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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Oxygen analogue of benzene [duplicate]

Cyclic ozone is theoretically possible although it has been found in some cases, so is a six-membered oxygen ring (oxygen analogue of benzene) theoretically possible too?
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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
26 views

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. $\ce{SO3^2-},$ $...
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What is the structures of 2-chloro-cis-2,trans-heptadiene? [closed]

I do not understand how to draw this structure. Is cis referring to the arrangement of the chlorine atome?
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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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1answer
42 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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1answer
55 views

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
64 views

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) because in ...
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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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120 views

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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How to know the size of a molecule? [closed]

I'd like to know the size of any molecule; in this case cocaine molecule. I got the 2D and 3D structure, however I need to know an approximately size to represent the molecule as an simple geometric ...
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1answer
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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
62 views

Why is dinitrogen tetroxide a planar molecule?

Why is $\ce{N2O4}$ a planar species in spite of having a σ-bond in between two $\ce{N}$ atoms for free rotation? Does it not form a conformer? Any clarification would be appreciated.
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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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1answer
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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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Phosphine inner structure problem [duplicate]

We all know that phosphine $\ce{PH3}$ is a Drago's molecule. Now, I have heard in my class lecture that since phosphorous is a large atom, it doesn't undergo steric crowdance like $\ce{CH4}$. Thus, ...
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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
45 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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Probability density of a particle in a 2D box with given coordinates

Wavefunction of particle in a $2$D box with sides $L$ in the $x$ and $y$-axis: $$φ = \sqrt{\frac {4}{L^2}} \sin\frac{n_1πx}{L}\sin\frac{n_2πy}{L}$$ For the different states ($n_1=1$, $n_2=2$), (...
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1answer
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What's the definition for mole before Avogadro's constant?

I have been searching for about 3 days how Avogadro's constant is found, and as all of us know the value is determined by division of charge of one mole of electrons (Faraday's constant) by the charge ...
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2answers
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Computing energy of Guassian basis set

Actually, I'd like to compute decay rate using : $$ \Gamma = 2\pi \ | \langle ab|V|cd \rangle|^2 \delta\ (\epsilon_f-\epsilon_i) $$ where a, b, c, d are the MOs and V is coulomb interaction, and $\...
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Is there any software that can do geometry optimization using machine learning?

DFT is a computational tool that is used in optimizing and calculating the electronic structure properties of molecules. Are there any machine learning codes that can do something similar in a ...
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1answer
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Determine and draw planes and axes of symmetry of a molecule using software (VESTA or Mercury)

I designed the $\text{MoS}_2$ molecule (bilayer), with polytype 2H in the VESTA. My goal is to draw the plans and axes of symmetry of the bilayer set. According to the information in the literature, ...
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What is the Structural Activity Relationship of Cocaine?

Cocaine, also known as coke is a widely known drug for both recreational and pharmacological use. What is exactly the relationship of it's structure to it's drug activity?
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What is diamagnetic in diamagnetic dilution?

I'm reading a paper where the authors study a peptide solution where each peptide may have two spin labels attached to them. They put the peptides on the surface and study them using a diamond sensor. ...
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Breaking bonds with magnetic fields

I was wondering if we could break a bond by applying a big magnetic field on a molecule. The magnetic would just cause the spin of cores of the atoms making the molecule to be aligned , raising the ...
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1answer
107 views

Application of the electronegativity effect on bond angles

There's a rule in determining molecular geometry that says that if the electronegativity of the central atom increases, the bond angle of the molecule increases. Is this is only applicable in the ...
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Change in chemical shift of geminal protons in the absence of conformational interconversions

In this post I would like to address a question regarding the chemical shifts of protons which are part of the same chemical environment. It is a known fact that they are not going to split each other ...
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1answer
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Molecular antibonding orbitals energy

When we heat hydrogen the energy of the molecular orbital of H2(1s) is increased .What happens to the energy of the antibonding molecular energy of hydrogen(1s*)?
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Are there any molecular modeling programs that can build materials made up of three or more elements into a cylindrical shape?

I would like to build a material similar to what is in the image below. I have tried programs such as Material Studio, Quantum ATK, and VNL, but most of them can only do materials with 2 elements.
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1answer
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Adding hydrogens to multiple pdb files using Openbabel GUI software [duplicate]

I am completely new to using OpenBabel software. I have about 9000 pdb files to which, I want to add hydrogens. It will be a very hectic task to open all of them 1 by 1 and then convert each of them....
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4answers
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How can you build a model of tetrahedral coordination from objects found at home?

Our college is switching to teaching online mid-semester in hopes of slowing the spread of Covid-19. All the molecular model kits are still on campus. How could you build a model of tetrahedral ...
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If all bond angles in AX₃ are the same, then which of the following are correct conclusions about AX₃?

Question If all bond angles in $\ce{AX3}$ are the same, then which of the following are correct conclusions about $\ce{AX3}?$ (A) $\ce{AX3}$ must be polar. (B) $\ce{AX3}$ must be planar. (...
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1answer
220 views

How to use Google’s Alpha-fold to predict a two-protein complex?

Alpha-fold won the CASP competition last year. It used deep learning to predict the secondary structure of a protein given the primary amino acid sequence. Google has released its code a few weeks ...
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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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1answer
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What is the largest, noncrystalline, non-polymer inorganic molecule?

A question came up in class from one of my chemistry students. He asked what the largest, non-crystal, non carbon-based, molecule is. We ruled out complex proteins, DNA, and other polymers, as well as ...
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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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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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3answers
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Do molecules with bridges through rings exist?

Do molecules with bridges through rings (in a manner illustrated by this) exist? I sometimes get results like this when doing Energy Minimization on molview.org. For example: Is this actually a ...
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2answers
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Substructure search with RDKit

I'm trying to search for substructures with RDKit. I would like to search for structure 1 as substructure in other structures. I don't understand why it doesn't find this structure in structures 3 ...
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2answers
219 views

Do isotopic groups cause optical activity?

I understood the simplified reason for optical activity of a compound based on the difference in the angular velocities of counter-rotating circularly polarized light. The difference is due to the ...
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1answer
72 views

Are there optically active molecules in which all atoms lie in the same plane?

I've learnt that when a molecule is non-superposable on its mirror image, it exists as a pair of enantiomers and is optically active. Absence of plane of symmetry is given to be one of the properties ...
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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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2answers
113 views

Why does strength of bond matter if melting only affects the the intermolecular of the molecules

So as I've been told, when a substance melts, the actual bonds of the substance aren't broken, only the IMFs (inter-molecular forces). So why is it that metal groups decrease in melting points going ...
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1answer
266 views

Geometry of Ni(acac)2

The complex $\ce{Ni(acac)2}$ is paramagnetic as expected , i.e it has two unpaired electrons giving rise to a magnetic moment of $ \sqrt{8}$ BM but doesn't have the tetrahedral geometry consistent ...
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1answer
60 views

What is the correct term of a chemical formula for very large molecules if not just “chemical formula”? [closed]

I know that many molecules, wihch I as a non chemist, might define as "small" if their two dimensional diagram can be sketched on an A4 page, are often formulated; ...
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1answer
21 views

Difference between a species and a phase in a solution? [closed]

Overview: As of my knowledge from metallurgical thermodynamics a phase is a thermodynamically stable and homogeneous entity made up of different species of a given concentration. e.g = 'Austenite' ...

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