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 don't molecules like water and hydrogen sulfide feature their two hydrogen atoms on exact opposite sides of the center?

I just saw a diagram of hydrogen sulfide, and it's two hydrogen form an angle of 92.1° with each other and the central sulfur atom.... With water its 104.45°... Why don't two identical atoms like two ...
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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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Troubleshooting an Autodock Vina Error on Chimera: "Could not find an atomic number for Hn Hn"

After having minimized a ligand (that I prepared on Marvinsketch), and after having prepared a target enzyme to dock said ligand onto (collected from RCSP PDB), I was met with an error by the reply ...
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Why bond angle of sulfur dioxide is higher than formaldehyde?

According to the VSEPR Model lone pair bond pair repulsive force is higher than bond pair - bond pair repulsive force. $\ce{SO2}$ has one lone pair so it's bond angle must be lower than formaldehyde. ...
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3answers
213 views

Orientation of amide bonds in a simplified polypeptide drawing

The syllabus for my course requires I draw protein polymers like this, where the patterned boxes represent different bodies (note that this is an extremely simplified drawing stripped down to its bare ...
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2answers
139 views

Why do CCl4 and CH4 have the same bond angle?

I was reading about the molecular shape of compounds. I learned that the electronegativity of the central atom and the terminal atom in a molecule both play a role in determining bond angle. In $\ce{...
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37 views

Contribution, and the way thereof, of the core 6p orbitals of compounds of plutonium(VIII)

According to the NIST database, the ground-state configuration of plutonium(VIII) is [Hg]5f³6p³, when intuitively it should be the same as neutral radon([Hg]6p⁶). Since plutonium(VIII) compounds are ...
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1answer
46 views

Continuous variable for graph of boiling point of different chain lengths

Looking at the boiling points of alkanes (for examples), many graphs plot boiling point against chain length : However, there is an issue with the line of best fit- since chain length is a discrete ...
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what do the asterisks in the molecule stand for?

My 7 year old nephew found a chemistry text book and started copying some pictures and diagrams. He drew this and asked me what do the asterisks mean ? He said he normally sees letters which means ...
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1answer
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Why this structure is diastereomers instead of enantiomers

In this diagram optical isomers has divided in to 2 categories, one is diastereomers and enantiomers. Is the example for diastereomers correct? For me its looks like enantiomers
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Where can i find accurate bond angles?

I am trying to find places where I can have accurate bond angles of certain molecules such as $\ce{F2Se}$, $\ce{Cl2S}$, or even $\ce{S2Se}. I have looked everywhere and have found only 3 sources that ...
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35 views

How to determine if all carbon atoms in a cyclic compound lie on the same plane?

I'm currently doing a-levels chemistry and came across a question asking if all 17 carbon atoms in cyclic rings of a cholesterol molecule lie on the same plane. I've done some googling and it turns ...
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1answer
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Error in calculating G-matrix

I have a question regarding the calculation of the $G$-matrix in the classic "Molecular vibrations" textbook by Wilson (1955, McGraw Hill). On page 63 it gives an example for the calculation ...
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What dodecahedral molecule is Linus Pauling likely holding in this photograph? Does it have 40 carbon atoms? [closed]

The video Quasicrystals ; Prof. Daniel Shechtman ; Nobel Prize in Chemistry shows Professor Dan Shechtman includes some photos of Linus Pauling who never believed in quasicrystals. From the video: ...
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What Chemical Database Extensions for Structure and Similarity Search are there?

I am looking for extensions/add-ons for relational databases (RDBMS) that enable storing and handling chemical structures including the possibility for substructure searches and similarity search. I ...
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Is each bag of plastic a polymer/macromolecule? If yes, why does it tear so easily? [duplicate]

For example, polyethene is a macromolecule. So each bag of polyethene should be one molecule. Doesn't tearing it therefore involve breaking strong covalent bonds? Shouldn't the energy needed to do ...
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1answer
86 views

What exactly is giant covalent molecule?

