Questions tagged [molecular-structure]

This tag should be applied to questions that deal with the particular arrangement of atoms in a molecule, the so-called molecular structure or geometry.

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14
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3answers
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How do I make 3d molecular graphics similar to those shown on Wikipedia?

I want to make 3d molecular graphics similar to those found on Wikipedia. In the page for benzene, you can see the structure looks like this: However, if I go to the interactive image as shown in ...
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0answers
17 views

For a structure of a compouund optically active, what is the number of stereo isomers if no geometrical isomers are present?

Suppose for example the compounds $\ce{M(AA)3}$ and $\ce{M(AA)3bc}$, with $\ce{M}$, the central metal atom and $\ce{AA}$, a bidentate ligand. What is the total number of stereo-isomers of both? I was ...
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1answer
32 views

What is "tail" in case of secondary structure of protein? [closed]

What is a "tail" in the case of the secondary structure of a protein? How does it influence the "protein assignment" task?
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2answers
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13C NMR peak location in butanone

The above is the correct $\ce{^{13}C}$-$\mathrm{NMR}$ spectrum of butanone. In the $\ce{^{13}C}$-$\mathrm{NMR}$ spectrum of butanone, I figure that the peak locations of the first $(\pu{27.3 ppm})$ ...
2
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2answers
110 views

Elucidating an unknown compound using 1H- and 13C-NMR spectral data [closed]

I am currently struggling with the following NMR spectrum for this compound: I know for sure that we should multiply the integrals of the hydrogen atoms by four, and that the compound contains at ...
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3answers
23k views

Identifying the number of bonding and lone pairs without a dot and cross diagram

I've just learned how to predict the shapes of molecules in class today using VSEPR theory. I would like to ask is there anyway to find the number of bond pairs and lone pairs without drawing a dot-...
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1answer
2k views

How to predict molecular geometry of acetylene using VSEPR model?

I need to determine the molecular geometry of acetylene. For this I performed the following procedure. First, I drew the correct Lewis structure which is a graphical representation that shows the ...
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1answer
34 views

How does addition of side chains affect solubility and processibility of polyphenylene vinylene?

I am studying electrical engineering and physics. In a recent lecture I was told the $\ce{OC1C10}\text{-PPV}$ molecule has the chains added to the oxygen atom down below because it allows for ...
0
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1answer
67 views

Why do isosteric molecules have similar shapes? [closed]

Isosteres (Definition): Isosteres are atoms, molecules, or ions of similar size containing the same number of atoms and valence electrons.[1] Questions: A. Why ...
2
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1answer
123 views

What molecule is pictured on the cover of Dead Sara's album "Ain't It Tragic?"

An album released today by Dead Sara, titled Ain't It Tragic, has a chemical structure on the album cover. Here's a close-up of that structure: As the structure is partially obscured, it's difficult ...
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1answer
629 views

What is the difference between expanded structural formula and Lewis dot structure?

I am teaching myself the basics of chemistry and I have done Lewis dot structure before. Right now I am going into carbon chemistry which often use structure formulas to represent compounds. There is ...
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1answer
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In the LCAO method for $H_2^+$, why do we only add or subtract orbitals but never alter one of the phases of the orbitals?

TLDR: Atkins' physical chemistry contains the quote "In general, from N atomic orbitals we can build N molecular orbitals". In the case of $H^+_2$, we use a combination of N=2 orbitals to ...
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1answer
49 views

Stereochemical relationship between the given compounds

Are the given compounds enantiomers or diastereomers? Or are they identical? The compound is trans-1,2-dimethylcyclobutane: My reasoning is that they are identical. They are not mirror images, and on ...
3
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1answer
36 views

What does "the natural bond angle" mean in the context of Universal Force Field (UFF) potential energy calculation and how are bond angles calculated?

As the title says, what does "the natural bond angle θ0" mean in the context of Universal Force Field (UFF) potential energy calculation? The reference appears in section D. Angular ...
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2answers
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PBP vs TBP geometry?

