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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Why there is no angle change observed in boron trifluoride (due to back bonding)? [on hold]

Could anyone explain me why there is no angle change in $\ce{BF3}$ because of back bonding like in substances $\ce{H3BO3},$ $\ce{N(GeH3)3}$ etc.?
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0answers
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Why isn't trinitramide planar?

The lewis structure of trinitramide has four major resonance structures, whereby the lone pairs of the central nitrogen can resonate with the nitro groups. This seems to indicate that each of the ...
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2answers
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Chemical Structures as Graph Labels in R

I asked the following question here https://stackoverflow.com/questions/56236135/chemical-structures-as-graph-labels-in-r but I ask it here for a different perspective. I want to make a plot that ...
3
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1answer
79 views

Why is the dz2 orbital so different from the rest?

What makes dz2 orbital so special? Although degenerate with other d orbitals, It has no nodal planes, instead it has 2 nodal "cones". Instead of having 4 lobes, it has 2 lobes and 1 ring. Also, ...
3
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1answer
101 views

What is the explanation of the structure of H2XeO4?

Using the obsolete VSEPR theory I had a hard time predicting the structure of $\ce{H2XeO4}$. So I looked it up. I found the molecule via chemapps.stolaf.edu: It looks weird to me. I can't explain the ...
7
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2answers
98 views

Software or library for creating images of ball and stick models?

Is there any code library (in any programming language) or software capable of producing images of ball and stick diagrams? Example of an image of a ball-and-stick model for Ammonia: (Image source) ...
2
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1answer
50 views

Is the -OCH3 group bulky?

Our teacher told us that $\ce{OCH3}$ is a less bulky group when compared to other bulky groups like $\ce{CH3}$, $\ce{NO2}$ etc. Is this true? If yes, why?
3
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1answer
168 views

Can anyone help me with this question on vibrational modes of free base porphyrin (C20H14N4)?

4 a. The structure of free-base porphyrin $(\ce{H2P}$, chemical formula: $\ce{C20H14N4})$ is shown below. Given that this molecule belongs to the $D_\mathrm{2h}$ point group (character table given ...
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30 views

What is molecular potency?

In the paper Junction Tree Variational Autoencoder for Molecular Graph Generation, the authors propose a ML model that is based on the message passing neural network, variational auto-encoder, the ...
3
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0answers
55 views

Do alkenes have priority over alkynes in R/S naming?

I am studying for an upcoming exam and I came upon a confusing question for the drawing of the molecule (3⁠R)-hex-1-en-5-yn-3-ol. Why is the stereocenter (3-carbon) R? Shouldn't it be S? After ...
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1answer
62 views

Structure of no2 molecule [closed]

Which is the correct structure of $\ce{NO2}$ ? While searching the internet I found out that - $\ce{NO2}$ have a coordinate and 2 covalent bonds. $\ce{N}$ will +ve charge. $\ce{O}$ (coordinate bond )...
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2answers
150 views

Chiral carbon in carvone molecules

This is the structure of carvone, with the chiral carbon noted by *. I don't understand why this is a chiral carbon, to my understanding a chiral carbon is a carbon with 4 different chemical groups ...
4
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3answers
66 views

What is the precise definition of Ramachandran angles?

The Wikipedia article Ramachandran plot is very schematic and doesn't even say when these angles are considered to be zero. It seems to assume that the peptide chain has no end, and always shows the ...
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0answers
63 views

Convert an image of a chemical structure to a ChemDraw file?

Is there a way to convert a bitmap (JPG, PNG) image of a chemical structure to a ChemDraw file so that you don't have to draw a structure you find in a paper yourself?
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1answer
109 views

Planarity of given molecules in all conformations

Which of these have all its atoms in one plane in all the possible conformations (if any): A) buta-1,3-diene B) but-1-en-3-yne C) $\ce{CH2=C=O}$ D) $\ce{CH2=C=CH2}$ While I was ...
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1answer
64 views

Why is casein hydrophobic?

According to this source hydrophobic behaviour occurs when a molecule does not have a charge or is neutral and therefore cannot be attracted to the negative nor positive parts of water. Casein has an ...
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1answer
50 views

Why is there a lone pair in thionyl fluoride?

