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.
615
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0
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What are the references in multi-reference methods? [closed]
There is this question: What exactly is meant by 'multi-configurational' and 'multireference'?
But I still don't understand what the multiple "references" are. I understand ...
2
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0
answers
188
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Physical interpreation of coulomb and exchange integral
When trying to solve the Schrodinger equation for the electronic hamiltonian:
$$H_{el} = \sum_{i=1}^{N} \bigg( - \frac{1}{2}\nabla_i^2 - \sum_A \frac{Z}{r_{i_A}} \bigg) + \sum_{i>j=1}^{N}\frac{1}{...
2
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0
answers
93
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Molecular dynamics simulation of a protein in acidic medium
I want to perform an MD simulation of a protein under acidic solvent conditions. A quick literature search seems to indicate that people are more interested in the protonation of protein side chains (...
2
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0
answers
107
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Negative coefficients for DIIS in SCF procedure
I am trying to implement the direct inversion of the iterative subspace (DIIS) algorithm in my simple HF program. After some problems it now seems to work. I can calculate the correct energies in ...
2
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0
answers
31
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expression of apparent reaction quotient
question
When computing the Gibbs energy change of a reaction using Legendre-transformed $\Delta_fG'$ values for a given $\mathrm{pH}$, the formula of the $\Delta_rG'$ of the reaction is:
$\Delta_rG' ...
2
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0
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115
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Can the Belousov-Zhabotinsky reaction be simulated with the Brusselator?
I'm trying to simulate the Belousov-Zhabotinsky reaction mathematically, with a system of ODEs. I know how to do this with the Oregonator and now I'm looking for another model to simulate the BZ-...
2
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0
answers
208
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Generate Surface with CubeFile from Gaussian in VMD or other free programm
I asked a question before, about how to save a mapped surface from GaussView. I don't get an answer, so I get much deeper in my internet research about it again.
Now I want to try to create a mapped ...
2
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0
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41
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Can Hartree-Fock be considered the quantum mechanical "Monopole" term in a quantum mechanical multipole expansion?
From what I understand, Hartree-Fock simplifies the exact electron-electron interaction with its two electron integrals. It reminds me of the classical energy of a charge distribution combined with ...
2
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0
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74
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Explosive reaction based on reaction rate
Question
We have the following chemical reactions:
$$
\begin{align}
\ce{A + B^* &-> C + D^*}\tag{1}\\
\ce{D^* &-> B^* + B^*}\tag{2}\\
\ce{B^* &-> B}\tag{3}
\end{align}
$$
...
2
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0
answers
94
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What is the largest known zero-point energy for a molecule?
I was surprised to find out that the zero-point energy (ZPE) for the ground state of $\ce{BH3}$ is a few thousand $\pu{cm-1}$, because for molecules I usually work with, it's much smaller. Does anyone ...
2
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2
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533
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Chaos in chemical reactions
I recently read about Chaos Theory and was wondering if a chemical reaction results in or shows characteristics of chaos (I found a few examples of such reactions here)
Chaos theory concerns ...
2
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0
answers
86
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Why does a 4-bonded nitrogen atom appears negatively charged after an optimization?
I have a molecule bearing a quaternary ammonium and I optimized it using M062X (also Hartree-Fock) using basis sets 6-31G(d,p) and 6-31G+(d,p) respectively. After optimization, I expect that the ...
2
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0
answers
123
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Antisymmetrized Product of Strongly Orthogonal Geminal (APSG) method
To get a deeper understanding of electronic structure methods, like Hartree-Fock, MP2, and Coupled Cluster method, there are many small programs (codes) available in Python, C++ or Fortran, for ...
2
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0
answers
34
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GVP(PP) orbital energies?
Hartree-Fock orbital energies can be interpreted physically, e.g. in Koopmans theorem, while one cannot assign active MCSCF orbitals to energies in general. What about GVB, say for example GVB(PP) ...
2
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0
answers
213
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What studies show that d orbitals don't play an important role in covalent bonding? (> period 2 elements) [closed]
Take a look at all the following molecules: $\ce{SO3^{2-}}$, $\ce{SO2}$, $\ce{SO4^2-}$, $\ce{PF5}$ and many more you can add. In all these there is a controversy of one of these two types:
Is formal ...
