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.
748
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How do you determine the number of nodes when shown the pi molecular orbits? [closed]
The pi MOs of deca-1,3,5,7,9-pentaene are shown below (from a top-down view). How many nodes does the highest-energy BONDING MO contain?
The choices are A) 1, B) 2, C) 3, D) 4. I know that pi*10 is ...
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In a molecular orbital is the antibonding orbital empy when electrons are found in the bonding orbital?
According to molecular theory when 2 atomic orbitals combine, 2 molecular orbitals will be created. So if the electrons are in the bonding orbital will the antibonding orbital exist and just be empy? ...
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How to make bonds thicker in ChemDraw?
I often see molecules depicted using ChemDraw with all or selected bonds visibly thicker than those used with the style defined with ACS-1996 template.
For example, see the PDF handouts for Baran's ...
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Are meso compounds also included in optical isomers or are they just stereoisomers
Our teacher has taught us today about optical isomers . And at the end given a formula for finding number of optical isomers of a symmetrical molecule( n is number of chiral atoms and the n is odd for ...
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At the atomic or molecular level, why are some macroscopic materials more flexible, compared to others?
Before answering this question, keep in mind that I am a 2 year Biology student, with limited experience in studying chemistry. I am going to make assumptions which I explain, feel free to correct ...
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What do consecutive letters A and B in the 4th column of PDB file signify?
What do the consecutive A and B in the 4th column identify in a PDB file downloaded from rcsb.org?
The molecule name is 3CZ3 (...
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Are physical space filling molecular modelling kits still available anywhere?
In the 1980s when software for drawing 2D chemical structures was in its infancy and most chemists didn't have access to the workstations that could convert 2D to 3D structures, many labs had physical ...
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Why does zircon hate lead? How do these tiny crystals so effectively exclude lead atoms during formation enabling accurate uranium-lead (U-Pb) dating?
Background
From the December 29, 2022 NPR article To peer into Earth's deep time, meet a hardy mineral known as the Time Lord:
"(Zircons) are really the best markers of Earth's time, or the ...
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Does propene have resonance structures? [closed]
Propene is an alkene with a double bond between 2 carbon atoms. $\ce{C3H6}$ may have 2 resonance structures due to 2 possible placings of the double bond. E.g. it can be C=C-C or C-C=C (ignoring ...
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Why are these structural formulas not isomers of C5H12? [closed]
A Biology textbook question stated that there are three isomers of C5H12, the structural formula of the first two isomers pentane and 2-methylbutane were pictured, the reader was then asked to draw ...
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Is the number of atoms per unit cell for Hexagonal Close-packed (HCP) really 6?
I am questioning whether the conventional N=6 for HCP is accurate. This question is spawned from an image in ZYbooks Material Science and Engineering textbook by Callister and Rethwisch, where they ...
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How can atoms get very close together even without direct covalent bonds between them? [closed]
Generally speaking, because of the Pauli exclusion principle, it’s difficult for the electron clouds of two atoms to overlap unless they are covalently bound together. The degree of overlap can be ...
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Why is the imine (C=N) bond so weak?
Nitrogen is similar to carbon in terms of electronegativity and size. MO theory suggests that the more electronegative N would result in a lowering of the of the π-bonding energy, E(πCN), below the E(...
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Is it possible to create Fischer projections (or similar) from SMILES expressions? [closed]
I've recently begun experimenting with drawing molecules from smiles expressions for use in an educational website. I am looking for a way to create simple structural representations of various ...
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Reproducing Hydrogen Molecule Hamiltonian in OpenFermion
I am learning quantum chemistry at the moment and I'm trying to understand the Hamiltonian generated by the OpenFermion package. I'm now stuck at understanding how openfermion calculates the ...
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Self Consistent Field method and LCAO
I am reading about the Self Consistent Field Method and Linear Combination of Atomic Orbitals.
Suppose we have one electron and one nucleus, then we can solve the Schrodinger equation explicitly.
If ...
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Input file details for rigid PES scan
I have a planar molecule and a hydrogen atom. I wish to perform single point energy calculation for different configurations of this system where I would place the hydrogen at a certain distance away ...
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Is there a molecular orbital equivalent of rehybridization?
