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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Hybridized orbitals and molecular orbital theory

When hybridization was introduced in the late 30's to explain the structure of methane , first it was considered that bonds between valence electrons of carbon in different atomic orbitals will have ...
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Given a molecule, is it possible to predict changes in its geometry? [closed]

Applying high temp and pressure to graphite turns it into diamond, which means the molecular structure goes from trigonal planar to tetrahedral. Does it naturally take the tetrahedral shape? Diamond ...
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How many condensed tetracyclic aromatic hydrocarbons are there? [closed]

Recently I have been asked to sketch the chemical structures for every condensed tetracyclic aromatic hydrocarbon. I have managed to find 7 structures, but my chemistry teacher's solution was ...
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166 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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54 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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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
160 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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55 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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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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184 views

Flexibility of long-chain aliphatic compounds

PubChem is unable to generate the conformers of Z-6-Heneicosen-11-one? The website says that the molecule is too flexible What does flexibility of a molecule mean in this context? I understand that ...
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Why are basal bonds longer than apical bonds in square pyramidal structure?

In trigonal pyramidal molecules such as $\ce{SF4}$, the axial bonds are longer than the equatorial bonds because of the 3c-4e bond. But in square pyramidal molecules such as $\ce{IF5}$ and $\ce{BrF5}$,...
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Optimization completed on the basis of negligible forces

I am performing relaxed scan in Gaussian (B3LYP/6-31G(d,p)). There are two small organic molecules, one of which is a radical, the other has a benzene ring. I'm trying to understand the optimization ...
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Why does SiH4 have unusually large bond angles?

The bond angles of $n > 2$ hydrides are usually around $90^\circ$, such as $\ce{PH3, H2S},$ $\ce{H2Se},$ $\ce{H2Te}.$ I understand that this is from increased $\mathrm{p}$ character in the bonding ...
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275 views

How can an Organic chemist know the chemical formula of a natural product she isolated from an organism? [closed]

As a non scientist I several times wondered how can an Organic chemist successfully isolate a single molecule which a natural product of an organism; Whether a plant-part/mushroom-part/algae-part or a ...
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Why do PBr3 and PCl3 have larger bond angles than PH3?

According to the Colby Chemistry Database, the bond angle of $\ce{PBr3}$ and $\ce{PCl3}$ are around $101$ degrees, but the bond angle of $\ce{PH3}$ is $92$ degrees. (Source: PCl3 PBr3 PH3) There was ...
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Why are Newman Projections drawn with 120 degrees when actually sp3 carbons are 109.5 degrees?

Title says the question, pretty much. For example, in the Newman projection of ethane, the carbon hydrogen bond angles are $120$ degrees, not $109.5$ degrees, as they actually are in an $\text{sp}^3$ ...
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Structure of CCl₂

I read that $\ce{CCl2}$ is non-polar. When I read about the reason on the net it stated that $\ce{CCl2}$ has a linear structure, but according to VSEPR theory it should have bent V-shaped geometry. ...
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Why there is a huge difference between the basicity of urea and guanidine?

The two molecules have very similar structures, but urea has a $\mathrm{p}K_\mathrm{b}$ of $13.9,$ while guanidine have a $\mathrm{p}K_\mathrm{b}$ of $0.4.$ If guanidine cation can be stabilized by ...
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54 views

Why is the Sulphur Dioxide molecule polar? [closed]

I am in 12th standard and was revising the concept of determining which polyatomic molecule can be polar and which can be non polar. So when this example was given we were told that vertical dipole ...
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Why is the bond angle of sulphur dioxide close to 120°, not 90°?

Figure 1: Structural data of $\ce{SO2}$. Taken from Wikimedia, where a full list of authors is available. As can be seen from the structural data, the bond angle of $\ce{SO2}$ is almost precisely $...
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Software to assist drawing of complex, three-dimensional skeletal formula from scratch or from existing crystal structure

Is there a tool that would help in creating rather intricate line drawings (not pre-rendered balls-and-sticks/wireframe/sticks/ORTEP diagrams) for a skeletal formula in 3D space? To illustrate the ...
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Structure of dihydrogen peroxy-phosphate ion

In structure of Dihydrogen peroxy-phosphate ion $\ce{H2PO5-}$, shouldn't negative charge be on oxygen linked directly to phosphorus, rather than on oxygen linked through peroxy linkage with another ...
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Preferred Lewis structure for sulphate anion and XeO4 [closed]

In a section reviewing Lewis structure, the textbook Atkins' Physical Chemistry, 10th Edition, by Atkins, Paula, and Keeler, gives the following illustration of hypervalence and octet expansion: I ...
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Question about d-orbitals [closed]

I saw somewhere that, "in PF5, the 3d orbitals of phosphorus end up in the anti-bonding molecular orbitals, and thus contribute less to the final molecule" and that "the hypervalency of some ...
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Does H3CO3+ ion exist and what is its structure? [closed]

Why doesn't $\ce{H3CO3+}$ ion exist and why doesn't the carbonyl group in carbonic acid $(\ce{H2CO3})$ seem reactive?
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Identifying molecule with three adjacent six-membered rings from blurry image

I have found this isolated image on one of my old hard drives and I would like to know what molecule does the image represent:
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Meaning of the term “vertex” in the topic of skeletal formulae

From the Wikipedia article on skeletal formula: Hydrogen atoms attached to carbon are implied. An unlabeled vertex is understood to represent a carbon attached to the number of hydrogens required ...
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Chromium cyanide complexes

I have rarely seen any chromium $(\ce{Cr})$ square planar complexes and I have been told that $\ce{[Cr(CN)4]-}$ is tetrahedral. So, if the statement is actually correct, are there any other known ...
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Can stimulated Raman processes be strong enough to drive out of equilibrium?