2
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0
answers
163
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How to obtain the distance of maximum probability of finding an electron on x axis
I have the radial component of the wavefunction
$R_{nl}(r)=r^2e^{-2r/3a_{0}}$ so to obtain the maximum distance on x axis I do not know if I have to compute the second derivative of $R_{nl}^2(r)$ or $...
2
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0
answers
155
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How does the phosphate ion look like? [duplicate]
I am trying to understand how a phosphate ion looks like using the VSEPR theory.
The phosphorus element has an atomic number of 15, and therefore it has a electron configuration as follow by the ...
2
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0
answers
99
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Why is it impossible to liquefy a gas with only pressure? [duplicate]
Why is it impossible to turn it to liquid by using only pressure after it reaches critical temperature? What happens in the molecular level? If we put enough pressure, the molecules are supposed to ...
2
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0
answers
55
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Dexamethasone radius of gyration source
I am looking for a source for the radius of gyration of dexamethasone in aqueous solution. Does anyone know where I could get it from? Even better would be an estimation of the Stokes radius, but the ...
2
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0
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1k
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Why is conjugation not possible if there is not present alternate $\pi$ molecules according to MO theory?
I was reading this page at Chemwiki; there they were discussing conjugated-$\pi$ bond.
In order to show that conjugation requires alternate double bonding, they cited the example of 1,3,6-...
2
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0
answers
311
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kinetic reaction rate greater than extent of reaction for equilibrium
I'm comparing a model with chemistry at equilibrium versus a kinetic one.
I take a network of two reactions: methane steam reforming (MSR) and water gas shift (WGS) at 700°C.
I calculated extent of ...
2
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0
answers
287
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Graph theory, isomer enumeration and chemical graph theory
Where could we find a good description of graph theory applied to the general problem of isomer enumeration and chemical graph theory?
1
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4
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1k
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What are the fundamental principles that are found throughout chemistry? [closed]
In the same way that biology has the fundamental idea that all organisms want to reproduce and pass on their genetic information, and that evolution accounts for the diversity of life, what are some ...
1
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1
answer
370
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How to derive the number of spectral lines?
Recently, I found that when electrons in an atomic sample de-excite from a higher energy level ($n_2$) to a lower energy level ($n_1$), the number of spectral lines observed in the spectrum is
$$\frac{...
1
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2
answers
4k
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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?
1
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2
answers
2k
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Spectroscopic constants - explanation
I'm a beginner in spectroscopy and I have troubles understanding papers describing values of spectroscopic constants. This paper, for example, describes constants $T_e, R_e, \omega_e, \omega_ex_e, B_e,...
1
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1
answer
33k
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Why x in equilibrium calculations can be "ignored"
You don't need to work out anything for me. I am just giving an example so you can explain something to me.
For example:
$$\ce{ClF3(g) <=> ClF(g) + F2(g)}\\ \ \ K_c=8.77\times10^{-14} \ \ @\ ...
1
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1
answer
169
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Potential energy of electron density at the nucleus
Consider the hydrogen atom for simplicity.
The electronic density at the nucleus is not null.
The attractive potential between a small volume of electronic density $\mathrm dV$ (at position $\vec r$)...
1
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1
answer
4k
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Why are there 3N-6 degrees of freedom in molecules?
Count the degrees of freedom using the minimum number of coordinates required to specify a position.
Let's say there are 3 atoms, 3 coordinates for center of mass, and 3 for an axis. But we need 6 ...
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5
answers
2k
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What are the effects of radio waves on matter?
Different regions of the electromagnetic spectrum interact differently with matter:
Microwave radiation can induce molecular rotation.
Infrared radiation can induce molecular vibration.
Visible and ...
1
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1
answer
3k
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How many empty orbitals do elements have?
A student was contemplating a question regarding elements with "no empty valence orbitals." An argument was made that elements all have infinite number of valence orbitals.
Every atom basically ...
1
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2
answers
224
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Concept of enthalpy at a given temperature
In thermodynamics, we always quote a fixed temperature, whenever we mention enthalpy of a reaction. For instance, one can determine the enthalpy of combustion of methane at 25 °C. Now almost all ...
1
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2
answers
157
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Can we really beat the speed of light? [closed]
This is a rather physics question but I wanted to get an insight from a chemistry perspective. I heard from some that you can beat the speed or go faster than it but is that really true. Physicists as ...
