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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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0answers
88 views

What is the AXMEN classification for CHBrCLF? [on hold]

What does the Lewis Dot Structure look like like and how can you determine the AXMEN classification for CHBrCLF?
0
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0answers
178 views

Why is the perchlorate anion non-polar?

I just want to confirm that my approach is right. I found that since the hybridisation of this molecule is sp3, the structure is tetrahedral and since all the $\ce{O-Cl}$ bonds are of the same ...
2
votes
1answer
27 views

Automated Identification of Isomeric Relationship from 3D Structure?

Is there a software package that when given two sets of 3D structures can return the isomeric relationship between them? Even if it was only able to state that they are conformational isomers that ...
9
votes
1answer
97 views

How can the solid state structure of cyclopentadienyllithium be explained?

In the solid state, LiCp adopts a polymeric multidecker structure where Li atoms are sandwiched between two Cp rings (shown in this diagram from Organometallics 1997, 16 (17), 3855–3858): If we ...
0
votes
2answers
45 views

Unique carbons on long carbon chains

If we have a long carbon chain like octane for example, do we determine if a carbon is unique by just looking at the immediate surrounding atoms of each carbon (in this case 3 unique carbons), or do ...
2
votes
1answer
302 views

Unique carbons on rings

In rings in general, how do I determine how many unique carbons there are? In this example, I am thinking that there are 2 unique carbons (one on top and one with a double bond) since this molecule is ...
0
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0answers
35 views

R/S descriptors in long carbon chain

I'm trying to figure out how to assign R/S descriptors using a Fischer model without transforming it into a spacial one. What I learned so far is the method to assign it for 'terminal' (I'm gonna use ...
1
vote
1answer
38 views

PCl3 vs SCl2 boiling point

Why does sulfur dichloride have a lower boiling point than phosphorus trichloride? Is it to do with the higher number of electrons causing stronger id-id interactions in PCl3, or do we need to compare ...
2
votes
1answer
29 views

How to determine net charge of a polycation using Wade's rules?

In order to determine the net charge of polycations, which adopt a Wade-like structure (octahedral, trigonal bipyramidal, ...), Wade's rules can be used. For example, the charge $x$ of the ...
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votes
1answer
49 views

Interatomic distances between hydrogens in allene

If $d_1$ and $d_2$ are the interatomic distances between the pairs of hydrogens shown above, what is the relation between $d_1$ and $d_2$? I think that $d_1$ and $d_2$ might be equal since the ...
5
votes
1answer
71 views

Is there an algorithm that takes atom coordinates and produces VSEPR geometries?

That is, you would give the coordinates of an atom, the coordinates of four (for example) other atoms, and it would return "tetrahedral" or "square planar" or whatever. I'm currently writing a ...
-1
votes
1answer
53 views

Molecular Geometry [duplicate]

Why is it that for a molecule with trigonal bipyramidal geometry, the lone pair is located in the equatorial region whereas for a molecular with an octahedral geometry, the lone pair is located in the ...
0
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0answers
104 views

Bond Angle in Diborane, B2H6

Why are the bond angles in the diborane $\ce{B2H6}$ ring much less than $\ce{109.5^o}$? Below is the structure: This source says that the boron atoms are approximately $\ce{sp^3}$ hybridized, so I ...
3
votes
1answer
108 views

How do I visualise bicyclo[4.4.1]undeca-1,3,5,7,9-pentaene?

While reading my organic chem book, I came across this compound: Since this is an exercise question, I do not know the name of this compound. I am unable to visualize this compound (how it looks out ...
1
vote
1answer
69 views

Would an (NH3)2+ molecule be trigonal planar like BH3 rather than trigonal pyramidal?

I've been learning about using MO theory to explain why $\ce{BH3}$ and $\ce{NH3}$ have different geometries and by following the line of reasoning used to rationalise the differences in geometry I ...
2
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0answers
34 views

Which natural orbitals are better for CASSCF calculations for organic diradicals?

