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Questions tagged [molecular-structure]

This tag should be applied to questions that deal with the particular arrangement of atoms in a molecule, the so-called molecular structure or geometry.

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Why does F replace the axial bond in PCl5?

Why does $\ce{F}$ replace an axial bond in $\ce{PCl5}$? I realize that it would be more stable there than at equatorial bond, but what is the reason of its stability? Similarly in $\ce{AB4}$ type of ...
Shubham's user avatar
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49 votes
5 answers
90k views

Why does bond angle decrease in the order H2O, H2S, H2Se?

I know that bond angle decreases in the order $\ce{H2O}$, $\ce{H2S}$ and $\ce{H2Se}$. I wish to know the reason for this. I think this is because of the lone pair repulsion but how?
Yomal Amarathunge's user avatar
45 votes
3 answers
5k views

Do molecules with bridges through rings exist?

Do molecules with bridges through rings (in a manner illustrated by this) exist? I sometimes get results like this when doing Energy Minimization on molview.org. For example: Is this actually a ...
schuelermine's user avatar
34 votes
3 answers
6k views

Has anyone even taken a picture of a molecule to confirm the geometry predicted by theory?

Have the geometries of molecules been proven, or are we operating strictly on mathematical theory? To put it over-simplistically: has anyone ever taken a picture of a molecule to compare against their ...
Jonathon Anderson's user avatar
33 votes
1 answer
6k views

What is the molecular structure of xenon hexafluoride?

Xenon hexafluoride, $\ce{XeF6}$, can be obtained by reaction of xenon with excess fluorine gas. What is the gas-phase structure of the molecule? What experimental evidence is there to support it, ...
orthocresol's user avatar
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29 votes
1 answer
9k views

Why is cyclooctateraene shaped like a "tub" rather than a "chair"?

I understand that for cyclooctatetraene (COT) to "escape" the horrible prospect of becoming an anti-aromatic molecule, it must adopt a non-planar conformation. The widely touted conformation of COT ...
paracetamol's user avatar
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26 votes
2 answers
38k views

Why is water a dipole?

Water ($\ce{H2O}$) is a dipole. The reason why is simply because it is not symmetrical, there are more electrons on the oxygen side than on the hydrogen side, and the electronegativity of oxygen. But ...
Friend of Kim's user avatar
26 votes
1 answer
4k views

Why do the atoms in molecular models have the colors they have?

Molecular models are a great tool for visualizing a molecule in three-dimensional space. These models even appear on the web (practically every chemical's Wikipedia page), and there is a very specific ...
ringo's user avatar
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26 votes
1 answer
1k views

Do vinyl cations adopt a classical or non-classical structure?

Whilst reading this question today, I remembered something that I had seen previously here. In the second linked question, @Martin provided a reference to suggest that vinyl cations actually adopt a ...
bon's user avatar
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25 votes
3 answers
195k views

How does one tell if a specific molecule is acidic or basic?

Let's take the $\ce{KOH}$ molecule into account. I know it is a base from literature, but how would one go about determining if a molecule is acidic or basic simply based on the structure of the ...
2567655222's user avatar
23 votes
3 answers
11k views

Why is the inversion barrier larger in PH3 than it is in NH3?

The inversion barrier in $\ce{NH3}$ is approximately $5~\mathrm{kcal~mol^{-1}}$ and that of $\ce{PH3}$ is $35~\mathrm{kcal~mol^{-1}}$. This has well-known stereochemical consequences in that amines ...
wuschi's user avatar
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23 votes
1 answer
23k views

Structure of Br3O8

What is the structure of $\ce{Br3O8}$? It has an odd number of electrons; does that make it a free radical? The structure given in my book shows Where did the 7th electron of the central atom go? ...
ghosts_in_the_code's user avatar
23 votes
1 answer
10k views

PBP vs TBP geometry?

