Questions tagged [conformers]

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

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Stable conformer of protonated ethane-1,2-diamine

I had been studying on the stable conformers of ethylene glycol and ethane-1,2-diamine. Due to hydrogen bonding in the vicinal $\ce{-OH}$ groups, ethylene glycol prefers to show gauche conformer. The ...
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5 votes
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Why 5-member rings prefer being cis-fused?

It always bothers me how whenever I am doing practice problems I never got a proper explanation as to why 5-member rings prefer(thermodynamically) being cis- rather than trans-fused( as opposed to ...
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3 votes
2 answers
198 views

What are skew positions in the conformation of cyclohexane?

I encountered a question which mentioned the skew position during discussion of the conformers of cyclohexane (chair/boat). Here is the question (grammatical errors have been emended): Which of the ...
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0 votes
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144 views

Chirality of conformations of butane

I have read that the conformations of butane are as follows: I came across a question about number of chiral conformations of butane. My Attempt : The total or fully eclipsed is achiral because it ...
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How many conformations are possible for ethane?

I am talking on the basis of observations made on the Newman projection of ethane. According, to the various sources, that I found on many websites, the number of conformational isomers are 2. They ...
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5 votes
1 answer
265 views

Why does α-ᴅ-glucose form at a lower temperature than β-ᴅ-glucose?

β-ᴅ-glucose is more stable than its α-anomer due to the fact that all the −OH groups occupy the equatorial position. If this is the case, then why does α-ᴅ-glucose predominate at 30 °C while β-ᴅ-...
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10 votes
1 answer
385 views

Why is a conformer of hydrogen peroxide rotationally inactive?

Hydrogen peroxide may exist in four different forms depending on the dihedral angle, $d = \angle\,\ce{H-O-O-H}$. The four conformers are: Conformer I with $d = 0^\circ$, Conformer II with $d = 60^\...
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4 votes
1 answer
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Why is the A-value of methoxy group lower than that of the hydroxyl group?

I am studying conformational analysis of monosubstituted cyclohexane. "A-value" refers to the energy difference between conformers with substitutent in equatorial (more favored) and axial ...
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7 votes
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Stereochemistry & mechanism of β-cyano enone methylation

I am helping a friend with some upper-level mechanism problems. We came across this one. This is my proposal. Do you agree/disagree? Thank you for any input. Source question:
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small negative frequencies in DF T optimizations with organic molecules containing CF3 groups [duplicate]

When optimizing by DFT medium-sized organic molecules containing aromatic CF3 groups (for example, adducts involving takemoto's catalyst), the frequency calculation on optimized structures have always ...
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Staggered Conformation Classification

I was working on an assignment I had a question about conformations of a molecule about a single bond. Given a random molecule like this with multiple large substituents on one side of the $\ce{C-C}$ ...
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3 votes
1 answer
132 views

Representing conformers using SMILES and Graph representations

I was wondering if either of SMILES or graph representations (in their vanilla form) can distinguish between two conformers of the same molecule. Can this be enhanced by adding additional metadata on ...
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Why does there need to be a planar intermediate in 2,2'-dibromobiphenyl when one of the phenyl groups rotates?

I was in class and my professor brought up the example of 2,2'-dibromobiphenyl: In her example, one of the bromines was actually pointing into the page and the two phenyl groups were not actually on ...
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3 answers
3k views

How to identify cis and trans forms of cyclohexane [closed]

How can identify which one is cis and which one is trans . If I consider it as a planar molecule (though it is not) I understand that if the substituents are in same side it is cis else trans but this ...
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Conformers with extremely high energy barriers?

What are some conformers with very high energy barriers? When we think of e.g. the butane conformers, at room temperature, the conformational change plays almost no role. I was wondering how molecules ...
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How many gauche butane interactions are present in cis-1,2-dimethylcyclohexane?

We were asked to find out the number of Gauche-Butane interactions for this compound: I proceeded by drawing the Newman Projection for this chair conformation as follows and marked the Gauche-Butane ...
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1 answer
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Newman projections: how to tell which groups are bulkiest to determine what is the most stable conformation?

The scenario Let's say we have a molecule where in the Newman projection the front carbon has a hydrogen, methyl and an ethyl, and in the back carbon there's a hydrogen, something like a S, Cl or Br (...
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1 answer
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Total number of stereoisomers of truxillic acid

Total number of stereoisomers of the compound will be: This was a question asked in our mock test. I've tried by considering pseudo-chirality on the carbon atoms. But I don't know where to start. I ...
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3 votes
1 answer
139 views

Which ethanol derivatives display the gauche effect?

How many of the following ethanol derivatives of the form $\ce{GCH2CH2OH}$ have a more stable gauche conformer compared to their anti conformer? $G = \ce{F}, \ce{Cl}, \ce{OH}, \ce{NH2}, \ce{OMe},...
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4 votes
0 answers
31 views

Covering conformers in a molecular modelling; consider them as a static entity or work with modelling shifts as well?

I am currently working with a molecular docking project, examining potential affinities of a solvent on a protein in an assay to evaluate potential error margin. The solvent is cyclohexanol (referred ...
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2 votes
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75 views

Strains in conformations of cyclohexane

I know some the basic kind of strains that can exist in molecules namely Torsional strain (Vanderwaals' strain), steric strain and angle strain. Is it possible to associate a particular type of ...
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3 votes
1 answer
98 views

Determining the torsion energy profile of butadiene by molecular dynamics

Disclaimer: this question is related to my previous question, although it is much more detailed Consider the following rotation of butadiene: I want to determine the relative energy of each dihedral ...
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Is it possible to estimate the abundance of conformers from J values?

I have a system of two disubstituted cyclohexanes and I want to estimate the abundance/ratio of the two based on the J values and if possible, roughly estimate the difference in free energy. To get ...
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3 votes
1 answer
75 views

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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0 votes
0 answers
71 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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2 votes
2 answers
2k views

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

Question 1: Which of the following Newman projections represent the most stable confirmation of the diastereomer of the molecule given below? I guess my main question is looking only at the Newman ...
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6 votes
1 answer
360 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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1 vote
0 answers
52 views

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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5 votes
1 answer
236 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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-1 votes
1 answer
220 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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1 vote
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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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3 votes
0 answers
209 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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1 vote
1 answer
402 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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2 votes
0 answers
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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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2 votes
0 answers
47 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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1 vote
1 answer
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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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3 votes
0 answers
271 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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16 votes
5 answers
3k views

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 ...
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3 votes
1 answer
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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 ...
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5 votes
1 answer
251 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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0 votes
1 answer
253 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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2 votes
2 answers
1k 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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  • 133
2 votes
2 answers
916 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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  • 113
1 vote
0 answers
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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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  • 179
7 votes
2 answers
2k views

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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8 votes
2 answers
3k views

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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15 votes
1 answer
348 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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6 votes
1 answer
3k views

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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2 votes
1 answer
551 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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10 votes
1 answer
382 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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