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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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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What “physical method” does Feynman refer to in The Feynman Lectures on Physics (Vol 1)

In the introductory chapter, Atoms in Motion, of the Feynman Lectures on Physics (Volume One), Feynman alludes to a certain "physical method", which can be used to determine the structure of ...
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Interstitial sites: edge and face sharing?

In close packed structures there is one octahedral hole per close packed atom. In a HCP unit cell these octahedra form a chain of face sharing polyhedra. Is this this universal in close packing or ...
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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-...
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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 ...
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Warning during geometry optimization via Gaussian

I have some recurrent problem with my DFT calculations [functional: hseh1pbe; basis:6-31+g(d,p), object: porphyrin derivative]. During the MO setting I get: **** Warning!!: The largest alpha MO ...
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57 views

Type of chirality in polycyclic compounds

Ignoring whether or not this molecule could exist, is there a name for this type of chirality? This molecule's mirror image cannot be superimposed on itself but there are no chiral centres. Even ...
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107 views

Geometry of a free radical at the bridgehead carbon

With reference to J. Am. Chem. Soc. 1968, 90 (19), 5266–5267, they state: The most favorable geometry of aliphatic free radicals remains an unsolved problem, since existing data are consistent with a ...
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41 views

Does a [B4O8]4- anion really exist?

I am currently collecting information for an abstract and therefore I wanted to discuss different $\ce{[BO3]^3-}$ and $\ce{[BO4]^5-}$ connectivities. I also found a book on crystallography and the ...
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94 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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553 views

Difference of aggregate and cluster?

Can anyone tell me the difference of aggregates and clusters from the molecular point of view? Thank you so much.
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1answer
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Geometry of AsF5 molecule

Which of the following is the best description of the arragement of fluorine atoms around the arsenic atom in a molecule of $\ce{AsF5}$? (a) trigonal bipyramid (b) octahedron (c) tetrahedron (...
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2answers
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Geometries of SCl2(OCH3)2 and SF2(OCH3)2

I am not able to understand the difference between structure of $\ce{SCl_{2}(OCH_{3})_{2}}$ and $\ce{SF_{2}(OCH_{3})_{2}}$. I am already well versed with Molecular Orbital and VSEPR theories. I found ...
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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: ...
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168 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 ...
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120 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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54 views

Is azonine planar?

I came across aza[9]-annulene, which is given to be aromatic. I can clearly see it follows Hückel's rule with 8 π-electrons in the ring and the lone pair of nitrogen. But the thing that concerns me ...
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Is there a Python module for calculating Ovality of a molecule?

Ovality gives a measure of how the shape of a molecule approaches a sphere (at one extreme) or a cigar shape (at the other). Ovality is described by a ratio of volume to area (see https://en.wikipedia....
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54 views

Why are branched isomers less polarisable?

This fact was given as an explanation as to why branched isomers of a compound have lower boiling points. How are branched isomers less polarisable and how does this relate to London dispersion ...
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212 views

What exactly are the frontier orbitals in diradical species like O2?

I read about frontier orbitals, namely HOMO, LUMO. But what's exactly HOMO/LUMO? I know HOMO stands for highest occupied molecular orbital and LUMO stands for lowest unoccupied molecular orbital. But ...
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642 views

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 $...
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55 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 ...
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313 views

Do alkenes have priority over alkynes in R/S naming?

I am studying for an upcoming exam and I came upon a confusing question for the drawing of the molecule (3⁠R)-hex-1-en-5-yn-3-ol. Why is the stereocenter (3-carbon) R? Shouldn't it be S? After ...
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154 views

X-ray structure analysis mirrored coordinates?

How to ensure, that X-ray crystallography structure analysis was done right to provide correct, non-mirrored atomic coordinates? Example: Following Wikipedia image, is generated from data taken from ...
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297 views

Compound class naming convention: heteropoly-acid vs isopoly-acid

There are heteropoly-acids and isopoly-acids, two classes of polynuclear compounds with and without heteroatoms within its molecular structures, respectively. These are the names widely used in the ...
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Springer Materials database molecule visualizer's 'crooked' straight-chain alkanes — science or art?