Why are the axial bond lengths greater than those of the equatorial bonds in a trigonal bi-pyramid (TBP) geometry molecule; but the opposite is true for pentagonal bi-pyramid (PBP) geometry molecules? ...
tkhanna42's user avatar
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23 votes
3 answers
6k views

What is the geometry of an alkyl radical?

I encountered this question which asks how many possible radicals are formed when $\ce{CH3CH2C(CH3)3}$ is monosubstituted by $\ce{Br2}$. The answer given is 3 while I think it should be 4, reasoning ...
ℵ_ϵ's user avatar
  • 826
22 votes
1 answer
869 views

Why does the image of cyclo[18]carbon look like a nonagon?

The $\ce{C18}$ allotrope cyclocarbon has been synthesized and imaged.[1] Science has most details behind a paywall, but this discussion includes an image: In this octakaidecagonal molecule, each $\ce{...
J.G.'s user avatar
  • 513
20 votes
2 answers
1k views

Why do we not generally have "enneane"?

Most numerical prefixes are based on Greek roots, but for "nine" we use the Latin root instead which seems inconsistent. Thus, for instance, "nonane" instead of "enneane", or in mathematics "nonagon" ...
Oscar Lanzi's user avatar
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19 votes
2 answers
843 views

What are the important implications to the field of chemistry, if any, of the hexavalent carbon species confirmed in 2017?

I’m struggling to understanding the true nature and implications of recent confirmations of the existence of stable species containing carbon atoms bound six (in another case 5) other carbon atoms. Is ...
airhuff's user avatar
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19 votes
3 answers
45k views

Bond order for carbonate ion for resonance

I saw in a textbook that for carbonate ion, there are 3 resonance forms and the bond order is 1 and 1/3. So in general, how should we calculate the bond order for resonance structures? Is there any ...
user avatar
18 votes
3 answers
47k views

Why is tetraamminecopper(II) a square planar and not a tetrahedral species?

In $\ce{[Cu(NH3)4]^2+}$, the $\ce{Cu^2+}$ ion has 9 electrons in the $\mathrm{3d}$ orbital with only one unpaired electron. How is it a square planar geometry? Where is that unpaired electron going?
Dhruba Banerjee's user avatar
18 votes
2 answers
732 views

(Computationally) finding similarity between two organic compounds

I have been struggling to find an acceptable answer for this question for my purposes. There are many ways to find similarity between two organic compounds - some of which are particularly popular ...
kosyumote's user avatar
  • 381
17 votes
4 answers
4k views

Aside from carbon, what other substances can be made "superhard"?

So diamonds are an allotrope of carbon, that is formed when carbon is put under immense pressure, right? What other elements or compounds can you make into "diamonds", as in more durable, harder ...
ArborianSerpent's user avatar
17 votes
3 answers
3k views

Portable library to render 2D structural formulas as vector graphics from SMILES or InChI

For a web-based project, I am looking for a piece of software to create a 2D vector graphics structural formula from a textual structure encoding scheme such as SMILES or InChI, running on the server ...
Niels Heidenreich's user avatar
16 votes
4 answers
4k views

How can you build a model of tetrahedral coordination from objects found at home?

Our college is switching to teaching online mid-semester in hopes of slowing the spread of Covid-19. All the molecular model kits are still on campus. How could you build a model of tetrahedral ...
Karsten's user avatar
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16 votes
1 answer
18k views

Basicity Alteration Due To Ortho Effect In Methoxy Aniline System

I wanted to ask something more in reference to this question. Suppose instead of toluidine, 2-methoxyaniline and 3-methoxyaniline are present. Now, why is 2-methoxyaniline more basic than 3-...
user avatar
16 votes
1 answer
6k views

What is quasi-aromaticity?

During my study of aromaticity, I came through this topic of quasi-aromaticity. Can you please elaborate what Quasi aromatic compounds are and how are they designated?
chail10's user avatar
  • 688
16 votes
1 answer
11k views

What is a stereochemically active or inactive s orbital?

