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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9
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3answers
734 views

How do I figure out how many hydrogens my compound actually has using a mass and NMR spectrum?

Question 3: It said $m/z = 122,$ and $m/z = 124$ is in a $3:1$ ratio, so I figured that meant that chlorine is present. Then I thought $m/z$ was the actual compound's molecular mass. So I used ...
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1answer
430 views

About Fe(III) and Fe(II) coordination complexes

Why does Fe(III) form octahedral coordination complexes if it has 5 electrons in its d-orbitals? I understand that Fe(II) has 6 electrons in its d-orbitals and 6 lone pairs from 6 ligands as the 12 ...
8
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1answer
204 views

Any way to see “cubic-active” vibrational modes in molecules?

For molecular complexes with a moderate amount of symmetry there are usually vibrational modes that are neither infrared nor Raman active. Sometimes these modes transform as some cubic polynomial in x,...
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0answers
53 views

Calculating the Molecular Orbitals of a Molecular State [closed]

I am performing ab initio calculations on a heteronuclear diatomic compound using the MRCI method on the MOLPRO quantum chemistry package. I obtained the molecular states of the compound but I was ...
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0answers
36 views

Changing toothpaste to a more stable structure

I am using charcoal toothpaste for an actor to spit bile on stage during a show. The paste is not the correct state for our needs. I know that you can freeze toothpaste and it becomes "more" solid ...
6
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1answer
813 views

How can I find out a substance name based on its structural formula?

When visiting a botanical garden in Stockholm, I stumbled across the following mosaic tile: I have tried to identify it using MolView, but it does not seem to identify it. Also, I have tried their ...
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0answers
61 views

How is it possible to melt diamonds? [duplicate]

On another thread on this website it mentioned how it was possible to melt diamonds, but what would be the micro-level occur for that to happen. This question applies to Silicon Oxide aswell. They ...
3
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1answer
109 views

How does resonance fail in approximating chemical structures?

In the book "Concise Inorganic Chemistry" by Prof. JD Lee, it says here: These contributing structures do not actually exist. The $\ce{CO3^2-}$ does not consist of a mixture of these structures, ...
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0answers
162 views

Dipole moments of dibromoethene isomers

There was an exercise in my textbook asking to compare the dipole moments of 1,1-dibromoethene and 1,2-dibromoethene(Z). The answer in the textbook says that the dipole moment of 1,1-dibromoethene is ...
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1answer
625 views

Provide a condensed structure for the following compound [closed]

I keep getting, (CH3)3CCH2CH2CHNH2CHCHCH3. However, the homework system keeps counting it as incorrect, and I don't know what part is incorrect. Thanks for the help!
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1answer
107 views

Software that determines whether a molecule can exist and draw it from a formula?

I have run calculations that predict atomic configurations. As a simple example, in a system that contains H and O, I might get a list like: ...
6
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2answers
322 views

Freely available software for generating 3D coordinates of molecules

As part of some research I am doing, I want to do a head-to-head comparison of software for generating 3D atomic coordinates for molecules. Is there a list anywhere of chemical software that does this?...
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1answer
282 views

Is sugar in mead different from “regular sugar”?

My understanding of the process of making mead is that you combine honey, yeast and water in an anaerobic environment. The yeast-bacteria ferments the sugar in the honey and produces ethanol (among ...
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0answers
50 views

Is bonds in CO is all 3 coordinate bonds or 2 covalent and 1 coordinate bonds?

Below image is as available in India's Class 11 NCERT Chemistry book vol 1 Page 104. I am confused as it states all 3 bonds are kind of coordinate bonds. Should it not start with 2 covalent bonds and ...
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0answers
243 views

Bonding in Sulphur dioxide [duplicate]

In Concise Inorganic Chemistry by J.D.Lee (Adapted by Sudarsan Guha, Fourth Edition), on page 82, under section 3.8 - Types of Covalent Bonds (Sigma and Pi Bonds) it is given (for Sulphur dioxide ...
9
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1answer
134 views

What is the biggest known difference between rₑ and r₀?

