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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33 views

What is the 3D shape of an ethane molecule?

I am currently teaching a course on groups, and want to give my students "real life" examples of symmetry groups to think about. The ethane molecule would be one such. But, the on-line ...
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19 views

Why is T-shaped geometry preferred to trigonal planar geometry for the bonds around atoms with 3 bonds and 2 lone pairs?

This is regarding a situation where an atom has five electron domains; two domains are lone pairs, and three are bonds to other atoms. The course materials I am using (focusing on VSEPR theory) ...
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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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Deciding which group twists out of the plane when ortho effect takes place

I'm going to take a few stills from 3D conformers of the following compounds available on PubChem in which ortho effect is applicable to show what I'm referring to. 2-Nitrobenzoic acid: N,N-Dimethyl-...
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What is the difference between a quaternary center and a stereogenic center? [closed]

In other words, can a carbon with 4 substituents be quaternary but not stereogenic? For example, a carbon with an R1 group, an R2 group, and two R3 groups? Thank you!
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Predict the geometry of molecules using MO theory

How can we use MO theory and diagram to predict the geometry of AH3 molecules? I encountered a question which asks to predict the geometries of CH3+, NH3+ and H3O+ whilst I am given the MO diagram to ...
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1answer
60 views

Identifying the molecular structure of compound with sum formula C8H14O3 formula using NMR and IR spectrometry data

I am looking to identify the molecular structure of a compound with the sum formula $\ce{C8H14O3}$ using the NMR and IR spectrometry data below. I was able to figure out the molecule as My friend ...
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1answer
47 views

Lack of elaboration in IR spectra of compounds

I've recently started learning about IR spectroscopy, and a common trend I'm seeing in my textbook and other sources is that not all the features in the IR spectrum are explained in detail. The focus ...
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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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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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130 views

Is it rigorous enough to change a DFT functional after geometry optimization to calculate excited state properties?

I have done the geometry optimization with the B3LYP functional, however, there is a need to calculate the excited state energy, so the CAM-B3LYP functional should be better suited for that. Do I need ...
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What is the geometry of a tri-substituted methyl free radical?

My teacher explained that free radicals could have a geometry that is planar or pyramidal(tending to tetrahedral) based on whether or not it is substituted by lone-pair containing atoms. For example, $...
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41 views

Do changing opt=modredundant to opt in Gaussian makes geometry optimization not to take into account frozen angles?

I am a newbie to Gaussian and just generated an input for the geometry optimization for some molecules with multi ring system. However, in the article that was a reference for those calculations, some ...
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209 views

Is selenium disulfide polar or non-polar?

So I saw in some internet site that $\ce{SeS2}$ is a polar molecule. When I drew the Lewis structure of the molecule, it showed up as a linear molecule like this: $$\ce{S=Se=S}$$ The electronegativity ...
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63 views

How does X-Ray Crystallography determine the components (as opposed to the structure) of a molecule?

Thanks for some online resources (i.e. here) I have an understanding of what X-Ray Crystallography does. By blasting X-Rays at a crystal and recording the scattering patterns on a plate behind the ...
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44 views

Can molecule have just h-bonds between its parts

I'm just starting to study chemistry so sorry for the probably obvious question to you, guys. According to the definition of molecule in Wikipedia: A molecule is an electrically neutral group of two ...
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60 views

Energy levels of combined orbitals

I saw the MO diagram for a NH3 molecule but couldn't understand why the combined atomic orbitals were in the positions they were, and if these positions were fixed. Why is the sigma anti bonding ...
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2answers
127 views

What is intermolecular distance in water? [closed]

I am wondering what is an average intermolecular distance in liquid water (say under normal pressure and room temperature). I need just order of magnitude. A reference would be helpful.
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36 views

What does a filled, solid circle mean in a chemical structure?

I'm looking in a textbook at an asphaltene molecule. The two aromatic rings next to the Nitrogen are shaded. What does that mean? I think the Nitrogen's create delocalized electrons in this ...
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Does the non-serotonin-like half of LSD resemble anything of significance?

LSD's resemblance to serotonin explains many of its effects on the brain, but I noticed only half of it resembles serotonin. The question I have, is does the other half resemble anything, particularly ...
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1answer
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Forcing atoms closer together [closed]

Is there a method in chemistry to alter the energy of atomic bonds by forcing atoms closer together in a smaller volume? Similar to how pressure squeezes atoms closer together.
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1answer
328 views

Why are square planar molecules drawn from the side plane as opposed to the top plane?

Simply put, why can't you draw square planar molecules top down (so you don't have to use depth bonds)?
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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-...
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How can I determine the size of tropolone molecule?

How can I determine the size of a tropolone molecule? It's a seven-membered aromatic ring with =O on the first carbon and -OH on the second carbon. Is there any software available?
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Why is chlorpromazine not characterized as tricyclic? [closed]

Chlorpromazine is an old ("typical") anti-psychotic medication with a chemical structure which I as a non chemist find almost identical to that of all "ine" tricyclic anti ...
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A question about ligand binding

I have done part a and part b but I keep getting a negative concentration for part c. For part a I got $\pu{2 \mu M}$ For part b I got $\pu{5.051 \mu M}$ For part c, I get $2=3.2 + \text{[bound ...
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Examples of application of surface area maximization to crystallography or molecular geometry

Suppose that N points are chosen from the unit ball (or its boundary, the sphere) in three-dimensional space R^3. Consider the convex hull of these N points (assume N is at least 4). The resulting ...
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71 views

If Electronegativity of Cl is greater than H2 then why is the bond angle of Cl2O greater than H2O? [duplicate]

If Electronegativity of Cl is greater than H2 then why is the bond angle of Cl2O greater than H2O? Cl2 has more EN than H2 and size of Cl2 is more than H2 but if we go according to EN then more angle ...
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47 views

how to obtain potential curves from database?

