Questions tagged [theoretical-chemistry]
For questions seeking answers deduced from or composed of theories regarding the chemical substances and about models and methods of theoretical chemistry.
612
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How to find the global minima of a supramolecular complex in computational chemistry?
So this is more of a complex problem, and my masters thesis could greatly benefit if I find an answer to this.
Essentially, I have a supramolecular inclusion complex. There is this molecule A (the ...
6
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0
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53
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How does graphite content affect the conductivity of pencil lead?
My peers and I started an experiment to test whether we could use the conductivity of a piece of pencil lead to determine its grade (that is, whether it is 2H, HB, 3B etc.). The paper Observational ...
1
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0
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33
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Define a rate-determining step and an energy barrier for a multi-step reaction profile
I am currently making reaction profile by means of DFT calculations. I am able to correctly draw a whole reaction profile.
However, I am struggling to find what exactly is the energy barrier of a ...
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0
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37
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Would methylenedioxy-methylhexanamine induce seretonin release? [closed]
DMAA (Dimethylamylamine, methylhexanamine, forthane, geranamine) is a norepinephrine/dopamine releasing agent and sympathomimetic.
Could methylenedioxy-DMAA or a similar chemical have serotonergic ...
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2
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75
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Question about conservation of amount of substance
if I consider the reaction : $$A \longrightarrow B+C$$
by what we call conservation of the amount of substance, we have $$nA_{0}=nA+nB=nA+nC$$
But for me the conservation says that $$nA_{0}=nA+nB+nC$$,...
0
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0
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33
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How to calculate theoretical value of mass output using electrolysis with different electrolyte concentrations?
I am writing a research paper on a zinc-copper electrolysis experiment observing the mass output of Zinc on a copper cathode, in which I am changing the concentration of the zincsulfate electrolytic ...
0
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0
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47
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Energy Decomposition Analysis for SN2 involving ambident nucleophiles and an alkali metal counterion
I am wanting to perform an EDA on transition state structure of the nucleophilic attack of an ambident nucleophile (2 atoms that could be used in nucleophilic attack on the same molecule) on a benzyl ...
1
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0
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34
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Force contribution of image atom using periodic boundary conditions
This is maybe a stupid question but lead to a discussion between me an my colleagues. If we use periodic boundary conditions and an atom has itself as neighbor do we need special care of this ...
2
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0
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76
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Gaussian16 optical rotation calculation using a deuterated species
I am running into issues preparing an input file for DFT calculations. Currently, I am trying to submit an optical rotation calculation for an alpha-deuterated benzyl bromide (1 deuterium on the ...
2
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0
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38
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What is the meaning and unit of the integral in the local density approximation (LDA)?
According to Parr and Weitao (1995), the Dirac exchange-energy formula (1930) comes from
[I am looking only at the last line of the equation and the rest for completeness]
It's an energy, so I'd ...
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1
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85
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Doubt on vibronic transitions
When we justify the presence of electronic transitions forbidden by Laporte selection rule, the coupling between electronic and vibrational states help us. Why we say that in this way we are ...
2
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1
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117
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Can the ionisation energy of hydrogen be calculated using Coloumb’s Law?
Using Coloumb’s Law: $$F=k\frac{qQ}{r^2}$$
and the potential energy function: $$U(r)=\int_\infty^r F dr$$
I get:
$$U(r)=k\frac{qQ}{r}$$
Where k is the Coloumb constant and q and Q are the values of ...
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1
answer
169
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Why does Euler's Number appear in so many equations? [closed]
Is there an intuitive explanation for $e$ in those randomly chosen equations from my theoretical chemistry book:
$$\Phi(x,t)=(2\pi \hbar)^{-1/2}\int_{-\infty}^\infty C(p){\color{red}e}^{i(px-E(p)t)/\...
0
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0
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88
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Why can we use stoichiometric coefficients in the equilibrium-constant expression? [duplicate]
I just studied the chapter on chemical kinetics on Coursera, wherein I was repeatedly admonished not to use the stoichiometric coefficients in the rate law formula. I was told that this formula has to ...
0
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1
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109
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How to find the ligand field splitting of d orbitals in a square planar complex?
I am working with a Iron square planar complex with $\ce{NH2-}$ and $\ce{OH-}$ ligands having cis and trans conformation. My question is how to theoretically/computationally calculate the ligand filed ...
