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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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7
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3answers
272 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 ...
-3
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0answers
21 views

Movement and Position of Electrons in Atoms and Compounds with respect to various models [on hold]

This may sound vague, but here goes. I've often wondered how electrons revolve in compounds (and not just atoms). That was before I came across various theories / models of the atom and I found out ...
0
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1answer
26 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
155 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,...
1
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0answers
32 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 ...
0
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0answers
30 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 ...
5
votes
1answer
299 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 ...
1
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0answers
45 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
61 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, ...
1
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0answers
27 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 ...
-1
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1answer
151 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!
1
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1answer
72 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: ...
5
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2answers
55 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?...
0
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1answer
47 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 ...
1
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0answers
30 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 ...
1
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0answers
44 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
votes
1answer
102 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 ...
1
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0answers
54 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
votes
1answer
109 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 ...
2
votes
1answer
101 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 ...
2
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0answers
38 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?
19
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1answer
672 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{...
0
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0answers
16 views

Lewis structure of chlorine dioxide [duplicate]

The central atom in the molecule of $\ce{ClO2}$ is chlorine. Draw the ‘dot-and-cross’ diagram for $\ce{ClO2}.$ Show outer electrons only. How to draw Lewis structure of $\ce{ClO2}?$ Please explain ...
2
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2answers
148 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 ...
1
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1answer
72 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
votes
1answer
137 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 ...
6
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0answers
74 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 ...
1
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0answers
33 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
vote
1answer
385 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 ...
-1
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1answer
60 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
50 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 ...
0
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2answers
47 views
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0answers
38 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 ...
3
votes
1answer
644 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
votes
1answer
147 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
165 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) ...
2
votes
1answer
138 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
votes
1answer
175 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 ...
1
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0answers
33 views

What is molecular potency?

In the paper Junction Tree Variational Autoencoder for Molecular Graph Generation, the authors propose a ML model that is based on the message passing neural network, variational auto-encoder, the ...
3
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0answers
103 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 ...
-4
votes
1answer
573 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 2 covalent bonds. $\ce{N}$ will +ve charge. $\ce{O}$ (coordinate bond )...
4
votes
2answers
180 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 ...
4
votes
3answers
114 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
votes
0answers
186 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
vote
1answer
156 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 ...
3
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1answer
77 views

Why is casein hydrophobic?

According to this source hydrophobic behaviour occurs when a molecule does not have a charge or is neutral and therefore cannot be attracted to the negative nor positive parts of water. Casein has an ...
0
votes
1answer
74 views

Why is there a lone pair in thionyl fluoride?

Why is there a lone pair in $\ce{SOF2}$? I drew its structure, which according to me should look like this: Why is there a lone pair on sulfur? Isn't its octet complete? If yes, why should it expand ...
2
votes
0answers
80 views

Spin state change during crystallisation for [NiCl2(PPh3)2]

$\ce{NiCl2(PPh3)2}$ is a complex that is borderline between tetrahedral(high spin) and square planar(no unpaired electron, high splitting parameter) because $\ce{Cl-}$ is a weak field ligand and $\ce{...
-2
votes
2answers
203 views

Why is manganate ion paramagnetic [closed]

When I tried to figure out why manganate ion is paramagnetic, given that its oxidation number is +6, I am not able to understand why there are unpaired electrons. Is it the case that six of the seven ...