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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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12 views

Finding molecular formula by bandgap energy [closed]

How to solve for x: GaxIn(1-x)N need to find x when emission wavelength is given and the bandgap energy of GaN and InN is given Also, it's given that the Bandgap energy is a linear function of Ga
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2answers
104 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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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 ...
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1answer
61 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
117 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
46 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 ...
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33 views

Does crystallisation at 78 degree possible for disufenton sodium (a specific nitrone compound) without causing to degrade? [closed]

As a more detailed explanation to my question: I want to recrystallise a nitrone of a synthesis I did. The compound is disufenton sodium, a variant of the $\alpha$-phenyl-N-tert-butylnitrone which has ...
3
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1answer
70 views

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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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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49 views

Where should the double bonded C attached to Sulphur be at? Equatorial or Axial position?

The maximum number of atoms that may lie in the same plane in $\left(\mathrm{CH}_{3}\right)_{2} \mathrm{C}=\mathrm{SF}_{2}\left(\mathrm{CH}_{3}\right)_{2}$ is ____ : Where should the the S=C bond lie ...
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2answers
65 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 ...
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1answer
43 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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3answers
304 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 ...
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0answers
32 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 $\...
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1answer
53 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? ...
2
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1answer
70 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 ...
3
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0answers
50 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^{\...
8
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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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8 views

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
114 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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0answers
41 views

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
101 views

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
66 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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1answer
124 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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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 ...
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1answer
106 views
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3answers
274 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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1answer
127 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
71 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 ...
2
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1answer
73 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
47 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 ...
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0answers
70 views

Molecular orbitals energy under pressure

Suppose we have a hydrogen molecule $\ce{H2}.$ At room temperature the average distance of the nuclei is $r_0$ (without applying pressure). If we put $n$ hydrogen molecules in a box with volume $V_\...
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1answer
327 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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0answers
61 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 ...
1
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1answer
163 views

Are all chiral carbons sp3 hybridised? [closed]

I had this doubt, whether all asymmetric chiral carbons must necessarily be $\mathrm{sp^3}$ hybridized. For sure, we know that double or triple bonded carbon atoms don't shows such chirality, but is ...
0
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1answer
71 views

Finding the molecule with the smallest bond angle in the following lists of elements

For each of the following lists of elements, find (and give a justification for your choice) the molecule with the smallest bond angle: a) $\ce{OSF_2, OSCl_2, OSBr_2}$ b) $\ce{SbCl_3, SbBr_3, SbI_3}$ ...
2
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1answer
338 views

Why is the bond angle of trifluoromethane higher than that of difluoromethane?

The bond angle $\ce{\angle(F-C-F)}$ of $\ce{CHF_3 > CH_2F_2}$ whereas that of $\ce{\angle(Cl-C-Cl)}$ is $\ce{CH_2Cl_2 > CHCl_3}$ why is this the case? Some explanations I read suggest the Bent's ...
4
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1answer
157 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 ...
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1answer
69 views

D and L configuration of monosaccharides

I got this question in the last week's test from Organic Chemistry. I am a bit confused in assigning D and L configuration. Help me understand the topic of D and L configuration and help with this ...
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0answers
34 views

References for the Molecular Distance Geometry Problem

Note: This question has also been posted here. The molecular distance geometry problem (MDGP) consists of two sub-problems: Given observations of noisy distances between atoms in a molecule, ...
7
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2answers
236 views

Why does a larger bond angle correspond to greater s-character?

In trialkylamines $\ce{NR3}$, the $\ce{R}$ alkyl group attached to nitrogen increases the electronegativity of the nitrogen atom. I also found in this question that this happens due to the repulsion ...
4
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3answers
111 views

How are compounds within a complicated mixture detected?

I was reading an article about an independent pharmaceutical watchdog group called Valisure which recently released a report stating that they found Benzene, a toxic substance, in many bottles of ...
5
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1answer
170 views

What is a correct primitive hexagonal unit cell to describe a monolayer of molybdenum sulfide?

I searched the coordinates or reduced coordinates of primitive cell of mono layer hexagonal $\ce{MoS2}$, but there are lots of different structures and coordination. For example, material project give ...
4
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2answers
260 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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1answer
325 views

Odd/Even swap rule for chiral compounds in stereochemistry

I had this question asked in my exam, where I was supposed to find if this pair is a diastereomer: Now, I have learnt this rule where: Making odd number of swaps in a molecule means they both are ...
3
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2answers
73 views

Predicting product ratio by rearrangement in Dehydration Reactions

I came across this question recently, which would have a clear major product. The OP has given satisfactory explanation for the product ratio, but wasn't sure about the major product. When I was ...
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1answer
90 views

Major product of the dehydration of alcohols

Well I was doing some questions and I have a bit of confusion on dehydration reaction. For instance, consider following reaction: How do I decide which adjacent hydrogen gets attracted by $\ce{HSO4-}$...
0
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1answer
97 views

Why are the hydrogen-carbon bonds bent in a graphical depiction of an alkene, but are straight horizontally and vertically in an alkane?

In propane, for example, the $\ce{C-H}$ bonds are depicted by straight vertical and horizontal lines. But in propene, the same bonds are bent. Is it a rule that $\ce{C-H}$ bonds are always bent if the ...

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