50
votes
Accepted
Do molecules with bridges through rings exist?
I'm not sure about the existence of molecules with bridges through rings. However, there are several publications of synthesis of molecules mimicking wheels and axles ([2]rotaxanes; The “[2]” refers ...
- 39.5k
49
votes
Accepted
Why is an S-S bond stronger than an O-O bond?
TL;DR: The $\ce{O-O}$ and $\ce{S-S}$ bonds, such as those in $\ce{O2^2-}$ and $\ce{S2^2-}$, are derived from $\sigma$-type overlap. However, because the $\pi$ and $\pi^*$ MOs are also filled, the $\pi$...
- 71.1k
36
votes
Accepted
Is it possible to achieve a level of "truly zero" concentration?
It depends how you dilute it. If you take an aqueous solution of A and just add pure water (absolutely 100% water), the concentration of A will never quite be null. In this case however, you will ...
- 1,618
30
votes
Do molecules with bridges through rings exist?
A variation on this theme is Ice VII, in which two cubic ice structures are intertwined with hydrogen bonds from each component structure passing through the hydrogen-bonded rings formed by the other ...
- 53.1k
27
votes
Accepted
Why do the atoms in molecular models have the colors they have?
There's an interesting article here - Illustrating Atoms and Molecules - that discusses atom colors:
In 1865, the chemist August Hoffman gave a Friday Evening Discourse at London’s Royal ...
- 1,725
21
votes
What is this fluorinated organic substance?
The name of the compound is 1-chloromethyl-4-fluoro-1,4-diazoniabicyclo[2.2.2]octane bis(tetrafluoroborate) (CAS #: 140681-55-6), which is commonly known as Selectfluor, a trademark of Air Products ...
- 39.5k
20
votes
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Why do we not generally have "enneane"?
Perhaps not a complete answer, but this might put you on the right track. It looks as though a lot of the system we have today grew out of recommendations made by August Wilhelm von Hofmann in a paper ...
- 11.6k
19
votes
Accepted
Is there a way to use free software to convert SMILES strings to structures?
According to the website, Open Babel should do the trick: Documentation - SMILES, Sourceforge.
For example, the following code will give you a neat SVG file of the molecule benzene:
...
- 43.8k
19
votes
Accepted
Why do methane molecules have 15 degrees of freedom?
15 is there because you have 5 atoms which can move independently, and we live in a 3D space, and $3\ \times\ 5\ =\ 15$.
3 of these are translational degrees of freedom, which you seem to agree with, ...
- 31k
18
votes
Symmetrize nearly symmetric molecule
I've done some work in both symmetry detection and in distance matrix methods. I think it's a great idea in concept, but the devil will be in the details for large, more complex molecules.
The first ...
- 27.7k
18
votes
Do symmetric hydrogen bonds in neutral molecules exist?
It appears that perhaps water may have symmetric hydrogen bonds between oxygen atoms, but it would take at least 60 GPa of pressure, or more, to make water to bond like that. I guess water stops being ...
- 4,578
18
votes
Accepted
Complex organic molecules
tl;dr: two different definitions. Astronomy: multiple carbon atoms in molecule. Chemistry: polymer
Interestingly enough, after reading about COMs here, as well as reading the Wikipedia page and the ...
18
votes
What is kekulization (in RDKit)?
This is a method to generate alternate Lewis structures of the same molecule. Here are two examples from the cumulative dissertation by Sascha Urbaczek[1]:
If you were to search for the left molecule ...
- 39k
17
votes
Do symmetric hydrogen bonds in neutral molecules exist?
This question crossed my mind during a lab today because we were making $\ce{Ni(dmg)2}$, which is shown below.
Well first, this is charged in some sense, but it is net-neutral. Also, the ...
- 12.9k
15
votes
Accepted
What is quasi-aromaticity?
In general, we can describe a quasi aromatic compound as a compound, which is ionic in nature with a counter ion, and the $\pi$ electrons in such compounds follow Huckel's rule ($4n+2$).
In other ...