What exactly is the definition of "giant covalent molecule"? All sources online don't give a definition but instead, allude to properties of examples of giant covalent molecules (such as ...
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For a structure of a compouund optically active, what is the number of stereo isomers if no geometrical isomers are present?

Suppose for example the compounds $\ce{M(AA)3}$ and $\ce{M(AA)3bc}$, with $\ce{M}$, the central metal atom and $\ce{AA}$, a bidentate ligand. What is the total number of stereo-isomers of both? I was ...
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1answer
34 views

What is "tail" in case of secondary structure of protein? [closed]

What is a "tail" in the case of the secondary structure of a protein? How does it influence the "protein assignment" task?
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2answers
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Elucidating an unknown compound using 1H- and 13C-NMR spectral data [closed]

I am currently struggling with the following NMR spectrum for this compound: I know for sure that we should multiply the integrals of the hydrogen atoms by four, and that the compound contains at ...
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35 views

How does addition of side chains affect solubility and processibility of polyphenylene vinylene?

I am studying electrical engineering and physics. In a recent lecture I was told the $\ce{OC1C10}\text{-PPV}$ molecule has the chains added to the oxygen atom down below because it allows for ...
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1answer
73 views

Why do isosteric molecules have similar shapes? [closed]

Isosteres (Definition): Isosteres are atoms, molecules, or ions of similar size containing the same number of atoms and valence electrons.[1] Questions: A. Why ...
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1answer
126 views

What molecule is pictured on the cover of Dead Sara's album "Ain't It Tragic?"

An album released today by Dead Sara, titled Ain't It Tragic, has a chemical structure on the album cover. Here's a close-up of that structure: As the structure is partially obscured, it's difficult ...
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79 views

Stereochemical relationship between the given compounds

Are the given compounds enantiomers or diastereomers? Or are they identical? The compound is trans-1,2-dimethylcyclobutane: My reasoning is that they are identical. They are not mirror images, and on ...
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In the LCAO method for $H_2^+$, why do we only add or subtract orbitals but never alter one of the phases of the orbitals?

TLDR: Atkins' physical chemistry contains the quote "In general, from N atomic orbitals we can build N molecular orbitals". In the case of $H^+_2$, we use a combination of N=2 orbitals to ...
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Mechanism of Action of Carbachol

Carbachol (carbamylcholine chloride) is known to be a cholinergic agent. Does it work as an indirect agonist by inhibiting acetylcholinesterase, as a direct agonist of acetylcholine receptors, or is ...
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what does the prefix tetrahydro actually means?

After encountering a few compounds which their name includes the prefix "TETRA HYDRO" I'm wondering what that prefix actually means? For example THC (tetrahydrocannabinol) and also THF folic ...
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1answer
58 views

How to identify 'water' mistakes in protein crystal structures: Are B-factors and occupancy good indicators?

When solving the structure of a protein from diffraction data (x-ray crystallography), it can sometimes be difficult know what should be modelled into small spheres of electron density that are not ...
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3answers
353 views

What is abnormal Beckmann rearrangement?

What is abnormal Beckmann rearrangement? I read this term in one of my solution papers but I am not able to find relevant literature for the same. Answers linking to some source, or giving the ...
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35 views

Spectroscopic constants weye and weze

I am using Morse potential to calculate the spectroscopic constants of a diatomic molecule. So far I was able to calculate $R_e$, $\omega_e$, $\omega_ex_e$, $B_e$ but wasn't able to calculate $\...
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63 views

What is a spiroketal compound?

I read a medicinal chemistry book about SGLT2 inhibitors. One of them is tofogliflozin. In that book, they refer to it as spiroketal. Is the spiroketal functional group the red part in this picture? ...
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1answer
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Does hydrogen bonding affect the structure of a molecule?

