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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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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 ...
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0answers
37 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
102 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 ...
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0answers
20 views

Bond formation of C2 [duplicate]

According to the molecular electronic configuration of C-C the remaining molecular orbitals are π2px^2 and π2py^2, does this mean that the first two bonds in C2 are π bonds how is this possible or do ...
1
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1answer
59 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
29 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
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2answers
50 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 ...
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1answer
39 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 ...
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0answers
48 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 ...
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0answers
19 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
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0answers
28 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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0answers
45 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
120 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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2answers
49 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
51 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
81 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
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0answers
38 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
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1answer
172 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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1answer
133 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
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1answer
77 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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0answers
35 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 ...
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0answers
35 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
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1answer
103 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
73 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
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5answers
92 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 ...
7
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1answer
236 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
57 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
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2answers
624 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
62 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
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0answers
61 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 ...
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2answers
114 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
83 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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0answers
39 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
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1answer
276 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
80 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
73 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?
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0answers
37 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
99 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 ...
12
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3answers
790 views

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 ...
9
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0answers
288 views

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
148 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 ...
0
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1answer
79 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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0answers
383 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 ...
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0answers
17 views

Does charge disperse the same way in a molecule as it does in an atom? [duplicate]

For the halide ions, it is known that charge density decreases from the fluoride ion to the iodide ion. This is because the ionic radius increases from the fluoride ion to the iodide ion. The larger ...
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1answer
204 views

Do 1s & 2s orbitals overlap of different atoms while forming sigma bond? I

Do 1s & 2s orbitals overlap of different atoms while forming sigma bond? I think they should overlap as there will not be enough energy difference between them.
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206 views

Why is there only one bond length for sulfur hexafluoride?

In sulfur hexafluoride, there are two 3-centre 4-electron bonds, according to the book I am reading (Essential Trends in Inorganic Chemistry by D. P. M. Mingos). The other two fluorines are bonded to ...
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0answers
31 views

How to find all published Pharmacophore Structure of a Drug target?

Other than literature review how do you find the structures of Pharmacophore of a drug target? I am searching Pyruvate Dehydrogenase Kinase (PDK) inhibitors and I have reviewed lots of literature but ...
3
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1answer
219 views

What are bond lengths and angles for picric acid? [closed]

I am working on a project in which I am required to create a model of picric acid. I do not understand how to find the bond lengths, bond angles, shape, and atom size of this molecule. Any help in ...