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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What makes glass so strong?

Recently, I am researching about the structure of glass and how it is so strong. However, I found that glass has an amorphous structure and has irregular crystal pattern. This means that glass would ...
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1 answer
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Formula of what substance is shown in the clip Disappointed by Electronic? [closed]

I'd like to know the substance (if any) the model of which is shown in the clip Disappointed by Electronic. The following screenshot is taken from the video electronicofficial — Electronic - ...
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How does the molecule consisting of two bridged aromatic rings look in 3D?

I can't understand how the following compound with bridged benzene rings looks like:
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Molecular modeling of basic diatomic molecule geometry [migrated]

Can anyone spare me a clue on this? I'm a self-taught student of Molecular Geometry trying to learn more about methods in modeling. After some extensive reading and study, it felt like it should be ...
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Monochlorination of (R)-2-chlorohexane: Number of possible chiral dichloro products

How many possible chiral dichloro products can be formed when (R)-2-chlorohexane reacted with one equivelent of $\ce{Cl2}$ in the presence of UV radiation (monochlorination only)? $$\ce{C6H11Cl + Cl2 -...
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1 answer
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Cl-P-Cl and Cl-S-Cl Bond angles in respective PCl3 and SCl2 compounds

Both $\ce{PCl3}$ and $\ce{SCl2}$ are $\mathrm{sp^3}$ hybrid. $\ce{PCl3}$ has 1 lone pair whereas $\ce{SCl2}$ has 2 lone pairs, so due to more lp-lp repulsion, $\ce{SCl2}$ should have smaller bond ...
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9 votes
1 answer
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Details of what actually happens in cold sulfuric acid between 80 and 90%; what molecular changes cause the viscosity to skyrocket?

AChem's answer to Why does the graph of the electrical conductivity of sulfuric acid/water solutions have this knee in the ~85%-~92% range? includes this plot from Horace E. Darling in "...
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Resource estimate for ab initio calculation [closed]

I have recently come across this very intriguing paper “The Fundamental Vibration of Molecular Hydrogen”. I have asked the authors the following naïve questions directly via email? What was the ...
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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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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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8 votes
2 answers
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When would a R-O-R bond be linear?

While rummaging in my molecular model kit, I noticed that it contains a surprising number of $180^\circ$ oxygen atoms, i.e., oxygen that is meant to be covalently bonded to two partners in a linear ...
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2 votes
1 answer
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Why am I getting a triplet instead of a singlet on NMR for aryl HH2-group?

I am trying to interpret an $\ce{^1H}$-$\mathrm{NMR}$ spectrum on the molecule 4-amino-N-(2-chlorophenyl)benzenesulfonamide that I produced in a lab session. I have managed to assign all the hydrogen ...
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1 vote
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Is there a good citation for the impact of inelastic neutron scattering on the measurement of the intramolecular geometry of H2O?

I have tried to find a good citation for the experimental measurement of the intramolecular geometry of H2O in the liquid phase and come across a problem: It seems that the method of choice for such a ...
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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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1 answer
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Crystal packing prediction for simple organic molecules?

Is it yet possible to predict a simple organic molecule's crystal structure or how the molecules arrange in a crystal without diffraction measurements? By crystal structure I mean, how would molecules ...
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4 votes
2 answers
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Hypothetical symmetric carbon peroxide

Could a hypothetical carbon peroxide $\ce{C5O12}$ with the following structure (MolView — 3D model) exist, and I what its properties would be (other than decomposing, of course)? I tried looking it ...
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Does the process of extraction of chondroitin sulfate change the molecular structure of the bovine source it is extracted from?

I have been prescribed Chondoritin Sulfate for my joints. For religious reasons, I don't have bovine. Hence my question. Does the process of extraction of chondroitin sulfate change the molecular ...
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How to draw Lewis structures of oxoacids?

I know the method of drawing Lewis structures of compounds containing two atom types such as $\ce{CO2}$ and $\ce{SO3}.$ What is the competent method for drawing Lewis structures of compounds like $\ce{...
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6 votes
2 answers
414 views

How does molecular structure contribute in the property of fluorescence?

