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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64
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1answer
10k views

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 ...
48
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5answers
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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?
40
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3answers
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 ...
34
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3answers
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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 ...
31
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1answer
4k 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, ...
28
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1answer
6k 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 ...
26
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2answers
34k 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 ...
26
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1answer
838 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 ...
25
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3answers
180k 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 ...
24
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1answer
2k 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 ...
23
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2answers
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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? ...
23
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3answers
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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 ...
22
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1answer
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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? ...
21
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3answers
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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 ...
20
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1answer
802 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{...
18
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2answers
955 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" ...
18
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3answers
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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 ...
18
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2answers
475 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 ...
16
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4answers
3k 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 ...
16
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2answers
687 views

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

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 ...
16
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3answers
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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?
16
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1answer
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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 ...
16
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1answer
670 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 ...
15
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4answers
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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 ...
15
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3answers
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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 ...
15
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2answers
713 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 ...
15
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1answer
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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-...
15
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1answer
2k 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 ...
15
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1answer
159 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 ...
15
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1answer
208 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 ...
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3answers
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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 ...
14
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3answers
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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 ...
14
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2answers
23k 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 ...
14
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1answer
3k 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?
14
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1answer
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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 ...
14
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1answer
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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 ...
13
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2answers
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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 ...
13
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1answer
23k 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}...
13
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2answers
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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 ...
13
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1answer
419 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-...
13
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1answer
424 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 ...
13
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1answer
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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 ...
12
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3answers
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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 ...
12
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2answers
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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. ...
12
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1answer
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Why are the two CH2 groups in allene perpendicular to each other?

Allene, $\ce{H2C=C=CH2}$, has two $\ce{=CH2}$ groups perpendicular to each other. This is the same as hydrogen peroxide's $\ce{H}$ atoms. Is there any reason why they adopt the perpendicular ...
12
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2answers
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What's the difference between a tetrahedron and a trigonal pyramid?

The shapes respectively denoted by 'tetrahedron' and 'trigonal pyramid' seem to be the same. Is there a difference between the two? If not, why are the two presented as different concepts in ...
12
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1answer
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Looking for a dye which emits around 680 nm

For a specific experiment, I'm looking for a dye which would emit around 680 nm. Preferably one I could buy easily commercially. Are there any databases which might give the emission spectra of ...
12
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7answers
19k views

Does NaOH react with K to form NaOK or KOH?

I realized that the $\ce{-OH}$ group when it reacts with some metal like $\ce{Na}$ or $\ce{K}$ will replace the $\ce{H}$ element to form $\ce{-OK}$ or $\ce{-ONa}$: \begin{align} \ce{H2O + Na &...
12
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1answer
733 views

Why is disilyne bent?

Why is disilyne $\ce{Si2H2}$ bent when the steric number of silicon is 2?
12
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1answer
654 views

How does the pyramidalization effect the bonding angles in a distorted octahedral environment?

This is a follow up on "Generally Octahedral - Meaning?". Since Dissenter asked in the comments to my answer: I'm not sure why the $\ce{F_{eq}-S-F'_{eq}}$ bond angles would be compressed, even if ...

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