Questions tagged [conformers]

For questions about conformational isomerism. Use this tag alongside [stereochemistry].

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All-Gauche Alkane: Is It Possible?

I've learned about anti and gauche conformations throughout my scholastic journey, and I have heard often that straight-chain alkanes always adopt an all-anti conformation in their lowest energy state....
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21 views

Gaussview GMMX grid seach: job completed before going through all the structures

I am recently using the GMMX add-on in gaussview to conduct conformer search. I was using the grid search method and the progrom suggested the number of structures is 729 (See picture below). I ...
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1answer
72 views

How to figure out the most stable conformation of the diastereomer?

I guess my main question is looking only at the newman projection how does one determine the stereochemistry? In the molecule to the right, I get for the first carbon, (et, H, Me,) R ( I flipped it ...
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1answer
97 views

Can a boat conformer of cyclohexane be most stable?

It is well-known that the "chair" conformation of cyclohexane is the most stable of its conformers. But is there any cyclohexane derivative where other notable conformers (boat, half-chair) are the ...
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Molecule with reversible exothermic conformational change?

I proposed some exotic biochemistry on the Worldbuilding stack. https://worldbuilding.stackexchange.com/questions/166814/digestive-system-of-the-ultimate-omnivore/166829#166829 Your creature ...
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1answer
184 views

Flexibility of long-chain aliphatic compounds

PubChem is unable to generate the conformers of Z-6-Heneicosen-11-one? The website says that the molecule is too flexible What does flexibility of a molecule mean in this context? I understand that ...
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1answer
30 views

Why are Newman Projections drawn with 120 degrees when actually sp3 carbons are 109.5 degrees?

Title says the question, pretty much. For example, in the Newman projection of ethane, the carbon hydrogen bond angles are $120$ degrees, not $109.5$ degrees, as they actually are in an $\text{sp}^3$ ...
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1answer
18 views

R and T conformations in relation to Activators and Inhibitors; Km of reaction in relation to uncompetitive and non-competitive inhibitor

Do -Activators -Competitive Inhibitors -Non-Competitive Inhibitors -Uncompetitive Inhibitors all change the conformation of the targeted enzyme from T to R (activator), and from R to T (the rest) ...
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70 views

Why does Pubchem show cis-1,3-cyclohexanediol with the hydroxyls in the equatorial position?

I am a beginning organic chemistry student and trying to reason about something based on information in my book, but seeing that Pubchem gives a different structure than I'd expect. In considering a ...
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1answer
114 views

Conformers of a meso-compound [duplicate]

In a particular question in one of my reference book, I was asked if the given compound (meso-butane-2,3-diol) was a meso compound or not. In it’s solution part, to show that the compound was ...
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How to apply the $parvo/amplo$ akamptisomeric stereodescriptors to this bicyclic system?

I'm looking for examples of akamptisomerism[1]. I'm try to find simple molecules able to (theoretically) show this kind of isomerism. I thought about the isomers of (2R)-2-methyl-9-oxabicyclo[3.3.1]...
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44 views

Finding out more stable conformer via molecular orbital interaction

Out of these two, which one is more stable? I'm unable to imagine the orientation of the lone pairs of O and ABMO of C and Cl bond. Any tips to tackle these kind of problems?
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1answer
98 views

Why does bromine increase the viscosity of olive oil? [closed]

Does bromine bond to the carbon in unsaturated fatty acids and break the double bonds between oxygen and carbon? Does this increase the viscosity of olive oil? Could someone give an elaborated ...
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155 views

Software for conformational search

I need a free software to perform a conformational search on molecules with 10 to 16 rotational bonds. What software would you recommend me? Where can I download it? Where can I find a manual of this ...
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5answers
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Define, (actually define) the “stability” and “energy” of a compound

When we say a conformer or compound is of "higher energy" than another, are we quantifying energy in terms of the bond strength? Or are we going off of how much energy it takes to break the bond? I ...
3
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1answer
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Bond rotation in buta-1,3-diene