In Concise Inorganic Chemistry by JD Lee (4th edition; adapted by Sudarshan Guha), page 73 under the section 3.6 (VSEPR Theory chapter Chemical Bonding): ...according to this theory, the position of ...
jyoti proy's user avatar
  • 1,014
16 votes
1 answer
3k views

Why isn't cyclobutane planar?

In short, cyclobutane adopts a certain, non-planar, configuration in order to reduce ring strain caused by the fact that carbons are $\mathrm{sp^3}$ hybridised. That much is understandable. In an ...
Αντώνιος Κελεσίδης's user avatar
16 votes
1 answer
215 views

How sure can we be about the structure of purine?

While answering the question Basicities of nitrogen atoms in purine, I noticed, that there might be a rapid interchange of the hydrogen bonded to the nitrogen atoms. I have found a crystal structure ...
Martin - マーチン's user avatar
16 votes
1 answer
2k views

Are there molecules that take the shape of every platonic solid?

Methane is the simplest molecule I know of that takes the shape of a platonic solid — in this case, the tetrahedron. Wikipedia has a page on platonic hydrocarbons that includes molecules with ...
Sean Lake's user avatar
  • 301
16 votes
1 answer
872 views

Band gap of fullerenes

From what I have read about fullerenes, the lower fullerenes like $\ce{C60}$ or $\ce{C70}$ have higher bandgaps around 3.5 eV or such, while the higher fullerenes have much smaller bandgaps of the ...
ubuntu_noob's user avatar
15 votes
2 answers
1k views

Help understanding how "steric effects" are distinct from "electronic effects"?

@jakebeal's excellent answer to Why do animal cells “mistake” rubidium ions for potassium ions? includes the following passage: In the case of potassium versus sodium, which are both very important ...
uhoh's user avatar
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15 votes
2 answers
26k views

Bond angles for the hydrides

I noticed the fact that all the hydrides of the elements belonging to group IV has bond angle 109.5° while in group V it varies from 107.3° for $\ce{NH3}$ to 91.3° for $\ce{SbH3}$. Similarly we see in ...
Aneek's user avatar
  • 830
15 votes
1 answer
239 views

Are there any non-Jahn-Teller type distortions?

My question is essentially, if ANY gradual type of deviation from a higher possible symmetric arrangement of the nuclei in a molecule is covered by the Jahn-Teller model. More specifically I have in ...
Raphael J.F. Berger's user avatar
14 votes
3 answers
2k views

How do I make 3d molecular graphics similar to those shown on Wikipedia?

I want to make 3d molecular graphics similar to those found on Wikipedia. In the page for benzene, you can see the structure looks like this: However, if I go to the interactive image as shown in ...
Pritt says Reinstate Monica's user avatar
14 votes
3 answers
14k views

Can Fe(CO)5 adopt both square pyramidal and trigonal bipyramidal geometries?

I know the hybridization of $\ce{Fe(CO)5}$ is $\mathrm{dsp^3}$. According to my book, coordination compounds with coordination number 5 can interchange between square pyramidal and trigonal ...
user avatar
14 votes
1 answer
26k views

How to rationalise the planar structre of I2Cl6?

$\ce{I2Cl6}$ is a dimer of $\ce{ICl3}$. $\ce{ICl3}$ is T-shaped, with $\ce{I}$ being $\mathrm{sp^3d}$ and having two lone pairs. I read in Inorganic Reaction Mechanisms by R. K. Sharma that $\ce{I2Cl6}...
Shodai's user avatar
  • 973
14 votes
1 answer
2k views

Bonding in Square Antiprismatic Compounds

Both $\ce{IF_8^-}$ and $\ce{XeF_8^{2-}}$ have (distorted) square antiprismatic geometries. I've been wondering how to explain the bonding in such compounds. Hypercoordinate bonding (as used to ...
ron's user avatar
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13 votes
2 answers
2k views

What is this fluorinated organic substance?