Why is there a lone pair in $\ce{SOF2}$? I drew its structure, which according to me should look like this: Why is there a lone pair on sulfur? Isn't its octet complete? If yes, why should it expand ...
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0answers
40 views

Spin state change during crystallisation for [NiCl2(PPh3)2]

$\ce{NiCl2(PPh3)2}$ is a complex that is borderline between tetrahedral(high spin) and square planar(no unpaired electron, high splitting parameter) because $\ce{Cl-}$ is a weak field ligand and $\ce{...
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2answers
136 views

Why is manganate ion paramagnetic [closed]

When I tried to figure out why manganate ion is paramagnetic, given that its oxidation number is +6, I am not able to understand why there are unpaired electrons. Is it the case that six of the seven ...
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0answers
47 views

How can nitrogen be quadruply bonded in tris(8-hydroxyquinoloinato)aluminum?

Nitrogen typically has five outer valence electrons. So how does a triply-bonded nitrogen in 8-hydroxyquinoline end up quadruply bonded in tris(8-hydroxyquinolinato)aluminum?
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0answers
13 views

Molecular weight of NiMnGaFe compund problem

I have a big problems calculating molar/molecular etc masses, because in my case I have a monocrystal, co I cannot imagine it as a molecule and my compound is made of Ni-Mn-Ga-Fe. I know the mass and ...
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2answers
76 views

What are the differences in shapes between molecular geometry and electronic geometry?

In my chemistry course we are told that molecular geometry considers only atoms as part of the shape, while electronic geometry considers atoms and electrons as part of the shape. However, I can't ...
2
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0answers
37 views

What does the dissociative mechanism for cis/trans interconversion of [Mo(CO)4(PPh3)2] look like?

All I can find in the literature is that the cis→trans interconversion proceeds via dissociation of one of the PPh3 ligands resulting in a square-pyramidal Cs intermediate, with the remaining PPh3 in ...
3
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1answer
55 views

Is the existence of chirality center equivalent to chiral?

To make my question more clear, I want to ask two questions: Is it possible for molecule to be achiral even though molecule has chirality center? Is it possible for molecule to be chiral even ...
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1answer
47 views

Mixing of molecular orbitals in polyatomic molecules

I am trying to solve the following Hamiltonian,$$H=-\frac{1}{2}\nabla^{2}-\sum_{i=1}^{10}\frac{1}{|\vec{r}-\vec{R_{i}}|}$$ Here $Z=1$ . To get all ther molecular orbitals of this system. I took the ...
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2answers
2k views

What would the chemical name be for C13H8Cl3NO

Formula C13H8Cl3NO SMILES C1=C(C(=CC(=C1)Cl)Cl)N(C(C2=CC=CC=C2)=O)Cl I found the diagram on the left in a book and drew the one on the right using https://pubchem.ncbi.nlm.nih.gov/...
4
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4answers
563 views

Structure of pyrophosphorous acid

What is the structure of pyrophosphorous acid? I asked this question here because the answer which I found on web and other resources are inconsistent which each other. For example, following data is ...
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2answers
56 views

Perpendicular orbitals in aryl and vinyl carbocations? [duplicate]

This point (iv) has been given under reasons for extremely low reactivity of aryl and vinyl halides. I cannot understand it. First of all, isn't the positive carbon atom in phenyl as well as vinyl ...
5
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2answers
161 views

Molecule with a quadrupole moment in an electric field

How does an uncharged non-polar molecule that has a quadrupole moment (such as carbon dioxide) behave in an electric field? I know that in a homogeneous electric field, ions travel while dipoles ...
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1answer
110 views

Bond-line structure of 2-methyl-3-phenyl-1-butanol

According to me the structure of 2-methyl-3-phenyl-1-butanol is the above one. Is my answer correct?
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0answers
51 views

Theory of symmetry breaking in water?

As we all know $\ce{H2O}$ is bent ($C_\mathrm{2v}$) in its ground state equilibrium structure, rather than linear ($D_\mathrm{\infty h}$), which can be readily understood e.g. from the MO diagram of ...
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119 views

Structure of (CH3COO)3Fe

I'm a grade 12 student trying to comprehend MOT & LFT in Co-ordination compounds. For one of our salt analysis(practicals), the test for acetate ion includes the addition of Neutral Ferric ...
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1answer
48 views

Expanded structure formula and Lewis dot structure, whats the difference?

