What's going on elsewhere?

I am trying to make a joint ternary plot where 6 triangular plots are put together in a hexagon shape in Python or MATLAB. I am using it to show the concentration of certain elements of a number of particles. I tried to make one in R and MATLAB, but to no avail. I would like to write it in Python...

I am trying correlate some experimental properties of a molecule to its calculated equilibrium geometry. To do so, I calculated the geometry and energy of some conformers. Now, I obtain mixed results when performing the same energetic calculation with dispersion-corrected (D3) and not corrected f...

One of the major features of semiempirical methods is that they significantly reduce the cost of evaluating 2-electron integrals. In general, they follow the formula for HF, but, introduce many simplifying assumptions. In HF for same spin electrons you need to calculate both coulomb and exchange...

I'm not sure the exact difference between the MCSCF and CASSCF methods. I know that the CASSCF method proceeds by optimizing both the CSFs and MOs (I mean the coefficients), but I don't know if this is also the case in MCSCF calculations. My guess is that in MCSCF only the coefficients of CSFs w...

I was thinking about an organic chemistry problem a few days ago but reached a dead end. There were 2 parts to this question. The first was thinking about the isomers of 'C4H3X2' [where X could be anything like a halogen or a deuterium etc]. I came up with the following 7 isomers: (I've really t...

To the best of my understanding Bq (or H-Bq) will add a ghost atom, remove the electrons and set the nuclear charge to 0. I was wondering if the x keyword behaves differently, I could not find any details on what the x keyword does.

I need to calculer the vibrational frequencies on a graphene oxide structure. Problem is, i am not sure what basis set should i use. Isn`t def-svp used for smaller molecules? Would it work with GO?

Yesterday a Reddit user posted a page from Morrison's Organic Chemistry in which it is said that singlet methylene is less stable than triplet methylene. Another user asked basically the same I'm asking here, as he got no answer and probably won't get any. I'm used to see radicals (and therefore ...

I'm reading McQuarrie's Physical chemistry textbook [1]. On p. 281, the author explains: If we use a more flexible trial function of the form in which $\psi(\mathbf{r_1},\mathbf{r_2})$ is a product of one-electron functions, or orbitals, $$\psi(\mathbf{r_1},\mathbf{r_2})= \phi(\mathbf{r_1})\phi(...

There's been ample work and media coverage on how to make a long C-C single bond. To my knowledge, the longest stable C-C bond is currently 1.704 Å, prepared by Schreiner Nature 477, 308–311 in 2011. All around us, there's considerable plastics, made from polymerizing alkenes like polyethylene. ...

A colleague of mine suggested to use TPSSh as a functional. Since I am applying Grimme's D3 dispersion correction by default, I was surprised that it wasn't implemented in the standard density functionals, cf. Gaussian Manual (Copy @ The Internet Archive). Since I might not be the only one to co...

I was reading a bit about this technique, Density Functional based Tight binding (DFTB). It's claimed it can provide a speed improvement of several fold when compared to plain DFT, still giving acceptable results. I downloaded one of its free implementations, the DFTB+ package, and started to wor...

I'm trying to do Normal Mode Analysis for my MD trajectory. I'm following Amber tutorial (http://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm) which uses an example of estrogen receptor protein and raloxifene ligand. Since I'm only getting errors from this, I'm having a couple ...

I'm new to SMILES strings, and have noticed that they're not standardised. Firstly, what is the reason for different structures of SMILES strings to represent the same compound? Why not have a standardised format? Secondly, are there any tools to convert between different SMILES strings for a gi...

Why is it so difficult to perform DFT calculations that consider temperature? I have seen that time-dependent DFT is needed to model systems at high temperature. Why is this the case? What about finite temperature functionals? Why is it also acceptable to use zero-temperature functional with TD...

Python module RDKit is great, but it cannot be installed by pip, and therefore it is difficult to use it sometimes in a virtual environment. I am wondering that if there are some alternative python modules that can convert smiles to chemical structures?

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-reaction. The Brusselator model is often mentioned as a model to simulate an oscillating reaction and...

I just recently began to study quantum chemistry and need some clarification for the construction of Kohn-Sham orbitals. Consider a system of several atoms. Let there be $N$ electrons in this system. We can reduce the description of such a system to the $\psi_i$ single-electron wave functions de...

I have written a code in Mathematica and have obtained the final energy of the hydrogen molecule. I have used Gaussian basis functions for this calculation. Now I need to plot the ground state wave function. How can I do so? I just know that the ground state wave function is defined as \begin{ali...

I have made e test with PBE; I used two different input geometries for the same structure and I got two different optimized geometry c lattice parameter difference = 0.06 Angstrom total energy difference = 0.0005 eV