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.

The molecular structure, geometry, or the structure of a molecule is the particular relative arrangement of atoms in a molecule. The term geometry is widely used in , and related branches.

A very common format for sharing geometries are cartesian coordinates (in Ångstrom). For example, in ammonia, $\ce{NH3}$ the structure is well defined by the following code (including the calculated electronic energy at the BP86/cc-pVDZ level of theory).

    4
AMMONIA, BP86/cc-pVDZ:   -56.553652 E(H)
 N     0.000000     0.000000     0.000000
 H     0.000000     0.000000     1.034364
 H     1.006493     0.000000    -0.238496
 H    -0.300271    -0.960659    -0.238496

A geometry can also be shared in different coordinates. The following is a z-Matrix in the Gaussian09 file format. It makes use of the internal symmetry of the molecule.

 n
 h                    1    hn2
 h                    1    hn2      2    hnh3
 h                    1    hn2      2    hnh3     3    dih4     

  hn2                   1.0344
  hnh3                103.3308
  dih4                107.3576

Most commonly the geometry is displayed in a picture:
enter image description here

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Has anyone even taken a picture of a molecule to confirm the geometry predicted by theory?

Have the geometries of molecules been proven, or are we operating strictly on mathematical theory? To put it over-simplistically: has anyone ever taken a picture of a molecule to compare against their math?
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What's the difference between a tetrahedron and a trigonal pyramid?

The shapes respectively denoted by 'tetrahedron' and 'trigonal pyramid' seem to be the same. Is there a difference between the two? If not, why are the two presented as different concepts in introductory chemistry courses?
Hal
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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 bond angle of $171$ degrees. However, this seems…
Tan Yong Boon
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Do molecules with a hexagonal planar geometry exist?

I recently read an article on Wikipedia about pentagonal planar geometry. There are only two molecules with this kind of geometry $\ce{XeF5-}$ and $\ce{IF5^2-}$ and it has two electron pairs at the axial positions. As soon as I looked at this, I…
user8167818
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Are there any chemicals with this structural skeleton?

Is there a chemical that has the bond structure like below? There are 5 atoms linking together. Two of them have 4 bonds. (They are different atoms.) Another two of them have 3 bonds. (They can be either same or different atoms.) The last atom has…
user1290
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Molecule with a quadrupole moment in an electric field

How does an uncharged non-polar molecule that has a quadrupole moment (such as carbon dioxide) behave in an electric field? I know that in a homogeneous electric field, ions travel while dipoles orient along the field (rotate) and non-polar…
Karsten
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What is distorted square pyramidal structure of a compound?

I have recently being studying structures of different types of compounds, when I came across the structure of $\ce{[XeF5]+}$ which have a structure distorted square pyramidal. I could not understand what "distorted" square pyramidal is and how it…
Alex McCoy
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Why does BCF (boron carbofluoride) not exist?

$\ce{BCF}$ (boron carbofluoride, or carbon borofluoride, not to be confused with another so-called BCF molecule that has nothing to do with it) should exist as a vapor molecule with the bonds $\ce{B≡C-F}$, it's simple; but it doesn't seem to exist,…
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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 molecules is unable to undergo Berry…
Russell Ng
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Planar transition-state of proline racemization facilitated by proline racemase

The racemization of proline can be facilitated by the enzyme proline racemase. Since the active sites of enzymes complement the conformation of the transition-states of the molecules they act upon, the most effective enzyme-inhibitors often…
Bob
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correct psilocybin molecular structure

I'm writing a research paper on psilocybin. I need to know the correct chemical structure. When I look online it it shows different ones. There is one with two OH molecules attached to the phosphorous and there is one with one OH and one O-…
Alex
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Pyramid Structure Name

I would like to know what the name is for the structure drawn below. This looks like a pyramid with 4 atoms at each vertex. Does the name of the structure depend on whether the atoms are all the same or if they are a combination of different ones?
mostafa
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what do the asterisks in the molecule stand for?

My 7 year old nephew found a chemistry text book and started copying some pictures and diagrams. He drew this and asked me what do the asterisks mean ? He said he normally sees letters which means atoms. But he can't found an atom that called…
learningtech
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Are there any theorems about packing of atoms in molecules subject to the Lennard-Jones potential?

Related to the problem of minimization of the Lennard-Jones potential in a molecule with $n$ atoms, where $n$ is, say, between $5$ and $10$, questions arise such as (but not limited to) the following: Is it possible to determine a lower bound on…
Jake
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Why is the bond angle of sulphur dioxide close to 120°, not 90°?

Figure 1: Structural data of $\ce{SO2}$. Taken from Wikimedia, where a full list of authors is available. As can be seen from the structural data, the bond angle of $\ce{SO2}$ is almost precisely $120°$, meaning that the σ-orbitals can be described…
Jan
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