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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150 views

Thermal properties of 301 stainless steel

So I know that 301 stainless steel was chosen for the SpaceX Starship rocket as it can handle high temperature differences. What about this alloy makes the steel harden when it gets colder?
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How do steric effects affect inductive effect in compounds with tetravalent nitrogen?

I want to compare the electron density on methyl group between tri‐tert‐butyl(methyl)azanium (1) and triisopropyl(methyl)azanium (2), i.e. essentially the inductive effects of $\ce{-\overset{+}{N}R3}$ ...
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Synthesis of 1-naphthaleneacetic acid: Methods

I am trying to synthesizing 1-naphthaleneacetic acid from naphthalene and monochloroacetic acid. I found some patents and papers, and I have tried to synthesis but the yield is low. I used iron powder ...
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Why is F a bad leaving group? [closed]

Why is F a bad leaving group? I thought that a good leaving group is one that tends to leave easily (=strong acid or weak base) and is stable (ergo a weak base or a strong acid). So wouldn't F be a ...
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1answer
168 views

Assigning E–Z configuration for alkenes with cyclic substituent groups [duplicate]

I was taught that according to CIP rules, we must check the priority order for the substituents. But how can we do the same for molecules with cyclic groups as substituents? How do we compare the ...
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small negative frequencies in DF T optimizations with organic molecules containing CF3 groups [duplicate]

When optimizing by DFT medium-sized organic molecules containing aromatic CF3 groups (for example, adducts involving takemoto's catalyst), the frequency calculation on optimized structures have always ...
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28 views

Relation between the number of hybridised orbitals and the number of sigma bonds

March's Advanced Organic Chemistry (8th Ed.), has in its first chapter several tantalizing statements of the following variety; Boron has only three valence electrons available to form bonds, hence ...
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1answer
92 views

How to find the largest cyclic substructure with RDKit?

I have a bunch of structures and of each I would like to find the largest cyclic substructure. I'm not a chemist, so I don't know if there is a common terminology for this. I hope, I made it clear ...
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Regarding stability and reactivity of m-xylene

I came across the following two details about m-xylene: m-Xylene is thermodynamically most stable compound among o-xylene, m-xylene, and p-xylene. m-Xylene is most reactive towards nitration and ...
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34 views

Is there a computer program capable of showing protein conformational changes based on pH?

As it is known, changes in pH change the attractions between the groups in the side chains of the protein. Acidification can, for example, cause protonation of the $\ce{COO-}$ end to $\ce{COOH},$ ...
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Molecular diffusivity of a three-component mixture

I usually used a following expression by Fuller & Schettler & Giddings to predict molecular diffusivities of binary mixtures: \begin{equation} D_i = \dfrac{1\cdot 10^{-4}\left(0.00143\cdot T^{...
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Where do I find data on 'molecular membership' sequences?

Techniques such as isotopic labeling allow for radioactive tracing of an element through a sequence of molecules. Using analytical instruments (such as LC-MS) we can then find out where labelled atoms ...
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Enantiomers or identical structures?

What is the relationship between the following pair of molecules? Is the underlined answer correct? Explain. I'm getting mixed answers. Some say these are identical molecules. Other say these are ...
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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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1answer
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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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32 views

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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1answer
96 views

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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1answer
82 views

What qualifies to be considered as a lone pair-lone pair repulsion?

Referring to ncert, Textbook for class XI Chemistry part I, pg no. 117 (At the top) Online downloadable one shows it to be pg no. 113. Here the text puts forward three structures of $\ce{ClF_3}$. My ...
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39 views

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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2answers
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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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1answer
84 views

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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1answer
80 views

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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2answers
647 views

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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1answer
64 views

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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2answers
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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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1answer
103 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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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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1answer
59 views

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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1answer
369 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
57 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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64 views

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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1answer
160 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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1answer
133 views

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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1answer
129 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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2answers
525 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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1answer
108 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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1answer
57 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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1answer
67 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
381 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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45 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
56 views

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
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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