What is the biggest known difference between $r_e$ and $r_0$? Where $r_0$ is the average bond length of the lowest vibrational state, and $r_e$ is the location where the potential is lowest. For a ...
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0answers
86 views

Question on identification of a compound

Question: Multiple correct answers are possible My Approach: I just found structure Q for all options A, B, C and D for which I have uploaded the structures below with their corresponding options. ...
2
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0answers
175 views

Which substitutent should be placed on axial position in SCl2(OCH3)2?

According to Bent's rule, in $\mathrm{sp^3d}$ more electronegative element is placed on the axial position, so between $\ce{Cl}$ and $\ce{OCH3}$ in $\ce{SCl2(OCH3)2}$ which should be placed on axial ...
9
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3answers
2k views

What is “super” in superphosphate?

This question is inspired from a previous question(marked unclear). I don't know about the context of that question but I was intrigued by a statement in that question: Superphosphate is used ...
3
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1answer
274 views

Number of stereoisomers of polysubstituted cubane

The molecule given below is a substituted cubane. a) How many stereoisomers exist for this molecule? b) How many pairs of enantiomers are possible? How do I calculate the number of stereoisomers? ...
2
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0answers
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?
20
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1answer
785 views

Why does the image of cyclo[18]carbon look like a nonagon?

The $\ce{C18}$ allotrope cyclocarbon has been synthesized and imaged.[1] Science has most details behind a paywall, but this discussion includes an image: In this octakaidecagonal molecule, each $\ce{...
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1answer
682 views

Do the groups involved in geometrical isomerism have to be in similar planes to show geometrical isomerism?

In my textbook, under the topic "Conditions for geometrical isomerism", the following has been given: Groups responsible to show geometrical isomerism must be nearly in the same plane. Is this ...
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2answers
716 views

How to convert Gaussian input file .gjf to SMILES?

Is there a way to convert Gaussian input files (.gjf) to SMILES-codes (.smi)? I'm aware of ...
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1answer
163 views

The influence of diffuse functions on electron density calculations

I am not a quantum chemist, but I am (starting to be) a user of electronic structure software. In the picture (screenshot) is the electron density of the same molecule. On the left I calculated the ...
3
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1answer
621 views

AB5E type molecule

In $\ce{AB5E}$-type molecules, why are the lone pairs in axial bonds? If the lone pair is present in axial bonds it repels four other bonds. On the other hand if the lone pair is in equatorial ...
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0answers
104 views

Can you use a photon's torque to change a molecule?

Can you use the torque of a photon to change bond angles, etc.? 11-Cis-Retinal to the all trans version, in the eye, is a good illustration [1]. Note: This phenomenon can be observed by closing ...
12
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1answer
1k views

Looking for a dye which emits around 680 nm

For a specific experiment, I'm looking for a dye which would emit around 680 nm. Preferably one I could buy easily commercially. Are there any databases which might give the emission spectra of ...
13
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2answers
2k views

What is this fluorinated organic substance?

The corresponding author of the paper where this formula was published as appendix passed away. Can someone help me with identifying what is the name of this compound and why have strange zig-zag ...
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0answers
65 views

Determining geometry of coordination compund without experimental data [closed]

How can I determine if a coordination compound has a tetrahedral or square planar geometry without any experimental data (such as magnetic spin) by just looking at its formula? For example, what is ...
1
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1answer
693 views

Which molecule has maximum bond angle amongst BF₃, BCl₃ and BBr₃? [closed]

$\ce{Br}$ is the least electronegative from the given compounds. So, in $\ce{BBr3}$ the electrons will be the closest towards boron and thus due to electron-electron repulsions $\ce{BBr3}$ will have ...
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1answer
397 views

Is fluorine also hybridised in carbon tetrafluoride?

I had read that when an atom forms multiple bonds, it hybridises it's orbitals to minimise the repulsion and decrease the overall energy. But do the terminal atoms also exist in hybridised form? E.g. ...
2
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0answers
275 views

Why isn't trinitramide planar?

The lewis structure of trinitramide has four major resonance structures, whereby the lone pairs of the central nitrogen can resonate with the nitro groups. This seems to indicate that each of the ...
2
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1answer
145 views

DCC coupling of N-hydroxysuccinimide and 2,2-dimethoxyacetic acid

I am forming N-hydroxysuccinimide ester (1) by DCC coupling with N-hydroxysuccinimide and 2,2-dimethoxyacetic acid using distilled THF as solvent. What I see on $\ce{^1H}$-NMR is three major singlets:...
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2answers
61 views

Optical activity of (1r,3R,5S)-3,5-dimethyl-4-methylidenecyclohexan-1-ol

Could anyone explain why compound L is not optically active?
14
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1answer
2k views

What is quasi-aromaticity?

