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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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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Order of stability of allotropes of phosphorus

I want to know the stability order of allotropes of phosphorus. Upon searching I realised that two types of stabilities are defined in their case kinetic thermodynamic But I am somewhat confused (...
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Lewis structure of R-COO-Na+ [closed]

I am studying Lewis structure and I have a question about an excercise. The question asks what is the Lewis structure of $\ce{R-COO^-Na+}$. I don't know how to draw it correctly.
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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 ...
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2answers
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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 ...
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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 ...
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Existence of an organic compound with carbon having six bonds [duplicate]

This article claims that scientists have found a compund where a carbon atom forms 6 bonds, by eliminating, through some means that the article doesn't talk about, 2 electrons from the ...
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64 views

Relations between different types of conformers [closed]

I am learning the classification of anti/gauche, staggered/eclipsed & anti/syn in conformation, but I feel my concepts are wrong: Question 1 During the addition of $\ce{Br2}$ to an alkene, only ...
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Ambiguity in ortho versus para product [closed]

In A Guide to Reaction Mechanism by Peter Sykes, Pg-150, there is a paragraph that states: [...] Thus nitration of nitrobenzene (Y=$\ce{NO2}$) is found to result in a mixture of $93 \text{%}$ m-...
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1answer
63 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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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:
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1answer
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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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$Q_3$ 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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Why does thionyl tetrafluoride have a double bond to oxygen rather than a single bond?

Why does the sulfur atom have a double bond to the oxygen in the $\ce{SOF4}$ structure, rather than a single bond? I think oxygen would still have an octet either way. When drawing the Lewis structure,...
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1answer
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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 ...
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1answer
61 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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Which of the compounds has the highest percentage of enol? [closed]

Which of the compounds has the highest percentage of enol? $\ce{CH3-CHO}$ $\ce{Ph2-CH-CHO}$ $\ce{Ph-CO-Ph}$ Parabenzoquinone How do I compare these?
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What is the CNC bond angle in methyl isothiocyanate?

According to VSEPR theory, for $\mathrm{sp^2}$ hybridisation the bond angle is approximately $120^\circ$. In $\ce{H3CNCS}$, the nitrogen has one lone pair. As lone-pair-bond-pair repulsion is greater ...
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1answer
84 views

Why is methyl parathion less toxic than ethyl parathion?

According to the PubChem pages on ethyl parathion and methyl parathion (pages 11 and 12 of the toxicity section, respectively), methyl parathion is significantly less toxic than ethyl parathion. The ...
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Is there a geometrically intuitive explanation of the equivalence of the numbers of irreducible representations and symmetry classes?

In group theory, as used in chemistry, we’re familiar with the idea that the number of irreducible representations of a symmetry group equals the number of classes of symmetry operations, e.g. three ...
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Hypervalency of orthonitrate

I have always believed that it is impossible for the atoms of period 2 elements (when they are the central atoms in polyatomic ions/molecules) to accommodate more than 8 electrons in their valence ...
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1answer
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Does Genistein remain in resonance stabilised form in physiological pH or acidic pH? [closed]

As a follow up, does the Carbonyl group at 4 position group get deprotonated or Hydroxyl group at 5 position get deprotonated? How does the resonance structure look? I have been looking through ...
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Difference between Soap and Detergent

In most articles and texts that I've read, soaps and detergents seem to be talked about collectively. I know that they are both surfactants and that soaps are usually natural, in comparison to ...
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How to compare three or more molecular structures? [closed]

Let's say you have three or more different geometry files (xyz) for the same structure and you want to compare them. What would be best way for that?
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1answer
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How to draw the structure and find the oxidation number of Phosphorous in H2P2O7 [closed]

Find the Oxidation number of Phosphorus in $\ce{H2P2O7^2-}$. So I thought of drawing the lewis structure to find the oxidation numbers. Because I wasn't sure if Oxygen was bonded to a Hydrogen or not. ...
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1answer
279 views

Do we consider the spatial orientation of a molecular orbital while assigning plane of symmetry?

I am following the video lectures by Neeraj Saini sir and in this video$^{\dagger}$ he said that $\ce{CO2}$ has infinite planes of symmetry. But I think that if we take into account the orientation of ...
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In what way trans alkenes are more symmetric than cis alkenes?

