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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18 views

Difference between a species and a phase in a solution?

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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1answer
172 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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26 views

Optimization completed on the basis of negligible forces

I am performing relaxed scan in Gaussian and I'm trying to understand the optimization output. Specifically, the line ...
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2answers
71 views

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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243 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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2answers
47 views

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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1answer
29 views

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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51 views

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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1answer
56 views

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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44 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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1answer
253 views

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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44 views

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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1answer
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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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2answers
134 views

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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1answer
182 views

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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2answers
300 views

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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40 views

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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2answers
169 views

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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1answer
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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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1answer
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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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73 views

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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3answers
547 views

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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1answer
45 views

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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1answer
166 views

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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32 views

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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1answer
393 views

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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1answer
76 views

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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1answer
230 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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2answers
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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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Is bonds in CO is all 3 coordinate bonds or 2 covalent and 1 coordinate bonds?

Below image is as available in India's Class 11 NCERT Chemistry book vol 1 Page 104. I am confused as it states all 3 bonds are kind of coordinate bonds. Should it not start with 2 covalent bonds and ...
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Bonding in Sulphur dioxide [duplicate]

In Concise Inorganic Chemistry by J.D.Lee (Adapted by Sudarsan Guha, Fourth Edition), on page 82, under section 3.8 - Types of Covalent Bonds (Sigma and Pi Bonds) it is given (for Sulphur dioxide ...
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What is the biggest known difference between rₑ and r₀?

What is the biggest known difference between $r_e$ and $r_0$? Where $r_0$ is the average bond length of the lowest vibrational state, and $r_e$ is the location where the potential is lowest. For a ...
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Question on identification of a compound

Question: Multiple correct answers are possible My Approach: I just found structure Q for all options A, B, C and D for which I have uploaded the structures below with their corresponding options. ...
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Which substitutent should be placed on axial position in SCl2(OCH3)2?

According to Bent's rule, in $\mathrm{sp^3d}$ more electronegative element is placed on the axial position, so between $\ce{Cl}$ and $\ce{OCH3}$ in $\ce{SCl2(OCH3)2}$ which should be placed on axial ...
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1answer
119 views

Number of stereoisomers of polysubstituted cubane

The molecule given below is a substituted cubane. a) How many stereoisomers exist for this molecule? b) How many pairs of enantiomers are possible? How do I calculate the number of ...
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Finding out more stable conformer via molecular orbital interaction

Out of these two, which one is more stable? I'm unable to imagine the orientation of the lone pairs of O and ABMO of C and Cl bond. Any tips to tackle these kind of problems?
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Why does the image of cyclo[18]carbon look like a nonagon?

The $\ce{C18}$ allotrope cyclocarbon has been synthesized and imaged.[1] Science has most details behind a paywall, but this discussion includes an image: In this octakaidecagonal molecule, each $\ce{...
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Lewis structure of chlorine dioxide [duplicate]

The central atom in the molecule of $\ce{ClO2}$ is chlorine. Draw the ‘dot-and-cross’ diagram for $\ce{ClO2}.$ Show outer electrons only. How to draw Lewis structure of $\ce{ClO2}?$ Please explain ...