I generally have seen the pyramidal inversion of NH3 explained in terms of rehybridization. The sp3 hybridized NH3 changes to sp2, with the lone pair in the p orbital, and then reverts to sp3 in the ...
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Is there any material that, subjected to electricity, extends in size in multiples without substantial change in heat for human use? [closed]
Is there any material that can molecularly restructure so as to expand its intra- or inter-molecular distance by no less than three-fold without substantially losing its structural integrity and ...
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Converting structures into Fisher projections
I am really struggling with converting pyrano/furanosides into their Fisher projection counterparts. Especially when they are drawn like in the shown projection. When do you know to connect the ...
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Bond symmetry in AX2 type triatomic molecules
Will triatomic molecules of the AX2, AX2E, AX2E2 etc. (e.g. H2O or CO2), where the central molecule is bonded to two identical atoms, always have symmetric bond lengths in the ground state? If so, is ...
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Improper dihedral angles: how to tell between 0 and 180 degress
How can I tell the difference between a 0 and 180 degree value when looking at an improper dihedral. For example, in the molecule below would the dihedral angle 4-2-3-1 have a value of 0 or 180 ...
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Bonding in hypervalent molecules
I don't know where they go the electrons of the extended-valence in molecules like $\ce{SF6}$ or $\ce{PCl5}$ for instance because my teacher said that the d orbitals can't interact with s and p (or ...
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Analog of chemical accuracy in vibronic energy calculation [closed]
Is there any analog of chemical accuracy in vibronic energy calculation? I understand that the unit is /cm however, probably, I shouldn't expect a given number in that unit as the analog.
I am ...
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Why are there FOUR $sp^3$ hybridized orbitals in methane?
(This may be a stupid question, but I've only learnt about hybridization yesterday.)
I will take the example of methane.
The valence shell electron configuration of ground state of carbon is $2s^2 2p^...
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Do disulfide bonds determine the 3-dimensional structure of a protein or do they just stabilise the 3D structure?
I noticed that most disulfide bonds occur when two cysteine side chains exist in close proximity to each other. Do those cysteine side chains "look out" for each other during folding, that ...
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Are glycosidic linkages considered ether linkages or not?
I’m quite confused about whether glycosidic linkages can be considered being ether bonds or not. My textbook has this written in the Carbohydrates chapter:
It is possible for a sugar hydroxyl group ($...
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Bond angle in ethers due to lone pair and bond pair repulsions
When I was learning VSEPR theory, we were taught that lone pair–lone pair repulsions are maximum followed by lone pair–bond pair and then bond pair–bond pair repulsions.
The bond angle in dimethyl ...
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Do the electronegativity of atoms affect the molecular geometry of molecules?
I would like to know whether the electronegativity of atoms will affect the molecular geometry of a molecule.
For example, the molecule $\ce{CHFCl2}$. Originally I thought that as fluorine was the ...
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When does the angle between the planes in tetrahedral molecule with central atom deviate from 90°?
Consider an atom X bonded to four other atoms A, B, C, D in a tetrahedral fashion with sp³ hybridisation. If A, B, C, D are the same, every bond angle is 109.47°, and the angle between the planes ...
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Formula of what substance is shown in the clip Disappointed by Electronic? [closed]
I'd like to know the substance (if any) the model of which is shown in the clip Disappointed by Electronic.
The following screenshot is taken from the video electronicofficial —
Electronic - ...
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How does the molecule consisting of two bridged aromatic rings look in 3D?
I can't understand how the following compound with bridged benzene rings looks like:
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Monochlorination of (R)-2-chlorohexane: Number of possible chiral dichloro products
How many possible chiral dichloro products can be formed when (R)-2-chlorohexane reacted with one equivelent of $\ce{Cl2}$ in the presence of UV radiation (monochlorination only)?
$$\ce{C6H11Cl + Cl2 -...
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Cl-P-Cl and Cl-S-Cl Bond angles in respective PCl3 and SCl2 compounds
Both $\ce{PCl3}$ and $\ce{SCl2}$ are $\mathrm{sp^3}$ hybrid. $\ce{PCl3}$ has 1 lone pair whereas $\ce{SCl2}$ has 2 lone pairs, so due to more lp-lp repulsion, $\ce{SCl2}$ should have smaller bond ...
