Software for atomic orbitals oveplap in molecules

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Discussion Overview

The discussion revolves around software tools for visualizing atomic orbital overlaps in molecules, particularly focusing on hybridized atomic orbitals rather than molecular orbitals. Participants explore the relationship between atomic orbitals, hybridization, and molecular bonding, with specific interest in chlorine and oxygen interactions in various chlorate ions.

Discussion Character

  • Exploratory
  • Technical explanation
  • Debate/contested

Main Points Raised

  • One participant seeks interactive software for visualizing hybridized atomic orbitals overlapping in molecules and questions the applicability of Mathematica for this purpose.
  • Another participant clarifies that hybridized orbitals are not part of molecular orbital (MO) theory and suggests using valence bond software for optimal hybrid orbitals, mentioning a specific program by Gerratt, Cooper, and Karadakov.
  • There is a discussion on how orbital overlap is influenced by the shape of the orbitals, with one participant suggesting that exchange interaction as a measure of overlap could depend on atom hybridization.
  • Participants express curiosity about the overlap of chlorine's (3d) orbitals and oxygen's (2p) orbitals in chlorate ions, with one participant indicating a desire for visual representations of this overlap.
  • It is noted that chlorine's d-orbitals are generally unimportant for bonding in main group compounds, with a reference to a specific academic article supporting this claim.
  • One participant questions the shapes of orbitals and considers the possibility of visualizing standard atomic orbitals overlapping, even if minimally.
  • A link to an article containing figures of valence bond orbitals in main group compounds is shared as a potential resource.

Areas of Agreement / Disagreement

Participants express differing views on the relevance of hybridized orbitals in relation to molecular orbitals, and there is no consensus on the significance of chlorine's d-orbitals in bonding. The discussion remains unresolved regarding the best methods for visualizing orbital overlaps.

Contextual Notes

Participants highlight the complexity of orbital shapes and their implications for bonding, but there are unresolved assumptions regarding the definitions and interpretations of hybridization and orbital overlap.

sludger13
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I would be most grateful for some tips of interactive software, which shows the hybridized atomic orbitals overlapping in the molecule (I don't mean resulting molecular orbitals but atomic orbitals of which overlapping forms MO).
And does this works also in Mathematica?
 
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You are mixing up something here. Hybridized orbitals aren't a concept of MO theory, i.e., molecular orbitals are not built up from hybrid orbitals but directly from atomic orbitals.
If you want to get best hybrid orbitals you have to use valence bond software and among those there are not many programs which do the hybrid optimization. The Spin coupled valence bond program by Gerratt, Cooper and Karadakov comes to my mind. You would have to contact this group to get access.
 
But the orbital overlap is dictated by the shape of orbitals, as I laically deduce. E.g. the exchange interaction as a measure of overlap could depend upon atom hybridization, isn't it true?

I'm curious how chlorine's (3d) orbitals and oxygen's (2p) orbitals are ovelapping in space, so that every (sp2) oxygen participate in delocalized orbital in (ClO2-, ClO3-, ClO4-). I would be satisfied just with a single picture, however I haven't found any.
 
sludger13 said:
But the orbital overlap is dictated by the shape of orbitals, as I laically deduce. E.g. the exchange interaction as a measure of overlap could depend upon atom hybridization, isn't it true?
Sure, but this is valence bond theory, not MO theory.
I'm curious how chlorine's (3d) orbitals and oxygen's (2p) orbitals are ovelapping in space, so that every (sp2) oxygen participate in delocalized orbital in (ClO2-, ClO3-, ClO4-). I would be satisfied just with a single picture, however I haven't found any.

Chlorines d-orbitals are unimportant for bonding. This is true in all main group element compounds, not only chlorine.
See, e.g.,
Reed, Alan E., and Paul V. R. Schleyer. "Chemical bonding in hypervalent molecules. The dominance of ionic bonding and negative hyperconjugation over d-orbital participation." Journal of the American Chemical Society 112.4 (1990): 1434-1445.
 
Ok, so the overlap is "nothing special" due to inefficient orbital's shapes. But what are their shapes? As the orbitals might be unhybridized, could I imagine "standard" atomic ((p) and one/two/three (d)) orbitals overlapping (just a little :))?
 

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