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.
124
questions with no upvoted or accepted answers
8
votes
0answers
1k 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 ...
8
votes
0answers
299 views
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 ...
7
votes
0answers
130 views
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 ...
6
votes
0answers
85 views
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-...
6
votes
0answers
102 views
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 ...
6
votes
0answers
2k views
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 ...
5
votes
0answers
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 ...
5
votes
0answers
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 ...
5
votes
0answers
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 ...
5
votes
0answers
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 ...
5
votes
0answers
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.
5
votes
1answer
3k views
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
(...
5
votes
2answers
2k views
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 ...
4
votes
0answers
40 views
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:
...
4
votes
0answers
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 ...
4
votes
0answers
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 ...
3
votes
0answers
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 ...
3
votes
0answers
94 views
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....
3
votes
0answers
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 ...
3
votes
0answers
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 ...
3
votes
0answers
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 $...
3
votes
0answers
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 ...
3
votes
0answers
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 ...
3
votes
0answers
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 ...
3
votes
0answers
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 ...
3
votes
0answers
77 views
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 ...
3
votes
0answers
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 ...
2
votes
0answers
16 views
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 ...
2
votes
0answers
20 views
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 ...
2
votes
0answers
35 views
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-...
2
votes
0answers
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. ...
2
votes
0answers
44 views
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 $...
2
votes
0answers
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 ...
2
votes
0answers
42 views
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 ...
2
votes
0answers
24 views
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.
2
votes
0answers
154 views
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 ...
2
votes
0answers
46 views
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?
2
votes
0answers
225 views
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 ...
2
votes
0answers
2k views
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?
2
votes
0answers
73 views
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 ...
2
votes
0answers
66 views
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 ...
2
votes
0answers
286 views
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 ...
2
votes
0answers
58 views
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/...
2
votes
0answers
141 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 ...
2
votes
0answers
2k 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 ...
2
votes
0answers
43 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 ...
2
votes
0answers
85 views
2
votes
0answers
50 views
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 ...
2
votes
0answers
54 views
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 ...
2
votes
0answers
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^...
