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Bond length from infrared spectra? - Matter Modeling Stack Exchange If you know the bond lengths of few such compounds, you can derive a very accurate linear correlation between the bond length and the frequency So while you can't directly predict bond lengths from IR alone, you can likely develop a correlation between a particular IR frequency and bond length for a series of related compounds
How may I calculate the bond length between two atoms? Bond formation could be something like 1-P $_ {break}$ You could also run quantum calculations for all possible pairs (or higher order clusters) of atoms or hit the literature to look up experimental bond strengths for greater accuracy
How to use rigid scan with dummy atoms in gaussian? For simplicity, I want to increase the bond lengths between the dummy atom and one O atom (I require a more complex scan) Here is my gaussian input, %chk=scan_test chk # scan hf 3-21g Title Card Required 0 1 X O 1 R1 H 1 R2 2 A1 H 1 R3 2 A2 3 D1
Visualise bonds in ASE - Matter Modeling Stack Exchange To visualize a trajectory in ASE, you have to use the default 'ase' viewer The 'x3d' viewer currently only allows visualizing one structure When you open the ase viewer GUI, you can simply press Ctrl+B to visualize bonds, and Ctrl+U to visualize unit cell In command line, you can simply do ase gui -b md traj to visualize bonds If you want to make a movie that shows the change of the bonds
Maximum bond length in Vesta - Matter Modeling Stack Exchange 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 atomic speci
How to plot molecules with angles and bond lengths I want to make a plot like the one in the picture, with bond lengths on top and a second one with bond angles Again, plotting the molecule, calculating the bond angles and lengths is easy
What is the difference between orbital localisation and NBO? Natural Bond Orbital Theory is basically (among plenty of other uses) providing an orbital localisation scheme to achieve similarity to Lewis structures In some of my answers you have probably read the term 'Lewis-like' structures for these occasions
Lost atoms in LAMMPS - Matter Modeling Stack Exchange 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 atom is lost But I know having a fixed z boundary is possible to run because that's what I found from several lammps papers
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 bonding Standard QTAIM just uses the value of $\nabla^2\rho$ at bond critical points (minimum electron density along the bond, max along orthogonal directions), but these values are unintuitive and often don