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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I need a good 3d drawing of ferropericlase
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
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529
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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 ...
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what are these two compounds genrally called and the difference in their property. Are they aromatic [duplicate]
Found these compound while looking at my notes, but have forgotten what they actually were.
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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 ...
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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 ...
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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 ...
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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
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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
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106
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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 ...
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2
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0
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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 = ...
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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 ...
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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 ...
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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 ...
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3
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1
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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 ...
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2
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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 ...
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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 ...
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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)?
4
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2
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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: ...
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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 ...
4
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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 ...
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2
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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 ...
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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?
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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? ...
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1
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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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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 ...
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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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2
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543
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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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218
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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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525
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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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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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