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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 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 ...
0
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1answer
42 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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Molecular basis of water in denying pseudoscience of water memory [closed]

In homeopathy, it is claimed that water, when diluted with homeopathic compounds and shaken, can hold the property of original compounds despite no molecule contained in final solutions. A detailed ...
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36 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
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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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45 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
47 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 ...
3
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1answer
51 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 ...
5
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1answer
45 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
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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
399 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
48 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
136 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
73 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?
2
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0answers
48 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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98 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 ...
0
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1answer
44 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
32 views

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
54 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
211 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
75 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 ...
2
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2answers
809 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 ...
5
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1answer
51 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
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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
213 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 ...
1
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2answers
63 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
71 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 ...
2
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0answers
47 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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0answers
144 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
281 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 ...
4
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1answer
816 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
25 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
32 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 ...
10
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1answer
120 views

How can the solid state structure of cyclopentadienyllithium be explained?

In the solid state, LiCp adopts a polymeric multidecker structure where Li atoms are sandwiched between two Cp rings (shown in this diagram from Organometallics 1997, 16 (17), 3855–3858): If we ...
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2answers
72 views

Unique carbons on long carbon chains

If we have a long carbon chain like octane for example, do we determine if a carbon is unique by just looking at the immediate surrounding atoms of each carbon (in this case 3 unique carbons), or do ...
2
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1answer
309 views

Unique carbons on rings

In rings in general, how do I determine how many unique carbons there are? In this example, I am thinking that there are 2 unique carbons (one on top and one with a double bond) since this molecule is ...
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1answer
145 views

PCl3 vs SCl2 boiling point

Why does sulfur dichloride have a lower boiling point than phosphorus trichloride? Is it to do with the higher number of electrons causing stronger id-id interactions in PCl3, or do we need to compare ...
2
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1answer
38 views

How to determine net charge of a polycation using Wade's rules?

In order to determine the net charge of polycations, which adopt a Wade-like structure (octahedral, trigonal bipyramidal, ...), Wade's rules can be used. For example, the charge $x$ of the ...
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1answer
63 views

Interatomic distances between hydrogens in allene

If $d_1$ and $d_2$ are the interatomic distances between the pairs of hydrogens shown above, what is the relation between $d_1$ and $d_2$? I think that $d_1$ and $d_2$ might be equal since the ...
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1answer
77 views

Is there an algorithm that takes atom coordinates and produces VSEPR geometries?

That is, you would give the coordinates of an atom, the coordinates of four (for example) other atoms, and it would return "tetrahedral" or "square planar" or whatever. I'm currently writing a ...
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1answer
66 views

Molecular Geometry [duplicate]

Why is it that for a molecule with trigonal bipyramidal geometry, the lone pair is located in the equatorial region whereas for a molecular with an octahedral geometry, the lone pair is located in the ...
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793 views

Bond Angle in Diborane, B2H6

Why are the bond angles in the diborane $\ce{B2H6}$ ring much less than $\ce{109.5^o}$? Below is the structure: This source says that the boron atoms are approximately $\ce{sp^3}$ hybridized, so I ...
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1answer
117 views

How do I visualise bicyclo[4.4.1]undeca-1,3,5,7,9-pentaene?

While reading my organic chem book, I came across this compound: Since this is an exercise question, I do not know the name of this compound. I am unable to visualize this compound (how it looks out ...
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1answer
130 views

Would an (NH3)2+ molecule be trigonal planar like BH3 rather than trigonal pyramidal?

I've been learning about using MO theory to explain why $\ce{BH3}$ and $\ce{NH3}$ have different geometries and by following the line of reasoning used to rationalise the differences in geometry I ...
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0answers
72 views

Which natural orbitals are better for CASSCF calculations for organic diradicals?

I am trying to perform CASSCF calculations for a series of diradicals. As input orbitals I have used two types of natural orbitals. One is unrestricted natural orbitals and the other MP2-based natural ...
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2answers
144 views

Bond angle in water vs in oxygen difluoride [duplicate]

My teacher taught that bond angle $\ce{H-O-H}$ is larger than $\ce{F-O-F}$ due to less repulsion in the latter's bond pairs. I know that bond angle $\ce{H-O-H}$ is $104.5^\circ$, but I'm confused with ...
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1answer
771 views

How to systematically find the reducible representation of a molecule? (eg: XeF4)

I am attempting to use the reduction formula to find the irreducible representation of $\ce{XeF4}$ to determine its IR stretching vibrations. I know the point group of $\ce{XeF4}$ is $D_{4h}$ and have ...
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415 views

How are bond lengths measured experimentally?

How is the bond length between any two atoms in a compound measured? For example, in the case of graphite, the bond between its two layers is 340 pm. This number must have been measured, so what are ...