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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59 views

Are all chiral carbons sp3 hybridised?

I had this doubt, whether all asymmetric chiral carbons must necessarily be $\mathrm{sp^3}$ hybridized. For sure, we know that double or triple bonded carbon atoms don't shows such chirality, but is ...
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Wade's rules for Zintl ions

How do you apply Wade's rules to Zintl polyhedral cluster anions ? For example, I believe $[\ce{Bi_3}]^{3-}$ is a triangle. My approach to justify would be: 5 electrons per each Bi atom 3 electrons ...
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How to rationalise the planar structre of I2Cl6?

$\ce{I2Cl6}$ is a dimer of $\ce{ICl3}$. $\ce{ICl3}$ is T-shaped, with $\ce{I}$ being $\mathrm{sp^3d}$ and having two lone pairs. I read in Inorganic Reaction Mechanisms by R. K. Sharma that $\ce{I2Cl6}...
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Finding the molecule with the smallest bond angle in the following lists of elements

For each of the following lists of elements, find (and give a justification for your choice) the molecule with the smallest bond angle: a) $\ce{OSF_2, OSCl_2, OSBr_2}$ b) $\ce{SbCl_3, SbBr_3, SbI_3}$ ...
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59 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 ...
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255 views

Why is the bond angle of trifluoromethane higher than that of difluoromethane?

The bond angle $\ce{\angle(F-C-F)}$ of $\ce{CHF_3 > CH_2F_2}$ whereas that of $\ce{\angle(Cl-C-Cl)}$ is $\ce{CH_2Cl_2 > CHCl_3}$ why is this the case? Some explanations I read suggest the Bent's ...
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Why does a larger bond angle correspond to greater s-character?

In trialkylamines $\ce{NR3}$, the $\ce{R}$ alkyl group attached to nitrogen increases the electronegativity of the nitrogen atom. I also found in this question that this happens due to the repulsion ...
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D and L configuration of monosaccharides

I got this question in the last week's test from Organic Chemistry. I am a bit confused in assigning D and L configuration. Help me understand the topic of D and L configuration and help with this ...
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1answer
249 views

Berry Pseudorotation

I was at a chemistry competition, and one of the questions they asked was on Berry pseudorotation Now the question gave 4 molecules, namely, $\ce{IF5, PF5, PCl5, and XeF5-}$, and asked which of these ...
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How can AuCl3 exist?

The reduction potential for $\ce{Au^3+ + 3e- -> Au}$ is $1.503 \text{ V}$. The reduction potential of $\ce{Cl2 + 2e- -> 2Cl-}$ is $1.36 \text{ V}$. So, the $E^o$ for $\ce{2Au^3+ + 6Cl- -> 2Au ...
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What is quasi-aromaticity?

During my study of aromaticity, I came through this topic of quasi-aromaticity. Can you please elaborate what Quasi aromatic compounds are and how are they designated?
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What is this fluorinated organic substance?

The corresponding author of the paper where this formula was published as appendix passed away. Can someone help me with identifying what is the name of this compound and why have strange zig-zag ...
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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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1answer
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How should I understand the geometry of a lone pair in resonance?

Consider: I'm a little confused as to why we ignore the effect the lone pair has on the geometry of the molecule when it is participating in resonance. Wouldn't it be the case that the molecule is ...
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Where would the lone pairs be placed in a sp3d3 hybrid structure? [duplicate]

$sp3d3$ has a pentagonal bipyramidal geometry. Lets say the structure is of the form that it contains $6$ equivalent bonds and $1$ lone pair. In case of $sp3d$ according to bent's rule the lone pairs ...
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References for the Molecular Distance Geometry Problem

Note: This question has also been posted here. The molecular distance geometry problem (MDGP) consists of two sub-problems: Given observations of noisy distances between atoms in a molecule, ...
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3answers
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How are compounds within a complicated mixture detected?

I was reading an article about an independent pharmaceutical watchdog group called Valisure which recently released a report stating that they found Benzene, a toxic substance, in many bottles of ...
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1answer
137 views

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

Referring to, NCERT Chemistry Part I, Textbook for Class XI[1]. Here the text puts forward three structures of $\ce{ClF3}$. My teacher said to me that (b) structure is unstable due to lone pair lone ...
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1answer
164 views

What is a correct primitive hexagonal unit cell to describe a monolayer of molybdenum sulfide?