6
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1
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201
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Non-Arrhenius temperature dependence of bimolecular reaction rates at very high temperatures
Once I have read that in some cases bimolecular reactions can exhibit a maximum as a function of temperature due to the short lifetime of the activated complex at very high temperatures.
At low ...
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1
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100
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Highest possible temperature [duplicate]
I know the lowest possible temperature in nature is 0 K although we have been able to only getting ever closer and closer to it but not at 0 K.
But on the opposite spectrum of temperature, what is the ...
6
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0
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66
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Are there examples of publications using DFT instead of HF as a coupled-cluster reference?
I have been searching for a while, and only managed to find an article by M. Saitow,[1] where CAM-B3LYP orbitals are used. I was wondering if this has been done elsewhere.
It was recommended to me by ...
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1
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139
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Can cyclopropane be synthesized from propan-1-ol?
I know the dehydration of propan-1-ol derives in prop-2-ene by removal of the hydroxyl group and a hydrogen atom from the second carbon, but could the hydrogen come from the ones bonded to the third ...
5
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1
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150
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Are there any examples of tricoordinate hydrogen?
There are cases where hydrogen forms two covalent bonds (of order 0.5 I assume) in certain molecules and ions such as $\ce{H3^+}$, $\ce{CH5^+}$, $\ce{B2H6}$, $\ce{HF2^-}$, and hydrogen-bridged cations ...
2
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2
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113
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Is there an algebraic form for the textbook reaction coordinate curves?
So here is a curve often used in textbooks to illustrate a reaction coordinate.
It's a nice short-hand device to learn the relationship between kinetic and thermodynamic parameters that control the ...
1
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1
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81
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How do you know if a bond according to VB theory consists of 2 "3 electron bonds" or one "fully paired" bond?
First of all, I want to discuss the whole thing strictly according to the VB - theory and not use any concepts of the MO - theory.
According to Linus Pauling, the "3 electron Bond" is the ...
3
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1
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112
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Why is the local coupling constant (vibronic coupling) given in eV?
Should the local coupling constant g not be without a unit, as the Holstein Hamiltonian suggests?
$
H=\underbrace{\sum_{P, Q} h_{P Q}^{(0)} a_P^{\dagger} a_Q}_{\text{Fixed geometry}}+\underbrace{\sum_{...
1
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0
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51
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Spin-preserving excitations
I'm currently working on quantum chemistry with quantum machine learning and one of the operations considered for the calculation is the excitation (and desexcitation) of an electron from an orbital ...
2
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1
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228
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Is there a difference between Hartree-Fock method and LCAO?
I have to dive in some quantum chemistry for a quantum machine learning project and I came across the so-called Hartree-Fock method.
In one of the reference I used, they considered electrons as ...
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1
answer
114
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Difficult in grasping "the extent/limit of conformational space of a compound until it change its stereochemistry"
I have heard that a conformational landscape encompasses all conformers that a compound has for a specific stereoisomer. I think it makes sense verbally, because if all conformers of a stereoisomer ...
2
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0
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68
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Diffusion vs mobility and the Einstein relation
This former question is about the mobility constant $M>0$ in the Cahn-Hilliard equation. To determine the value of such a mobility for a simulation study, Kim and Sanders (2020)
use the formula
$$
...
-3
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1
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103
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Does concentrated HNO3 oxidize aluminium to form a protective oxide layer, or is the oxide layer already present so HNO3 is unable to react? [duplicate]
Sources on the internet like this one only say that aluminium does not react with concentrated or dilute $\ce{HNO3}$.
I have seen other related questions on this site but none answers my question ...
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0
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24
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Rationalisation of stabilising dispersion interactions in HgS via QM
It is well-known that mercury(II) sulfide, HgS, is extremely inert- for example, it has one of the lowest solubilities of nearly all known compounds in water(check Wikipedia). There are two well-known ...
4
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2
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265
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Provide a mathematical explanation of why the non-relativistic Schrödinger equation for a Molecular system, cannot be solved analytically?
The non-relativistic Schrödinger Equation is:
$\widehat{H}|\psi\rangle=E|\psi\rangle$
Where $\widehat{H}$ is the Molecular Hamiltonian in Atomic Units and has the following terms:
$$ \widehat{H}
=...
9
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2
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592
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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 ...
0
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0
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511
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Reaction of copper(II) chloride and aluminium foil
So I did an experiment recently with copper(II) chloride and aluminum. As they reacted with each other the redox reaction made the aluminum a brown substance that is supposed to be copper and the ...