Why don't all the atoms in s-cis-1,3-butadiene lie in one plane? All carbon atoms are $\mathrm{sp^2}$ hybridised and I feel that there would be no $\ce{C-C}$ bond rotation due to the conjugation ...
5
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1answer
159 views

Conformer generation for radicals

Is there an automatic way to generate conformers for radical like systems (spin multiplicity is doublet)? My system for the study is a substituted fullerene with a missing H atom from the functional ...
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1answer
178 views

Trouble with Converting from Structural Formulas into Newman Projections

I have the following question from my Organic Chemistry textbook: I'm asked to convert the following line diagram into a Newman Projection. The arrow pointing to the carbon signifies "looking down ...
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2answers
954 views

What is the most stable conformation (Newman Projection) of CF3CH3?

Is a totally eclipsed Newman projection the most stable conformation for a 2 carbon compound, with one carbon bonded to more electronegative atoms (making them partially negative), and the other ...
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2answers
510 views

why does ring flip of L-fructose occur?

when drawing the chair conformation for beta-L-fructose, I got the structure above (in the picture). The answer said that the conformation above had a ring flip. Why does a ring flip occur and how can ...
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536 views

Cyclohexene conformation in fused ring

The picture (a) is from a organic chemistry book by Clayden, Chapter 32. That means drawing (a) is right expression of the molecule. What I wonder is that is it possible for (a) to ring-flip? If so, ...
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Hyperconjugation in ethane conformers

I refer you to this set of presentation slides. On slide 8, the author explains the preference for the staggered conformation of ethane by saying that there is a favourable hyperconjugative ...
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2answers
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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 for rotation (to convert into the other isomer). Given that ...
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1answer
291 views

Atropisomerism of naphthyl alcohol

In March's Advanced Organic Chemistry (6th ed.), it's stated that the above two are atropisomers. I don't get why is it so. How is the topmost $\ce{C}$ locked in its place? Surely, there's steric ...
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1answer
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Dipole moment of ferrocene conformations

Which conformation of ferrocene has a zero dipole moment? I thought that the answer should be the staggered conformation because it would have the cyclopentadienyl groups oriented away from each ...
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1answer
445 views

Is there a way to determine the orientation of a benzene-ring ethyl group in synthesis reactions?

On my study guide for synthesis reactions (specifically for the synthesis of disubstituted benzene derivatives), two of the problems look extremely similar. The question on the guide asks us to ...
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1answer
327 views

What is the correct way to notate conformation preferences of polysaccharides?

In some webpages (1 or 2) are found the way to notate the conformational preferences of monosaccharides such as furanose and pyranose. But, it lacks to give a brief description on how to do it with ...
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1answer
285 views

Reason for the greater energy of the eclipsed conformer of alkanes?

My textbook states: In the staggered form of ethane, the electron clouds of C-H bonds are as far apart as possible, thus there are minimum repulsive forces, minimum energy and maximum stability. On ...
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2answers
457 views

Any program for conformational searching for sugars?

I want to estimate mean Gibbs free energy of formation of glucose and for that purpose I think conformers of ring flip should be taken into account. Do you know if some free program can find those ...
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1answer
115 views

Estimating standard Gibbs free energy of a molecule

In order to estimate the standard Gibbs free energy of a molecule at room temperature and normal pressure, we use Maxwell Boltzmann average over rotational conformers. Question Should we consider ...
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1answer
86 views

How to determine the dimensions of a bixin molecule?

I need the dimension of a bixin molecule. I do not know where to look or how to calculate this information. I understand that this molecule has several rotational axes and conformation, so there is ...
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1answer
84 views

Could chromatography induce a conformational change?

We'd been studying chromatography in our instrumental analysis course and I was wondering if chromatography could induce a conformational change. For example, you have a straight chain with a ...
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1answer
109 views

Why is the boat form of paraldehyde not theoretically possible?

