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35 votes

Five-pointed crown alkane C25H40: does it exist?

These polyspiro compounds such as the one you gave are known as [m,n]rotanes, where m is the size of the central ring and n is the size of the decorating rings. So, your compound would be called [5,5]-...
orthocresol's user avatar
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21 votes

Atropisomerism of naphthyl alcohol

The hindered rotation is due to the hydrogens at the naphthyl moiety. The following shows the rotation calculated at the DF-B97D3/def2-SVP level of theory. To better visualise this, I have chosen a ...
Martin - マーチン's user avatar
17 votes

Why are conformational isomers considered as isomers?

Gaurang's answer deals well with the theory part I just wanted to give a visual aid. (Taken from Atropisomerism of naphthyl alcohol) Let's call the rotating substituent on the naphtahlene a fan. The ...
Avyansh Katiyar's user avatar
15 votes
Accepted

Multiplet shape in proton NMR of morpholines

It looks as if the NMR of morpholine is an AA′XX′ spectrum (the chemical shift difference is 0.80 ppm, or 320 Hz on your spectrometer, two orders of magnitude larger than the coupling constant). ...
NotEvans.'s user avatar
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15 votes

Why are conformational isomers considered as isomers?

I was taught that geometric (cis-trans) isomers are considered isomers because there is a high energy barrier to breaking the double bond... There's a problem here. Geometrical isomers are isomers ...
Gaurang Tandon's user avatar
14 votes
Accepted

Why is diequatorial trans-1,2-dimethylcyclohexane more stable than diaxial trans-1,2-dimethylcyclohexane?

The key concept is 1,3-diaxial interaction. See the figure 1 below using methylcyclohexane as an example. Figure 1: Equatorial and axial conformations of methylcyclohexane with 1,3-diaxial strain ...
Jan's user avatar
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12 votes

Five-pointed crown alkane C25H40: does it exist?

Fascinating molecule. I am not offering anything substantially, new or original here; merely here to confirm what has already been said. I couldn't find any evidence that suggests this particular ...
getafix's user avatar
  • 8,495
11 votes

Why is the cis isomer of 1,3-dimethylcyclobutane more stable than the trans isomer?

The four carbon atoms in cyclobutane are not coplanar, as that would lead to a large degree of unfavourable eclipsing interactions. So, it is not a flat square; it adopts a puckered conformation. One ...
getafix's user avatar
  • 8,495
11 votes
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Flexibility of long-chain aliphatic compounds

PubChem 3D has limits on the number of 'rotatable bonds' I recently answered a related question about PubChem 3D: Beyond the limits of MMFF94 and MMFF94s themselves, PubChem3D had several limits ...
Geoff Hutchison's user avatar
10 votes

Define, (actually define) the "stability" and "energy" of a compound

As a chemist, I would agree that textbooks are not clear about the term stability and energy. It is not your fault and undergraduate organic chemistry books make the situation worse. I cannot recall ...
AChem's user avatar
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10 votes
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Stable conformer of protonated ethane-1,2-diamine

I'm not 100% convinced that both amines will protonate at the same time, since protonation of a charged molecule is different than the neutral. At the moment, I don't have the time to calculate the $\...
Geoff Hutchison's user avatar
9 votes
Accepted

Hydrogen bonding in staggered vs eclipsed conformations

Disclaimer: I am not a computational chemist, I am completely new to this stuff. Just a humble student of @pentavalentcarbon However, my thought is that if you have interacting OH groups, the ...
getafix's user avatar
  • 8,495
9 votes
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Why is a conformer of hydrogen peroxide rotationally inactive?

"Rotationally inactive" is probably about the rotational spectrum of the molecule I'm assuming the (unsaid) context of the question is that it is about rotational spectroscopy as this is ...
matt_black's user avatar
8 votes

Which conformations of 2,3-dimethylbutane are more stable?

The correct arrangement (from least stable to most stable) is probably: $4 > 2 > 3 \gtrapprox 1$ based on my calculations for the four gas phase rotamers you can see in the figure below. Your ...
pH13 - Yet another Philipp's user avatar
8 votes
Accepted

What are the implications of having different conformations?