The corresponding author of the paper where this formula was published as appendix passed away. Can someone help me with identifying what is the name of this compound and why have strange zig-zag ...
SSimon's user avatar
  • 267
13 votes
2 answers
61k views

Why are lp-lp repulsions greater than bp-lp and bp-bp?

My teacher told me that lone pair and lone pair are closer together hence the repulsion is greater and they take up more space, but I do not understand? Can anyone explain it to me?
XQ. Matsci's user avatar
13 votes
3 answers
12k views

Why is the $\mathrm d_{z^2}$ orbital so different from the rest?

$\mathrm d_{z^2}$ orbital appears to be special: Although degenerate with other d orbitals, it has no nodal planes, instead it has two nodal "cones". Instead of having four lobes, it has ...
user226375's user avatar
13 votes
2 answers
16k views

Are carbocations necessarily sp2 hybridized and trigonal planar?

My copy of Pearson's Organic Chemistry (7e), Morrison and Boyd, under the section "Reaction intermediates", accords a succinct description on the structure of carbocations: The central $C$-atom (of ...
paracetamol's user avatar
  • 18.7k
13 votes
1 answer
518 views

What is the structure of trifluoromethanesulfonic acid in the gas phase?

During an interesting discussion in our group’s seminar, the question arose what actually causes trifluoroacetic acid to be a much better nucleophile than trifluoromethanesulfonic acid. Part of the ...
Jan's user avatar
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13 votes
1 answer
5k views

Double bond crossed lines representation

I have been studying organic chemistry for years, and I do not remember the spotting double bond represented with crossed lines, except maybe one ore two more times in addition to the following one ...
mykhal's user avatar
  • 6,212
13 votes
1 answer
521 views

2017 Nobel Prize; What does Cryo-electron microscopy data actually look like?

It was just announced that the 2017 Nobel Prize for Chemistry has been awarded to Jacques Dubochet, Joachim Frank and Richard Henderson "for developing cryo-electron microscopy for the high-...
uhoh's user avatar
  • 5,788
13 votes
1 answer
573 views

Steric hindrance of an unbonded electron pair

This question is half inspired by this question, and half inspired by the structure of molecules like hydrazine and hydrogen peroxide. When I was looking at the aforementioned molecules, I started ...
ringo's user avatar
  • 24.1k
13 votes
1 answer
13k views

How do electronegativity and lone pairs affect bond angles?

How do bond angles vary in molecules with a lone pair and central atom of different electronegativity, but in the same period so that electronegativity matters more than orbital size? Let's assume ...
Kat's user avatar
  • 131
12 votes
3 answers
1k views

Can a molecule contain a linear series of conjugated pi bonds twisted through 180 degrees?

Imagine a long chain of carbon atoms connected by single and double bonds in conjugated fashion. All of the p orbital pi bonds would normally be aligned to either side of the carbon atoms forcing the ...
Slarty's user avatar
  • 423
12 votes
3 answers
3k views

Complex organic molecules

I am studying astronomy and came across the following term in the astrochemistry course called 'complex organic molecules' or also written as COMs. My question is: What is exactly meant with these ...
Mathphys meister's user avatar
12 votes
2 answers
4k views

How are there two C3 rotation axes in ammonia?

If we look at the character table for the $C_\mathrm{3v}$ point group (which $\ce{NH3}$ is an example of), we see that these are the symmetry elements ${E, 2 C_3, 3 \sigma_v}$ present in the molecule. ...
PV.'s user avatar
  • 682
12 votes
3 answers
6k views

Which biphenyl is optically active?

Which biphenyl is optically active? I know that it can never be 1. I don't think it will be 4 either as I read that it should be ortho-substituted biphenyl. So, when I look at 2 and 3, I can't make ...
studious's user avatar
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