Wikipedia says the following about paraldehyde: Theoretically, four stereoisomeric structures are possible. The structures (1) and (2) are known as cis- and trans-paraldehyde. The structures (...
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2answers
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If α-glucose is less stable than β-glucose, why is glucose almost always α in its compounds?

Maltose, saccharose, turanose, trehalose, trehalulose, amylopectin, amylose - they are all α. Why? Also, why is cellulose β?
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lowest energy conformation of butan-2,4-diol

Do the OH groups want to be furthest apart? or the CH3 groups? I'm trying to determine the lowest energy conformation - and I don't know which group has the bigger steric effect?
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4answers
2k views

Five-pointed crown alkane C25H40: does it exist?

My 4 year old granddaughter, playing with molecular models, began making a cyclopentane ring, each of whose carbons bore a spiro-connected cyclopentane ring of its own , in the manner of spiro[4.4]...
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2answers
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Why is the cis isomer of 1,3-dimethylcyclobutane more stable than the trans isomer?

I expect there to be more steric repulsions between the two methyl groups if they are on the same face as each other. Why is this not the case?
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323 views

Workflow for many-molecule/many-conformer calculations in Spartan, GAMESS, AND Gaussian

I wish to investigate the antioxidant properties of several hydrocarbon compounds, which are each mono- or polyhydroxylated, specifically at the phenyl ring. I wish to gain insight into my workflow ...
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1answer
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Is the SN1 reaction faster with an axial or equatorial leaving group?

Why does compound 1 undergo the $\mathrm{S_N1}$ reaction faster than 2 even though both proceed via the same carbocation intermediate?
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3answers
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Which conformations of 2,3-dimethylbutane are more stable?

I am not sure what the proper arrangement of these conformations are from least to most stable. I got the wrong answer, but my thinking was this: First, I thought that because 2 and 4 are in eclipsed ...
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0answers
243 views

Confusion about gauche effect

This recent question about the gauche effect led me to read this rather older answer. The problem is that I notice I am still confused. To take the case of 1,2 difluoroethane, I drew these orbitals: ...
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676 views

Why is gauche conformer of 2,3 dimethyl butane more stable than its anti conformer?

Why is gauche conformer of 2,3-dimethylbutane seen along 2,3 bond more stable than its anti conformer? It seems to be anomalous to me as in most other butane like compunds anti form is more stable ...
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Multiplet shape in proton NMR of morpholines

I recently carried out a Buchwald–Hartwig reaction to attach a morpholin-4-yl group to an aromatic ring: In the proton NMR of the (columned) product, I found the peaks corresponding to the morpholine ...
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4k views

Cyclopentane conformations

What is the energy minimum of cyclopentane conformational diagram: the halfchair or envelope? How does cyclopentane flip?
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1answer
238 views

What are the implications of having different conformations?

I have seen videos explaining what conformations are. I am curious about whether different conformations can give rise to slightly different properties. Particularly of interest is whether you can ...
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4k views

Hydrogen bonding in staggered vs eclipsed conformations

In my first semester of organic chemistry, we learned that staggered conformations have lower energy/higher stability. However, my thought is that if you have interacting OH groups, the hydrogen ...
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1answer
5k views

Energy profile of cyclohexene conformations

The energy profile for cyclohexane flipping looks like this: How does the corresponding diagram for cyclohexene look like?
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Conformation of six-membered ring constituting a bridged compound

What is the conformation of the cyclohexane ring constituting [2.2.1]-bicycloheptane? Is it boat or twisted boat? Is that conformation abundant in other bicyclic systems containing a cyclohexane ring?...
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2answers
4k views

Relative rates of two acyclic dienes in the Diels-Alder reaction

As for factors that affect the rate of the Diels Alder reaction, having an s-cis conformation is primary. But in a case as shown below, what makes the second diene react faster compared to the third? ...
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804 views

Enolate formation and tosylate displacement in cis/trans decalin

What will happen in the following reactions? This is Problem 3d from Chapter 6 of Zweifel and Nantz's Modern Organic Synthesis. I thought that after the hydroxyl group is converted into a good ...