Why are the axial bond lengths greater than those of the equatorial bonds in a trigonal bi-pyramid (TBP) geometry molecule; but the opposite is true for pentagonal bi-pyramid (PBP) geometry molecules? ...
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0answers
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Mechanism of Action of Carbachol

Carbachol (carbamylcholine chloride) is known to be a cholinergic agent. Does it work as an indirect agonist by inhibiting acetylcholinesterase, as a direct agonist of acetylcholine receptors, or is ...
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6answers
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Free API to view 2D representation of Molecules

I'm looking for a free API that can accept a SMILE and produce the 2D structure of a molecule. I would like to include this in a web page. I have collection of SMILES and would like to have the 2D ...
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2answers
71 views

what does the prefix tetrahydro actually means?

After encountering a few compounds which their name includes the prefix "TETRA HYDRO" I'm wondering what that prefix actually means? For example THC (tetrahydrocannabinol) and also THF folic ...
2
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1answer
45 views

How to identify 'water' mistakes in protein crystal structures: Are B-factors and occupancy good indicators?

When solving the structure of a protein from diffraction data (x-ray crystallography), it can sometimes be difficult know what should be modelled into small spheres of electron density that are not ...
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1answer
55 views

What is a spiroketal compound?

I read a medicinal chemistry book about SGLT2 inhibitors. One of them is tofogliflozin. In that book, they refer to it as spiroketal. Is the spiroketal functional group the red part in this picture? ...
3
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1answer
75 views

Does hydrogen bonding affect the structure of a molecule?

We know an individual molecule of $\ce{H2O}$ has a bent structure, but if we consider a volume of water, then there are many molecules having hydrogen bonding with each other. Due to this, does the ...
5
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1answer
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Geometries of SCl2(OCH3)2 and SF2(OCH3)2

I am not able to understand the difference between structure of $\ce{SCl_{2}(OCH_{3})_{2}}$ and $\ce{SF_{2}(OCH_{3})_{2}}$. I am already well versed with Molecular Orbital and VSEPR theories. I found ...
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3answers
311 views

What is abnormal Beckmann rearrangement?

What is abnormal Beckmann rearrangement? I read this term in one of my solution papers but I am not able to find relevant literature for the same. Answers linking to some source, or giving the ...
4
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3answers
282 views

What is the difference between structure assignment and structure prediction?

I am absolutely new to structural bioinformatics (only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using machine learning. ...
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0answers
34 views

Spectroscopic constants weye and weze

I am using Morse potential to calculate the spectroscopic constants of a diatomic molecule. So far I was able to calculate $R_e$, $\omega_e$, $\omega_ex_e$, $B_e$ but wasn't able to calculate $\...
4
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2answers
299 views

Relationship between molar mass and density in solids

In ideal gases, it's pretty clear that 1 mole of gas occupies 22.4 L at STP. By knowing this, it's easy to calculate density given molar mass. However, this isn't true for solids. If I know molar mass ...
3
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0answers
51 views

Eigenenergies and states of Jahn–Teller molecule

I'm generally interested in numerical chemistry. In our lecture, we have discussed the $E \otimes e$ Jahn–Teller molecule with the following Hamiltonian \begin{align} H = \epsilon n_d + \omega ( a^{\...
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1answer
96 views

Weerman degradation on alpha-hydroxy amides

I came across this reaction scheme in the solutions of a test paper: I understand the formation of isocyanate intermediate as the first step. In the second step, I realized that hydrolysis will be ...
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0answers
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Finding Potential Depth of Multiple-Minimum in a PEC

Suppose we have the following curve with more than one well and different maximum points: My simple question is how to calculate the potential depth of each well? Do we calculate all the potential ...
4
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0answers
63 views

Planarity at the Junction between multiple Rings

My Approach: As cyclohexane should be in the chair form and cyclopentane should be in the envelope form, more the number of five-membered rings more should be its planarity, as envelope form is more ...
4
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1answer
134 views

The ways to determine if an ionic compound is paramagnetic or not

Find which of $\ce{Na2O2}$ and $\ce{CsO2}$ is paramagnetic. (Adapted from JEE advanced paper-1 2016, q.22) The given solution involves removing the cations and taking the anionic part, i.e. $\ce{O2^2-...
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1answer
130 views

Can resonance structures account for NMR spectroscopy chemical shifts?

I am unable to understand why the alpha carbon to the carbonyl group is of lower chemical shift compared to the beta carbon based on the effects of electronegativity and hybridisation. Since if ...
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1answer
728 views

Why is disilyne bent?

