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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38 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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25 views

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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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 ...
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2answers
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How to convert Gaussian input file .gjf to SMILES?

Is there a way to convert Gaussian input files (.gjf) to SMILES-codes (.smi)? I'm aware of ...
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1answer
69 views

The influence of diffuse functions on electron density calculations

I am not a quantum chemist, but I am (starting to be) a user of electronic structure software. In the picture (screenshot) is the electron density of the same molecule. On the left I calculated the ...
3
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1answer
124 views

AB5E type molecule

In $\ce{AB5E}$-type molecules, why are the lone pairs in axial bonds? If the lone pair is present in axial bonds it repels four other bonds. On the other hand if the lone pair is in equatorial ...
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Can you use a photon's torque to change a molecule?

Can you use the torque of a photon to change bond angles, etc.? 11-Cis-Retinal to the all trans version, in the eye, is a good illustration [1]. Note: This phenomenon can be observed by closing ...
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31 views

Determining geometry of coordination compund without experimental data [closed]

How can I determine if a coordination compound has a tetrahedral or square planar geometry without any experimental data (such as magnetic spin) by just looking at its formula? For example, what is ...
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1answer
352 views

Which molecule has maximum bond angle amongst BF₃, BCl₃ and BBr₃? [closed]

$\ce{Br}$ is the least electronegative from the given compounds. So, in $\ce{BBr3}$ the electrons will be the closest towards boron and thus due to electron-electron repulsions $\ce{BBr3}$ will have ...
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1answer
52 views

Is fluorine also hybridised in carbon tetrafluoride?

I had read that when an atom forms multiple bonds, it hybridises it's orbitals to minimise the repulsion and decrease the overall energy. But do the terminal atoms also exist in hybridised form? E.g. ...
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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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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 ...
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1answer
169 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, ...
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1answer
122 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 ...
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2answers
121 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
71 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?
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1answer
170 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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32 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 ...
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76 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
161 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 )...
4
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2answers
160 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 ...
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3answers
69 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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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
123 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
71 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
55 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
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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
152 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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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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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
96 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 ...
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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 ...
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1answer
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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
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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
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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/...
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4answers
661 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
60 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
178 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
131 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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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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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
51 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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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
75 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
315 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 ...
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1answer
99 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 ...
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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
60 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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0answers
80 views

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 ...