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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Molecular Orbital Diagram

Chemists have revealed that $1 \lambda^{2}, 2 \lambda^{2}$ -disilene $\left(\mathrm{Si}_{2}\right)$ is diamagnetic while disulfur $\left(\mathrm{S}_{2}\right)$ is paramagnetic $(\mathrm{S}=1)$. Draw ...
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Why do both bonding and antibonding molecular orbitals exist at the same time when two waveforms could only be in-phase or out-of-phase?

I am quite confused concerning the existence of both bonding and antibonding molecular orbitals. I understand from previous posts that the number of orbitals has to be conserved, and thus when two ...
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What does “the natural bond angle” mean in the context of Universal Force Field (UFF) potential energy calculation and how are bond angles calculated?

As the title says, what does "the natural bond angle θ0" mean in the context of Universal Force Field (UFF) potential energy calculation? The reference appears in section D. Angular ...
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Why does dilithium have a longer bond length than dihydrogen?

I've tried MO theory however they both have a bond order of 1. Which means we can not relate the bond order to the bond length. My thinking - I think that the h2 bond length is shorter due to only ...
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Does anyone know what program was used to make this molecular structure picture? [closed]

I am a quantum chemistry beginer, and this picture color scheme is classic. I wonder how to make such pictures by myself.
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Why is the shape of sulphates and perchlorates such that lattice enthalpy doesn't decrease down the group? [duplicate]

The solubility of carbonates, bicarbonates and hydroxides of s-block elements increases down the group. But, the solubility of their sulphates and perchlorates decreases down the group. The reason for ...
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Differences in AChE inhibition kinetics between paraoxon and methyl paraoxon

According to literature, dimethyl paraoxon has a reaction rate constant for the aging (spontaneous dealkylation) of acetylcholinesterase of $\pu{0.186 h-1}$, a spontaneous reactivation rate constant ...
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Why is the dihedral angle of solid hydrogen peroxide less than that of gaseous? [duplicate]

Hydrogen peroxide has an "open book" structure: The dihedral angle in gaseous H$_2$O$_2$ is close to what we might expect in a tetrahedral arrangement. However, in solid H$_2$O$_2$ it's ...
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Diatomic molecule under pressure

If we put a diatomic molecule under pressure the interatomic distance will be decreased and according to this graph the potential energy of the bonding molecular orbital will be increased. What will ...
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Net direction of dipole moment in oxygen difluoride

What is the net direction of dipole moment in $\ce{F2O}$ molecule? In the case of $\ce{NH3}$ and $\ce{NF3}$ molecules both have net dipole moment with direction reversed due to strong ...
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Structure-Activity Relationship of Chlormephos and Parathion

According to the book "The Chemistry of Organophosphorus Pesticides", the insecticide Chlormephos (S-(chloromethyl) O,O-diethyl phosphorodithioate) has an oral LD50 in rats of 7 mg/k. ...
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Comparing O−O bond length in hydrogen peroxide and dioxide(2−) ion

Problem How can we qualitatively compare the bond lengths between $\ce{H2O2}$ and $\ce{O2^2-}?$ Answer Attempt I tried using molecular orbital theory, but since both have peroxide $\ce{O2^2-},$ the ...
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Are phenyl and allyl groups in prop-2-enylbenzene coplanar?

Wouldn't C1 and C2 in prop-2-enylbenzene be on the same plane as that of the phenyl ring, right? If the double bond connected to C2 was between it and C1, they would be, but is it correct that now ...
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Help understanding how “steric effects” are distinct from “electronic effects”?

@jakebeal's excellent answer to Why do animal cells “mistake” rubidium ions for potassium ions? includes the following passage: In the case of potassium versus sodium, which are both very important ...
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How do point mutations affect complementary base-pairing and widths of the nucleotide pairs?

Point mutations are divided into two categories: transitions and transversions. Since point mutations only occur during DNA replication (an integral process of both mitosis and meiosis), the mutated ...
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How are there two C3 rotation axes in ammonia?

If we look at the character table for the $C_\mathrm{3v}$ point group (which $\ce{NH3}$ is an example of), we see that these are the symmetry elements ${E, 2 C_3, 3 \sigma_v}$ present in the molecule. ...
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Is N--O--N known to exist?

Commonly, the empirical formula $\ce{N2O}$ refers to the molecule with structure $\ce{N\bond{~--}N\bond{~-}O}$. Is the isomer $\ce{N-O-N}$ known to exist? I'm guessing it is significantly less stable ...
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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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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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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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53 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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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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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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391 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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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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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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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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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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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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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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330 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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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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118 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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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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957 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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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
28 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
272 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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