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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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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621 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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148 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
6k 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 ...
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1answer
83 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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174 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 ...
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1answer
829 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
129 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
92 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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58 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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152 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
2k 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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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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1answer
120 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 ...
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1answer
35 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 ...
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1answer
126 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
287 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 ...
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1answer
322 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
362 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 ...
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1answer
45 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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75 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
82 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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2k 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
145 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
230 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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105 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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374 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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4k 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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938 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 ...
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39 views

Determining global minimum structures for ion-water clusters

What is the best way to find the global minimum structure(or get close to it) for an ion and N waters? (i.e. ion cluster in vacuum) For example, consider Flouride ion cluster with N=5 waters. I want ...
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Lewis structure of ClO radical

The commonly shown structure of the ClO radical described here has a single bond between the chlorine and oxygen atoms. In that structure, chlorine has a formal charge of 1, and oxygen has a formal ...
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How do I make a ZMAT or XYZ file from scratch?

From a structure representation like the one below for Bacteriochlorophyll A, how do I make the ZMAT or XYZ file? The closest similar question asked here was about converting a PDB entry into XYZ, but ...
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906 views

Why do aluminum and air have low specific heats?

According to Wikipedia, ...specific heat capacity is a function of the structure of the substance itself. In particular, it depends on the number of degrees of freedom that are available to the ...
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123 views

Breaking degeneracy in phosphorus pentachloride

Recently, in a class discussion, the following point was brought up: Although the axial and equatorial bond lengths in $\ce {PCl5}$ are inequivalent, when we consider the time-averaged $\ce {P-Cl}$...
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759 views

What determines the geometry of Nitrogen to be planar or trigonal pyramidal?

In the following molecule (1-(4-fluorophenyl)-4-[[1-(2-methoxyethyl)tetrazol-5-yl]-phenyl-methyl]-piperazine) I have seen its 3D structure using Jmol, and I see that both nitrogens on the middle ring ...
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142 views

Berry Pseudorotation

I was at a chemistry competition, and one of the questions they asked was on Berry pseudorotation Now the question gave 4 molecules, namely, $\ce{IF5, PF5, PCl5, and XeF5-}$, and asked which of these ...
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1answer
2k views

Comparision of ONO Bond angle in NO2 and N2O4

How can I compare the bond angle between $\ce{O-N-O}$ atoms in $\ce{NO2}$ and $\ce{N2O4}$? In $\ce{NO2}$ there is lone pair-bond pair repulsion, and in $\ce{N2O4}$ there is bond pair-bond pair ...
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Generating geometries for substituted molecules

I would like to automate some of my calculations, and I am looking for a tool to generate reasonable good initial geometries. The details: I have already optimized molecular geometries, and I would ...
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134 views

Why does nitric acid have a different molecular structure from phosphoric and arsenic acids?

I remember that this really bugged me as an undergrad, and upon revisiting some inorganic chemistry notes I realized I still don't have a satisfactory answer for it. The structure of nitric acid, $\ce{...
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T shape molecule with three hydrogens

Is there any sort of AX3E2 molecule that consists of hydrogen atoms bonded to the main atom who is left over with two lone pairs of electrons? (Similar to ClF3 just with hydrogen instead of fluorine?)
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430 views

Is carbon suboxide planar?

I was asked to comment on the planarity of the carbon suboxide molecule. I thought that the Lewis structure of the molecule looks somewhat like an Allene and must have similar bonding. The two ...
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87 views

Dissociation energy of benzene dimer

It is known that the benzene dimer has two stable structures, T-shaped ($\ce{C_{2v}}$) or parallel-displaced ($\ce{C_{2h}}$) structure. Now the question is: does the dissociation energy ($\ce{D_0}$) $...
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5answers
570 views

Free API to view 2D representation of Molecules

I'm looking for a free API that can accept a SMILE and produce the 2D structure of a molecule. I would like to include this in a web page. I have collection of SMILES and would like to have the 2D ...
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538 views

How to simulate phase separation in a discrete system using LAMMPS?

I would like to simulate phase separation in LAMMPS and need advice what kind of two particle systems and interactions will yield phase separation. For example, a meta stable phase separation is ...
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933 views

How to determine the angle between non-bonding electron pairs?

Is there a way to determine the angle between non-bonding electron pairs that aren't obvious? Take $\ce{H2S}$ for example: The two non-bonding electron pairs would be at the yellow end of this ...
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π-ligands in trigonal prismatic complexes

We recently had a discussion here about the symmetry problems for the often postulated s- and p-mixing with the d-orbitals in complexes to somehow allow a d-d-transition. It was pointed out back then ...
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Is there a known crown ether analog to fullerenes?

It is well known that endohedral fullerenes have potential quantum computing applications example 1,example 2, and example 3. But, currently they are too expensive, around $167 million per gram at ...
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3k views

Determine the geometry of each nitrogen atom in formamidinium ion

The geometry at A seems to be straightforward: $\ce{N}$ is surrounded by $\ce{C}$ and two $\ce{H}$'s. By VSEPR, this is trigonal planar. For the geometry at B: $\ce{N}$ is surrounded by $\ce{C}$, two ...
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141 views

Why must the ground state of hydrogen molecule be gerade?

As we know, the electronic ground state of hydrogen molecule is $\Sigma_g^+$. My question is, how do we know it from the theoretical perspective? The nuclear potential in the hamiltonian of hydrogen ...
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135 views

How sure can we be about the structure of purine?

While answering the question Basicities of nitrogen atoms in purine, I noticed, that there might be a rapid interchange of the hydrogen bonded to the nitrogen atoms. I have found a crystal structure ...

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