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 orbitals energy under pressure

Suppose we have a hydrogen molecule $\ce{H2}.$ At room temperature the average distance of the nuclei is $r_0$ (without applying pressure). If we put $n$ hydrogen molecules in a box with volume $V_\...
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Why is a conformer of hydrogen peroxide rotationally inactive?

Hydrogen peroxide may exist in four different forms depending on the dihedral angle, $d = \angle\,\ce{H-O-O-H}$. The four conformers are: Conformer I with $d = 0^\circ$, Conformer II with $d = 60^\...
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Calculating the apparent molecule length from density of the bulk [closed]

I'm interested to estimate the apparent length of the water molecule assuming it could be approximated as a cube. This is an intentional simplification. Calculating molecule length from volume in ...
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How do you determine the Lewis formula using VSPER theory when one or more double or / and triple bonds occur? [closed]

I have some questions about determining the Lewis formulas of molecules. I basically proceed like this: if a molecule consists of two atoms, I draw it linearly, and select the bond so that if one ...
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1answer
96 views

Are all chiral carbons sp3 hybridised? [closed]

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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1answer
43 views

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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1answer
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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1answer
136 views

How to understand the role of the lone pair on the molecular structure when it participates in resonance?

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 actually in ...
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27 views

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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56 views

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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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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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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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
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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2answers
150 views

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
251 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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66 views

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
75 views

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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1answer
88 views

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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1answer
162 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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1answer
38 views

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
191 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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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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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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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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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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1answer
101 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
138 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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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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35 views

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
61 views

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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95 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
81 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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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
87 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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973 views

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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76 views

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
116 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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33 views

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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