Fluorescence is the property which is exhibited when electrons emit wavelength of light lower than the one they absorbed so does that mean we can make every molecule to become fluorescent? I wanted to ...
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2 votes
0 answers
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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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7 votes
1 answer
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Caffeine molecule representation and orientation

Almost all the representations of the caffeine molecule that I've come across have the two rings drawn next to each other on the horizontal axis. Any particular reason for this? Would it be sacrilege ...
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6 votes
0 answers
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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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9 votes
2 answers
572 views

Why are there two infrared vibrational frequencies for the terminal CO ligands of Fe2(CO)9?

I am struggling to rationalise why there are two infrared vibrational frequencies ($\pu{2082 cm^-1}$ and $\pu{2019 cm^-1}$) for the stretching of the terminal $\ce{CO}$ ligands of $\ce{Fe2(CO)9}$. ...
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Troubleshooting an Autodock Vina Error on Chimera: "Could not find an atomic number for Hn Hn"

After having minimized a ligand (that I prepared on Marvinsketch), and after having prepared a target enzyme to dock said ligand onto (collected from RCSP PDB), I was met with an error by the reply ...
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5 votes
3 answers
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Orientation of amide bonds in a simplified polypeptide drawing

The syllabus for my course requires I draw protein polymers like this, where the patterned boxes represent different bodies (note that this is an extremely simplified drawing stripped down to its bare ...
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1 vote
2 answers
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Why do CCl4 and CH4 have the same bond angle?

I was reading about the molecular shape of compounds. I learned that the electronegativity of the central atom and the terminal atom in a molecule both play a role in determining bond angle. In $\ce{...
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Contribution, and the way thereof, of the core 6p orbitals of compounds of plutonium(VIII)

According to the NIST database, the ground-state configuration of plutonium(VIII) is [Hg]5f³6p³, when intuitively it should be the same as neutral radon([Hg]6p⁶). Since plutonium(VIII) compounds are ...
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1 vote
1 answer
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Continuous variable for graph of boiling point of different chain lengths

Looking at the boiling points of alkanes (for examples), many graphs plot boiling point against chain length : However, there is an issue with the line of best fit- since chain length is a discrete ...
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3 votes
0 answers
292 views

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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Why this structure is diastereomers instead of enantiomers

In this diagram optical isomers has divided in to 2 categories, one is diastereomers and enantiomers. Is the example for diastereomers correct? For me its looks like enantiomers
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Where can i find accurate bond angles?

I am trying to find places where I can have accurate bond angles of certain molecules such as $\ce{F2Se}$, $\ce{Cl2S}$, or even $\ce{S2Se}. I have looked everywhere and have found only 3 sources that ...
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1 vote
0 answers
59 views

How to determine if all carbon atoms in a cyclic compound lie on the same plane?

I'm currently doing a-levels chemistry and came across a question asking if all 17 carbon atoms in cyclic rings of a cholesterol molecule lie on the same plane. I've done some googling and it turns ...
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3 votes
1 answer
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Error in calculating G-matrix

I have a question regarding the calculation of the $G$-matrix in the classic "Molecular vibrations" textbook by Wilson (1955, McGraw Hill). On page 63 it gives an example for the calculation ...
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2 votes
0 answers
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What dodecahedral molecule is Linus Pauling likely holding in this photograph? Does it have 40 carbon atoms? [closed]

The video Quasicrystals ; Prof. Daniel Shechtman ; Nobel Prize in Chemistry focuses on Professor Dan Shechtman but happens to include some photos of Linus Pauling who never believed in quasicrystals. ...
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1 vote
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What Chemical Database Extensions for Structure and Similarity Search are there?