I am trying to perform CASSCF calculations for a series of diradicals. As input orbitals I have used two types of natural orbitals. One is unrestricted natural orbitals and the other MP2-based natural ...
1
vote
2answers
57 views

Bond angle in water vs in oxygen difluoride [duplicate]

My teacher taught that bond angle $\ce{H-O-H}$ is larger than $\ce{F-O-F}$ due to less repulsion in the latter's bond pairs. I know that bond angle $\ce{H-O-H}$ is $104.5^\circ$, but I'm confused with ...
1
vote
1answer
108 views

How to systematically find the reducible representation of a molecule? (eg: XeF4)

I am attempting to use the reduction formula to find the irreducible representation of $\ce{XeF4}$ to determine its IR stretching vibrations. I know the point group of $\ce{XeF4}$ is $D_{4h}$ and have ...
2
votes
0answers
94 views

How are bond lengths measured experimentally?

How is the bond length between any two atoms in a compound measured? For example, in the case of graphite, the bond between its two layers is 340 pm. This number must have been measured, so what are ...
0
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0answers
32 views

Why doesn't the arsenate ion have two double bonds?

The commonly described arsenate anion has a double bond between the arsenic atom and one of the oxygen atoms. This makes the arsenic ion have a formal charge of 0, and all of the oxygens have a formal ...
2
votes
0answers
30 views

Determining global minimum structures for ion-water clusters

What is the best way to find the global minimum structure(or get close to it) for an ion and N waters? (i.e. ion cluster in vacuum) For example, consider Flouride ion cluster with N=5 waters. I want ...
1
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0answers
110 views

Lewis structure of ClO radical

The commonly shown structure of the ClO radical described here has a single bond between the chlorine and oxygen atoms. In that structure, chlorine has a formal charge of 1, and oxygen has a formal ...
4
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2answers
143 views

How do I make a ZMAT or XYZ file from scratch?

From a structure representation like the one below for Bacteriochlorophyll A, how do I make the ZMAT or XYZ file? The closest similar question asked here was about converting a PDB entry into XYZ, but ...
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votes
2answers
92 views

Why do aluminum and air have low specific heats?

According to Wikipedia, ...specific heat capacity is a function of the structure of the substance itself. In particular, it depends on the number of degrees of freedom that are available to the ...
4
votes
1answer
59 views

Breaking degeneracy in phosphorus pentachloride

Recently, in a class discussion, the following point was brought up: Although the axial and equatorial bond lengths in $\ce {PCl5}$ are inequivalent, when we consider the time-averaged $\ce {P-Cl}$...
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votes
2answers
127 views

What determines the geometry of Nitrogen to be planar or trigonal pyramidal?

In the following molecule (1-(4-fluorophenyl)-4-[[1-(2-methoxyethyl)tetrazol-5-yl]-phenyl-methyl]-piperazine) I have seen its 3D structure using Jmol, and I see that both nitrogens on the middle ring ...
2
votes
0answers
59 views

Berry Pseudorotation

I was at a chemistry competition, and one of the questions they asked was on Berry pseudorotation Now the question gave 4 molecules, namely, $\ce{IF5, PF5, PCl5, and XeF5-}$, and asked which of these ...
1
vote
1answer
308 views

Comparision of ONO Bond angle in NO2 and N2O4

How can I compare the bond angle between $\ce{O-N-O}$ atoms in $\ce{NO2}$ and $\ce{N2O4}$? In $\ce{NO2}$ there is lone pair-bond pair repulsion, and in $\ce{N2O4}$ there is bond pair-bond pair ...
6
votes
1answer
134 views

Generating geometries for substituted molecules

I would like to automate some of my calculations, and I am looking for a tool to generate reasonable good initial geometries. The details: I have already optimized molecular geometries, and I would ...
7
votes
1answer
82 views

Why does nitric acid have a different molecular structure from phosphoric and arsenic acids?

I remember that this really bugged me as an undergrad, and upon revisiting some inorganic chemistry notes I realized I still don't have a satisfactory answer for it. The structure of nitric acid, $\ce{...
0
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0answers
58 views

Resonance structures for acyl imidazole

I was asked to draw the four resonance structures of the acyl imidazole boxed in the picture. I'm not too confident with drawing resonance structures, so i'm really not sure if the answer i came up ...
1
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0answers
37 views

T shape molecule with three hydrogens

Is there any sort of AX3E2 molecule that consists of hydrogen atoms bonded to the main atom who is left over with two lone pairs of electrons? (Similar to ClF3 just with hydrogen instead of fluorine?)
6
votes
1answer
119 views

Is carbon suboxide planar?

