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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16
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2answers
695 views

What are the important implications to the field of chemistry, if any, of the recently confirmed hexavalent carbon species?

I’m struggling to understanding the true nature and implications of recent confirmations of the existence of stable species containing carbon atoms bound six (in another case 5) other carbon atoms. Is ...
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0answers
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Structure and bonding in ClO2 [duplicate]

To draw the structure of $\ce{ClO2}$, I tried to find the hybridization of the central atom i.e $\ce{Cl}$. I figured out that there would be two $\ce{Cl - O}$ double bonds, which means $\ce{Cl}$ would ...
9
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4answers
842 views

What free software exists to view molecule pictures within a file explorer?

I am testing my small api library that generates lots of chemical files such as MOL and SDF. I was wondering if there is a software that can show me the pictures of chemical structures inside each ...
8
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1answer
2k 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 ...
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0answers
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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 ...
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2answers
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If salt crystals make a cube shape, what is this 'X' marking?

I am an amateur, with very little professional chemistry knowledge. I was doing a demonstration / experiment with my 6 year old child. We took very warm normal tap water, and dissolved into it a ...
1
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1answer
385 views

What is the criteria for determining structure of a molecule?

Does the shape of the molecule depends on symmetry? Why is the shape of dinitrogen trioxide ($\ce{N2O3}$): (oxidation number of nitrogen atoms: +4, +2) Instead of my proposal, which is much more ...
2
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0answers
46 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 ...
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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
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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 ...
9
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1answer
204 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{...
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2answers
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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 ...
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1answer
182 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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2answers
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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 ...
7
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3answers
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Shape and polarity of the iodate ion

I am trying to figure out the shape of the iodate ion or $\ce{IO3^-}$. No matter how many times I draw it, I keep getting iodine in the centre, and 3 oxygen atoms surrounding it, 2 with single bonds, ...
1
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1answer
3k 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
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4answers
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Constrain bond angle In Gaussian molecular structure optimization

I am computing the optimized molecular structure of an organic molecule in the Gaussian 09 computational chemistry package. As I have it now, I do not think that the optimized structure that I am ...
6
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1answer
154 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 ...
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0answers
57 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?)
7
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1answer
878 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
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1answer
97 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 ($\ce{D_0}$) $...
8
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1answer
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What is the molecular structure of the fragment ion m/z 161 of rosmarinic acid?

Attached is an ESI-MS/MS spectrum of product ion scan of rosmarinic acid (m/z 359.10) (source). I'm trying to figure out the structure of the fragment m/z 161. It's not clear to me what the structure ...
26
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1answer
842 views

Do vinyl cations adopt a classical or non-classical structure?

Whilst reading this question today, I remembered something that I had seen previously here. In the second linked question, @Martin provided a reference to suggest that vinyl cations actually adopt a ...
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1answer
296 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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0answers
127 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 ...
7
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2answers
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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 ...
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1answer
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What is a stereochemically active or inactive s orbital?

In Concise Inorganic Chemistry by JD Lee (4th edition; adapted by Sudarshan Guha), page 73 under the section 3.6 (VSEPR Theory chapter Chemical Bonding): ...according to this theory, the position of ...
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1answer
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How can placing a lone pair in axial position differs from that in equatorial in number of electron domains?

I need help understanding the following statement in my book (regarding trigonal bipyramidal geometry): Placing a lone pair in an axial position would put it at 90 degree to three other electron ...
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1answer
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How can I tell whether or not a molecule is planar?

I am doing several questions involving judgment on the planarity of a compound. Which of the following is not a planar molecule? $\ce{H_2C=C=CH_2}$ $\ce{H_2C=C=C=CH_2}$ $\ce{H_2C=C=O}$ ...
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198 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 ...
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721 views

Molecular weight of Polymers

Addition polymerisation is defined in my textbook as the process in which a molecule or compound is formed by combination of small molecules (monomers) implicitly having greater molecular mass than ...
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2answers
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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.
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2answers
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Hydronium Structure

I was doing an acid-catalyzed mechanism and I ran into hydronium ($\ce{H3O}$) and I wasn't able to figure out why its structure is the way it is. If you look at the structure, you see the hydrogens, ...
3
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2answers
152 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 ...
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3answers
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Why can't oxygen in furan be sp-hybridized?

From the Chem LibreTexts article on Aromaticity and the Huckel $4n + 2$ Rule: So far, you have encountered many carbon homocyclic rings, but compounds with elements other than carbon in the ring can ...
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1answer
642 views

Dipoles and determining molecular (a)symmetry [closed]

What is a dipole? Also, how do you know if a molecule is symmetrical or asymmetrical? For example, are the following symmetrical or asymmetrical? Can you tell just from the molecular formula? Which ...
4
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2answers
335 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 ...
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0answers
91 views

Can a structure like this exist?

I was studying carbon compounds and this popped up in my mind:
10
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1answer
1k views

Geometry of the pentachloridoindate(III) anion

According to Brown et al.,1 the crystal structure of $\ce{[NEt4]2[InCl5]}$ reveals that the pentachloridoindate(III) anion, $\ce{[InCl5]^2-}$, adopts a square pyramidal $C_\mathrm{4v}$ geometry (VSEPR ...
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0answers
335 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 ...
5
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0answers
108 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 ...
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3answers
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Can a molecule contain a linear series of conjugated pi bonds twisted through 180 degrees?

Imagine a long chain of carbon atoms connected by single and double bonds in conjugated fashion. All of the p orbital pi bonds would normally be aligned to either side of the carbon atoms forcing the ...
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0answers
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Why is the bond angle of N-N-N in hydrogen azide not 180 degrees?

Chen and Wang (2009) have reported an $\ce {N-N-N}$ bond angle in the hydrazoic acid molecule of $171.5$ degrees using B3LYP/6-311G** model. The wikipedia page for the molecule also reports a similar ...
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1answer
308 views

Chiral Centers and Stereochemistry

I was just wondering how many chiral centers this molecule has. This question might be a bit simple but I was especially confused by the bottom left "chiral center" that is bonded to a wedged ch3 and ...
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1answer
214 views

Do all the angles change in cyclopropane and cyclobutane or it is only the C-C-C angles? [duplicate]

Are the angles other than the C-C-C angles in cyclopropane and cyclobutane still 109.5° as the acyclic compound, or what?
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1answer
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How to know it when I see a covalent network?

This is a well-known (better said: well-discussed) question in the internet. When you look for answers for popular questions, you usually see them with a variable degree of reliability and complexity. ...
23
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3answers
5k views

What is the geometry of an alkyl radical?

I encountered this question which asks how many possible radicals are formed when $\ce{CH3CH2C(CH3)3}$ is monosubstituted by $\ce{Br2}$. The answer given is 3 while I think it should be 4, reasoning ...
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0answers
2k views

How does the dx2-y2 orbital bond with four ligands in square planar metal-metal complexes

I understand that the complex [Re2Cl8]2- has a bond order of 4 between the ruthenium ions. The bond comprises of sigma interactions between Dz2 orbitals, two sets of pi interactions between dxz and d ...
15
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1answer
208 views

Are there any non-Jahn-Teller type distortions?

My question is essentially, if ANY gradual type of deviation from a higher possible symmetric arrangement of the nuclei in a molecule is covered by the Jahn-Teller model. More specifically I have in ...

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