Questions tagged [conformers]

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

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2
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1answer
42 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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1answer
45 views

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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3answers
140 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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0answers
17 views

When undergoing a ring flip, why doesn't the ring go directly from the half-boat confirmation to boat confirmation?

Why does the ring go through the twist-boat conformation when transitioning from half-boat to boat conformations? In other words, what is stopping the ring from transitioning directly from the half-...
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0answers
29 views

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 ...
1
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1answer
797 views

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 ...
4
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1answer
204 views

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 (...
3
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1answer
150 views

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 ...
3
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1answer
95 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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0answers
25 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 ...
2
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0answers
48 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 ...
3
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1answer
41 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 ...
5
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0answers
58 views

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 ...
2
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1answer
65 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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0answers
37 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 ...
2
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2answers
496 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 ...
6
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1answer
147 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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0answers
47 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 ...
4
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1answer
197 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
65 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 $\text{sp}^3$ ...
1
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1answer
20 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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0answers
100 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
202 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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0answers
60 views

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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0answers
45 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
161 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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0answers
186 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
2k 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 ...
3
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1answer
2k views

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
178 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
193 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 ...
2
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2answers
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 ...
2
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2answers
680 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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0answers
683 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, ...
6
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2answers
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 ...
7
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2answers
2k 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 ...
14
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1answer
310 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 ...
6
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1answer
2k 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 ...
2
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1answer
466 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 ...
10
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1answer
350 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 ...
2
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1answer
321 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 ...
10
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2answers
486 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
130 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 ...
4
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1answer
93 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 ...
4
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1answer
86 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 ...
1
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1answer
132 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
5k views

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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2answers
97 views

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?
2
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1answer
944 views

Best chair configuration for trimethylcyclohexane matching a specific Haworth projection?

Which option best depicts trimethylcyclohexane shown in the Haworth projection below? I thought B because All the methyl groups are equatorial and equatorial groups are more stable. All the methyl ...
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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]...