The Springer Materials database includes a molecule visualizer tool: Enhanced data visualization features display interactive crystal structures, data tables, and phase diagrams with export ...
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171 views

What is the structure of diferric hexaphenolate?

I was studying about the ferric chloride identification of phenol, where one product formed is diferric hexaphenolate. But I am having trouble drawing out the structure of it. With ferric ion having a ...
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Porous materials: Is the expression of a mean free path $\overline{\ell}$ of the gas molecule valid for a binary mixtures?

Suppose that I have a binary gas mixture at low pressure. Can I calculate the mean free path $\overline{\ell}$ of the gas molecule in a pores of solid material by substituting a molecular weight of a ...
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How do structural differences between neostigmine and TL-599 contribute to differences in toxicity?

Stevens and Beutel studied the activity of several carbamate anticholinesterases. Among other things, they found that the (4-trimethylammonio)phenyl dimethylcarbamate iodide (The para-analog of ...
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Double Bond Geometry

The double bond at position '4' appears to be showing a 'E' geometry because the priority 1's are on opposite sides of the double bond ie top-left of bond4 is '1' (because Oxygen > Carbon)); bottom-...
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319 views

CAS id to SMILES

How can I convert a list of CAS ids to structures (SMILES). I have been trying (Chemspider API, PubChem and the chemical identifier Resolver) but there are still some ids I can't find the structure. ...
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Can one describe the bonding of Na to F in terms of molecular orbital theory? What about valence bond theory?

I would kindly appreciate an explanation in terms of the two accepted quantum mechanical theories -valence bond & molecular orbitals- for the electronic energy level structure in natrium fluoride $...
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48 views

Steric inhibition of resonance in substituted benzoic acid

Why does attaching an $\ce{-NO2}$ group at the ortho position of benzoic acid cause $\ce{-COOH}$ to become perpendicular to the plane of the benzene ring? Why doesn't the nitro group get pushed out ...
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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 ...
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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.
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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 ...
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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?
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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 ...
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Convert an image of a chemical structure to a ChemDraw file?

Is there a way to convert a bitmap (JPG, PNG) image of a chemical structure to a ChemDraw file so that you don't have to draw a structure you find in a paper yourself?
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What does the dissociative mechanism for cis/trans interconversion of [Mo(CO)4(PPh3)2] look like?

All I can find in the literature is that the cis→trans interconversion proceeds via dissociation of one of the PPh3 ligands resulting in a square-pyramidal Cs intermediate, with the remaining PPh3 in ...
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Theory of symmetry breaking in water?

As we all know $\ce{H2O}$ is bent ($C_\mathrm{2v}$) in its ground state equilibrium structure, rather than linear ($D_\mathrm{\infty h}$), which can be readily understood e.g. from the MO diagram of ...
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Structure of (CH3COO)3Fe

I'm a grade 12 student trying to comprehend MOT & LFT in Co-ordination compounds. For one of our salt analysis(practicals), the test for acetate ion includes the addition of Neutral Ferric ...
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Reading Stereographs

On an old paper, I found an interesting representation of some symmetry operations: stereographs. Online I found a set of symmetry operations and related stereographs (see: http://newton.ex.ac.uk/...
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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 ...
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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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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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Can a structure like this exist?

I was studying carbon compounds and this popped up in my mind:
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Structural entity for the tattoo resembling spine surgery involving 6AL-4V ELI alloy

I have very little background in chemistry, so forgive me if I sound ridiculous and uneducated. I want to have a tattoo designed in honor if my spine surgery that I had. I think that molecular ...
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Looking for a pressure phase diagram of selenium at large ranges of pressure and temperature

I'm doing undergraduate research and our group is having a lot of difficulty finding a comprehensive pressure phase diagram or phase table for selenium (including most known packing geometries that ...
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196 views

How will Back-Bonding affect molecular geometry?

While going through a textbook, I came across the following line: $\ce{R3C-}$ is pyramidal while $\ce{(CN)3C-}$ is planar due to lack of back bonding from the lone pair of carbon atom into the $\pi^...