Stack Exchange Network

Stack Exchange network consists of 174 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit Stack Exchange

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.

0
votes
0answers
34 views

How does one plot molecular orbitals (probability electron density plot) for complex nonlinear molecules?

For molecules such as $\ce{H2}$, we can put the molecule along one of the Cartesian axes, with probability density along the other orthonormal axis and plot it. We can do the same for planar molecules ...
-1
votes
2answers
36 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 ...
-2
votes
0answers
14 views

Structure of chlorine trifluoride according to the VESPR model [duplicate]

It is said that the charge clouds are oriented in space as far away from one another as possible according to the VESPR model. Then why do the lone electron pairs from chlorine trifluoride occupy ...
4
votes
2answers
107 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 ...
-3
votes
1answer
44 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
votes
0answers
44 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 ...
2
votes
0answers
56 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
votes
1answer
34 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 ...
0
votes
0answers
28 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 ...
-2
votes
1answer
42 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?
0
votes
1answer
102 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
votes
1answer
62 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 ...
1
vote
2answers
271 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
votes
1answer
49 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 ...
1
vote
0answers
32 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 ...
-1
votes
1answer
107 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
vote
2answers
57 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 ...
1
vote
2answers
69 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
votes
0answers
44 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/...
3
votes
0answers
141 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 ...
-1
votes
1answer
133 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
votes
1answer
343 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 ...
2
votes
0answers
23 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
votes
1answer
30 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
votes
1answer
114 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 ...
0
votes
2answers
61 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
votes
1answer
308 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 ...
1
vote
1answer
106 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
votes
1answer
35 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 ...
-2
votes
1answer
59 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 ...
5
votes
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 ...
-1
votes
1answer
60 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 ...
0
votes
0answers
468 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 ...
3
votes
1answer
115 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 ...
1
vote
1answer
104 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 ...
2
votes
0answers
46 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 ...
1
vote
2answers
93 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 ...
2
votes
1answer
421 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 ...
2
votes
0answers
298 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 ...
0
votes
0answers
65 views

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 ...
2
votes
0answers
31 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 ...
1
vote
0answers
427 views

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 ...
4
votes
2answers
314 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 ...
-1
votes
2answers
284 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 ...
3
votes
1answer
75 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 $\ce {P-Cl}$...
-2
votes
2answers
267 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 ...
2
votes
0answers
75 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 ...
1
vote
1answer
658 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 ...
6
votes
1answer
136 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 ...
8
votes
1answer
91 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{...