24 votes

Linear algebra and Hess's law?

To convert this into a generic linear algebra problem you'd rewrite it in the form $Ax=b$ where $A$ is a matrix of stoichiometric coefficients of size $m \times n$; $x$ is a vector of length n of ...
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  • 18.7k
15 votes
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Why don't the MO energies sum up to Hartree-Fock SCF value?

The key misconception you have is that the sum of the orbital energies is equal to the electronic energy. Compare the formulas for the two (taken from Chapter 3 of Szabo and Ostlund's Modern Quantum ...
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  • 11.3k
12 votes
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How do computational programs decide how many virtual orbitals to compute?

The basis functions you use describe a space within which your orbitals are vectors. If you have $N$ basis functions this space is $N$-dimensional, and in a $N$-dimensional space you can have at most $...
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  • 2,463
10 votes
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What material properties are unpredictable (not reproducible) but can be measured consistently and at a low cost?

Impossible for a homogeneous material, however ... basically every nonhomogeneous material fits your description. Say the pattern of microphase separation in a copolymer. Or the arrangement of filler ...
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  • 11.4k
9 votes

Why is chemistry based on rules and exceptions when everything can be simulated?

I wondered why we can't/don't have perfect knowledge about how things work on an atomic level Well... we do. The things you have suggested (like VSEPR theory) are very crude, though, and not suitable ...
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9 votes
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Given a CIF (crystallographic interchange format) file (and thus cartesian atomic coordinates), how can you find the bonds between atoms?

Your question does not detail out what you mean by how is it done. Indeed, your question may be answered twice: determine the distances between atoms, pairwise compare the sum of van der Waals radii;...
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  • 23.6k
8 votes
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Listing all possible structures for a given Markush structure automatically

Preface: Since you mention familiarity with/access to Python, and I assume you want to process batches from .sdf from a script rather than from a GUI (note, ...
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  • 23.6k
8 votes
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Is there an error at page 138, 4.4 of Introduction of Computational Chemistry 3rd Edition?

There is an updated list of errata* for the 3rd edition of Jensen's book at https://chem.au.dk/~frj/corrections_ICC3.html, which includes the mistake you pointed out (and more). It reads: page 138, (...
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  • 65.8k
8 votes

How to estimate the temperature needed to overcome an activation energy barrier?

From the Eyring equation, we can simply calculate the $k$ value for it. \begin{align} k &= \frac{k_\mathrm{b} T}{h}\exp\left(\frac{-\Delta G^\ddagger}{RT}\right)\\ k_\mathrm{b} &= \pu{1.38E-9 ...
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  • 1,160
8 votes

How to estimate the temperature needed to overcome an activation energy barrier?

You could convert the rate constant($k$) to half-life($t_{1/2}$) which would give you an idea of the time scale required for the reaction to finish at a certain temperature. The equation to obtain ...
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  • 5,249
8 votes
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STO-1G in Gaussian

I don't believe there is a "STO-1G." Even if there were, it would exhibit poor performance. The STO-nG basis sets were first published by Hehre, Stewart, and Pople in 1969: "Self-...
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7 votes
Accepted

Why are MD simulations necessary for obtaining Boltzmann populations?

In principle you can, assuming you are given $V(\{\bf{r_i}\})$ where $\{\bf {r_i} \}$ is the set of variables that define a configuration in the system - this is typically the coordinates of the atoms,...
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  • 2,463
7 votes

Why is chemistry based on rules and exceptions when everything can be simulated?

We can't simulate everything because there isn't enough computing power to do it The fundamental problem of making chemical predictions is that they are extremely hard to do because of the ...
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  • 32.2k
7 votes

Given a CIF (crystallographic interchange format) file (and thus cartesian atomic coordinates), how can you find the bonds between atoms?

You didn't ask about macromolecules, but I'll write about it anyway. Macromolecular CIF files (mmCIF) also don't contain bonds. This information is stored in separate dictionaries. In particular, the ...
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  • 361
6 votes

Why is chemistry based on rules and exceptions when everything can be simulated?

What you have in mind sounds like Molecular Mechanics. Atoms are treated there like classical particles and are simulated using classical physics, including Coulombic forces. But we know that this is ...
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6 votes

Given a CIF (crystallographic interchange format) file (and thus cartesian atomic coordinates), how can you find the bonds between atoms?

