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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0answers
2k views

Why does [Co(NO2)6]4- ion have 3 unpaired electron as opposed to 1?

Why does $\ce{[Co(NO2)6]^4-}$ ion have 3 unpaired electron as opposed to 1? The book says that it has 3 unpaired electrons. I thought $\ce{NO2-}$ was a strong field ligand, making $\ce{Co^2+}$ a $\ce{...
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1answer
106 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
62 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 ...
13
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3answers
352 views

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
73 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 ...
3
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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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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 ...
1
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1answer
59 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 ...
72
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4answers
31k views

Bonding in diatomic C2, a carbon-carbon quadruple bond?

Carbon is well known to form single, double, and triple $\ce{C-C}$ bonds in compounds. There is a recent report (2012) that carbon forms a quadruple bond in diatomic carbon, $\ce{C2}$. The excerpt ...
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47 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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How to Calculate Transition Dipole Moment from Two Known Wavefunctions

I am interested in calculating the transition dipole moment (TDM) from the information from two wavefunctions of different states. This is somewhat similar to calculating the molecular dipole moment ...
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2answers
179 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
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What would follow in the series sigma, pi and delta bonds?

I realise, that this question is a stretch, but I was wondering, how would a bonding orbital be called if it was formed from two $f_{x(x^2−3y^2)}$ or $f_{y(3x^2−y^2)}$ orbitals. Have there been any ...
3
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1answer
66 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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2answers
485 views

How different are molecule with same connectivity

Let us represent molecules by graphs (atoms are vertices and bonds are edges). Let $A$ be the adjacency matrix of the molecular graph. $A_{ij} = b$ where $b$ is either binary: 0 when atom i and j are ...
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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 ...
34
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1answer
3k views

Natural Bond Orbital analysis: Significance of stabilization energy determined by 2nd order perturbation

PREFACE: I am no expert on this topic. My questions at the bottom may be off base. I have some experience with symmetry-adapted perturbation theory (SAPT) when it comes to analyzing intermolecular ...
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3answers
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Do filled Orbitals also hybridize?

Recently I was watching a video on Valence Bond Theory, on the MIT Open-Course youtube channel. The teacher there said that For hybridization to occur, electron promotion from fully filled ...
2
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1answer
69 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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0answers
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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3answers
12k views

Which areas of chemistry require calculus?

I didn't have much chemistry in school/college, and am now building up my knowledge again. I am studying maths in parallel, building up to calculus. I noticed that the introductory chemistry books (...
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44 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 ...
7
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1answer
389 views

Is the Lowdin Orthogonalization used in diagonalizing the atomic orbitals really a basis change?

This is kind of more on the mathematics side of quantum chemistry, but I can't quite figure out why the Lowdin Orthogonalization is called a basis set change. I get how it works from the perspective ...
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0answers
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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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, ...
3
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1answer
78 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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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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43 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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1answer
110 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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2answers
314 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
171 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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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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0answers
70 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
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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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0answers
77 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
164 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 ...
6
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2answers
163 views

Tunneling in chemical reactions

We know that quantum tunneling is the reason behind several natural phenomenon like alpha decay and thermonuclear fusion inside the stars. How can it influence chemical reactions by tunnelling a ...
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0answers
52 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 ...
12
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1answer
309 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 ...
16
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1answer
1k views

What exactly is meant by 'multi-configurational' and 'multireference'?

Some topics here have touched on this before (see 1, 2, 3), but I haven't found a clear definition yet. I would like to know what exact property of the wave function these terms refer to. It would ...
4
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1answer
105 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
67 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 $\vec r$)...
4
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1answer
89 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 ...
10
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1answer
153 views

Spin in meta-GGAs

In density functional theory (DFT) we know that the local density approximation (LDA) leads to an exchange-correlation energy kernel of the form: $$E_\mathrm{xc}^\mathrm{LDA} =\int e_\mathrm{xc}\left(...
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4answers
153 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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5answers
167k views

How to calculate the concentration H3O+ in a solution with pH=6.99?

What is the correct way to calculate the concentration $\ce{H3O+}$ in a solution with $\ce{pH}=6.99$? Attempt 1. pH<7, therefore there are only $\ce{H3O+}$ particles in the solution. $[\ce{H3O+...
6
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1answer
337 views

When is it better to use coupled-cluster (CC) over configuration interaction (CI) calculations?

My experience with different theoretical methods in computational chemistry primarily comes from use and reading papers. My experience is that people almost always use CCSD instead of CISD if they ...
6
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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 ...
3
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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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