How may I estimate the bond energy of a molecule?
Feb 20, 2025 · Can I estimate the bond energy by running a single Gaussian calculation of the fragments at very long separation (say, 40 angstroms)? Or do I have to calculate each …
What is the method to examine atomic bonds and hydrogen …
May 1, 2025 · Bond path can be straight line or curve, obviously for the latter case the length of bond path is longer than the sum of the distances between BCP and associated two (3,-3) …
What are the types of bond orders? - Matter Modeling Stack …
Laplacian Bond Order This method is an extension of the QTAIM (Quantum Theory of Atoms In Molecules) concept of using the Laplacian of the electron density $\nabla^2\rho$ to …
Number of hydrogen bonds - Matter Modeling Stack Exchange
Aug 26, 2024 · I'm studying hydrogen bonds in a water system. The commonly accepted parameters are: D-A distance = 3.5 Å and H-D-A angle = 30°. To analyze the hydrogen bonds, …
How to carry out BSSE correction in ORCA?
Jan 22, 2025 · 2 I'm working on a diatomic molecule and need to accurately describe its bond dissociation energy. I plan to perform BSSE correction (Counterpoise or some other) for this …
Is it possible to do a Gaussian redundant scan with some fixed …
Jun 18, 2021 · The last line indicates that the bond (B) between atoms 5 and 6 are scanned (S) with 20 steps of size -0.1 Angstrom. In the image you posted in the question, the bond …
Maximum bond length in Vesta - Matter Modeling Stack Exchange
Dec 30, 2022 · I need some cutoff radii to count bonds between different atoms in my system. When a .cif file is opened in Vesta, there are some default values of min and max bond …
Lost atoms in LAMMPS - Matter Modeling Stack Exchange
Nov 1, 2022 · HI @Magic_Number, after running with more recorded timestep, I think the main reason is because the molecule pass through zlo and have atom deleted, as result, the bond …
proteins - From a PDB file, how may I know which atoms have …
Sep 29, 2023 · A bond is present when the distance between two atoms is lower than the sum of the Van der Waals radii of the two atoms. Van der Waals radii are typically looked up from a …
Generate structure using atomic coordinates - Matter Modeling …
Feb 22, 2023 · 10 To understand the new coordinates after altering the bond length of the C-O bonds you can use the below approach: Let us first visualize the positions of all the atoms …