I am looking for extensions/add-ons for relational databases (RDBMS) that enable storing and handling chemical structures including the possibility for substructure searches and similarity search. I ...
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1 answer
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Is each bag of plastic a polymer/macromolecule? If yes, why does it tear so easily? [duplicate]

For example, polyethene is a macromolecule. So each bag of polyethene should be one molecule. Doesn't tearing it therefore involve breaking strong covalent bonds? Shouldn't the energy needed to do ...
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1 vote
1 answer
208 views

What exactly is giant covalent molecule?

What exactly is the definition of "giant covalent molecule"? All sources online don't give a definition but instead, allude to properties of examples of giant covalent molecules (such as ...
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For a structure of a compouund optically active, what is the number of stereo isomers if no geometrical isomers are present?

Suppose for example the compounds $\ce{M(AA)3}$ and $\ce{M(AA)3bc}$, with $\ce{M}$, the central metal atom and $\ce{AA}$, a bidentate ligand. What is the total number of stereo-isomers of both? I was ...
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0 votes
1 answer
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What is "tail" in case of secondary structure of protein? [closed]

What is a "tail" in the case of the secondary structure of a protein? How does it influence the "protein assignment" task?
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2 votes
2 answers
134 views

Elucidating an unknown compound using 1H- and 13C-NMR spectral data [closed]

I am currently struggling with the following NMR spectrum for this compound: I know for sure that we should multiply the integrals of the hydrogen atoms by four, and that the compound contains at ...
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0 votes
1 answer
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How does addition of side chains affect solubility and processibility of polyphenylene vinylene?

I am studying electrical engineering and physics. In a recent lecture I was told the $\ce{OC1C10}\text{-PPV}$ molecule has the chains added to the oxygen atom down below because it allows for ...
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0 votes
1 answer
79 views

Why do isosteric molecules have similar shapes? [closed]

Isosteres (Definition): Isosteres are atoms, molecules, or ions of similar size containing the same number of atoms and valence electrons.[1] Questions: A. Why ...
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3 votes
1 answer
133 views

What molecule is pictured on the cover of Dead Sara's album "Ain't It Tragic?"

An album released today by Dead Sara, titled Ain't It Tragic, has a chemical structure on the album cover. Here's a close-up of that structure: As the structure is partially obscured, it's difficult ...
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1 vote
1 answer
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Stereochemical relationship between the given compounds

Are the given compounds enantiomers or diastereomers? Or are they identical? The compound is trans-1,2-dimethylcyclobutane: My reasoning is that they are identical. They are not mirror images, and on ...
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3 votes
1 answer
98 views

In the LCAO method for $H_2^+$, why do we only add or subtract orbitals but never alter one of the phases of the orbitals?

TLDR: Atkins' physical chemistry contains the quote "In general, from N atomic orbitals we can build N molecular orbitals". In the case of $H^+_2$, we use a combination of N=2 orbitals to ...
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0 answers
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Mechanism of Action of Carbachol

Carbachol (carbamylcholine chloride) is known to be a cholinergic agent. Does it work as an indirect agonist by inhibiting acetylcholinesterase, as a direct agonist of acetylcholine receptors, or is ...
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2 answers
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What does the prefix tetrahydro mean?

I'm wondering what is the meaning of tetrahydro when used as a prefix. For example, THC (tetrahydrocannabinol) and also THF folic acid (tetrahydro folate) or THF (tetrahydrofuran). I couldn't ...
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2 votes
1 answer
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How to identify 'water' mistakes in protein crystal structures: Are B-factors and occupancy good indicators?

When solving the structure of a protein from diffraction data (x-ray crystallography), it can sometimes be difficult know what should be modelled into small spheres of electron density that are not ...
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7 votes
3 answers
485 views

What is abnormal Beckmann rearrangement?

What is abnormal Beckmann rearrangement? I read this term in one of my solution papers but I am not able to find relevant literature for the same. Answers linking to some source, or giving the ...
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0 votes
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Spectroscopic constants weye and weze

I am using Morse potential to calculate the spectroscopic constants of a diatomic molecule. So far I was able to calculate $R_e$, $\omega_e$, $\omega_ex_e$, $B_e$ but wasn't able to calculate $\...
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