaching chemistry, and I'm having trouble getting past the first paragraph. Specifically, the following excerpt is what I'm struggling with:

"MO theory is often presented as a superior or more advanced theory citing “failures” of VB such as the paramagnetism of O2 and the explanation of excited electronic states. However, a more in-depth application of VB (1) shows that resonance between two paramagnetic structures with two 3-electron π bonds (Figure 1A) is more stable than resonance between two diamagnetic spin paired structures each with a 2-electron π bond and a 4-electron repulsion (Figure 1B)."

I don't understand several points about this. Firstly, isn't the double bond in dioxygen a sigma bond and and pi bond, not two pi bonds as per the text? I understand that the two bonds are actually equivalent (not one sigma and one pi, but two equivalent bonds of mixed character), but to make that point clear you'd need to invoke hybridization, and in their description and drawing they haven't done so.

Secondly, don't bonds involving three electrons imply that at least two electrons would have the same set of quantum numbers and therefore be in violation of the Pauli principle? I've never heard anything about 3 electron bonds before, and I don't understand how they can be made to fit with either VBT or MOT as both are quantum based theories and as such must conform to Pauli. Figures 1A and 1B don't help me much either. Assuming that the solid line between the nuclei indicates a sigma bond, figure 1A seems to show a triple bond between the atoms. The existence of two p orbital on each atom also seems to indicate sp hybridization, whereas O2 has sp2 hybridization. Actually, a VBT description that explains the paramagnetism of O2 would make more sense to me if they showed 2 sp hybridized O atoms triply bonded (1 sigma bond between the sp orbitals, and two pi bonds between p orbitals) with an unpaired electron in each of the remaining sp orbitals. This would not account for the lone pairs though, and would imply a far shorter bond length. Handschuh-talk to me 09:39, 22 September 2018 (UTC)
 * "O2 has sp2 hybridization" is either circular reasoning or an unsupported underlying premise:) You are rightly concerned about putting a third electron into a single π molecular orbital, but when you add two p atomic orbitals, you get both a π and a π* and that latter can hold up to two more electrons. If you hybridize two p, which can hold a total of 4, your result can also hold a total of 4. Their diagram 1A represents two p orbitals interacting rather than a single unified π. They casually call it "π", but it's really also π* (which also actually does have π symmetry). So there are two sets of π/π* in addition to the σ, but each bonding π (populated by 2 electrons) is weakened by 1 electron in its associated antibonding π. That means each of the two π/π* has net effect of approximately "half bonding". So "1σ+2[half-π]" rather than "1σ+1π" still gives a net appearance of 4 bonding electrons exactly as "O=O" represents. Our triplet oxygen discusses the MO approach in detail and also links to the idea of three-electron bonds. DMacks (talk) 10:31, 22 September 2018 (UTC)
 * "when you add two p atomic orbitals, you get both a π and a π* and that latter can hold up to two more electrons"
 * Except this is supposed to be a VBT description of the bonding. Bonding and anti-bonding orbitals are a MOT concept..aren't they? Handschuh-talk to me 10:50, 22 September 2018 (UTC)
 * No, at the introductory level we usually gloss over that aspect, but Modern valence bond theory is entirely compatible with MOT, and uses many of the same tools to deduce electronic properties. -- Jayron 32 23:08, 22 September 2018 (UTC)