I was asked to comment on the planarity of the carbon suboxide molecule. I thought that the Lewis structure of the molecule looks somewhat like an Allene and must have similar bonding. The two ...
5
votes
1answer
74 views

Dissociation energy of benzene dimer

It is known that the benzene dimer has two stable structures, T-shaped ($\ce{C_{2v}}$) or parallel-displaced ($\ce{C_{2h}}$) structure. Now the question is: does the dissociation energy ($\ce{D_0}$) $...
4
votes
5answers
127 views

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 ...
8
votes
1answer
360 views

How to determine the angle between non-bonding electron pairs?

Is there a way to determine the angle between non-bonding electron pairs that aren't obvious? Take $\ce{H2S}$ for example: The two non-bonding electron pairs would be at the yellow end of this ...
4
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0answers
59 views

π-ligands in trigonal prismatic complexes

We recently had a discussion here about the symmetry problems for the often postulated s- and p-mixing with the d-orbitals in complexes to somehow allow a d-d-transition. It was pointed out back then ...
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0answers
35 views

Is there a known crown ether analog to fullerenes?

It is well known that endohedral fullerenes have potential quantum computing applications example 1,example 2, and example 3. But, currently they are too expensive, around $167 million per gram at ...
6
votes
2answers
796 views

Determine the geometry of each nitrogen atom in formamidinium ion

The geometry at A seems to be straightforward: $\ce{N}$ is surrounded by $\ce{C}$ and two $\ce{H}$'s. By VSEPR, this is trigonal planar. For the geometry at B: $\ce{N}$ is surrounded by $\ce{C}$, two ...
1
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0answers
69 views

Why must the ground state of hydrogen molecule be gerade?

As we know, the electronic ground state of hydrogen molecule is $\Sigma_g^+$. My question is, how do we know it from the theoretical perspective? The nuclear potential in the hamiltonian of hydrogen ...
8
votes
0answers
62 views

How sure can we be about the structure of purine?

While answering the question Basicities of nitrogen atoms in purine, I noticed, that there might be a rapid interchange of the hydrogen bonded to the nitrogen atoms. I have found a crystal structure ...
0
votes
2answers
152 views

Structure of Dolomite [closed]

This the structure of Dolomite. Can someone explain this structure to me?( like what are the blue, yellow etc atoms are? why are they arranged this way?) Any help would be appreciated.
3
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2answers
91 views

Can carbon be the central atom of a complex? Can it form a quadruple bond with itself? [closed]

Why does $\ce{[C(NH3)2]}$ not exist as a complex? Here, $\ce{C}$ is carbon and the configuration of $\ce{C}$ in ground state is $\ce{[He] 2s^2 2p^2}$. Can't the two $\ce{NH3}$ molecules pair the two ...
0
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0answers
45 views

Why is the structure of xenon hexafluoride called “distorted octahedral”? [duplicate]

"Octahedral" is a polyhedron having 8 faces, but this compound has clearly 7 faces. Image from NCERT Chemistry book (standard book in India).
8
votes
1answer
278 views

How to dock aggregated structures comprised of “elementary” protein units like LEGO pieces?

There are proteins with intrinsic symmetries. For example: I was wondering how to use transformations such as: rotations, translation, replications to construct possible structures using 2 types of ...
4
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2answers
101 views

Ice Crystal Matrix measurements of H2O molecules?

I want a mathematically generated 3D STL copy of this image, however it's represent algorithmically. If I do all the H2O's as individual pieces with female connections prepared for chopped bike ...
2
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0answers
74 views

Can a structure like this exist?

I was studying carbon compounds and this popped up in my mind:
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0answers
34 views

Structures of Fe(CO)5 [duplicate]

Why is $\mathrm{d}_{z^2}$ orbital used in hybridisation of $\ce{Fe(CO)5}$ resulting in trigonal bipyramidal geometry?
5
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0answers
39 views

Wade's rules applied to metallic elements

There are many examples of metallic clusters that distort from the structure predicted by Wade's rules to a more 'spherical', closo-like arrangement. For example, $\ce{Bi8^2+}$ is a square antiprism ...
2
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0answers
122 views

3D similarity search software [closed]

What software / webservice can one use to find a compound that has similar 3D structure/dimension to another compound? eg. say we are tying to find a 'better' version of atropine, so naturally we try ...