I searched the coordinates or reduced coordinates of primitive cell of mono layer hexagonal $\ce{MoS2}$, but there are lots of different structures and coordination. For example, material project give ...
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1answer
414 views

Why does calcium phosphate dissolve at low pH

Why does calcium phosphate dissolve at low $\mathrm{pH}$? What makes its solubility $\mathrm{pH}$ dependent? This question arises after reading about the calcium phosphate bridges in casein micelles ...
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Relationship between molar mass and density in solids

In ideal gases, it's pretty clear that 1 mole of gas occupies 22.4 L at STP. By knowing this, it's easy to calculate density given molar mass. However, this isn't true for solids. If I know molar mass ...
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1answer
249 views

Odd/Even swap rule for chiral compounds in stereochemistry

I had this question asked in my exam, where I was supposed to find if this pair is a diastereomer: Now, I have learnt this rule where: Making odd number of swaps in a molecule means they both are ...
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Basicity Alteration Due To Ortho Effect In Methoxy Aniline System

I wanted to ask something more in reference to this question. Suppose instead of toluidine, 2-methoxyaniline and 3-methoxyaniline are present. Now, why is 2-methoxyaniline more basic than 3-...
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1answer
682 views

Do the groups involved in geometrical isomerism have to be in similar planes to show geometrical isomerism?

In my textbook, under the topic "Conditions for geometrical isomerism", the following has been given: Groups responsible to show geometrical isomerism must be nearly in the same plane. Is this ...
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Major product of the dehydration of alcohols

Well I was doing some questions and I have a bit of confusion on dehydration reaction. For instance, consider following reaction: How do I decide which adjacent hydrogen gets attracted by $\ce{HSO4-}$...
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Predicting product ratio by rearrangement in Dehydration Reactions

I came across this question recently, which would have a clear major product. The OP has given satisfactory explanation for the product ratio, but wasn't sure about the major product. When I was ...
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1answer
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Why are the hydrogen-carbon bonds bent in a graphical depiction of an alkene, but are straight horizontally and vertically in an alkane?

In propane, for example, the $\ce{C-H}$ bonds are depicted by straight vertical and horizontal lines. But in propene, the same bonds are bent. Is it a rule that $\ce{C-H}$ bonds are always bent if the ...
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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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What is the mechanism for this reaction?

The closest reaction I can find is Lossen rearrangement but in that hydroxyamic acid is first converted to its derivative but how will that be possible here? Moreover, even if I make an amine in this ...
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296 views

Determining covalent bond strengths without hybridisation

Assuming pure $\ce{2s}$ and $\ce{2p}$ orbitals of carbon are used in forming $\ce{CH4}$ molecule, which of the following statements is false? (single choice question) Three $\ce{C-H}$ bonds ...
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1answer
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Why is this structure impossible?

I'm asked the following: Explain why the structure $\ce{H-C=C-H}$ doesn't make sense chemically. Not only am I just looking for a check up of my answer, but am I making any sense in what I'm ...
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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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369 views

Compound class naming convention: heteropoly-acid vs isopoly-acid

There are heteropoly-acids and isopoly-acids, two classes of polynuclear compounds with and without heteroatoms within its molecular structures, respectively. These are the names widely used in the ...
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1answer
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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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1answer
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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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550 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
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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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1answer
141 views

Analysis of multiple spectra to determine an unknown structure

I've been trying to solve the structure of a molecule from a $^{13}\ce{C}$ and proton NMR as well as a MS spectrum, but I've been stumped, I've been staring at it for a while with no improvement. I've ...
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Are there square planar complexes with sp2d hybridization?

We were taught (Under the section 'Valence Bond Theory') seven types of geometries a transition metal complex may assume and its corresponding hybridization states, Linear - $\ce{sp}$ Trigonal planar ...
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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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1answer
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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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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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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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1answer
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Geometries of SCl2(OCH3)2 and SF2(OCH3)2

I am not able to understand the difference between structure of $\ce{SCl_{2}(OCH_{3})_{2}}$ and $\ce{SF_{2}(OCH_{3})_{2}}$. I am already well versed with Molecular Orbital and VSEPR theories. I found ...
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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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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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179 views

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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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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2answers
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How to use Google’s Alpha-fold to predict the structure of a two-protein complex?

Alpha-fold won the CASP13 and CASP14 competitions last year and this year. It used deep learning to predict the secondary structure of a protein given the primary amino acid sequence. Google has ...
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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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