That's an interesting question. To start off, what Mith said in the comments is absolutely right. Let's say that two conformations of a molecule have different smells (which is in fact not an absurd ...
orthocresol's user avatar
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8 votes
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Is there a way to determine the orientation of a benzene-ring ethyl group in synthesis reactions?

Unless the temperature is really low, you will not be able to distinguish the two conformation isomers (conformers). Rotation about single C-C bonds is rarely hindered. It can be, by using bulky ...
TAR86's user avatar
  • 6,881
8 votes

Define, (actually define) the "stability" and "energy" of a compound

Finding minimums: a general view When minimizing energy you are searching (using numerical methods) for the minimum of Potential Energy). You are at the minimum when the derivative(Jacobian) is equal ...
B. Kelly's user avatar
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8 votes
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All-Gauche Alkane: Is It Possible?

At Last! Success! I found this research paper, which describes a "Self-assembling nanocapsule", which is held together by plenty of hydrogen bonding, and can assemble around a linear ...
mpprogram6771's user avatar
7 votes
Accepted

Dipole moment of ferrocene conformations

To find out whether a compound can have a nonzero dipole moment, consider its symmetry. A dipole moment is a vector which must be transformed onto itself by every symmetry operation present in the ...
Jan's user avatar
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7 votes
Accepted

How to determine the dimensions of a bixin molecule?

There is a paper on bolaamphiphiles (1) where it is stated that measured surface area corresponding to the area of a bixin molecule lying on the water surface with most methyl groups pointing outside ...
andselisk's user avatar
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7 votes
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Cyclopentane conformations

As you mention, there are two main conformations that cyclopentane may adopt. In the absence of substituents around the ring, there is actually only a $\pu{0.5 kcal/mol}$ energy difference between ...
NotEvans.'s user avatar
  • 17.2k
7 votes

Effect of periodic acid on cyclohexane derivatives

The literature reveals that cis-1,2-cyclohexanediol 1 cleaves about 20-times faster than trans-1,2-cyclohexanediol 2 although the equilibrium between the diol and the cyclic periodate intermediate ...
user55119's user avatar
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7 votes
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Bond rotation in buta-1,3-diene

1,3-Butadiene (Preferred IUPAC name: Buta-1,3-diene) is the organic compound, which is industrially important as a monomer in the production of synthetic rubber. It is also the simplest conjugated ...
Mathew Mahindaratne's user avatar
7 votes
Accepted

Can a boat conformer of cyclohexane be most stable?

TL;DR: It is highly unlikely that there is a non-multicyclic derivative with a stable boat conformation. It needs a lot of convincing and quite bulky groups to destabilise the chair conformation and ...
Martin - マーチン's user avatar
6 votes

Hydrogen bonding in staggered vs eclipsed conformations

Since I posted this question several months ago, I've come across some evidence in the form of published papers that explore cases where eclipsed conformations are favored over their staggered ...
Melanie Shebel's user avatar
6 votes
Accepted

Enolate formation and tosylate displacement in cis/trans decalin

I went looking for this question again today after talking to someone about a similar reaction, then realised I never got round to trying to actually answer it. Leading reference: Tetrahedron 1969, ...
NotEvans.'s user avatar
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6 votes

Five-pointed crown alkane C25H40: does it exist?

Scifinder, the online tool of the Chemical Abstracts Service of the American Chemical Society shows no results. Thus, unfortunately, to the best of any chemist’s knowledge this beautiful molecule has ...
Jan's user avatar
  • 68.3k
6 votes

Five-pointed crown alkane C25H40: does it exist?

The topologically closest analogue with a well-established crystal structure I found is 3a-Hydroxy-trispiro(octahydropentalene-1,1':2,1'':3,1'''-tris(cyclopentane))-2'''-one ($\ce{C20H30O2}$). Its ...
andselisk's user avatar
  • 38.3k
6 votes
Accepted

Any program for conformational searching for sugars?

Use RDKit It sounds like you're only considering free or open source conformer generation tools. In that case, I highly recommend using RDKit, since the distance-geometry (and in turn ETKDG) methods ...
Geoff Hutchison's user avatar
6 votes

Define, (actually define) the "stability" and "energy" of a compound

The answer is complicated because there are different kinds of stability and when we talk about energy, we also can mean different kinds of energy. When we speak of energy, we generally refer to a ...
Zhe's user avatar
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