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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 the structure of ozone not an equilateral triangle? [duplicate]

In the structure of ozone, there is a double bond and a coordinate bond, which causes the accumulation of positive charge on the central oxygen due to sharing of the lone pair. Wouldn't a triangular ...
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Do the lone pair of electrons on the outside atoms play a part in the molecular geometry of a molecule?

I'm currently learning about VSEPR theory. I am a bit confused about the electron repulsion part. My textbook states that the electron densities around the central atom determine the molecular ...
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Planarity of molecules in organic chemistry [on hold]

So, I wanted some information regarding organic chemistry. Here is my question: how to determine whether a cyclic compound is planar or not?
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1answer
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Lewis structure draw [on hold]

I have the next organic compound: $\ce{(NH2)2CHCOOH}$. I need to do a Lewis structure for it. This is what I have done: Is it correct? Thank you for the help.
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What is dissociation limit for molecules? [closed]

In research papers, I read the terms like "at the dissociation limit of hydrogen molecule". How dissociation limits are calculated for molecules (like H$_{2}$, H$_{2}^{+}$) etc? Is there a database ...
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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
43 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
40 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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59 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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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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126 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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Conjugaison and mesomerism in no planar molecules

In my textbook(french general chemistry textbook) it says: if a molecule is conjugated( alternance of pi/Lone pair and sigma bonds) then the molecule is planar, but of we look at SO4 (2-) the ...
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1answer
50 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
118 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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22 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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439 views

Why is the perchlorate anion non-polar?

I just want to confirm that my approach is right. I found that since the hybridisation of this molecule is sp3, the structure is tetrahedral and since all the $\ce{O-Cl}$ bonds are of the same ...
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1answer
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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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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
54 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
307 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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37 views

R/S descriptors in long carbon chain

I'm trying to figure out how to assign R/S descriptors using a Fischer model without transforming it into a spacial one. What I learned so far is the method to assign it for 'terminal' (I'm gonna use ...
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1answer
72 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
32 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
56 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
74 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
58 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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226 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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108 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
81 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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39 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
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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
250 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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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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Why doesn't the arsenate ion have two double bonds?

The commonly described arsenate anion has a double bond between the arsenic atom and one of the oxygen atoms. This makes the arsenic ion have a formal charge of 0, and all of the oxygens have a formal ...
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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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191 views

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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192 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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1answer
70 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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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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70 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
467 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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134 views

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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1answer
87 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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Resonance structures for acyl imidazole

I was asked to draw the four resonance structures of the acyl imidazole boxed in the picture. I'm not too confident with drawing resonance structures, so i'm really not sure if the answer i came up ...
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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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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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1answer
74 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
176 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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1answer
225 views

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

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