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Details of what actually happens in cold sulfuric acid between 80 and 90%; what molecular changes cause the viscosity to skyrocket?
AChem's answer to Why does the graph of the electrical conductivity of sulfuric acid/water solutions have this knee in the ~85%-~92% range? includes this plot from Horace E. Darling in "...
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Resource estimate for ab initio calculation [closed]
I have recently come across this very intriguing paper “The Fundamental Vibration of Molecular Hydrogen”.
I have asked the authors the following naïve questions directly via email?
What was the ...
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How do the spin-matrices change in systems without spherical symmetry?
The (non-relativistic) spin matrices of a free electron, with $z$ as the quantization axis, read:
$$
\boldsymbol{S}_{x}=\frac{\hbar}{2}\left[\begin{array}{ll}
0 & 1 \\
1 & 0
\end{array}\right],...
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O-C-O bond angles in carboxylates vs carboxylic acids?
I am wondering how different the O-C-O angle is in a carboxylate vs its acid form.
Does it (noticeably) increase because of the electron-electron repulsion caused by an additional lone pair?
Bond ...
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When would a R-O-R bond be linear?
While rummaging in my molecular model kit, I noticed that it contains a surprising number of $180^\circ$ oxygen atoms, i.e., oxygen that is meant to be covalently bonded to two partners in a linear ...
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Why am I getting a triplet instead of a singlet on NMR for aryl HH2-group?
I am trying to interpret an $\ce{^1H}$-$\mathrm{NMR}$ spectrum on the molecule 4-amino-N-(2-chlorophenyl)benzenesulfonamide that I produced in a lab session. I have managed to assign all the hydrogen ...
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Is there a good citation for the impact of inelastic neutron scattering on the measurement of the intramolecular geometry of H2O?
I have tried to find a good citation for the experimental measurement of the intramolecular geometry of H2O in the liquid phase and come across a problem:
It seems that the method of choice for such a ...
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Radius ratio of capped octahedral coordination (CN=7)
I was asked to work out the Radius ratio of capped octahedral coordination when CN = 7. How to define a capped octahedral? Is there any restrictions on the lengths of the edges or the distances of the ...
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1
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Crystal packing prediction for simple organic molecules?
Is it yet possible to predict a simple organic molecule's crystal structure or how the molecules arrange in a crystal without diffraction measurements?
By crystal structure I mean, how would molecules ...
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Hypothetical symmetric carbon peroxide
Could a hypothetical carbon peroxide $\ce{C5O12}$ with the following structure (MolView — 3D model) exist, and I what its properties would be (other than decomposing, of course)?
I tried looking it ...
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Does the process of extraction of chondroitin sulfate change the molecular structure of the bovine source it is extracted from?
I have been prescribed Chondoritin Sulfate for my joints. For religious reasons, I don't have bovine. Hence my question. Does the process of extraction of chondroitin sulfate change the molecular ...
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How does molecular structure contribute in the property of fluorescence?
Fluorescence is the property which is exhibited when electrons emit wavelength of light lower than the one they absorbed so does that mean we can make every molecule to become fluorescent? I wanted to ...
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How to determine positions of groups on compound based on H-NMR spectroscopy (C9H13NO)
Based on the below $\pu{200 MHz}$ $\ce{^1H}$-$\mathrm{NMR}$ spectroscopy, I have to determine the molecular structure of compound $\bf{B}$, which oxidises to a compound $\bf{A}$ with molecular formula ...
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Caffeine molecule representation and orientation
Almost all the representations of the caffeine molecule that I've come across have the two rings drawn next to each other on the horizontal axis.
Any particular reason for this?
Would it be sacrilege ...
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Why are the unsaturated fatty acids usually unconjugated?
My textbook gives the structures of the unsaturated fatty acids in food including oleic acid, linoleic acid, linolenic acid and docosatetraenoic acid. I figure that when two or more $\ce{C=C}$ double ...
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Why are there two infrared vibrational frequencies for the terminal CO ligands of Fe2(CO)9?
I am struggling to rationalise why there are two infrared vibrational frequencies ($\pu{2082 cm^-1}$ and $\pu{2019 cm^-1}$) for the stretching of the terminal $\ce{CO}$ ligands of $\ce{Fe2(CO)9}$. ...
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