 * Also, as shown in the paper, especially the diagram, it isn't a 3-electron, 1-orbital bond, it's a 3-electron, 2-orbital bond; that is you have 3 electrons distributed (via Resonance between two perpendicular pi-bonds). In the case between VBT and MOT here, the difference is in the explanation of the paramagnetism: VBT explains it via resonance, MOT explains it via bonding/anti-bonding orbitals.  Either way, however, Pauli is preserved, look at the diagram on the right: You have two perpendicular p-orbitals, and neither ever has more than 2 electrons in them.  Ultimately, however, they are both still useful theories which is why we keep them both: VBT is powerful in explaining geometry (angles, positions, and bond lengths), whereas MOT is useful in such matters as visualizing energy and bond order.  Each can kind-of come up with explanations the other is better at (i.e. "resonance", which is still an inelegant kludge that MOT avoids entirely), but the point of the paper is that BOTH theories are valid because even VBT can explain observed behavior.  -- Jayron 32 23:16, 22 September 2018 (UTC)
 * Well, if VBT can include bonding and anti-bonding orbitals then I don't even understand what the distinction between the two theories is. As I understand VBT, a bond is created by overlapping two atomic orbitals. This allows the electrons to be counted as being in atomic orbitals from both atoms in the bond. In the diagram, no atomic orbital has more than 2 electrons, but two atomic orbitals are indicated to be bonding i.e. overlapping to form a bond with a total occupancy of 3 electrons.
 * Secondly, if VBT is only able to accurately describe the bonding of dioxygen after we update the theory with concepts borrowed from MOT, then that doesn't say much for the paper's argument that VBT is just a good a description of the phenomenon. Handschuh-talk to me 00:10, 23 September 2018 (UTC)
 * Whatever this is, it is not the familiar approach. The original cited article is  - I have to go, so I haven't looked to see if it's in Sci-Hub. Wnt (talk) 12:48, 22 September 2018 (UTC)
 * I should note that Sci-Hub now gives a message to "use a proxy to download articles" (but in Russian) rather than a download link if you just go there. Maybe they're doing us a favor; for all I know local authorities have taken to cracking down on academics for making interlibrary loans.  Sci-Hub's .onion address doesn't work, but visiting their regular domain names in Tor seems to count as a proxy.  Anyway, to return to topic, it would seem that their prototype of three electron bonds is in F2-, which has an energy of -30 kcal/mol, versus -38 kcal/mol for F2.  They point out that the molecular orbital model doesn't predict that correctly - it would predict a bond energy only half as large (-19 kcal/mol I assume) for F2-.  They have an odd "breathing orbital" model that I don't necessarily understand as of yet, where they draw the p orbitals for the F atom with a full shell bigger than the ones for the one missing an electron.  I'm not sure what that signifies but they say that "the three-electron bond which is made entirely of charge fluctuation".
 * When they get to oxygen, the deal is this: each oxygen starts with six electrons.  Two go into a lone pair at their rear end, and one goes to a sigma bond between the oxygens (the standard single bond), leaving three pi electrons left for each to contribute.  They point out that these can be put with a singlet pi bond and a "four-electron repulsion" (that's the VB-speak for a pi bond plus a pi antibond, I assume), but they don't have to be:  they can be put with the F2- situation in each of the two pi planes.  That gives two unpaired electrons for a triplet ground state as they say.  Now what I don't see is the usual assumption that you end up with two lone pairs rather than one, and I'm not sure why, but they surely have a point in there about the fluorine radical.  These three-electron bonds seem like a necessary and useful addition to the valence bond toolkit, and it allows us to draw the oxygen as a bona fide diradical with unpaired electrons in some specific location rather than in molecular orbitals.  (Well, alright, it's the same location because it's only 2 atoms but I imagine you can come up with some giant organic peroxide (duh, no, let me think...) where saying the unpaired electrons are in molecular orbitals might seem pretty bizarre??) Wnt (talk) 20:51, 28 September 2018 (UTC)

