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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2
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1answer
311 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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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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5answers
770 views

How can I determine the size of this Tropolone molecule?

How can I determine the size of a Tropolone molecule? It's a 7 ring aromatic with O on the 1st C and OH on the 2nd C. Is there some software available? The image is available below.
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0answers
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Why is chlorpromazine not characterized as tricyclic?

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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1answer
33 views

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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0answers
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Why AlCl6-3 and AlBr6-3 does not exist but PCl6- exist?

Both $\ce{Al}$ and $\ce{P}$ is of third period so if $\ce{P}$ can gain extra electron to accommodate 6 chlorine so why $\ce{Al}$ cannot gain 3 electrons for accommodating 6 chlorine? Furthermore as $\...
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0answers
12 views

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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1answer
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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 ...
4
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1answer
42 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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0answers
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What is the molecular geometry of HClO? [duplicate]

I'd like to know the molecular geometry of HClO based on its number of bonding groups on the central atom and the number of lone pairs.
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1answer
146 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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Identifying a given structural formula [duplicate]

I came across this formula and have no idea what it is for: Would someone be able to enlighten me?
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0answers
33 views

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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0answers
76 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
25 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 ...
2
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1answer
139 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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0answers
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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 ...
2
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2answers
53 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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0answers
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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 ...
5
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2answers
121 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 ...
4
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0answers
71 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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1answer
31 views

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 ...
2
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1answer
414 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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0answers
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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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3answers
560 views

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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0answers
39 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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1answer
56 views

Anthracycline nomenclature - doxorubicin [closed]

Why $\ce{-OCH3}$ is Number 3? I think that $\ce{-OCH3}$ Appropriates Number one.
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1answer
47 views

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 ...
5
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2answers
78 views

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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0answers
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
67 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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1answer
51 views

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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2answers
592 views

Why is borole not considered aromatic

I came across a problem which stated that borole isn't aromatic. I thought that borole is similar to pyrrole so it should be aromatic, but that isn't the case. Can I know why isn't it aromatic? I was ...
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0answers
40 views

Normal (Regular) or Inverted Terms?

I have a question on the order of the spin-orbit molecular states. I understand how to find the terms that split from a parent molecular state in a diatomic molecule. But my question is on how to find ...
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1answer
40 views

Do different alkyl groups affect chirality?

I am a bit confused on the definition of a chiral center; A carbon atom is chiral if it has four different items bonded to it at the same time. source However I am not sure whether different alkyl ...
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0answers
33 views

Cross-conjugation and aromaticity in pyrene

I have read about non-huckel double bonds and clar's rule, but what made me confuse is that huckel's perception gives me the feeling that central bonds in polycyclic aromatic hydrocarbons (ex: pyrene) ...
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1answer
22 views

How to interpret BRICS fragments

I have a molecule with a SMILES string as given below. smi='c1ccccc1OCCOC(=O)CC' I want to obtain BRICS based fragments which I did as follows. ...
4
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1answer
148 views

Converting SMILES string into valid sub-strings

I have a SMILES string as follows. smi= 'CCOC(=O)C1=C(COCCN)NC(C)=C(C(=O)OC)C1c1ccccc1Cl' Is there anyway that I convert this SMILES string into valid sub-strings ...
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1answer
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Molecular Structure

What's the meaning of the triangle and striped line in this structure of $\ce{H3O+}$: Can someone suggest me a site to learn about this? (I'm quite a novice in chemistry.) Thanks
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Dipole moments of cis and gem alkenes [duplicate]

The procedure for comparing dipole moments for cis- and trans-alkenes is quite easy, but how to compare dipole moments of 1,1 dichloroethene (1); and cis-dichloroethene (2)? My teacher told me that ...
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2answers
47 views

Aspartic acid conjugate base acidity

Question Which hydrogen among the four in the conjugate base of aspartic acid is most acidic? Answer My attempt I am confused between Hb and Hc I know Hd has $\mathrm pK_\mathrm a \approx 9$, so ...
3
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2answers
113 views

What is the mechanism for this intramolecular SN1 reaction?

What is the mechanism for the following intramolecular $\mathrm{S_N1}$ reaction? For this question, my professor hinted at an intramolecular reaction, and he asked us to recall the bromonium ion as ...
3
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1answer
210 views

Is hybridization of the cyclopropyl anion sp5?

I have read some answers about the $\mathrm{sp^5}$ hybridisation of carbon atoms in the $\ce{C-C}$ bond in cyclopropane as well as the $\sigma$-bond resonance in methylcyclopropyl cation. Overall, the ...
5
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1answer
73 views

How is bond angle of a molecule measured?

Simply, how are (average?) bond angles for simple (or complex) molecules such as methane or ethene measured (determined)? I'm guessing that X Ray crystallography can be used to determine bond angles ...
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0answers
22 views

Any open-source to animate 2D materials in 3D. (e.g. van der Waals heterostructures, 2D crystal layers etc.)

I want to model different 2D nano-structures, layered materials in 3D (animated version). Is there any open source where I can build these structures. Like this:
4
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1answer
53 views

What is the origin of rotational energy barrier in ethane?

What is the origin of rotational barrier in ethane? In most organic chemistry textbooks, we learned that it's originated from steric repulsion between two methyl groups. But recently I heard that ...
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0answers
42 views

$Q_3$ is symmetric with respect to the $\sigma_v$ operation?

I am currently studying the textbook Infrared and Raman Spectroscopy: Principles and Spectral Interpretation, second edition, by Peter J. Larkin. Section 8. Symmetry: Infrared and Raman Active ...
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1answer
51 views

How to control the optimization step size in Gaussian?

I would like to perform a geometry optimization for a weakly bound methane dimer structure with Gaussian 16. During this process, the Newton-Raphson step should be controlled such that its length ...
6
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2answers
441 views

Identification of the organic compound

An organic compound A $(\ce{C10H14O})$ exhibits following characteristics. A) It reacts with metallic sodium to give a colorless odorless gas. B) It is oxidized by $\ce{KMnO4}$ to benzoic acid. C) It ...
1
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1answer
71 views

Steric Effects in Friedel-Crafts Reactions

I recently came across a Friedel-Crafts reaction happening between benzoyl chloride and mesitylene with $\ce{AlCl3}$ as a catalyst. Apparently this reaction doesn't occur due to steric effects even ...

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