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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How do structural differences between neostigmine and TL-599 contribute to differences in toxicity?

Stevens and Beutel studied the activity of several carbamate anticholinesterases. Among other things, they found that the (4-trimethylammonio)phenyl dimethylcarbamate iodide (The para-analog of ...
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Is it rigorous enough to change a DFT functional after geometry optimization to calculate excited state properties?

I have done the geometry optimization with the B3LYP functional, however, there is a need to calculate the excited state energy, so the CAM-B3LYP functional should be better suited for that. Do I need ...
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137 views

What is the geometry of a tri-substituted methyl free radical?

My teacher explained that free radicals could have a geometry that is planar or pyramidal(tending to tetrahedral) based on whether or not it is substituted by lone-pair containing atoms. For example, $...
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151 views

Do changing opt=modredundant to opt in Gaussian makes geometry optimization not to take into account frozen angles?

I am a newbie to Gaussian and just generated an input for the geometry optimization for some molecules with multi ring system. However, in the article that was a reference for those calculations, some ...
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2answers
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Is selenium disulfide polar or non-polar?

So I saw in some internet site that $\ce{SeS2}$ is a polar molecule. When I drew the Lewis structure of the molecule, it showed up as a linear molecule like this: $$\ce{S=Se=S}$$ The electronegativity ...
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1answer
120 views

How does X-Ray Crystallography determine the components (as opposed to the structure) of a molecule?

Thanks for some online resources (i.e. here) I have an understanding of what X-Ray Crystallography does. By blasting X-Rays at a crystal and recording the scattering patterns on a plate behind the ...
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1answer
58 views

Can molecule have just h-bonds between its parts

I'm just starting to study chemistry so sorry for the probably obvious question to you, guys. According to the definition of molecule in Wikipedia: A molecule is an electrically neutral group of two ...
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1answer
74 views

Energy levels of combined orbitals

I saw the MO diagram for a NH3 molecule but couldn't understand why the combined atomic orbitals were in the positions they were, and if these positions were fixed. Why is the sigma anti bonding ...
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608 views

What is intermolecular distance in water? [closed]

I am wondering what is an average intermolecular distance in liquid water (say under normal pressure and room temperature). I need just order of magnitude. A reference would be helpful.
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What does a filled, solid circle mean in a chemical structure?

I'm looking in a textbook at an asphaltene molecule. The two aromatic rings next to the Nitrogen are shaded. What does that mean? I think the Nitrogen's create delocalized electrons in this ...
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Does the non-serotonin-like half of LSD resemble anything of significance?

LSD's resemblance to serotonin explains many of its effects on the brain, but I noticed only half of it resembles serotonin. The question I have, is does the other half resemble anything, particularly ...
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Forcing atoms closer together [closed]

Is there a method in chemistry to alter the energy of atomic bonds by forcing atoms closer together in a smaller volume? Similar to how pressure squeezes atoms closer together.
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Why are square planar molecules drawn from the side plane as opposed to the top plane?

Simply put, why can't you draw square planar molecules top down (so you don't have to use depth bonds)?
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Double Bond Geometry

The double bond at position '4' appears to be showing a 'E' geometry because the priority 1's are on opposite sides of the double bond ie top-left of bond4 is '1' (because Oxygen > Carbon)); bottom-...
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How can I determine the size of tropolone molecule?

How can I determine the size of a tropolone molecule? It's a seven-membered aromatic ring with =O on the first carbon and -OH on the second carbon. Is there any software available?
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Why is chlorpromazine not characterized as tricyclic? [closed]

Chlorpromazine is an old ("typical") anti-psychotic medication with a chemical structure which I as a non chemist find almost identical to that of all "ine" tricyclic anti ...
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A question about ligand binding

I have done part a and part b but I keep getting a negative concentration for part c. For part a I got $\pu{2 \mu M}$ For part b I got $\pu{5.051 \mu M}$ For part c, I get $2=3.2 + \text{[bound ...
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Examples of application of surface area maximization to crystallography or molecular geometry

Suppose that N points are chosen from the unit ball (or its boundary, the sphere) in three-dimensional space R^3. Consider the convex hull of these N points (assume N is at least 4). The resulting ...
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159 views

If Electronegativity of Cl is greater than H2 then why is the bond angle of Cl2O greater than H2O? [duplicate]

If Electronegativity of Cl is greater than H2 then why is the bond angle of Cl2O greater than H2O? Cl2 has more EN than H2 and size of Cl2 is more than H2 but if we go according to EN then more angle ...
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1answer
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how to obtain potential curves from database?

