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  1. What are the types of bond orders? - Matter Modeling Stack Exchange

    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 characterize …

  2. 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) CPs. If you are …

  3. 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 fragment …

  4. Scanning two bond lengths G-16 - Matter Modeling Stack Exchange

    May 9, 2023 · When you are scanning two bond lengths in Gaussian, you step once through the first bond scan, and complete stepping through the second bond scan. For example, consider the case …

  5. 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 …

  6. Generate structure using atomic coordinates - Matter Modeling Stack ...

    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 before and after …

  7. 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 lengths between two …

  8. 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, I plotted the …

  9. 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 connecting that …

  10. proteins - From a PDB file, how may I know which atoms have bonds ...

    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 preexisting …