Species identification (Unknown spiders)
2 unknown spiders for Species identification:





Based on uploaders talk page, most probable region is North Eastern US, maybe New York?

(Aside: A photo subject identification refdesk would be useful.) ShakespeareFan00 (talk) 10:30, 22 September 2018 (UTC)
 * For photo identification the TinEye service, an example of Content-based image retrieval, is useful for checking whether an image is already on the web, though it cannot interpret an image. DroneB (talk) 11:07, 22 September 2018 (UTC)


 * The lower one looks like a Dolomedes tenebrosus - in fact they may both be. Mikenorton (talk) 12:25, 22 September 2018 (UTC)


 * Uploader responded to my query about region, Long Island, New York is where one (probably both) of the photos were taken. ShakespeareFan00 (talk) 23:17, 24 September 2018 (UTC)


 * This link gives a distribution for dolomedes tenebrosus, which is consistent with that location. Mikenorton (talk) 23:48, 24 September 2018 (UTC)

When An Idea appears on your conscious mind
What makes ideas pop up into your conscious mind? Is there a brain mechanism for that? — Preceding unsigned comment added by 37.252.180.177 (talk) 23:11, 22 September 2018 (UTC)
 * See this for example. Before the idea becomes conscious it is sometimes called preconscious though our article uses that term in a somewhat different way. 173.228.123.166 (talk) 00:59, 23 September 2018 (UTC)
 * Yes, the word did not pop up into my mind when I wrote the question. But it remains unanswered. There is probably loads of preconscious processing. How come only some become conscious? --31.4.136.202 (talk) 09:52, 23 September 2018 (UTC)
 * I have had occasions where I would need for some reason to remember some obscure fact, like who was some unsuccessful presidential candidate’s vice president candidate, knowing that I knew the answer at least during the campaign. Hard concentration does not bring the answer to mind, but I can leave the search to the unconscious processes and go on to to some other task. After thirty seconds or so the answer pops up without any conscious effort at all. It is literally like the file search is being done by a separate mental process from conscios awareness or mental effort. Edison (talk) 15:54, 23 September 2018 (UTC)
 * Related may be Working memory. I cannot remember the name of another possibly related bias (similar to confirmation bias), although we tend to notice what we expect to see or what we're looking for.  We routinely think and remember things that are not considered immediately important and quickly discard, but if such normally mundane event is recently seeked for, we'll tend to focus on it (or finally remember what was "tagged for retrieval").  An example is when we notice we need to buy an item (it may have recently stopped working, or a newly perceived need), then we start noticing it in stores and ads, although we never would normally care about the particular item...  But that's of course not explaining the internal details of preconscious processing, a lot of which is still mysterious... — Paleo  Neonate  – 17:23, 23 September 2018 (UTC)
 * See subliminal advertising. 92.31.140.53 (talk) 18:12, 23 September 2018 (UTC)
 * This is not what I was talking about, but the aim here is indeed to influence using the unconscious (interestingly, that article seems to need work, including mention on how some of the methods are pseudoscience)... — Paleo  Neonate  – 20:24, 23 September 2018 (UTC)


 * See also Hard problem of consciousness on why the question is tricky. -- Jayron 32 15:07, 24 September 2018 (UTC)


 * Wouldn't it be a safe guess that there is some sort of filing system used by the mind, and if so, wouldn't thoughts be associated with other thoughts, and if thoughts are associated with other thoughts, wouldn't it be unsurprising that thoughts of no known relevance would always be popping up as mere associates of the thoughts to which we attribute relevance? Bus stop (talk) 16:12, 24 September 2018 (UTC)


 * I usually don't respond on this page, but this is an interesting question of a subject that fascinates me and I have studied in great detail. The first thing to understand is that no one really knows what consciousness is or what we even need it for. Next to "what lies outside our universe" this is the biggest unanswered question in science today. There are many theories about the mechanisms of consciousness, with one of the most intriguing being the "single-cell theory of consciousness", but it all is really a mystery. What we do know is that there are many, many levels of consciousness, with the highest level (full, waking consciousness) being the smallest part of the mind. And I mean extremely small (microscopic) compared to all the unconscious things going on. We're basically running on autopilot most of the time. The best idea for why we even have it is that it allows us to solve unsolvable problems by viewing it in some big picture, and using intuition to literally guess the correct answer. (Those stupid captcha letters are an excellent example of this.)


 * Then you have to distinguish between, consciousness, imagination, memory, and cognition. Our mind operates using two separate languages (similar to computer languages). Freud discovered this and wrote extensively on it. Our conscious language is in words, which we have to learn. The subconscious language is not in words, but in terms of meaning and sensory input. The subconscious language is not learned but instinctual, and is the same for all humans (possibly all mammal or even all animals). Nearly all our thoughts are processed in this subconscious language at incredibly fast speed, right up to the point where it is on the tip of your tongue. It doesn't become conscious until you put it into words, which takes much longer.


 * Coming up with an idea involves imagination, which is what the brain constructs as being an illusion we call the future. Imagination involves combining known information in new ways, thus involves memory. Memory creates an illusion we call the past. But then there is also cognition, which is the ability to attribute a meaning to a thing or event, and differentiate it from other things and events.


 * Nothing becomes a memory (thus nothing is cognized) until after it passes through the amygdala to the hippocampus. The amygdala is like a filter, that in computer terms compresses our memories into small, easily-stored packets. When you drive across country, you don't remember every tree or house along the way. Your amygdala changes these into generic "forest" and "neighborhood"s. Only those things which really stand out to you are fully committed to memory, and this is determined by emotional saliency (how hard does it tug at my emotions). Thus, the amygdala is also the emotion center of the brain.


 * So after barely grazing all of the factors involved, back to the original question. It all depends on these unconscious processes. Imagine your brain is running millions of computer programs, simultaneously, and each are always talking and communicating with each other in a very random and chaotic manner (remind you of any particular encyclopedia out there?). It is only when enough parts of your unconscious mind get together (collaborate) and decide (consensus), "ok, this is emotionally important enough for me to cognate, that the thought begins to take shape in your subconscious. And only after some more debate --if it seems important enough--, it may enter what is known as your stream of consciousness, which is that little voice that blabs on endlessly in our minds, using words but still in random order. Some people talk using their stream of consciousness, but this is really incoherent, so most then take that idea and put it into a coherent form that others can understand, which requires another aspect of processing reality called metaperception. (Figure that consciousness starts developing about the age of two and finishes by four. Metaperception begins forming around the age of four and doesn't finish until you're 25, which is most of the reason kids act the way they do.) Zaereth (talk) 00:25, 27 September 2018 (UTC)