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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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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Why are the unsaturated fatty acids usually unconjugated?

My textbook gives the structures of the unsaturated fatty acids in food including oleic acid, linoleic acid, linolenic acid and docosatetraenoic acid. I figure that when two or more $\ce{C=C}$ double ...
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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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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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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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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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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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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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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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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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Is N--O--N known to exist?

Commonly, the empirical formula $\ce{N2O}$ refers to the molecule with structure $\ce{N\bond{~--}N\bond{~-}O}$. Is the isomer $\ce{N-O-N}$ known to exist? I'm guessing it is significantly less stable ...
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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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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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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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O-C-O bond angles in carboxylates vs carboxylic acids?

I am wondering how different the O-C-O angle is in a carboxylate vs its acid form. Does it (noticeably) increase because of the electron-electron repulsion caused by an additional lone pair? Bond ...
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Radius ratio of capped octahedral coordination (CN=7)

I was asked to work out the Radius ratio of capped octahedral coordination when CN = 7. How to define a capped octahedral? Is there any restrictions on the lengths of the edges or the distances of the ...
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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 ...
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Eigenenergies and states of Jahn–Teller molecule

I'm generally interested in numerical chemistry. In our lecture, we have discussed the $E \otimes e$ Jahn–Teller molecule with the following Hamiltonian \begin{align} H = \epsilon n_d + \omega ( a^{\...
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Planarity at the Junction between multiple Rings

My Approach: As cyclohexane should be in the chair form and cyclopentane should be in the envelope form, more the number of five-membered rings more should be its planarity, as envelope form is more ...
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3 votes
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Molecular diffusivity of a three-component mixture

I usually used a following expression by Fuller & Schettler & Giddings to predict molecular diffusivities of binary mixtures: \begin{equation} D_i = \dfrac{1\cdot 10^{-4}\left(0.00143\cdot T^{...
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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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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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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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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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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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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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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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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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How do the spin-matrices change in systems without spherical symmetry?

The (non-relativistic) spin matrices of a free electron, with $z$ as the quantization axis, read: $$ \boldsymbol{S}_{x}=\frac{\hbar}{2}\left[\begin{array}{ll} 0 & 1 \\ 1 & 0 \end{array}\right],...
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How to determine positions of groups on compound based on H-NMR spectroscopy (C9H13NO)

Based on the below $\pu{200 MHz}$ $\ce{^1H}$-$\mathrm{NMR}$ spectroscopy, I have to determine the molecular structure of compound $\bf{B}$, which oxidises to a compound $\bf{A}$ with molecular formula ...
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2 votes
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Molecular orbitals energy under pressure

Suppose we have a hydrogen molecule $\ce{H2}.$ At room temperature the average distance of the nuclei is $r_0$ (without applying pressure). If we put $n$ hydrogen molecules in a box with volume $V_\...
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2 votes
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Regarding stability and reactivity of m-xylene

I came across the following two details about m-xylene: m-Xylene is thermodynamically most stable compound among o-xylene, m-xylene, and p-xylene. m-Xylene is most reactive towards nitration and ...
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Differences in AChE inhibition kinetics between paraoxon and methyl paraoxon

According to literature, dimethyl paraoxon has a reaction rate constant for the aging (spontaneous dealkylation) of acetylcholinesterase of $\pu{0.186 h-1}$, a spontaneous reactivation rate constant ...
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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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2 votes
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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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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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2 votes
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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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2 votes
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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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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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2 votes
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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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