I'm sorry if this is a really super basic question. I am looking at the potential curves of a diatomic molecule in a book , and to plot them. I google the molecule and got to the NIST website, there I ...
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1answer
1k views

Maximum number of coplanar atoms in difluorotrimethylphosphorane

In $\ce{PF2(CH3)3},$ what is the maximum number of atoms lying in one plane? $\ce{P}$ is the central atom with the hybridization $\mathrm{sp^3d}.$ Two $\ce{F}$ atoms will form axial bonds with it, ...
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How to use Clausius-Mossotti equation to determine the molecular structure of a compound? [closed]

A question in my exam came as follows: Explain the Clausius-Mossotti equation. How is it used in establishing the molecular structure of a compound? I have studied the Clausius-Mossotti equation and ...
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80 views

How to use NMR readings to determine the molecular structure of a compound? [closed]

A question in my exam came as follows: How is NMR used in the determination of structure of organic compounds? I have studied NMR spectroscopy and I know how to determine values using an NMR ...
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1answer
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How to remove CH3 labels from a molecule's image? [OpenBabel in Python]

I would like to remove CH3 labels from svg images generated in openbabel in Python. I am thinking I should use ...
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1answer
289 views

How many covalent bonds are there in carbon suboxide?

Calculate the number of covalent bonds in $\ce{C3O2}$. Structure: I am confused. I can count covalent bonds as 8 by counting single-single bonds, but also I can say that there are 4 "double ...
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What do you call different formations of polycyclic molecules, such as the 'bent' phenanthrene vs. the 'linear' anthracene?

Are there terms, IUPAC or not, that describe multiple carbon rings fused in different shapes, like the aforementioned anthracene and phenanthrene? Also, I thought I read about a term describing carbon ...
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2answers
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Effective core potential and Gaussian basis set

Is using the effective core potential (ECP) and Gaussian basis set simultaneously in ab initio calculation a valid approach? For example, is it correct to use ECP for one of the atoms and, instead of ...
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Type of chirality in polycyclic compounds

Ignoring whether or not this molecule could exist, is there a name for this type of chirality? This molecule's mirror image cannot be superimposed on itself but there are no chiral centres. Even ...
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277 views

Molecular structure of iodine nonoxide

A question in an exam was as follows: Iodine reacts with ozone gas to form a dark yellow solid $\ce{X}.$ Let the number of lone pair of electrons in un-ionised form of $\ce{X}$ be $m,$ number of lone ...
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Geometry of a free radical at the bridgehead carbon

With reference to J. Am. Chem. Soc. 1968, 90 (19), 5266–5267, they state: The most favorable geometry of aliphatic free radicals remains an unsolved problem, since existing data are consistent with a ...
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Change of ionic packing upon crystals are pressurized

When rock salt crystal is pressurized, its FCC structure changes to BCC structure whereby coordination ratio changes from 6:6 to 8:8. At the same time packing efficiency of the crystal decreases from ...
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1answer
431 views

Can the molecule POOF exist?

Obviously, it really would be $\ce{O=P-O-F}$. Since $\ce{F-O-O-F}$ exists the $\ce{-O-F}$ part is obviously possible and the rest of it doesn't strike me as unreasonable, but whether it can actually ...
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Why can't an “upside down” chiral molecule neutralize the polarized light effect? [duplicate]

Steve Mould did a nice video a few months back called "Why Sugar Always Twists Light To The Right" (link is timestamped at the critical part). However his explanation was not complete. He ...
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3answers
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What do (2S,3S) and similar notations mean?

