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.

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65 views

Is it possible to have an allotrope of carbon with formula $(=C=)_n$?

Well, let's actually leave alone the separate question like from which "monomer" would one produce such a thing (can one actually consider it being a polymer? Or a covalent crystal?), because it seems ...
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29 views

Does the natural atomic orbital analysis result in natural electron configurations of molecules?

In my understanding, the natural atomic orbital (NAO) analysis is a method of calculation to get occupancy of electrons in center of each atoms. In other words, the result of NAO-occupancy indicates ...
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1answer
258 views

Is it good practise to mix double and triple zeta basis sets?

I need to compute extremely accurate single point energies using the coupled cluster method. The methods to be employed scale largely with the number of basis functions. A few basis functions may have ...
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1answer
57 views

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 $\vec r$)...
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15 views

Applying the constant number of electrons in DFT density optimisation

(Previous related question: Finding mathematically the ground state density in DFT) I am studying the density optimisation procedure (in particular for Orbital-Free DFT) this thesis. The derivative ...
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1answer
73 views

Cauchy-Schwarz integral screening different inequalites

Eq. (9.12.23) in [1] states that: $$\sum_{abcd}c_{ab}c_{cd}g_{abcd}>0\tag{MEST 9.12.23}\label{91223}$$ with $c_{ab}=c_ac_b$ for $c_a$ being some distribution coefficients and $g_{abcd}$ being the ...
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1answer
68 views

Finding mathematically the ground state density in DFT

To find the ground state density in DFT, you set the following Lagrangian: $$L = E[\rho(\vec r)] - \mu\left(\int \rho(\vec r) \mathrm{d}\vec r - N\right)$$ While minimising with respect to the ...
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4answers
127 views

Heisenberg's uncertainity principle(HUC)

I know the mathematical form of HUC and its statement i.e.It is impossible to determine simultaneously. , the exact position and momentum of an electron. i don't know why this ...
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1answer
45 views

What are the constraints on the two electron integral matrix?

In semi-empirical methods, the two electron integral matrix is simplified and the entries are replaced by actual values instead of integrals to evaluate. However, while doing that, the variational ...
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48 views

Modelling the Oregonator

Assuming this is the correct place for a post like this, I need to write a piece of code to show the oscillations in the Oregonator. I have successfully done so for the Brusselator, but have been ...
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109 views

Where to find experimental spin-orbit coupling constants?

I am searching for experimental spin-orbit coupling constants, particularly for main group elements and Cr(0) to calculate correlation consistent Composite Approach (ccCA) energetics. This method ...
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1answer
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Reaction of sulphur with calcium carbonate

Can sulphur react with calcium carbonate to form sulphur trioxide and calcium carbide, as the energy of 3(S=O) is greater than ((C=O) +2(C-O))? EDIT: i forgot to say that this is in an oxygen-free ...
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Catalyzing the breakdown of Si-O bonds

What catalysts can catalyze the breakdown of (Si-O) bond ? Can you mention some books(ebooks or hard cover) or websites that cover a lot of information about (Si-O) bond characteristics? I have ...
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1answer
49 views

Doubt on Element [duplicate]

I read the definition of element: Element consists of only one kind of atom and cannot be broken down into a simpler type of matter by either physical or chemical means. Then as per definition, $\...
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1answer
138 views

How to calculate the amount charge transfer from a natural population analysis?

I am trying to reproduce the quantity referred to as the degree of charge transfer reported in this publication by Zhu et al. [Ref. 1] for the F4-TCNQ molecule. I am interested in section 3.2 in the ...
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30 views

What makes determining entropy changes theoretically so hard compared to enthalpy?

It is really hard to determine the entropy change of a reaction accurately because of subtle solvent effects and a lack of standard entropies. On the other hand, enthalpy is relatively easy and ...
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99 views

Is there a reliable chemical theory that predicts pKa based on structure?

Obviously, there are general stability arguments that can be made to estimate relative pKas, such as evaluating the stability of the conjugate base of an acid, or thinking about how polarized the bond ...
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Do “random” “2D” polymers constrained to a box actually form “space filling” curves?

Background: The self avoiding walk model is (allegedly) a reasonable model for polymers, at least with respect to certain "universal" (i.e. lattice independent) constants -- see section 1.1. in this ...
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1answer
110 views

How to calculate S² value of a broken-symmetry wave function?

$S$ represents spin, signifies the number of unpaired electrons in the system. For example, if the number of unpaired electrons is $1$, then $S=1/2$. $S^2$ is calculated as $S(S+1)$. From what I have ...
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2answers
364 views

Kolmogorov backward equations in active biological systems

I am trying to understand the following equations from a paper by Wang et al. [1, p. 5 at the SI]: Michaelis–Menten Representation of the Kinesin Cycle We assumed that there is a strong ...
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28 views

Explaining hypervalency in the framework of molecular orbital theory

In preparing for teaching duties in an introductory course in inorganic chemistry, I seem to have made a digression into how we understand the hypervalent molecules. Just to re-iterate what this ...
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34 views

All possible determinants forms a complete basis [closed]

How do we mathematically prove that the set of all possible excited determinants forms a complete basis for expanding the wavefunction (as in full configuration interaction)?
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43 views

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 ...
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Is there an easy explanation of MP2 calculation [closed]

for my master thesis I calculated some ring strains with MP2 calculation. It was not hard to calculate these things but I'm struggling to understand what the theory is about. Now I'm defending my work ...
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60 views

Variational method: Hydrogen atom ground state in STO-3G basis expansion

I computed numerically the ground state energy of hydrogen by variational procedure, firstly expanding the wave function over the s-wave basis set STO-3G $$\psi(r)=\sum_{i=0}^3 C_{i} e^{-\alpha_ir^2}$$...
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Is there a mathematical basis behind the HSAB theory?