During my study of aromaticity, I came through this topic of quasi-aromaticity. Can you please elaborate what Quasi aromatic compounds are and how are they designated?
5
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2answers
2k views

How do α,β-unsaturated acids undergo decarboxylation?

I know the concerted mechanism for β-keto acids, but neither could I figure out, nor was I able to find out the mechanism for α,β-unsaturated acids. Any help is appreciated.
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0answers
127 views

Chemical Structures as Graph Labels in R

I asked the following question here https://stackoverflow.com/questions/56236135/chemical-structures-as-graph-labels-in-r but I ask it here for a different perspective. I want to make a plot that ...
5
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1answer
7k views

Why is the dz2 orbital so different from the rest?

What makes dz2 orbital so special? Although degenerate with other d orbitals, It has no nodal planes, instead it has 2 nodal "cones". Instead of having 4 lobes, it has 2 lobes and 1 ring. Also, ...
3
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1answer
435 views

What is the explanation of the structure of H2XeO4?

Using the obsolete VSEPR theory I had a hard time predicting the structure of $\ce{H2XeO4}$. So I looked it up. I found the molecule via chemapps.stolaf.edu: It looks weird to me. I can't explain the ...
7
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2answers
887 views

Software or library for creating images of ball and stick models?

Is there any code library (in any programming language) or software capable of producing images of ball and stick diagrams? Example of an image of a ball-and-stick model for Ammonia: (Image source) ...
4
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1answer
917 views

Is the -OCH3 group bulky?

Our teacher told us that $\ce{OCH3}$ is a less bulky group when compared to other bulky groups like $\ce{CH3}$, $\ce{NO2}$ etc. Is this true? If yes, why?
3
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1answer
247 views

Can anyone help me with this question on vibrational modes of free base porphyrin (C20H14N4)?

4 a. The structure of free-base porphyrin $(\ce{H2P}$, chemical formula: $\ce{C20H14N4})$ is shown below. Given that this molecule belongs to the $D_\mathrm{2h}$ point group (character table given ...
3
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0answers
381 views

Do alkenes have priority over alkynes in R/S naming?

I am studying for an upcoming exam and I came upon a confusing question for the drawing of the molecule (3⁠R)-hex-1-en-5-yn-3-ol. Why is the stereocenter (3-carbon) R? Shouldn't it be S? After ...
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1answer
5k views

Structure of no2 molecule [closed]

Which is the correct structure of $\ce{NO2}$? While searching the internet I found out that $\ce{NO2}$ have a coordinate and two covalent bonds. $\ce{N}$ will have a positive charge. $\ce{O}$ (...
11
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3answers
379 views

What is the mechanism for this reaction?

The closest reaction I can find is Lossen rearrangement but in that hydroxyamic acid is first converted to its derivative but how will that be possible here? Moreover, even if I make an amine in this ...
4
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2answers
827 views

Chiral carbon in carvone molecules

This is the structure of carvone, with the chiral carbon noted by *. I don't understand why this is a chiral carbon, to my understanding a chiral carbon is a carbon with 4 different chemical groups ...
6
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3answers
351 views

What is the precise definition of Ramachandran angles?

The Wikipedia article Ramachandran plot is very schematic and doesn't even say when these angles are considered to be zero. It seems to assume that the peptide chain has no end, and always shows the ...
2
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0answers
3k views

Convert an image of a chemical structure to a ChemDraw file?

Is there a way to convert a bitmap (JPG, PNG) image of a chemical structure to a ChemDraw file so that you don't have to draw a structure you find in a paper yourself?
1
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1answer
639 views

Planarity of given molecules in all conformations

Which of these have all its atoms in one plane in all the possible conformations (if any): A) buta-1,3-diene B) but-1-en-3-yne C) $\ce{CH2=C=O}$ D) $\ce{CH2=C=CH2}$ While I was attempting this ...

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