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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
How may I estimate the bond energy of a molecule? 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 without the other?
How to carry out BSSE correction in ORCA? 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 molecule While Gaussian handles this in a single step, I'm struggling with how to carry out this correction in ORCA
Is it possible to do a Gaussian redundant scan with some fixed bonds? 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 between 5 and 6 is long, so during the scan, the bond length would have to decrease which is why the step size is negative
Number of hydrogen bonds - Matter Modeling Stack Exchange 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 number of hydrogen bond
proteins - From a PDB file, how may I know which atoms have bonds . . . 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 table, not calculated We can find such tables in chemical reference books or online For instance, here is a link that supplies the following Van der Waals radii
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
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