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 antibonding orbitals energy

When we heat hydrogen the energy of the molecular orbital of H2(1s) is increased .What happens to the energy of the antibonding molecular energy of hydrogen(1s*)?
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Checking how chemically plausible a molecular structure is? [closed]

I was working on a project, which dealt with the plausibility of a chemical structure. So i wanted to know on what basis can i check it? It would be nice if someone could list down all the features ...
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Are there any molecular modeling programs that can build materials made up of three or more elements into a cylindrical shape?

I would like to build a material similar to what is in the image below. I have tried programs such as Material Studio, Quantum ATK, and VNL, but most of them can only do materials with 2 elements.
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113 views

Adding hydrogens to multiple pdb files using Openbabel GUI software [duplicate]

I am completely new to using OpenBabel software. I have about 9000 pdb files to which, I want to add hydrogens. It will be a very hectic task to open all of them 1 by 1 and then convert each of them....
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How can you build a model of tetrahedral coordination from objects found at home?

Our college is switching to teaching online mid-semester in hopes of slowing the spread of Covid-19. All the molecular model kits are still on campus. How could you build a model of tetrahedral ...
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If all bond angles in AX₃ are the same, then which of the following are correct conclusions about AX₃?

Question If all bond angles in $\ce{AX3}$ are the same, then which of the following are correct conclusions about $\ce{AX3}?$ (A) $\ce{AX3}$ must be polar. (B) $\ce{AX3}$ must be planar. (...
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1answer
191 views

How to use Google’s Alpha-fold to predict a two-protein complex?

Alpha-fold won the CASP competition last year. It used deep learning to predict the secondary structure of a protein given the primary amino acid sequence. Google has released its code a few weeks ...
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40 views

Why are branched isomers less polarisable?

This fact was given as an explanation as to why branched isomers of a compound have lower boiling points. How are branched isomers less polarisable and how does this relate to London dispersion ...
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1answer
85 views

What is the largest, noncrystalline, non-polymer inorganic molecule?

A question came up in class from one of my chemistry students. He asked what the largest, non-crystal, non carbon-based, molecule is. We ruled out complex proteins, DNA, and other polymers, as well as ...
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54 views

What exactly are frontier orbitals? [closed]

I read about frontier orbitals, namely HOMO, LUMO. But what's exactly HOMO/LUMO? I know HOMO stands for highest occupied molecular orbital and LUMO stands for lowest unoccupied molecular orbital. But ...
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Steric inhibition of resonance in substituted benzoic acid

Why does attaching an $\ce{-NO2}$ group at the ortho position of benzoic acid cause $\ce{-COOH}$ to become perpendicular to the plane of the benzene ring? Why doesn't the nitro group get pushed out ...
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Do molecules with bridges through rings exist?

Do molecules with bridges through rings (in a manner illustrated by this) exist? I sometimes get results like this when doing Energy Minimization on molview.org. For example: Is this actually a ...
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222 views

Substructure search with RDKit

I'm trying to search for substructures with RDKit. I would like to search for structure 1 as substructure in other structures. I don't understand why it doesn't find this structure in structures 3 ...
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184 views

Do isotopic groups cause optical activity?

I understood the simplified reason for optical activity of a compound based on the difference in the angular velocities of counter-rotating circularly polarized light. The difference is due to the ...
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Are there optically active molecules in which all atoms lie in the same plane?

I've learnt that when a molecule is non-superposable on its mirror image, it exists as a pair of enantiomers and is optically active. Absence of plane of symmetry is given to be one of the properties ...
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Are there any theorems about packing of atoms in molecules subject to the Lennard-Jones potential?

Related to the problem of minimization of the Lennard-Jones potential in a molecule with $n$ atoms, where $n$ is, say, between $5$ and $10$, questions arise such as (but not limited to) the following: ...
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Why does strength of bond matter if melting only affects the the intermolecular of the molecules

So as I've been told, when a substance melts, the actual bonds of the substance aren't broken, only the IMFs (inter-molecular forces). So why is it that metal groups decrease in melting points going ...
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1answer
198 views

Geometry of Ni(acac)2

The complex $\ce{Ni(acac)2}$ is paramagnetic as expected , i.e it has two unpaired electrons giving rise to a magnetic moment of $ \sqrt{8}$ BM but doesn't have the tetrahedral geometry consistent ...
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56 views

