# Tag Info

20

B3LYP is still a decent functional at its level of theory (single-hybrid functional), but you're right that there's a general criticism of it, which I largely hear in the form of people saying things like "all they did was B3LYP/6-31G*" to criticize non-experts that blindly use this combination which became the "default" in chemistry for ...

18

You can see it with VESTA software. For example, we can see the different lattice planes of NaCl crystal. [001] plane of NaCl: [101] plane of NaCl: [111] plane of NaCl:

17

I think this review¹ by Head-Gordon is a useful supplement to Nike's answer. Its combines a review of functional development, a benchmarking of various functionals, and an explanation of the design process for the $\omega$B97 functionals. Its also open access, so its a great resource if you are interested in DFT functionals in general. They benchmarked 200 ...

16

I don't have too much to add to the answers of Nike Dattani and Tyberius, but I think the crux is that its capabilities have been historically overestimated. One particular failing of B3LYP is that it tends to underestimate bond energies. However, since the small (and fast) 6-31G* basis set will lead to overbinding, the famous combination B3LYP/6-31G* ended ...

13

Assuming a generic chemistry background I wouldn't assume that knowledge of crystal structure would be too in depth at an undergraduate level. It is definitely encountered, but depending on the type of chemistry you want to go into, you probably never deal with solid state chemistry. I would first explain briefly how crystals are described by periodic ...

13

I highly recommend using pymatgen for this. I coded a surface slab generator for Avogadro and in addition to being slow (since it generates a supercell before carving up the slab) it has a variety of weird hard-to-debug issues. There's a nice example of cutting $\ce{LiFePO4}$ online from materialsvirtuallab.org # Import the neccesary tools to generate ...

12

In the example you highlighted and indeed in most plane-wave DFT codes, there is periodicity in all three dimensions including for surface slab calculations. In the case of a surface slab, vacuum space is commonly added in the $z$ dimension. The vacuum space is there so that an adsorbate can bind of course, but it's also there because of the boundary ...

11

The identification of cavities, for drug design, is beyond the geometric characterization (aka volume). The server and individual software, beside the geometrical cavity determination, characterize them following their functionality and extent of solvent exposure, what sites are suitable for occupancy by hydrophobic groups or by ligand hydrogen-bond donors,...

11

To address the question in the title, I went to Catalysis-Hub and sorted the computed energies from most exothermic to most endothermic. Ignoring the C (g) entries adsorbing onto surfaces (which have computed adsorption energies around -7 eV), the most exothermic entry is $\mathrm{I_{2}\ (g)} + 2* \rightarrow 2 \mathrm{I}^*$ on a Pt(111) surface with a value ...

10

First of all, it's better to define the terms here because probably not all the people here are familiar with SQS right away. SQS is an abbreviation for special quasirandom structures. The illuminating reference here is the work of Zunger et. al. that basically show you that the most relevant parameter to consider when you want if SQS truly resembles a ...

9

Determining a surface energy requires a few steps. Calculate a bulk structure Cut a surface termination manually or using a tool Calculate the surface structure Calculate the surface energy I will try to provide some references to tools and methodology rather than attempting to describe this entire process since it is out of the scope of an SE question. To ...

8

There is currently no tool built into ASE to do this sort of detective work on surface terminations. I highly suggest that you take the approach of trying to eliminate dangling bonds first (for example, Se atoms with only 1 neighbor). This will give you a more reasonable termination, but may not give you the desired Ni-Se ratio. With a complex unit cell ...

8

I'll try to outline an approach in plane-wave DFT. The main idea is to build up the system step-wise and reuse previous results as the number of atoms and therefore the computational burden will grow quickly. Lets start with the simulation using a bulk material with $N$ atoms and assume the surface direction is orientated facing the z-axis. Make sure this ...

8

As mentioned by @GeoffHutchison, PACKMOL is probably the most used one for random dense packing of molecules. Sometimes this might however not suit your needs, e.g. if the shape you want to fit molecules into is not supported by PACKMOL or you want to achieve a certain distance. I achieved good results using the surface tools of ASE. Since it's Python you ...

8

I did some work during my rotation in the Brooks group on surfaces that could act as abiogenesis sources (self-sustaining chemical reactions that become living organisms). Key considerations for Heterogeneous catalysis are: The timescales of your reaction, in our case it was a 24hr high pressure/temperature reaction so we required a driving force to have ...

