Questions tagged [conformers]
For questions about conformational isomerism. Use this tag alongside [stereochemistry].
122
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Why is the 'cis-1,3-dimethylcyclobutane' conformation of both methyl groups at the bottom more unstable than both at the top?
I'm having trouble understanding why both methyl groups on top of the ring is a more stable conformation than both at the bottom of the ring.
I found a reasoning that says the steric strain between ...
- 81
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Conformational analysis [closed]
In organic chemistry, much emphasis is given to the study of the conformers of alkanes and the broader topic of conformational analysis. Can you elucidate why the spatial arrangements and rotations ...
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455
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How to convert SMILES to 3D (with higher accuracy than RDKit)?
I am interested in assigning 3D coordinates to (atoms in) some 10K molecules that I have, currently represented by SMILES. This is because as have been shown by many chemoinformatics papers, 3D and 2D ...
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Difficult in grasping "the extent/limit of conformational space of a compound until it change its stereochemistry"
I have heard that a conformational landscape encompasses all conformers that a compound has for a specific stereoisomer. I think it makes sense verbally, because if all conformers of a stereoisomer ...
- 25
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Calculating energy difference between two 1-4 dimethylcyclohexane conformers
The following question was asked in a quiz at my college
Draw the most stable and least stable chair conformer for 1,4-dimethylcyclohexane and calculate the
energy difference between these two. Given ...
2
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Can we always use the planar representation of cycloalkanes instead of their true conformations to study their stereochemistry and chirality?
When I have drawn stereoisomers of substituted cyclohexanes and checked if they are chiral, I typically represent the ring as a planar hexagon and look for symmetry elements. For example, I would use ...
- 325
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Are the physical and chemical properties of a molecule an average of the properties of its conformers? [closed]
Conformers sometimes differ in chemical reactivity. For example, only certain alkyl bromide conformers have the appropriate geometry to undergo elimination via an E2 mechanism. I imagine that ...
- 325
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Why is diequatorial trans-1,2-dimethylcyclohexane more stable than diaxial trans-1,2-dimethylcyclohexane?
Consider diequatorial trans-1,2-dimethylcyclohexane and diaxial trans-1,2-dimethylcyclohexane as shown in the figure below [1, p. 178]. In both compounds, the ring is free of angle strain.
trans-1,2-...
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303
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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 ...
- 192
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541
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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 ...
- 93
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438
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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 ...
- 53
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502
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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 ...
- 27
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231
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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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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-...
- 173
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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^\...
- 6,840
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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 ...
- 752
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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 $\ce{C-C}$ ...
3
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236
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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 ...
- 1,495
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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 ...
- 119
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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 ...
- 297
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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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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 ...
- 143
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177
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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},...
- 6,208
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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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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 ...
- 777
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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 ...
- 1,618
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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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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....
- 1,298
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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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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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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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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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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 $\text{sp}^3$ ...
- 2,049
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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) ...
- 131
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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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571
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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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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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Nucleophilicity and basicity of compounds with or without nitrogen inversion
In nitrogen inversion, the lone pair changes its direction continuously.
Does this in any way delocalize the charge density on the nitrogen making it less nucleophilic and less basic than, say, a ...
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611
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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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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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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 ...
- 169
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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 ...
- 1,007
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309
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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 ...
- 51
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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 ...