1
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0
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85
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Are diffuse functions necessary for modeling unbound conjugated anions?
According to this paper, and contrary to popular belief, diffuse functions are far from being necessary for the calculation of the electron affinities of the polycyclic aromatic hydrocarbon(PAH)s, due ...
4
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1
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179
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How is a Barrierless Reaction Confirmed in Quantum Chemistry?
Background:
Some quantum chemistry papers explore potential energy surfaces by characterizing critical points with an ab initio method. Reactants, products, intermediates, and transition states are ...
7
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175
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Mathematical models of oscillatory chemical reactions
I am a mathematician working on real-life models in ordinary differential equations. I want to know if there are any models of oscillatory chemical reactions that consist of three ordinary ...
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2
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Are there any monocations with negative electron affinities known?
It is known that most dianions are unbound per se, i.e. that the corresponding monoanions have negative electron affinities, and the "dianions" we see in e.g. metal oxides can exist as such ...
4
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186
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Ferrocene's band gap is supposed to make it colorless but it isn't. Why is it so?
Wang and Islam [1] state that the ferrocene molecule's band gap, i.e. the HOMO-LUMO gap at the Kohn-Sham level, is 5.03 eV, which corresponds to an absorption wavelength of at most 240 nm.
So, ...
5
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2
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What are observationally stable elements?
According to Wikipedia, a lot of the elements that have higher atomic numbers than dysprosium have isotopes that say "Observationally stable" instead of stable, for example in Isotopes of ...
1
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0
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How to calculate <ab|ab> integrals to carry out Schwarz pre-screening of molecular integrals
During writing my own two-electron integration library I faced an issue of dealing with integrals that have very small values beyond the C/C++ double data type. ...
1
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0
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291
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Solubility of water in toluene
I'm interested in studying the solubility of water molecules in toluene.
I already know that some water can dissolve in toluene. I've also done some calculations at DFT level using the C-PCM solvation ...
1
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0
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68
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Alternate electronegativity measures for exotic atoms?
An exotic atom is an otherwise normal atom in which one or more sub-atomic particles have been replaced by other particles of the same charge. For example, electrons may be replaced by other ...
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53
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Why probability for an atom is fraction for population?
In the canonical ensemble the probability of finding an atom (or molecule) in its $i$-th energy state is given by the Boltzmann factor.
This probability is interpreted as the number of microstates ...
3
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1
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392
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STO-1G in Gaussian
I don't see the STO-1G basis set in the available sets on the Gaussian website and the software (g16) throws an error if I try. I see how it seems possible to use a custom basis but I'm not entirely ...
4
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759
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How do computational programs decide how many virtual orbitals to compute?
How do computational programs decide how many virtual orbitals to compute? For example, a Gaussian job of benzene at the TD-DFT B3LYP/3-21G level of theory calculates from 42 electrons a total of 66 ...
3
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99
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What is the physical significance of the damping function in calculation of vdW interaction energy?
In order to take care for the singularity (also removing the double counting of exchange-correlation) obtained with this expression,
$$E_\mathrm{vdW} = \frac{C^6}{R^6}$$
many type of damping functions ...
7
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1
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253
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Variational (Rayleigh-Ritz) method and multielectron wavefunction
I am studying Rayleigh-Ritz method and I have some problem to understand what the final wavefunction looks like. Suppose that we have a system with $N$ electrons, atom or molecule. We are interested ...
3
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0
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83
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State-of-the-art results on molecular vibronic energy calculation
Could someone kindly point me to the latest records in scale, accuracy, or timescale for molecular vibronic energy calculation?
I tried to start with Google Scholar: https://scholar.google.com/scholar?...
6
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109
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Why is carbon monoxide non-Brönsted-basic in aqueous solution when it has a lone pair on carbon?
Carbon monoxide is not protonatable in aqueous solution; a quick Google search even leads to a paper that talks about using carborane acids, i.e. extreme superacids, to protonate the molecule.
However,...
4
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114
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Schrodinger operator with matrix potential and Green's function
Clearly Schrodinger operators with matrix potentials appear very naturally in molecular dynamics/quantum chemistry, particularly when considering a crude adiabatic basis or diabatic basis for an ...
6
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2
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752
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Hypothetical symmetric carbon peroxide
Could a hypothetical carbon peroxide $\ce{C5O12}$ with the following structure (MolView — 3D model) exist, and I what its properties would be (other than decomposing, of course)?
I tried looking it ...