1
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1
answer
326
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What is a chemical daily life experience that can be modelled by superior mathematics? [closed]
I'm searching for a chemical daily life experience that can be modelled by superior mathematics so that the origin of the equations involved can be easily explained to a beginner in chemistry.
By ...
1
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1
answer
107
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Methods: Does failing at intermolecular properties mean the same for intramolecular properties?
Let us consider the following:
1.) Method X fails at describing intermolecular non-covalent interactions.
2.) Method X excels at describing molecules of type Y.
3.) Method X ___?___ at describing ...
1
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2
answers
112
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Software to perform molecular dynamic simulation
I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require ...
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1
answer
2k
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How to control the optimization step size in Gaussian?
I would like to perform a geometry optimization for a weakly bound methane dimer structure with Gaussian 16. During this process, the Newton-Raphson step should be controlled such that its length ...
1
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2
answers
2k
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Dipole moment of water using the definition [closed]
In many Chemistry books, the dipole moment of molecules is calculated through algebraic formulas. However, another definition of the dipole moment is
$$\vec{\mu} = \sum_i q_i \, \vec{r}_i$$
So, how ...
1
vote
1
answer
416
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Confusion about atomic/molecular orbital terminology
I have come across several different orbital terms: atomic orbitals, natural orbitals, split-localized orbitals, molecule-intrinsic orbitals, quasi-atomic orbitals.
I don't know what the difference ...
1
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1
answer
2k
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Why do noble gases like Xe and Kr form compounds, despite offending the octet rule?
According to the octet rule noble gases should not form compounds but xenon and krypton form compounds like $\ce{XeF2}$, $\ce{XeF4}$, $\ce{XeOF2}$ and $\ce{KrF2}$ respectively. Why?
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2
answers
189
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Why does orbital optimization remove spin contamination?
I've come across numerous articles asserting that orbital optimized methods, where minimization of the energy is achieved through a series of unitary rotations (achieved by exponentiated single-...
1
vote
1
answer
140
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Number of stable molecules of artificial molecule XY4 [closed]
Suppose element X has $5$ stable isotopes, and element Y has $6$ stable isotopes. Find the number of natural molecules, knowing that an X has a charge of $+4$ and Y has a charge of $-1$.
What I tried ...
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1
answer
92
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Small but modest displacements at negligible forces from DFT
When looking at a Gaussian log file today, I noticed the following information in the convergence criterion section after an analytical frequency calculation was performed:
...
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1
answer
341
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Fixed cell parameters, TINKER
I am using TINKER package to calculate the external reorganization energy for pentacene crystal. But I have problems with that - I've generated .xyz file of 5 molecules with VESTA and I need to ...
1
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1
answer
324
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Nuclear zero-point energy and quantum delocalization effects of water molecules
What do we mean by "Nuclear zero-point energy" and "quantum delocalization effects" of water molecules ? It's said that without these effects "water" becomes somewhat unbounded, which is not very well ...
1
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2
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2k
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deduce chemical properties of a compound from elements
If we know the properties of two elements e.g Oxygen and Hydrogen.
We know the following properties
sound speed
boiling point
melting point
refractive index
etc.
given that information, is it ...
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1
answer
122
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Question on theoretical existence (or lack thereof) of spherical symmetry of flerovium and/or oganesson
It is known that flerovium, with a [core]7s²7p² configuration, is predicted to be noble-gas-like; this is due to the "7p²" part of flerovium actually being (7p(1/2))², i.e. mathematically ...
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1
answer
31
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Is there a way of finding solubility/solvent from basic information? [closed]
Let's say I have a compound and I want to find a solvent for it.
Looking on some where like Wikipedia, it is quite easy to find solubility, in various solvents for common compounds. However it can be ...
1
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1
answer
58
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Explanation of terminology in equation used for energy calculation using Hartree–Fock method
I found in the literature that the energy of the Hartree–Fock method is given by the following equation:
$$E_\mathrm{HF} = \int (\Psi^* \hat{H}\Psi)\,\mathrm d\tau$$
The term $\Psi$ is the wave ...
1
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1
answer
385
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What are the steps of Hartree-Fock Theory?
Outline the steps involved in the Hartree–Fock method for the calculation of molecular electronic structure.
I understand the basics of HF, in that it does not account for electron correlation (...