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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26 views

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 ...
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4answers
328 views

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 ...
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Why is the carbon monoxide triple bond stronger than the nitrogen-nitrogen triple bond?

The $CO$ triple bond has a bond enthalpy of 1072 kJ/mol while the $N_2$ triple bond has a bond enthalpy of 945 kJ/mol, at least according to my source. The molecules are isoelectronic, so I couldn't ...
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1answer
52 views

Are Hartree-Fock solutions eigenfunctions of the electronic hamiltonian?

$\newcommand{\Ket}[1]{\left|#1\right>}$ $\newcommand{\Bra}[1]{\left<#1\right|}$ I'm currently revising for my qualifiers, and I've come across a point of confusion, one that several places give ...
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1answer
74 views

How to perform Mulliken population analysis by hand with GAMESS output?

I did a simple calculation on hydrogen fluoride with GAMESS and I wanted to reproduce the Mulliken population analysis for atomic orbitals. A molecular orbital is a linear combination of atomic ...
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1answer
101 views

Unexpectedly low melting point of Aluminium

According to Wikipedia, the melting point of aluminium is 933.47K (660 oC) while the melting point of magnesium is 923K (650 oC), yet the melting point of sodium is merely 370.87K (98 oC). With huge ...
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1answer
22 views

MOPAC: can we run THERMO immediately after the geometry optimzation?

With MOPAC, I am trying to set up single run with geometry optimization followed by calculation of THERMOdynamic parameters. Is there viable way for that?
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41 views

Is there a software that can predict the shape of a custom protein, given its amino acid sequence?

I know that the internet is full of enzyme and protein simulators which can show active site and 3D structure (like bioblender), but the problem with these programs is that they use predefined ...
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1answer
71 views

Is there a rule of thumb to predict when coupled cluster might dip below the variational limit?

Coupled cluster is a non-variational method, meaning that it can give energies that are below the true FCI energy (the "variational limit" for variational methods). Often coupled cluster still gives ...
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1answer
128 views

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 (...
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1answer
75 views

What does ³D mean in energy level diagram for helium?

I'm coming from a Physics background and am trying to make sense of the energy level diagram for para-helium and ortho-helium. From what I've gathered each column shows the different energy levels ...
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2answers
248 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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1answer
75 views

Catalyst discovery

How are catalysts for chemical reactions found? Given a hoped for reaction, let's take the hydrogenation of carbon monoxide to methanol as an example, do chemists: Proceed directly from some ...
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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 ...
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1answer
71 views

Is there a hypervalent molecule which has no contribution of d-orbitals at all?

I thought that d-orbitals were used to "extend the octet rule" in these molecules until I looked it up on Google and saw that they actually contributed only a little to the molecule. A little, but not ...
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49 views

Is it possible to create an arbitrary, stable, unique chemical fingerprint? [closed]

Context: I want to be able to hash real-world objects Is it possible to create a substance containing a combination of elements (or isotopes?) in a random and difficult to reproduce (but simple to ...
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61 views

How to achieve Löwdin transformation?

I use Gaussian 09 to obtain the Hamiltonian and overlap matrices, $H_0$ and $S_0,$ where the B3LYP functional and the 6-31G basis set are adopted. Then how to transform the system to an orthogonal ...
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1answer
82 views

How does resonance fail in approximating chemical structures?

In the book "Concise Inorganic Chemistry" by Prof. JD Lee, it says here: These contributing structures do not actually exist. The $\ce{CO3^2-}$ does not consist of a mixture of these structures, ...
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54 views

Is there any publicly available software that can do deterministic CCSDTQP other than MRCC?

MRCC can do arbitrary order coupled cluster but much of the code is computer-generated (not hand-coded by a human) so it can be slow. There are some stochastic codes for high-order coupled cluster, ...
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50 views

Explosive reaction based on reaction rate

Question We have the following chemical reactions: $$ \begin{align} \ce{A + B^* &-> C + D^*}\tag{1}\\ \ce{D^* &-> B^* + B^*}\tag{2}\\ \ce{B^* &-> B}\tag{3} \end{align} $$ ...
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1answer
1k views

Will Proving or Disproving of any of the following have effects on Chemistry in general?

I am working on a project relating to- https://en.wikipedia.org/wiki/Millennium_Prize_Problems I wanted to list the effects of them being proved or disproved in different aspects of science and maths....
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44 views

Psi4 gradient calculation with complete basis set? [closed]

I'm trying to set up a gradient calculation for psi4. In my input.dat file, I have tried the following keywords: set basis cc-pVTZ gradient('CCSD(T)') which is ...
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39 views

Why are the OV and VO blocks of the CIS 1RDM zero?

I know the reduced density matrix has the form: $$ \gamma(\alpha,\beta) = \langle\Psi_N|c^{\dagger}_{\alpha} c_{\beta}|\Psi_n \rangle $$ but when $\Psi_N$ is the configuration interaction singles (CIS)...
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2answers
416 views

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 ...
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3answers
184 views

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 ...
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0answers
73 views

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 ...
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0answers
78 views

How to formulate the 1 dimensional time-dependent Schrodinger’s equation from a given function?

Assuming $f(t) =e^{−iωt}$, formulate the 1 dimensional time-dependent Schrodinger’s equation. I started solving the problem as \begin{align} E &= hf, \tag1\label{eq:1}\\ E &= ħw, \tag2\...
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2answers
170 views

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 ...
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1answer
115 views

What is the biggest known difference between rₑ and r₀?

What is the biggest known difference between $r_e$ and $r_0$? Where $r_0$ is the average bond length of the lowest vibrational state, and $r_e$ is the location where the potential is lowest. For a ...
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1answer
103 views

Is it possible to have an allotrope of carbon as a long unbranched chain of itself?

Is it possible to have an allotrope of carbon with formula $\ce{(=C=)_n}$? Well, let's actually leave alone the separate question like from which "monomer" would one produce such a thing (can one ...
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1answer
882 views

Dipole moment in NF3 versus NH3

The usual explanation for the molecular dipole moment of $\ce{NF3}$ being smaller than that of $\ce{NH3}$, despite the $\ce{N-F}$ dipole being stronger than the $\ce{N-H}$ dipole, is that influence of ...
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55 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
315 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
74 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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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
107 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
91 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
158 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
54 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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0answers
54 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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0answers
123 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
296 views

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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16 views

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
58 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
220 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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33 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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122 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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73 views

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
143 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
390 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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