- 39.5k
15
votes
Is it possible to achieve a level of "truly zero" concentration?
For an analytical chemist, the concept of zero concentration does not exist. The concentration cannot be exactly 0! Only a limit of detection can be developed in terms of statistics. This is why a ...
- 38.9k
14
votes
What is the difference between "molecular mass", "average atomic mass" and "molar mass"?
Atomic mass refers to the average mass of an atom. This has dimensions of mass, so you can express this in terms of daltons, grams, kilograms, pounds (if you really wanted to), or any other unit of ...
- 71.1k
14
votes
Accepted
What is this fluorinated organic substance?
That is generally known as Selectfluor, a source of electrophilic fluorine. The zig-zag line is a 2-D representation of the third ethylene $\ce{-CH2-CH_{2} -}$ unit that links the two nitrogens. more ...
- 21.6k
14
votes
Accepted
Why is borole not considered aromatic
A very basic way to do this would be to draw a diagram that shows the p-orbitals going above and below the plane.
For Borole, the bonding orbitals would look like as shown below (taken from the ...
- 6,905
14
votes
Can sugars dissolve in liquid ammonia?
Can sugars dissolve in liquid ammonia?
Yes, according to Ref.1, liquid ammonia is used to extract sugars in sugar-beet chips:
5.88 kilograms of sugar-beet chips having a moisture content of 5.4 ...
- 39.5k
13
votes
Why do we not generally have "enneane"?
I believe Tyberius gave an extremely reasonable answer for the question and it deserves to be the best answer. I just want to provide some supporting facts for his argument. For example, there are a ...
- 39.5k
13
votes
Accepted
How do I visualise bicyclo[4.4.1]undeca-1,3,5,7,9-pentaene?
This compound is 1,6-methano[10]annulene, and a classic example of an unusual compound displaying aromaticity.
Aromaticity requires the pi-system to lie in a plane. One might speculate that [10]...
- 10.6k
13
votes
Are physical space filling molecular modelling kits still available anywhere?
Note, CPK (for Corey–Pauling–Koltun) is a colour scheme, i.e., a convention to symbolize atoms of carbon in black, oxygen in red, nitrogen in blue, etc. which took ...
- 28.4k
12
votes
How does a molecule search work by drawing in visual editor?
Usually, structure search is implemented using a graph model. For example, let's take cyclohexane. On screen this is a hexagon - but this is converted on the server to a simple atom/bond graph model ...
- 1,725
12
votes
Accepted
How are organic compounds with radioactive atoms synthesized?
The current methods employed for synthesis fall into the following three categories1:
Chemical synthesis
Biochemical methods
Isotope exchange reactions
Chemical Synthesis:
Most chemical syntheses ...
- 6,218
11
votes
Does NaOH react with K to form NaOK or KOH?
The question: Will $\ce{NaOH + K}$ form $\ce{NaOK}$ or $\ce{KOH}$?
This is a redox reaction regardless of what species $\ce{K}$ would react with. The answer is two-fold: (a) Having potassium added to ...
- 39.5k
11
votes
Is there a way to use free software to convert SMILES strings to structures?
In addition to the other good answers, I'd recommend rdkit, an open-source, freely available software for chemoinformatics. Most people use ...
- 21.8k
11
votes
Accepted
Which biphenyl is optically active?
Biphenyl 2 is the only optically active compound here. These stereoisomers are due to the hindered rotation about the 1,1'-single bond of the compound (Ref.1). Biphenyl 3 is not optically active, ...
- 39.5k
11
votes
Are physical space filling molecular modelling kits still available anywhere?
Is there any current source of those 3D CPK kits?
You have to distinguish space-filling and semi-space filling, see below:
For semi-space filling, many ball-and-stick models also have pegs instead ...
- 39k
10
votes
Accepted
What is difference between intramolecular redox and disproportionation redox
Disproportionation is a redox reaction where one element works both ways, with part of it being oxidized and another part reduced. It does not have to be intramolecular in the strict sense, since the ...
- 31k
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