When my textbook is discussing stereoisomers with more than one chiral centers, it's using notation like (2S,3S) being an enantiomer with (2R,3R) and so forth. I understand R and S configuration, and ...
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1answer
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ATP chemical structure: phosphate groups with Oxygen anions or with OH groups?

I've googled repeatedly (with multiple search queries) to try and get an answer to this question but nothing comes up. Embarrassingly, I seem to be the only person who is confused by: ATP with oxygen ...
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1answer
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Anthracycline nomenclature - doxorubicin [closed]

Why $\ce{-OCH3}$ is Number 3? I think that $\ce{-OCH3}$ Appropriates Number one.
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1answer
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Is a tautomer's stability compared with refernce to its initial compund [closed]

Considering the following example while comparing the enolic content in the product, am I supposed to compare its stability with reference to its initial state or am I supposed to compare it between ...
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How is nomenclature decided in this case (formyl vs oxy)?

I was asked the IUPAC Name of the following compound in JEE Mains (2nd September, Shift 1) 2020. There were two names occuring to me: 5-formyl-2-methyl-hex-2-enoic acid (2,5)-dimethyl-6-oxo-hex-2-...
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What is one formula unit? [duplicate]

I am really sorry if this is a beginner question but please still help me. In this website, which explains balancing chemical equations mentioned the word formula unit here: $\ce{3Ca(NO3)2}$ (just ...
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1answer
152 views

Book Recommendation for Molecular Orbital Theory [duplicate]

I posting my question here since I have seen similar questions but I haven't found the specific answer I am searching for. I am seeking textbook recommendations on Molecular Orbital Theory with ...
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1answer
91 views

Sucrose skeletal formula - missing Carbon and Hydrogen [duplicate]

I was reading the Wikipedia article about Sucrose, when I noticed that the skeletal formula was missing some $\ce{C}$ and $\ce{H}$ atoms. The chemical formula being $\ce{C12H22O11}$, I counted the $11$...
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Why is borole not considered aromatic

I came across a problem which stated that borole isn't aromatic. I thought that borole is similar to pyrrole so it should be aromatic, but that isn't the case. Can I know why isn't it aromatic? I was ...
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Normal (Regular) or Inverted Terms?

I have a question on the order of the spin-orbit molecular states. I understand how to find the terms that split from a parent molecular state in a diatomic molecule. But my question is on how to find ...
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50 views

Do different alkyl groups affect chirality?

I am a bit confused on the definition of a chiral center; A carbon atom is chiral if it has four different items bonded to it at the same time. source However I am not sure whether different alkyl ...
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Cross-conjugation and aromaticity in pyrene

I have read about non-huckel double bonds and clar's rule, but what made me confuse is that huckel's perception gives me the feeling that central bonds in polycyclic aromatic hydrocarbons (ex: pyrene) ...
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1answer
62 views

How to interpret BRICS fragments

I have a molecule with a SMILES string as given below. smi='c1ccccc1OCCOC(=O)CC' I want to obtain BRICS based fragments which I did as follows. ...
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217 views

Converting SMILES string into valid sub-strings

I have a SMILES string as follows. smi= 'CCOC(=O)C1=C(COCCN)NC(C)=C(C(=O)OC)C1c1ccccc1Cl' Is there anyway that I convert this SMILES string into valid sub-strings ...
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Molecular Structure

What's the meaning of the triangle and striped line in this structure of $\ce{H3O+}$: Can someone suggest me a site to learn about this? (I'm quite a novice in chemistry.) Thanks
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Dipole moments of cis and gem alkenes [duplicate]

The procedure for comparing dipole moments for cis- and trans-alkenes is quite easy, but how to compare dipole moments of 1,1 dichloroethene (1); and cis-dichloroethene (2)? My teacher told me that ...
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2answers
119 views

Aspartic acid conjugate base acidity

Question Which hydrogen among the four in the conjugate base of aspartic acid is most acidic? Answer My attempt I am confused between Hb and Hc I know Hd has $\mathrm pK_\mathrm a \approx 9$, so ...

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