I'm sorry if this is a really super basic question. I am looking at the potential curves of a diatomic molecule in a book , and to plot them. I google the molecule and got to the NIST website, there I ...
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848 views

Maximum number of coplanar atoms in difluorotrimethylphosphorane

In $\ce{PF2(CH3)3},$ what is the maximum number of atoms lying in one plane? $\ce{P}$ is the central atom with the hybridization $\mathrm{sp^3d}.$ Two $\ce{F}$ atoms will form axial bonds with it, ...
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How to use Clausius-Mossotti equation to determine the molecular structure of a compound? [closed]

A question in my exam came as follows: Explain the Clausius-Mossotti equation. How is it used in establishing the molecular structure of a compound? I have studied the Clausius-Mossotti equation and ...
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79 views

How to use NMR readings to determine the molecular structure of a compound? [closed]

A question in my exam came as follows: How is NMR used in the determination of structure of organic compounds? I have studied NMR spectroscopy and I know how to determine values using an NMR ...
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1answer
27 views

How to remove CH3 labels from a molecule's image? [OpenBabel in Python]

I would like to remove CH3 labels from svg images generated in openbabel in Python. I am thinking I should use ...
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1answer
209 views

How many covalent bonds are there in carbon suboxide?

Calculate the number of covalent bonds in $\ce{C3O2}$. Structure: I am confused. I can count covalent bonds as 8 by counting single-single bonds, but also I can say that there are 4 "double ...
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What do you call different formations of polycyclic molecules, such as the 'bent' phenanthrene vs. the 'linear' anthracene?

Are there terms, IUPAC or not, that describe multiple carbon rings fused in different shapes, like the aforementioned anthracene and phenanthrene? Also, I thought I read about a term describing carbon ...
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2answers
69 views

Effective core potential and Gaussian basis set

Is using the effective core potential (ECP) and Gaussian basis set simultaneously in ab initio calculation a valid approach? For example, is it correct to use ECP for one of the atoms and, instead of ...
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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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154 views

Molecular structure of iodine nonoxide

A question in an exam was as follows: Iodine reacts with ozone gas to form a dark yellow solid $\ce{X}.$ Let the number of lone pair of electrons in un-ionised form of $\ce{X}$ be $m,$ number of lone ...
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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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Change of ionic packing upon crystals are pressurized

When rock salt crystal is pressurized, its FCC structure changes to BCC structure whereby coordination ratio changes from 6:6 to 8:8. At the same time packing efficiency of the crystal decreases from ...
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1answer
420 views

Can the molecule POOF exist?

Obviously, it really would be $\ce{O=P-O-F}$. Since $\ce{F-O-O-F}$ exists the $\ce{-O-F}$ part is obviously possible and the rest of it doesn't strike me as unreasonable, but whether it can actually ...
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Why can't an “upside down” chiral molecule neutralize the polarized light effect? [duplicate]

Steve Mould did a nice video a few months back called "Why Sugar Always Twists Light To The Right" (link is timestamped at the critical part). However his explanation was not complete. He ...
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What do (2S,3S) and similar notations mean?

When my textbook is discussing stereoisomers with more than one chiral centers, it's using notation like (2S,3S) being an enantiomer with (2R,3R) and so forth. I understand R and S configuration, and ...
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72 views

ATP chemical structure: phosphate groups with Oxygen anions or with OH groups?

I've googled repeatedly (with multiple search queries) to try and get an answer to this question but nothing comes up. Embarrassingly, I seem to be the only person who is confused by: ATP with oxygen ...
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57 views

Anthracycline nomenclature - doxorubicin [closed]

Why $\ce{-OCH3}$ is Number 3? I think that $\ce{-OCH3}$ Appropriates Number one.
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Is a tautomer's stability compared with refernce to its initial compund [closed]

Considering the following example while comparing the enolic content in the product, am I supposed to compare its stability with reference to its initial state or am I supposed to compare it between ...
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How is nomenclature decided in this case (formyl vs oxy)?

I was asked the IUPAC Name of the following compound in JEE Mains (2nd September, Shift 1) 2020. There were two names occuring to me: 5-formyl-2-methyl-hex-2-enoic acid (2,5)-dimethyl-6-oxo-hex-2-...
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37 views

What is one formula unit? [duplicate]

I am really sorry if this is a beginner question but please still help me. In this website, which explains balancing chemical equations mentioned the word formula unit here: $\ce{3Ca(NO3)2}$ (just ...
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1answer
98 views

Book Recommendation for Molecular Orbital Theory [duplicate]

I posting my question here since I have seen similar questions but I haven't found the specific answer I am searching for. I am seeking textbook recommendations on Molecular Orbital Theory with ...
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Sucrose skeletal formula - missing Carbon and Hydrogen [duplicate]

I was reading the Wikipedia article about Sucrose, when I noticed that the skeletal formula was missing some $\ce{C}$ and $\ce{H}$ atoms. The chemical formula being $\ce{C12H22O11}$, I counted the $11$...

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