7

I have used ASE to create slaps of complex, anisotropic materials in the past. However, ase.lattice is not for creating slabs, it's a module containing functions for creating three dimensional Bravais lattices. Some functions you could use are ase.build.surface or ase.build.cut (for lower level control). Examples: from ase.build import surface s1 = surface('...

7

Generally, if you want to perform simulations with some force field, you will have to search the literature for published FFs tailored for your problem. The Stillinger-Weber (SW) model is very popular to describe bulk (diamond) silicon, for which it was designed in the first place. But several reparametrizations have also been published. If you happen to ...

6

For calculating the energy of a surface, we need to split the contribution of the surface and the contribution of the bulk to the total energy. $$E_\mathrm{total} = E_\mathrm{surface} + E_\mathrm{bulk}$$ The term $E_\mathrm{total}$ is obtained from a calculation on a simulation cell that models the surface (let this be Calculation 1). The term $E_\mathrm{... 5 This may be a bit of a rough answer, so apologies in advance... Since the eigenvalues obtained using non-energy-consistent pseudopotentials (i.e. the situation in VASP as far as I know) do not themselves have physical meaning, we typically use a slab system with an explicit vacuum, in order to make reference to vacuum. A more common situation is calculating ... 5 What is surface termination? The following figure should give you a clear understanding of the surface termination. Note that the vacuum should be large enough to avoid the interaction between slabs. How to make the surface termination of a crystal structure? There are lots of methods to realize this. For example, you can use ASE that Tristan Maxson ... 5 The reconstructed$(\sqrt{3} \times \sqrt{3})R30$surface unit cell can be obtained by first applying the rotation matrix$ \begin{pmatrix} 1.0 & 2.0 & 0.0 \\ -1.0 & 1.0 & 0.0 \\ 0.0 & 0.0 & 1.0 \end{pmatrix}$to the primitive bulk unit cell, and then the reconstructed$(001)$surface can be cleaved from this unit cell, or ... 5 I would propably explain that there are different planes within a crystal, show some of them in an animation or pyhsical prop and depending on the depth of the presentation just omit the numbering and details. 4 Wannier90 might not be good at preserving the symmetry. But they probably include a few new methods to enforce symmetry in Wannier90.v.3.1.0. Maybe you can check this. http://www.wannier.org/features/ Also, WannierTools can symmetrize the hr.dat, but from my personal experience it sometimes gives you worse results than the original hr.dat. http://www.... 4 Just some thoughts... All depends on what type of study do you want to do. An aside note: studying the interaction or behavior of a ligand attached to a surface is different to study the passivation of that surface with the same ligand. For only one ligand, you can search the surface for symmetry sites and then, manually (just adding it to a distance lower ... 4 Take care in the figure posted by Jack that the [hkl] notation actually represents the vector plane, that is the direction perpendicular to the plane. The plane are indexed as (hkl). for example, the first figure should be read as (001) plane of NaCl, whereas [001] represents the direction along the c-axis. 4 If your molecules form not too many types of adsorption complexes on your surfaces, then you can built a lattice model with SuSMoST ( http://SuSMoST.com/ ) and run a short Monte Carlo simulation at high temperature. High temperature Monte Carlo gives you essentially a random structure. 4 The work function is surface-dependent, and sensitive to surface reconstructions and passivation, amongst other things. The Fermi level of the infinite bulk material would be a rather crude proxy for the workfunction. You also need to be aware that the Fermi level as computed in most periodic DFT codes is calculated with respect to an arbitrary ... 4 Also, you can use Atomsk and Nanocut. Both are free. Atomsk info (from the site): A free, Open Source command-line program dedicated to the creation, manipulation, and conversion of data files for atomic-scale simulations. "Atomsk: A tool for manipulating and converting atomic data files" Pierre Hirel, Comput. Phys. Comm. 197 (2015) 212-219 doi:10.1016/j.... 4 To answer your first question: the theory has certainly been worked out in some detail. The most accurate approach (a) would involve a quantum transport calculation in the non-equilibrium Green function formalism, describing the tip (L) and the sample (R) as semi-infinite leads, connected by a central region (C), and using the Meir-Wingreen formula to ... 3 I would just like to point out that the question explicitly mentions adsorbing atomic oxygen rather than$\mathrm{O_{2}}\$ (without mentioning the oxygen source or the surface). One can therefore somewhat simplify the question to: what is the strongest bond the oxygen atom can form? In molecules, the strongest bond is the C≡O triple bond in carbon monoxide at ...

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