35

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]-rotane. A Reaxys search unfortunately doesn't show anything for [5,5]-rotane, but in general, many such compounds have been made. A lot of the articles are in ...


18

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 mode with large atoms (not actually using the van-der-Waals radii, because that looked very strange; click here for a ball and stick version): We can observe ...


17

I'm not a transition-state physical chemist, but I think a good approach to this problem is transition-state theory, specifically the Eyring equation: $$k = \kappa \frac{k_b T}{h} e^{\frac{-\Delta G^{\ddagger}}{RT}}$$ This equation tries to predict the rate constant $k$ from an assumed pseudo-equilibrium between the transition-state and the starting ...


15

Conformation B is probably correct because of the hydrogen bonding, if we assume this substance is either pure or in a polar solvent. The Me-Me gauche interaction is on the order of +3.8 kJ/mol (see most textbooks, or it is one half of methyl's A value, which involves two gauche interactions), while the hydrogen bond can be on the order of −5 to −25 kJ/mol. ...


15

TL;DR Torsional strain can be thought as the repulsion due to electrostatice forces between electrons in adjacent MOs. Meanwhile steric strain (also known as van der Waals strain) can be thought as the repulsion when two bulky groups which are not directly bonded to each other become too close to each other and hence there isn't enough space for them. Here ...


15

The gauche effect is commonly explained with LCAO-based bond orbitals. LCAO is short for linear combination of atomic orbitals and implies that we can take two atomic orbitals $\phi_1, \phi_2$ and create two molecular orbitals $\psi_1, \psi_2$ from them by linear combination: $\psi_1 = a_1 \phi_1 + b_1 \phi_2$ and $\psi_2 = a_2 \phi_1 + b_2 \phi_2$. ...


14

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). Unlike linear AA′XX′ systems where the bonds can rotate, in the morpholine it very much has a fixed conformation. In this fixed conformation, the protons are ...


12

In alkanes staggered conformers (all anti) are local minima, while eclipsed conformers represent transition states. The first is "stable", while the latter is not. The rotational barrier has been measured and calculated often, it is around 12 kJ/mol.[1] In alkenes the eclipsed conformers are local minima, while the staggered, or more accurately ...


12

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 molecule has been synthesised. In particular, I wonder if the five outer rings would be exactly perpendicular to the center one (eclipsed), or somewhat ...


11

Short answer, no. There is not a "twist-chair." To convince yourself, it probably helps to make a physical model with a chemistry model kit. If you try to twist the chair, you can't do it without significantly moving at least one atom, in which case, the conformation is basically a "skew" or "twist boat." Try it. The boat and chair conformations are indeed ...


11

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 of the carbon atoms makes a $25^\circ$ angle with the plane formed by the other three carbons, and this mitigates some of the eclipsing interactions, at the ...


11

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 fan has two black fins one red fin. Now let us consider two conformations Red fin at 3'o clock And Red fin at 9'o clock If you were to take ...


10

First off this is SMARTS not SMILES. Think of SMARTS as like a regular expression language for molecules (e.g., SMILES). So let's break down some of those characters: ~ is "any bond" ! is "not" $ indicates a recursive SMARTS expression. @ indicates "any ring bond" The $(*#*) means "two atoms with a triple bond between them". The !D1 means and not an atom ...


10

Cyclobutane and its substituted derivatives readily undergo a ring flip (or ring inversion) as pictured below. The barrier to ring flipping is very low, around 1.5 kcal/mole, so at room temperature the flipping process is very rapid. The lowest energy conformation of cyclobutane exists in a puckered geometry as depicted in $\ce{A}$ and $\ce{B}$. In the ...


10

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 the text, it was an old book, however it clearly said that stability of a compound does not mean anything. We should always ask, stability with respect to what? ...


10

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 indicated in the accompanying manuscript: Bolton et. al. "PubChem3D: a new resource for scientists" J Cheminf. (2011) v. 3, art. 32) Not too large (with ≤...


9

The argument made by Ben can be supported by computational chemistry. I calculated three conformers of the compound. Conformation B1 includes an intramolecular hydrogen bond, while in conformation B2 the proton was rotated away from the second hydroxyl group. Conformation C is the staggered one. The displayed structures were optimised in the gas phase. ...


9

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 because the arrangement of different groups around the pi bond is different. Consider the following molecule: It also has a pi bond, we might be tempted to say ...


8

Page 11699 of this paper has one approach to what you want: basically, you compute the relative Gibbs free energies of the possible stable conformers, assume they can interconvert, and use a Boltzmann distribution to work out what the percentages are. First, we selected a reference structure $R$ for a given species (neutral or protonated). Next, for ...


8

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 reasoning for 4 over 2 sounds good, that would also be my point. For the two minima 1 and 3 (with Boltzmann weights of 46%:54% at the highest calc. niveau (red), ...


8

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 groups or a tether, but neither is the case here. I expect the benzyl*-methyl bond and the phenyl*-ethyl bond to rotate freely at reasonable temperatures (say, ...


8

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 to zero. However, there are a couple unstable places that also have a derivative of zero, namely saddle points and maximums (top of a circle). We are after the ...


7

It's a little hard to tell from this angle, but that looks like a pretty sensible representation of the axial methyl geometry given on the website you linked to. I'm not entirely sure what you mean by "push to the center of the molecule", though. ETA: These might help a little more: this isn't exactly the most accurate geometry, but it's a pretty good ...


7

When we sight down a carbon-carbon single bond and draw a Newman projection of a particular conformation, any two groups on the adjacent (vicinal) carbons that have a dihedral angle of 60° between them are said to have a gauche relationship. In the following figure, the $\ce{X}$ and $\ce{Y}$ have a gauche relationship. $\ce{X}$ and $\ce{Y}$ can be the same ...


7

The IUPAC recommends s-cis and s-trans for the rotamers of conjugated dienes. The nomenclature derives from having a "cis-like" or "trans-like" geometry about a sigma bond. I feel like something similar should be appropriate, however that same IUPAC link recommends E/Z or sp/ap (syn-periplanar/anti-periplanar) for the N-alkyl amides (5,6). Amide 5 ...


7

According to structure determined by electron diffraction, norbornane is present in bridged boat conformation. http://pubs.acs.org/doi/abs/10.1021/ja01014a032, see Figure. Norbornane and its derivatives are often used for studying effect of equatorial and axial substitution of cyclohexane and is considered rigid. Therefore, I don't expect significant ...


7

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 hydrogen bonding would make the eclipsed conformations more stable. Is this be the case? Why or why not? For example, a small molecule containing two carbons, each ...


7

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 is approx. $\pu{1.0 nm^2/molecule}$ at zero pressure. If the methyl groups were parallel to the water surface, a molecular area of approx. $\pu{1.7 nm^2/...


7

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 stable another conformation like the twist-boat. Conformations of cyclohexane There are quite a few imaginable conformations,[1] but for cyclohexane itself ...


7

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 molecule of all-anti tetradecane, $\ce{(C14H20)}$ using the energy afforded by the hydrogen bonding to squeeze/twist the alkane into a helical all-gauche conformation. ...


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