While providing the reason for the higher melting point of trans molecules, everyone says that trans molecules are more symmetric than cis molecules. An example can be found over here, where the OP ...
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1answer
169 views

Identify the structure of compound with C₉H₁₀ formula using IR and NMR data [closed]

Use IR and NMR data to define the structure of the molecule, the formula of the given structure $\ce{C9H10}.$ On what basis do we conclude that its structure is that (the answer) only? On what points ...
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SMILES string convertors

I'm new to SMILES strings, and have noticed that they're not standardised. Firstly, what is the reason for different structures of SMILES strings to represent the same compound? Why not have a ...
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1answer
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C₂ axis of symmetry in 1,3-dichloroallene

Is there an $C_2$ axis of symmetry in $\ce{Cl-CH=C=CH-Cl}$? A $C_2$ axis of symmetry means that I should be able to rotate the molecule about an axis by $180^\circ$. But I would need a composition ...
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47 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. ...
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1answer
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What is the structure of CF3 radical? [duplicate]

In the class, I was told that $\ce{H3C^.}$ has a trigonal planar structure with the unpaired electron in $\mathrm{2p_z}$ orbital. But $\ce{H3C -}$ has a trigonal pyramidal structure. But why does ...
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Will ipso substitution work in both cases of vanillic and isovanillic acids here or not?

What will be the product of the 2 reactions when bromine is taken in excess? I think ipso substitution will work here and there will be two $\ce{Br}$ substituting in both products, but in the book it ...
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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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Alternative python modules to RDKit to convert SMILES to structure

Python module RDKit is great, but it cannot be installed by pip, and therefore it is difficult to use it sometimes in a virtual environment. I am wondering that if ...
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1answer
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Fastest way to determine if molecule has resonance structures [closed]

I came across this old exam problem: For which of the following choices, is every molecule a resonance hybrid with resonance structures? A. $\ce{SO2},$ $\ce{NH3},$ benzene B. $\ce{SO3^2-},$ $\ce{NH3},...
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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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49 views

An automated approach to visualize several xyz structures

I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.
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How to draw the 2D representation of ammonia molecule

In the 2D representation of the ammonia molecule, we see one solid line, one solid triangle and one dashed triangle A plane can be made to pass through any three given points. In other words, we can ...
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1answer
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Carboxylic acid bond lengths in 3-carboxycyclobutane-1-carboxylate

Select correct order of bond length of the above bond P, Q, R & S: (A) P > R > S > Q (B) Q > R = S > P (C) S > Q > R > P (D) None of these I think the answer should be (D) ...
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Would it be accurate to say that hydrazine (N2H4) forms dative bonds with H+ ions?

I understand that the lone pair on the 2 nitrogen atoms allows N2H4 to form hydrogen bonds with other hydrazine molecules, but a question in my chemistry worksheet indicated that N2H4 forms dative ...
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MolView is unable to generate correct 3D structure for hydroxypropadiene

MolView is unable to generate the correct structure of hydroxypropadiene. It instead generates the structure of acrolein (which has the same molecular formula). Why is this so? Is it because ...
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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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1answer
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On the assignment of axial and equatorial to substiuents of polyhexacyclics

Must the assignment of axial and equatorial substituents of polyhexacyclics always be with respect to each six-membered ring or is there a shorthand? For example, how would X, Y, and Z be assigned ...
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1answer
108 views

Bonding and coordination of oxygen in a Ga2O3 crystal structure [duplicate]

I'm trying to find the crystal structure of gallium oxide ($\ce{Ga2O3}$). However, I find the images of the crystal structure in the peer-reviewed journals problematic. First, I hop to the wikipedia ...
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1answer
88 views

Why is dinitrogen tetroxide a planar molecule?

I was wondering why $\ce{N2O4}$ is a planar species in spite of having a σ-bond in between the two $\ce{N}$ atoms for free rotation. Does it not form a conformer?
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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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Can MCM-41 (mesoporous materials) be used for ion exchange?

Wikipedia, and this journal article talk of a microporous and mesoporous material MCM-41. Although MCM-41 has dynamic sized pores which can be changed, but it is hydrothermally unstable. Can this ...
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How to calculate Wiener index for aromatic and cyclic organic compounds?

I have been searching for literature on calculating the Wiener index for aromatic and cyclic organic compounds. For acyclic aliphatic compounds the methodology is straightforward obtained from ...
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1answer
46 views

What is the name and formula of this structure? [closed]

Could anyone please let me know the formula and name of this structure? Any answer is helpful. Could you also summarize how to deduce the formula? Here is an image:

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