What is the correct term of a chemical formula for very large molecules if not just “chemical formula”? [closed]

I know that many molecules, wihch I as a non chemist, might define as "small" if their two dimensional diagram can be sketched on an A4 page, are often formulated; ...
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1answer
20 views

Difference between a species and a phase in a solution? [closed]

Overview: As of my knowledge from metallurgical thermodynamics a phase is a thermodynamically stable and homogeneous entity made up of different species of a given concentration. e.g = 'Austenite' ...
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1answer
184 views

Flexibility of long-chain aliphatic compounds

PubChem is unable to generate the conformers of Z-6-Heneicosen-11-one? The website says that the molecule is too flexible What does flexibility of a molecule mean in this context? I understand that ...
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Why are basal bonds longer than apical bonds in square pyramidal structure?

In trigonal pyramidal molecules such as $\ce{SF4}$, the axial bonds are longer than the equatorial bonds because of the 3c-4e bond. But in square pyramidal molecules such as $\ce{IF5}$ and $\ce{BrF5}$,...
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Optimization completed on the basis of negligible forces

I am performing relaxed scan in Gaussian (B3LYP/6-31G(d,p)). There are two small organic molecules, one of which is a radical, the other has a benzene ring. I'm trying to understand the optimization ...
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Why does SiH4 have unusually large bond angles?

The bond angles of $n > 2$ hydrides are usually around $90^\circ$, such as $\ce{PH3, H2S},$ $\ce{H2Se},$ $\ce{H2Te}.$ I understand that this is from increased $\mathrm{p}$ character in the bonding ...
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277 views

How can an Organic chemist know the chemical formula of a natural product she isolated from an organism? [closed]

As a non scientist I several times wondered how can an Organic chemist successfully isolate a single molecule which a natural product of an organism; Whether a plant-part/mushroom-part/algae-part or a ...
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2answers
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Why do PBr3 and PCl3 have larger bond angles than PH3?

According to the Colby Chemistry Database, the bond angle of $\ce{PBr3}$ and $\ce{PCl3}$ are around $101$ degrees, but the bond angle of $\ce{PH3}$ is $92$ degrees. (Source: PCl3 PBr3 PH3) There was ...
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Why are Newman Projections drawn with 120 degrees when actually sp3 carbons are 109.5 degrees?

Title says the question, pretty much. For example, in the Newman projection of ethane, the carbon hydrogen bond angles are $120$ degrees, not $109.5$ degrees, as they actually are in an $\text{sp}^3$ ...
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60 views

Structure of CCl₂

I read that $\ce{CCl2}$ is non-polar. When I read about the reason on the net it stated that $\ce{CCl2}$ has a linear structure, but according to VSEPR theory it should have bent V-shaped geometry. ...
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1answer
105 views

Why there is a huge difference between the basicity of urea and guanidine?

The two molecules have very similar structures, but urea has a $\mathrm{p}K_\mathrm{b}$ of $13.9,$ while guanidine have a $\mathrm{p}K_\mathrm{b}$ of $0.4.$ If guanidine cation can be stabilized by ...
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1answer
69 views

Why is the Sulphur Dioxide molecule polar? [closed]

I am in 12th standard and was revising the concept of determining which polyatomic molecule can be polar and which can be non polar. So when this example was given we were told that vertical dipole ...
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Why is the bond angle of sulphur dioxide close to 120°, not 90°?

Figure 1: Structural data of $\ce{SO2}$. Taken from Wikimedia, where a full list of authors is available. As can be seen from the structural data, the bond angle of $\ce{SO2}$ is almost precisely $...
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Software to assist drawing of complex, three-dimensional skeletal formula from scratch or from existing crystal structure

Is there a tool that would help in creating rather intricate line drawings (not pre-rendered balls-and-sticks/wireframe/sticks/ORTEP diagrams) for a skeletal formula in 3D space? To illustrate the ...
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Structure of dihydrogen peroxy-phosphate ion

In structure of Dihydrogen peroxy-phosphate ion $\ce{H2PO5-}$, shouldn't negative charge be on oxygen linked directly to phosphorus, rather than on oxygen linked through peroxy linkage with another ...
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1answer
135 views

Preferred Lewis structure for sulphate anion and XeO4 [closed]