We know an individual molecule of $\ce{H2O}$ has a bent structure, but if we consider a volume of water, then there are many molecules having hydrogen bonding with each other. Due to this, does the ...
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Eigenenergies and states of Jahn–Teller molecule

I'm generally interested in numerical chemistry. In our lecture, we have discussed the $E \otimes e$ Jahn–Teller molecule with the following Hamiltonian \begin{align} H = \epsilon n_d + \omega ( a^{\...
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1answer
114 views

Weerman degradation on alpha-hydroxy amides

I came across this reaction scheme in the solutions of a test paper: I understand the formation of isocyanate intermediate as the first step. In the second step, I realized that hydrolysis will be ...
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Finding Potential Depth of Multiple-Minimum in a PEC

Suppose we have the following curve with more than one well and different maximum points: My simple question is how to calculate the potential depth of each well? Do we calculate all the potential ...
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64 views

Planarity at the Junction between multiple Rings

My Approach: As cyclohexane should be in the chair form and cyclopentane should be in the envelope form, more the number of five-membered rings more should be its planarity, as envelope form is more ...
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1answer
207 views

Can resonance structures account for NMR spectroscopy chemical shifts?

I am unable to understand why the alpha carbon to the carbonyl group is of lower chemical shift compared to the beta carbon based on the effects of electronegativity and hybridisation. Since if ...
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68 views

Dative Bond in Nitrogen Dioxide

I learnt that a coordinate covalent bond forms only when Donor atom has a complete octet and also has at lest 1 lone pair. The receiving atom must have an incomplete octet and possess at least 1 ...
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What molecule is this. Pretty sure its not ethanol? [closed]

This is the molecule in question This in advance.
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119 views

Of 2-bromobutan-2-ol and trans-1,2-dimethylcyclobutane which is chiral as well as dissymmetric?

In an examination I was asked to determine the molecules which are chiral as well as dissymmetric. There were four options, and among them, two were achiral, as they had an improper axis of symmetry. ...
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87 views

What is the difference between structure and morphology in polymer blends?

When talking about polymer blends there is a difference between its structure and morphology, but I am not sure what it is. These two terms are used interchangeably in materials I use to study, but I ...
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177 views

The ways to determine if an ionic compound is paramagnetic or not

Find which of $\ce{Na2O2}$ and $\ce{CsO2}$ is paramagnetic. (Adapted from JEE advanced paper-1 2016, q.22) The given solution involves removing the cations and taking the anionic part, i.e. $\ce{O2^2-...
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What is the difference between structure assignment and structure prediction?

I am absolutely new to structural bioinformatics (only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using machine learning. ...
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209 views

Reactions of P2O5 and P4O10 with sulfuric acid [closed]

I have seen two reactions of $\ce{H2SO4}$, in one it reacts with $\ce{P2O5}$ and in the other $\ce{P4O10}$. The Reactions are as follows: $$\ce{H2SO4 + P2O5 -> SO3 + 2HPO3}$$ $$\ce{6H2SO4 + P4O10 -...
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103 views

Why does adding excess NaOH prove amphoteric nature?

When 3+ hexaaqua ions react with hydroxide ions, the following set of reactions occurs: When we get to stage 3, a neutral ion has formed, and a white precipitate is created. Now, we know that for ...
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1answer
79 views

Dehydration reaction of an alcohol, 2,3-dimethyl-2-phenylbutan-1-ol, with conc. sulfuric acid (at high temperature)

What's the major product of the dehydration reaction of 2,3-dimethyl-2-phenylbutan-1-ol with conc. $\ce{H2SO4}$ (at high temperature)? I am aware that in this reaction $\mathrm{E}$1 mechanism will be ...
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Molecular orbitals energy under pressure

Suppose we have a hydrogen molecule $\ce{H2}.$ At room temperature the average distance of the nuclei is $r_0$ (without applying pressure). If we put $n$ hydrogen molecules in a box with volume $V_\...
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345 views

Why is a conformer of hydrogen peroxide rotationally inactive?

Hydrogen peroxide may exist in four different forms depending on the dihedral angle, $d = \angle\,\ce{H-O-O-H}$. The four conformers are: Conformer I with $d = 0^\circ$, Conformer II with $d = 60^\...

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