Why is disilyne $\ce{Si2H2}$ bent when the steric number of silicon is 2?
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Dative Bond in Nitrogen Dioxide

I learnt that a coordinate covalent bond forms only when Donor atom has a complete octet and also has at lest 1 lone pair. The receiving atom must have an incomplete octet and possess at least 1 ...
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2answers
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1answer
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Of 2-bromobutan-2-ol and trans-1,2-dimethylcyclobutane which is chiral as well as dissymmetric?

In an examination I was asked to determine the molecules which are chiral as well as dissymmetric. There were four options, and among them, two were achiral, as they had an improper axis of symmetry. ...
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1answer
69 views

What is the difference between structure and morphology in polymer blends?

When talking about polymer blends there is a difference between its structure and morphology, but I am not sure what it is. These two terms are used interchangeably in materials I use to study, but I ...
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0answers
40 views

Carbonate Ion and it's structure

I recently began learning about resonance in molecules- I drew the following Lewis dot structure for $\ce{CO^{2-}_3}$ ion and accounted for resonance in it. Now I was asked about hybridisation and ...
4
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2answers
11k views

Bond angles in BrF5

If in an octahedral structure there is one lone pair placed on any two of the axial position then will the lone pair distort all the 90 degree angles due to repulsion from lone pair or the angles will ...
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1answer
110 views
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1answer
636 views

If all bond angles in AX₃ are the same, then which of the following are correct conclusions about AX₃?

Question If all bond angles in $\ce{AX3}$ are the same, then which of the following are correct conclusions about $\ce{AX3}?$ (A) $\ce{AX3}$ must be polar. (B) $\ce{AX3}$ must be planar. (C) $\ce{AX3}...
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1answer
81 views

What are the limits of size differences in a host–guest complex?

We learn in my chemistry course that there must be a snug fit for a host-guest complex to form. So, something like benzene (0.6 nm in diameter) can form a host-guest complex with a β-cyclodextrin host ...
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1answer
147 views

Reactions of P2O5 and P4O10 with sulfuric acid [closed]

I have seen two reactions of $\ce{H2SO4}$, in one it reacts with $\ce{P2O5}$ and in the other $\ce{P4O10}$. The Reactions are as follows: $$\ce{H2SO4 + P2O5 -> SO3 + 2HPO3}$$ $$\ce{6H2SO4 + P4O10 -...
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1answer
75 views

Dehydration reaction of an alcohol, 2,3-dimethyl-2-phenylbutan-1-ol, with conc. sulfuric acid (at high temperature)

What's the major product of the dehydration reaction of 2,3-dimethyl-2-phenylbutan-1-ol with conc. $\ce{H2SO4}$ (at high temperature)? I am aware that in this reaction $\mathrm{E}$1 mechanism will be ...
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1answer
79 views

Why does adding excess NaOH prove amphoteric nature?

When 3+ hexaaqua ions react with hydroxide ions, the following set of reactions occurs: When we get to stage 3, a neutral ion has formed, and a white precipitate is created. Now, we know that for ...
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2answers
13k views

Why does dimethyl ether have a bond angle bigger than 109.5 degrees?

Why does dimethyl ether have a bond angle bigger than 109.5 degrees, in contradiction with VSEPR theory?
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1answer
52 views

Why is the shape of xenon difluoride linear and not trigonal bi-pyramidal? [closed]

My explanation is, the shape of $\ce{XeF2}$ is actually trigonal bi-pyramidal, but as the 3 lone pairs of $\ce{Xe}$ remain so close to the $\ce{Xe}$ atom itself, it seems that $\ce{XeF2}$ has a linear ...
4
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1answer
159 views

How to understand the role of the lone pair on the molecular structure when it participates in resonance?

I'm a little confused as to why we ignore the effect the lone pair has on the geometry of the molecule when it is participating in resonance. Wouldn't it be the case that the molecule is actually in ...
3
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2answers
1k views

1H-NMR of vanillin details in Nilered video

The image below is from a Nilered video How to extract Vanillin from Vanilla Sugar, where he displays the $\ce{^1H}$-$\mathrm{NMR}$ of the final product created: The labels A, F, & E make sense ...
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0answers
62 views

Calculating the apparent molecule length from density of the bulk [closed]

I'm interested to estimate the apparent length of the water molecule assuming it could be approximated as a cube. This is an intentional simplification. Calculating molecule length from volume in ...

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