In a section reviewing Lewis structure, the textbook Atkins' Physical Chemistry, 10th Edition, by Atkins, Paula, and Keeler, gives the following illustration of hypervalence and octet expansion: I ...
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1answer
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Question about d-orbitals [closed]

I saw somewhere that, "in PF5, the 3d orbitals of phosphorus end up in the anti-bonding molecular orbitals, and thus contribute less to the final molecule" and that "the hypervalency of some ...
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2answers
238 views

Does H3CO3+ ion exist and what is its structure? [closed]

Why doesn't $\ce{H3CO3+}$ ion exist and why doesn't the carbonyl group in carbonic acid $(\ce{H2CO3})$ seem reactive?
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Identifying molecule with three adjacent six-membered rings from blurry image

I have found this isolated image on one of my old hard drives and I would like to know what molecule does the image represent:
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1answer
189 views

Meaning of the term “vertex” in the topic of skeletal formulae

From the Wikipedia article on skeletal formula: Hydrogen atoms attached to carbon are implied. An unlabeled vertex is understood to represent a carbon attached to the number of hydrogens required ...
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Chromium cyanide complexes

I have rarely seen any chromium $(\ce{Cr})$ square planar complexes and I have been told that $\ce{[Cr(CN)4]-}$ is tetrahedral. So, if the statement is actually correct, are there any other known ...
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Can stimulated Raman processes be strong enough to drive out of equilibrium?

In the (spontaneous) Raman process, incident light $\hbar \omega_1$ scatters and transfers some energy $\hbar \omega$ to a vibrational excitation of molecule or solid. Typically this is a very rare ...
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2answers
229 views

Is PCl5 really trigonal bipyramidal in shape?

We know that the structure of $\ce{CH4}$ is tetrahedral, and not planar tetragonal, as a tetrahedron enables maximum distribution of $\ce{H}$-atoms in space, as they repulse from each other. This is ...
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Are all stable Xenes (graphene-like 2D honeycomb sheets) buckled?

background: Per this abstract Silicene, germanene and stanene are part of a monoelemental class of two-dimensional (2D) crystals termed 2D-Xenes (X = Si, Ge, Sn and so on) which, together with ...
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Computational tool for identification of activity cliff

Are there computational tools for identification of activity cliff between two analog compounds? This paper list chemotypes that with a high propensity to induce activity cliff.
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1answer
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Drawing bicarbonate ion in different way [closed]

I don't know why can't I draw $\ce{[HCO3]-}$ like that: I tried to draw it like that and checked everything. I checked formal charge and all was good. Why they draw it OH I know its also alright but ...
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Does H2SO or H2CO have a higher dipole moment? [closed]

Given these two molecules, I realize that the molecules are pretty identical in terms of the individual atoms' electronegativities (with Sulfur only being a small bit higher than Carbon). So then, the ...
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121 views

Bond length comparison in substituted phosphorus pentahalide

What would be the comparison between $\ce{P-F}$ and $\ce{P-Cl}$ bond length in phosphorus tetrafluoride chloride $\ce{PF4Cl}$ and phosphorus trifluoride dichloride $\ce{PF3Cl2}$ in the equitorial ...
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What is the Lewis dot structure for ozone? [duplicate]

Currently I studying about the Lewis dot structure for different compounds and my textbook says that the Lewis structure for ozone may be drawn as(as shown in the image): And then it goes on to ...
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3answers
553 views

How do I figure out how many hydrogens my compound actually has using a mass and NMR spectrum?

Question 3: It said $m/z = 122,$ and $m/z = 124$ is in a $3:1$ ratio, so I figured that meant that chlorine is present. Then I thought $m/z$ was the actual compound's molecular mass. So I used ...
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1answer
87 views

About Fe(III) and Fe(II) coordination complexes

Why does Fe(III) form octahedral coordination complexes if it has 5 electrons in its d-orbitals? I understand that Fe(II) has 6 electrons in its d-orbitals and 6 lone pairs from 6 ligands as the 12 ...
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1answer
169 views

Any way to see “cubic-active” vibrational modes in molecules?

For molecular complexes with a moderate amount of symmetry there are usually vibrational modes that are neither infrared nor Raman active. Sometimes these modes transform as some cubic polynomial in x,...

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