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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11
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1answer
214 views

Software to assist drawing of complex, three-dimensional skeletal formula from scratch or from existing crystal structure

Is there a tool that would help in creating rather intricate line drawings (not pre-rendered balls-and-sticks/wireframe/sticks/ORTEP diagrams) for a skeletal formula in 3D space? To illustrate the ...
4
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0answers
31 views

Structure of dihydrogen peroxy-phosphate ion

In structure of Dihydrogen peroxy-phosphate ion $\ce{H2PO5-}$, shouldn't negative charge be on oxygen linked directly to phosphorus, rather than on oxygen linked through peroxy linkage with another ...
0
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1answer
76 views

Preferred Lewis structure for sulphate anion and XeO4 [closed]

In a section reviewing Lewis structure, the textbook Atkins' Physical Chemistry, 10th Edition, by Atkins, Paula, and Keeler, gives the following illustration of hypervalence and octet expansion: I ...
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1answer
40 views

Question about d-orbitals [closed]

I saw somewhere that, "in PF5, the 3d orbitals of phosphorus end up in the anti-bonding molecular orbitals, and thus contribute less to the final molecule" and that "the hypervalency of some ...
1
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2answers
113 views

Does H3CO3+ ion exist and what is its structure? [closed]

Why doesn't $\ce{H3CO3+}$ ion exist and why doesn't the carbonyl group in carbonic acid $(\ce{H2CO3})$ seem reactive?
-2
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1answer
48 views

Identifying molecule with three adjacent six-membered rings from blurry image

I have found this isolated image on one of my old hard drives and I would like to know what molecule does the image represent:
7
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1answer
181 views

Meaning of the term “vertex” in the topic of skeletal formulae

From the Wikipedia article on skeletal formula: Hydrogen atoms attached to carbon are implied. An unlabeled vertex is understood to represent a carbon attached to the number of hydrogens required ...
4
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2answers
291 views

Chromium cyanide complexes

I have rarely seen any chromium $(\ce{Cr})$ square planar complexes and I have been told that $\ce{[Cr(CN)4]-}$ is tetrahedral. So, if the statement is actually correct, are there any other known ...
2
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0answers
40 views

Can stimulated Raman processes be strong enough to drive out of equilibrium?

In the (spontaneous) Raman process, incident light $\hbar \omega_1$ scatters and transfers some energy $\hbar \omega$ to a vibrational excitation of molecule or solid. Typically this is a very rare ...
2
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2answers
137 views

Is PCl5 really trigonal bipyramidal in shape?

We know that the structure of $\ce{CH4}$ is tetrahedral, and not planar tetragonal, as a tetrahedron enables maximum distribution of $\ce{H}$-atoms in space, as they repulse from each other. This is ...
6
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1answer
85 views

Are all stable Xenes (graphene-like 2D honeycomb sheets) buckled?

background: Per this abstract Silicene, germanene and stanene are part of a monoelemental class of two-dimensional (2D) crystals termed 2D-Xenes (X = Si, Ge, Sn and so on) which, together with ...
2
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0answers
17 views

Computational tool for identification of activity cliff

Are there computational tools for identification of activity cliff between two analog compounds? This paper list chemotypes that with a high propensity to induce activity cliff.
-1
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1answer
51 views

Drawing bicarbonate ion in different way [closed]

I don't know why can't I draw $\ce{[HCO3]-}$ like that: I tried to draw it like that and checked everything. I checked formal charge and all was good. Why they draw it OH I know its also alright but ...
2
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0answers
71 views

Does H2SO or H2CO have a higher dipole moment? [closed]

Given these two molecules, I realize that the molecules are pretty identical in terms of the individual atoms' electronegativities (with Sulfur only being a small bit higher than Carbon). So then, the ...
1
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0answers
56 views

Bond length comparison in substituted phosphorus pentahalide

What would be the comparison between $\ce{P-F}$ and $\ce{P-Cl}$ bond length in phosphorus tetrafluoride chloride $\ce{PF4Cl}$ and phosphorus trifluoride dichloride $\ce{PF3Cl2}$ in the equitorial ...
0
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0answers
24 views

What is the Lewis dot structure for ozone? [duplicate]

Currently I studying about the Lewis dot structure for different compounds and my textbook says that the Lewis structure for ozone may be drawn as(as shown in the image): And then it goes on to ...
9
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3answers
540 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 ...
0
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1answer
37 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
164 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
38 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
31 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
367 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
47 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
73 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
30 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
205 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!
0
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1answer
77 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
58 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
50 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
32 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
56 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
106 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
60 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
125 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
113 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
41 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
702 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
23 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
235 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
83 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
165 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
38 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
411 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
90 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
64 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
51 views
1
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0answers
52 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
1k 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
187 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 ...