I learnt about the HSAB concept about a year ago, and found that it helped rationalise many of the solubilities/reactivities that “pure” Lewis acid/base theory could not. Is there a mathematical ...
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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 ...
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101 views

Hartree Fock for an atom (Beryllium)?

I'm working on solution of Hartree-Fock equation for Beryllium in configuration $1s^2 2s^2$, expanding the orbital with STO-3G basis $$\phi_k=\sum_{p=0}^3 C_{kp}e^{-\alpha_{kp}r^2}$$ I know the values ...
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2answers
61 views

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,...
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Why does the exchange interaction in Hartree-Fock theory lower the total energy?

In Hartree-Fock theory, the expectation value of the total energy can be written as $$E = \langle\Psi| H |\Psi\rangle = \sum_{a} \langle a| h |a \rangle + \frac{1}{2}\sum_{ab} \big( [aa |bb] - [ab|ba]...
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1answer
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Charge, multiplicity, level of theory and coordination coordinates of gold compleaxes [closed]

Good day, I need to learn a trick in answering the following questions: How to come up with cartesian coordinates of a complex say, [Au(CH2)2(S)PPh2]2, to be ran on Gaussian? The charge and its ...
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1answer
33 views

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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1answer
199 views

What is the difference between a configuration state function and a Slater determinant?

I do not understand the distinction between configuration state functions and Slater determinants. Is not every Slater determinant a CSF ? Please explain the difference and the use/need of ...
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2answers
92 views

Dissociation degree hell, Ostwald's law of dilution

Greetings dear chemists! I got a nice exam problem on wich i am stuck for hours, well maybe the problem is with me. I know the problem can be solved. So here we go. We got a weak monoprotic acid, we ...
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95 views

What is the ANO-RCC basis set and how does it work?

On the basis set exchange, the ANO-RCC basis looks huge, even for hydrogen: ...
2
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1answer
36 views

A theoretical framework for the formalization of chemical interaction and configuration based properties

Is there an attempt in any area of chemistry to formalize the way a molecule's properties change based on its configuration and the resulting changes in interaction with other molecules. For example, ...
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50 views

GAMESS Gaussian qst2 method alternative

I've heard about the qst2 Gaussian method but I don't have any licence so I use the free GAMESS-US. Nevertheless, I didn't find any Gamess method which allows a TS finding like qst2. Have you heard ...
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2answers
85 views

Intuition for why catalyst affects both forward and reverse reactions equally?

I have looked for quite a long time on the site however all the answers involve mathematical explanations involving Arrhenius's equation. I would really like an intuitive reason (or one using ...
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193 views

What is the largest coupled cluster calculation that has ever been done (as of March 2019)?

I am doing some research and trying to make sure the numbers I am reporting are accurate. I found that the paper by Sylvetsky et. al. says:[1] We were, however, able to complete a ...
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1answer
251 views

Pauli exclusion principle

Pauli exclusion principle states that 'No two electron can exist in same state' or 'No two electron can have same set of quantum numbers'. But in reality there is no state of electron. The state is ...
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2answers
164 views

Ab initio calculations

Why are quantum mechanical calculations so computationally expensive? What exactly is the process that makes it so time taking? What I mean is, one can perform classical dynamics simulations on a ...
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0answers
106 views

Good software/module in python to determine nuclear attraction integral in Slater type orbital basis sets

I am trying to solve a Hamiltonian of one electron and 10 stationary nuclear centers. here, the electron is treated quantum mechanically and nuclear centers are treated classically objects. The ...
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105 views

How to evaluate the expectation value of the Hamiltonian for a three electron Slater determinant?

I'm having trouble with a few concepts dealing with slater determinants and many electron systems. In particular, when dealing with 3 electron systems, I know that $$ \psi_0 = \frac{1}{\sqrt{6}} \det ...
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23 views

Why do identical protons not couple with each other in 1H NMR? [duplicate]

So basically I'm wondering why the different protons in ...let's say trans-stilbene do not couple with each other. I'm aware of the fact that they are chemically and magnetically equivalent. They ...
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2answers
92 views

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 ...
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150 views

Strange “far out” orbitals in HF and DFT calculations. Why do they occur?

I calculated some orbitals and I get quite strange results with orbital geometries I wouldn't expect from MO theory. A more experienced colleague just said: "That's always the case with big basis sets,...
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1answer
102 views

Simulation of Miller-Urey experience [closed]

The Miller-Urey experiment shows that it easy in a primordial atmosphere similar to early earth to generate amino acids,my question: is it theoretically possible to simulate this experience on any ...
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1answer
119 views

Conformer generation for radicals

Is there an automatic way to generate conformers for radical like systems (spin multiplicity is doublet)? My system for the study is a substituted fullerene with a missing H atom from the functional ...
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1answer
61 views

Is the neutral di-µ-oxo-bridged manganese dimer with eight ammonia ligands a reasonable structure?

In its guide to model antiferromagnetic couplig, Gaussian uses $\ce{Mn2O2(NH3)8}$ as a model compound.[1] It argues that manganese is in II oxidation high spin state; in other words, in both manganese ...
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1answer
48 views

What determines the coefficients in the wavefunction of a hybrid orbital?

I was studying the hybridization of carbon atoms and I came to figure out that the $sp$ hybridization wavefunction is given as $$|sp_{+}\rangle =\frac{1}{\sqrt{2}}\left(\psi_{2s}+\psi_{2p_x}\right)$$ ...