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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Molecular structure strength

Why is it that bent molecular structures have more strength as far as hydrogen bonding is concerned? And linear molecular structures do not. Take the example of H2O molecule hydrogen bonding and the ...
Hasham Beyg's user avatar
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Xe-F bond lengths and geometry of XeF6 [duplicate]

My teacher states that the geometry (not shape) of XeF6 is distorted octahedral but according to VSEPR theory I conclude it should be pentagonal bipyramidal. Please tell why is there such deviation. ...
Madhav Mittal's user avatar
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Behavior of polyanionic silicate chains in silico

I am trying to understand the stability of charged linear molecules, more specifically these, which contain periodically repeated high electron affinity parts, such as single-bonded oxygen (radicals). ...
Paul Kolk's user avatar
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Why cant H2O be linear? [duplicate]

My understanding is that a H2O molecule cannot be linear due to repulsions between the electrons of the non-bonding domains and the hydrogen: However i was wondering why the structure could not take ...
Varshil MVH Pets's user avatar
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Why can't the fructose monomer in sucrose be α-fructose?

In all academic sources, sucrose is identified as α−glucose (1-->2) β−fructose. However, I cannot find any explanation anywhere as to why the fructose monomer has to be in the β configuration. ...
MD P's user avatar
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What is happenning with that single hydrogen in Phosphorous acid?

As an oxyacid, Phosphorous acid intuitively should have the structure since the hydrogens should be on the oxygens. However, the major form of this acid is actually with the hydrogen attached to the ...
Captain Chicky's user avatar
-2 votes
1 answer
53 views

Is methylpropane actually butane?

My notes from my teacher says that 1- chloromethylpropane can be prepared from methylpropane under sunlight with chlorine. However I am confused as I think there is no such thing as methylpropane ...
gatiskandis's user avatar
4 votes
1 answer
130 views

How to draw endo-bicyclo[2.2.1]hept-5-ene-2,3-dicarboxylic anhydride on ChemDraw?

I'm struggling to draw endo-bicyclo[2.2.1]hept-5-ene-2,3-dicarboxylic anhydride on ChemDraw. I currently have this: How can I draw it in the chair conformation side on view? I know what it is ...
avogadros_pupil's user avatar
1 vote
1 answer
49 views

Best representation of 1310384-76-9 / 1104637-53-7, a molecule with a coordination bond between nitrogen and boron

If you look up the above CAS numbers, you will sometimes find this structure: which, I think correctly, our chemistry validation software tags as 'bad valence'. In other websites you will find the ...
user6376297's user avatar
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29 views

How to integrade a group of disconnected smiles descriptors from molecular into a single smiles descriptor?

I am new to cheminfo so this question may sound stupid. I am trying to calculate the RDF(radial distribution function) of these two compounds below: https://pubchem.ncbi.nlm.nih.gov/compound/155293646 ...
Yuuya's user avatar
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I need a good 3d drawing of ferropericlase [closed]

I'm not a scientist, I'm an artist and I need a good 3d drawing of ferropericlase, where can I find that? Thank you! Niki
Nicoletta Barolini's user avatar
8 votes
1 answer
669 views

Does concept of degree of unsaturation not work for fullerene molecule?

Commonly known buckminsterfullerene has molecular formula C60 if we calculate it's degree of unsaturation by formulae, it comes out to be 61 and it is also known that this fullerene has 12 pentagon ...
worksifitdoes's user avatar
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1 answer
192 views

Are all bond lengths equal in [8]annulene? [closed]

I know [8]annulene is non-planar, but are all bond lengths equal?
user avatar
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1 answer
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Why does the two OH bonds in H2O have different bond disassociation enthalpies? How does the bond cleavage happen here?

I came across this question, and in the text it was written as 'change in the chemical environment'. I wasn't satisfied with this explanation, so I am looking for a more detailed answer on this matter ...
goldi mathews's user avatar
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3 answers
212 views

How many molecules in DNA?

This seems to be a simple question but I have failed to find an answer by searching. Let's consider human DNA so 23 chromosomes. The first question is on the double helix, is that considered as one or ...
badjohn's user avatar
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From chemfig to .mol file/SMILES

I usually draw molecules using the markup language known as LaTeX. In particular, I use the chemfig package. I much prefer this method over WYSIWYG apps because it ...
user3204810's user avatar
-5 votes
1 answer
78 views

What does the colon (the pairs of dots) mean in chemical structures? [closed]

What do the two dots mean, for example, the "Ö" in Wikipedia.org - Hydroxonium-cation.svg
11pro12's user avatar
2 votes
2 answers
184 views

Cyclopentadiene planar

Cyclopentadiene has a sp3 carbon yet it is said to be planar. I am not able to understand and haven't been able to find a credible source. Some sources say it to be non-planar
gsam7's user avatar
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Correct structure of compound tetraiodine nonoxide [duplicate]

I have a confusion about the correct structure of tetraiodine nonoxide. I came to know about it while reading the equation : $$\ce{6 I2 (dry) + 11 O3 -> 3I4O9 + 3O2 }$$ Now again I saw the equation ...
Prince Nagar's user avatar
2 votes
0 answers
154 views

Are there any compounds with pentagonal pyramidal molecular geometry?