I am teaching my self the basics of chemistry and I have done lewis dot structure before. Right now I am going into carbon chemistry which often use structure formulas to represent compounds. There is ...
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0answers
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Why does fulminate not minimize formal charge in its structure?

The official structure of fulminate looks like this: from wikipedia: https://en.wikipedia.org/wiki/Fulminate However, this structure does not minimize formal charge, since nitrogen has a formal ...
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1answer
67 views

Is 1-(1-Methyl cyclopropyl) carbocation [1] as stable as Cyclopropyl Methyl Carbocation[2]

Does the extra Methyl group interfere with the exceptional stability of Cyclopropyl Methyl Carbocation?
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1answer
269 views

Why CO2 has 4 vibrational degrees of freedom?

If I have a diatomic molecule, so a linear molecule, $3N-5=6-5=1$ holds, since this vibrational degree of freedom corresponds to the stretching coordinate beetwen the two nuclei. If I consider water ...
4
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1answer
87 views

The carbon-13 NMR for 1,1,1-trichloroethane

I was working the following spectroscopy problem from Clayden 2e that asks us to identify the structure of a compound from information about its carbon-13 NMR peaks. Problem 3.5: The solvent ...
3
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2answers
2k views

The real structure of difluoro(dioxo)xenon (XeO2F2)

I have a problem regarding structure of difluoro(dioxo)xenon ($\ce{XeO2F2}$). I have posted a image above. my teacher is saying that the structure B is correct as there is very less repulsion in ...
4
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1answer
56 views

Is the neutral di-µ-oxo-bridged manganese dimer with eight ammonia ligands a reasonable structure?

In its guide to model antiferromagnetic couplig, Gaussian uses $\ce{Mn2O2(NH3)8}$ as a model compound.[1] It argues that manganese is in II oxidation high spin state; in other words, in both manganese ...
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Dichlorine monoxide molecular geometry

I need to predict the geometry of Dichlorine monoxide, using the main link theory: Lewis model, VSEPR and hybridization of molecular orbitals. First, the Lewis structure is a graphical representation ...
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1answer
349 views

Molecular geometry of acetylene

I need to determine the molecular geometry of acetylene, for this I have performed the following procedure: First, we represent the correct Lewis structure. Remember that the Lewis structure is a ...
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2answers
69 views

Do molecules with polar bond, but with no dipole moment experiences a greater effect from the london dispersion forces?

Do molecules that have polar bonds and a structure that makes the polarity of those bonds cancel each other out, experience a greater effect from the London dispersion force, than molecules with a ...
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2answers
75 views

How is it that earth's inner core is still solid?

Earth's inner core is made up of an alloy of Iron and Nickel. The important note here is that it is solid. The temperature at the inner core is about $5,763K = 5,490\text{ degrees C}$. Now the ...
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0answers
48 views

Reading Stereographs

On an old paper, I found an interesting representation of some symmetry operations: stereographs. Online I found a set of symmetry operations and related stereographs (see: http://newton.ex.ac.uk/...
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148 views

X-ray structure analysis mirrored coordinates?

How to ensure, that X-ray crystallography structure analysis was done right to provide correct, non-mirrored atomic coordinates? Example: Following Wikipedia image, is generated from data taken from ...
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1answer
474 views

Explain the structure of HNC (Hydrogen Isocyanide)

What are the different types of bonds present in the structure? Does Nitrogen donates one electron from its lone pair to carbon and acquires a positive charge? How do I determine the Oxidation state ...
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1answer
1k views

Shape of urea molecule around N atom

I was doing a question where I was supposed to predict the shape of the urea molecule $[\ce{H2N(CO)NH2}]$ using Lewis and VSEPR. I identified that the N atoms will have a lone pair on them and so I ...
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0answers
31 views

Reverse Image Searching a ChemDraw Figure

Is there any image-recognition software out there that can read in a high-resolution image of a ChemDraw-generated figure and back out the structure (such as the SMILES or INChI)? I have a bunch of ...
3
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1answer
33 views

Automated Identification of Isomeric Relationship from 3D Structure?

Is there a software package that when given two sets of 3D structures can return the isomeric relationship between them? Even if it was only able to state that they are conformational isomers that ...