The most software find bonds in a structure from cartesian coordinates by finding atom pairs that are closer than a certain threshold distance (something shorter than the vdw radius of the given atoms)...
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  • 5,240
6 votes

Given a CIF (crystallographic interchange format) file (and thus cartesian atomic coordinates), how can you find the bonds between atoms?

how could one algorithmically find all bond pairs Here is a sketch of an algorithm that takes crystal symmetry into account: Move all atoms into a single asymmetric unit Apply all symmetry operators ...
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5 votes

What material properties are unpredictable (not reproducible) but can be measured consistently and at a low cost?

The OP asks: What process, material and/or measurement could be used? Answer: Snowflake maker, dihydrogen monoxide, photograph (with metric ruler included). "Snowflake maker" is a vapor ...
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  • 12.4k
5 votes
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Practical use of the partition function in molecular simulations

The actual partition function is unimaginably formidable. For just $N$ point particles in a 3D box, it's already got $3N$ dimensions. If the box is length $L$, GROMACS would probably divide the box ...
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4 votes

What is the format of mol2vec featurize?

To quote from a documentation of the program here (still assuming only it were the one of the question): Subcommand 'featurize' Featurizes new samples using pre-trained Mol2vec model. It saves the ...
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  • 23.6k
4 votes
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Computational determination of the diagram of molecular orbitals of a polyatomic chemical species

You can visualize isosurfaces of the molecular orbitals in gview. This allows you to identify the orbitals visually. That is a way to determine that the HOMO is a lone p-orbital of the oxygen atom. I ...
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4 votes
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Matrix elements evaluation in Hartree-Fock method

Electronic structure theory at the end of the day is "advanced quantum mechanics". IMO, one should understand the symbols from a QM perspective before applying it here. Is $1/r_m$ an ...
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  • 65.8k
4 votes
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How can I formally justify the description of an electronic excitation that includes only the relevant orbitals?

The answer here depends on what you mean by "formal procedure" and "physically valuable". The potential flaw in your approach is the assumption that $$\Psi=\cos(\Omega_R)\sigma_\...
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  • 8,860
3 votes

How to give different color to each type of heteroatom during substructure matching in RdKit

If you scale the visual representation of the molecule, i.e. replace the current definition of the image by IPythonConsole.molSize = (400,400) instead of (250,250),...
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  • 23.6k
3 votes

On the definition of eigenframe

I can't find anything definitive but both https://www.thestudentroom.co.uk/showthread.php?t=4172326 and https://www.physicsforums.com/threads/eigenframe-definition-please.876035/ suggest that an ...
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  • 2,463
3 votes

Why does exchange integral 1s2p not vanish for Helium excited state?

Introduction I start off this derivation more generally and analyize the configuration where $(n_A,\ell_A) \neq (n_B,\ell_B)$. By $E_{ n_A\ell_Am_A,n_B\ell_Bm_B}^{Z_1,Z_2}$. Later, I restrict my ...
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3 votes
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Variational (Rayleigh-Ritz) method and multielectron wavefunction

One Electron Starting with your trial wavefunction: $$ \Phi = \sum^k_{i=1} c_i \chi_i, $$ you seem to be thinking about one-electron orbitals $\chi_i(r)$ which will add up to a one-electron molecular ...
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  • 1,899
3 votes
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Gaussian type orbitals and p-type orbital

No, your understanding is not correct. Let the third centre at which the gaussian product is centred be $R_P$. Now we can write $$(x-x_A)=((x-x_P)-(x_A-x_P))=(x-x_P)-x_{PA}$$ so defining $x_{PA}$. ...
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  • 2,463
2 votes

What is the main difference between computational methods such as Hartree–Fock and tight binding?

In a nutshell The tight-binding model relies on the assumption that we can forgo the GLOBAL antisymmetry of fermions and instead purely work with a LOCALLY antisymmetric basis. In that sense, the ...
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2 votes

Obtaining orbitals from a many-body wave function

For any wave function, you can define the one particle density matrix $\int \psi(x_1, \dots, x_n)\psi^\ast(x_1^\prime, x_2, \dots, x_n) dx_2\cdots dx_n$. The eigenfunctions of this operator are single ...
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