As a high school student, I am curious whether there are any compounds with pentagonal pyramidal molecular geometry. I know that most compounds having hexacoordinated central atom and having $\sigma = ...
Bongo Man's user avatar
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1 answer
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Transform raw atomic coordinate data into SDF file

I have raw data of the atom types and their coordinates. For example, water molecule is: O -0.034 0.977 0.007 H 0.064 0.020 0.001 H 0.871 1.300 0.0006 Here, I ...
neco's user avatar
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5 votes
1 answer
271 views

Why is pyramidal structure observed in trisilylphosphine?

Why does trisilylphosphine $\ce{P(SiH3)3}$ (ICSD Entry: 72676, [1]) have a pyramidal structure while trisilylamine $\ce{N(SiH3)3}$ (ICSD Entry: 201428, [2]) is planar? I think since silicon has a ...
Substitute_Y's user avatar
-3 votes
1 answer
106 views

Can glycerol in substituted natural fats be a monomer according to European REACH Regulation? [closed]

European REACH regulation for registration of chemical substances has an own definition of a polymer according to this regulation. I've noticed the following problem. I want to discuss here only the ...
IV_'s user avatar
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3 votes
1 answer
127 views

Dipole moments of trans and cis nitrous acid

I have a paper due about the isomers of nitrous acid, using various calculations methods to find molecular properties like their dipole moment. I've found the dipole moment of trans isomer to be 1.987 ...
silvermacabre's user avatar
-4 votes
2 answers
103 views

Mechanism of S2Cl2 and NaHSO3 [closed]

I learned that NaHSO3 reacts with S2Cl2 to give Na2S4O6 as product. After looking up the structure of Na2S4O6, it confuses me that four sulfur atoms connect together. I couldn't figure out the exact ...
Shira's user avatar
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1 answer
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Does I2 form coordinate covalent bond with PI3 in PI3.I2 (PI5)

As PI5 is uncertainly stated as the combination of PI3 and I2. There are suggestions that phosphorus donates its 3s electron pair to molecular orbital of I2 or I2 donates its electron to 3d orbital of ...
Shira's user avatar
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0 votes
1 answer
126 views

Which group takes CIP priority CH2OH or CH2OCH3?

I am confused why this structure is (2R, 3R) when CH2COMe takes priority over CH2OH which takes priority over CH3, surely it should be (2S, 2R)?
Michael Heron's user avatar
4 votes
2 answers
760 views

Is HC(=NH)OH a stable compound?

The molecule $\ce{HC(=NH)OH}$ has been shown to derive from hydrogen cyanide and water (compound 7). Is it a stable compound? source: Das, T.; Ghule, S.; Vanka, K. Insights Into the Origin of Life: ...
nightcod3r's user avatar
-4 votes
1 answer
127 views

What is the structure of quinine? [closed]

I am very confused on what the inner lines in the hexagons mean, are these representing double bonds? If yes, does that mean quinine has 6 double bonds? Also what would be considered a central atom ...
Ahmad Ghaddar's user avatar
5 votes
1 answer
1k views

How to convert SMILES to 3D (with higher accuracy than RDKit)?

I am interested in assigning 3D coordinates to (atoms in) some 10K molecules that I have, currently represented by SMILES. This is because as have been shown by many chemoinformatics papers, 3D and 2D ...
jasperhyp's user avatar
-1 votes
2 answers
296 views

Why does the conjugate base of peracetic acid not have any resonance structures?

Peroxyacetic acid, $\ce{CH3C(O)OOH}$ has its anion form when a proton is detached, like $\ce{CH3C(O)OO-}$. I think it can have two resonance forms like I drew (even though they have several charge ...
NIH's user avatar
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3 votes
0 answers
71 views

Why does gallium expand on solidification

I've heard that Ga exist as Ga2 molecules in its crystal lattice. Does that have anything to do with expansion of Ga while solidifying? Why and how does it actually expand?
Neet aspirant's user avatar
-3 votes
1 answer
84 views

According to molecular orbital theory, 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? ...
CaptainAmerica Whyso's user avatar
-2 votes
1 answer
3k views

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 ...
Lanagan's user avatar
-4 votes
1 answer
197 views

Planarity of rings [closed]

Can a 7 or less than 7 membered homocyclic ring with unsaturated C atoms and fully conjugated system, lose planarity? The smallest homocyclic non-planar ring that I know is cyclooctatetraene which is ...
Shubhayu Basak's user avatar
0 votes
0 answers
104 views

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 ...
Growing6884's user avatar
4 votes
2 answers
554 views

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 (...
majumderS's user avatar
10 votes
4 answers
1k views

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 ...
matt_black's user avatar
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8 votes
1 answer
518 views

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 ...
uhoh's user avatar
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1 vote
1 answer
1k views

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 ...
Yitian Chen's user avatar
-1 votes
1 answer
197 views

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 ...
Simon's user avatar
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-1 votes
1 answer
151 views

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 ...
TriGnome's user avatar
1 vote
0 answers
72 views

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 ...
哲煜黄's user avatar
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2 votes
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172 views

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(...
JAClarke's user avatar
1 vote
0 answers
118 views

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 ...
Dr Acme Isme's user avatar
1 vote
0 answers
56 views

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 ...
QF2QP's user avatar
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4 votes
1 answer
253 views

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 ...
Iti's user avatar
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0 answers
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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 ...
Arun's user avatar
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1 vote
0 answers
44 views

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 ...
Akash's user avatar
  • 335
-3 votes
1 answer
61 views

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 ...
Kortelly Zamatosh's user avatar

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