In the (spontaneous) Raman process, incident light $\hbar \omega_1$ scatters and transfers some energy $\hbar \omega$ to a vibrational excitation of molecule or solid. Typically this is a very rare ...
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Is PCl5 really trigonal bipyramidal in shape?

We know that the structure of $\ce{CH4}$ is tetrahedral, and not planar tetragonal, as a tetrahedron enables maximum distribution of $\ce{H}$-atoms in space, as they repulse from each other. This is ...
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Are all stable Xenes (graphene-like 2D honeycomb sheets) buckled?

background: Per this abstract Silicene, germanene and stanene are part of a monoelemental class of two-dimensional (2D) crystals termed 2D-Xenes (X = Si, Ge, Sn and so on) which, together with ...
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Computational tool for identification of activity cliff

Are there computational tools for identification of activity cliff between two analog compounds? This paper list chemotypes that with a high propensity to induce activity cliff.
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Drawing bicarbonate ion in different way [closed]

I don't know why can't I draw $\ce{[HCO3]-}$ like that: I tried to draw it like that and checked everything. I checked formal charge and all was good. Why they draw it OH I know its also alright but ...
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Does H2SO or H2CO have a higher dipole moment? [closed]

Given these two molecules, I realize that the molecules are pretty identical in terms of the individual atoms' electronegativities (with Sulfur only being a small bit higher than Carbon). So then, the ...
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Bond length comparison in substituted phosphorus pentahalide

What would be the comparison between $\ce{P-F}$ and $\ce{P-Cl}$ bond length in phosphorus tetrafluoride chloride $\ce{PF4Cl}$ and phosphorus trifluoride dichloride $\ce{PF3Cl2}$ in the equitorial ...
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What is the Lewis dot structure for ozone? [duplicate]

Currently I studying about the Lewis dot structure for different compounds and my textbook says that the Lewis structure for ozone may be drawn as(as shown in the image): And then it goes on to ...
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How do I figure out how many hydrogens my compound actually has using a mass and NMR spectrum?

Question 3: It said $m/z = 122,$ and $m/z = 124$ is in a $3:1$ ratio, so I figured that meant that chlorine is present. Then I thought $m/z$ was the actual compound's molecular mass. So I used ...
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About Fe(III) and Fe(II) coordination complexes

Why does Fe(III) form octahedral coordination complexes if it has 5 electrons in its d-orbitals? I understand that Fe(II) has 6 electrons in its d-orbitals and 6 lone pairs from 6 ligands as the 12 ...
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Any way to see “cubic-active” vibrational modes in molecules?

For molecular complexes with a moderate amount of symmetry there are usually vibrational modes that are neither infrared nor Raman active. Sometimes these modes transform as some cubic polynomial in x,...
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Calculating the Molecular Orbitals of a Molecular State [closed]

I am performing ab initio calculations on a heteronuclear diatomic compound using the MRCI method on the MOLPRO quantum chemistry package. I obtained the molecular states of the compound but I was ...
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Changing toothpaste to a more stable structure

I am using charcoal toothpaste for an actor to spit bile on stage during a show. The paste is not the correct state for our needs. I know that you can freeze toothpaste and it becomes "more" solid ...
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How can I find out a substance name based on its structural formula?

When visiting a botanical garden in Stockholm, I stumbled across the following mosaic tile: I have tried to identify it using MolView, but it does not seem to identify it. Also, I have tried their ...
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How is it possible to melt diamonds? [duplicate]

On another thread on this website it mentioned how it was possible to melt diamonds, but what would be the micro-level occur for that to happen. This question applies to Silicon Oxide aswell. They ...
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How does resonance fail in approximating chemical structures?

In the book "Concise Inorganic Chemistry" by Prof. JD Lee, it says here: These contributing structures do not actually exist. The $\ce{CO3^2-}$ does not consist of a mixture of these structures, ...
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Dipole moments of dibromoethene isomers

There was an exercise in my textbook asking to compare the dipole moments of 1,1-dibromoethene and 1,2-dibromoethene(Z). The answer in the textbook says that the dipole moment of 1,1-dibromoethene is ...
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289 views

Provide a condensed structure for the following compound [closed]

I keep getting, (CH3)3CCH2CH2CHNH2CHCHCH3. However, the homework system keeps counting it as incorrect, and I don't know what part is incorrect. Thanks for the help!
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Software that determines whether a molecule can exist and draw it from a formula?

I have run calculations that predict atomic configurations. As a simple example, in a system that contains H and O, I might get a list like: ...
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Freely available software for generating 3D coordinates of molecules

As part of some research I am doing, I want to do a head-to-head comparison of software for generating 3D atomic coordinates for molecules. Is there a list anywhere of chemical software that does this?...
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Is sugar in mead different from “regular sugar”?

My understanding of the process of making mead is that you combine honey, yeast and water in an anaerobic environment. The yeast-bacteria ferments the sugar in the honey and produces ethanol (among ...

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