# Tag Info

## Hot answers tagged x-ray-diffraction

24

Our group uses both methods a lot so here are some examples why you would use X-ray, in addition to NMR, in organic synthesis. Your compound isn't soluble enough: Colleagues produce very large aromatic systems for organic electronics which are basically insoluble in all solvents. With a good NMR machine (600MHz and up) it might still be enough to get ...

20

I agree with @andselisk that this question is quite broad. I will focus on two specific questions asked The only equation I know for x-ray diffraction is Bragg's Law but is this the only equation used to interpret the data? [...] How do you translate the spots on a detector to electron density plots using Braggs law? Apart from Bragg's law (which tells ...

16

Coming from natural product chemistry, of course the structure elucidation by NMR is the most commonly used method, especially in isolation. NMR requires only a little substance dissolved in whichever deuterated solvent you have on your shelf and is rapidly set up. The only downside is that for very small amounts of sample you will be blocking the strongest ...

11

There are a few reasons, but the most direct answer is that the wavelength of X-ray photons is on the order of the distance between atomic nuclei in solids, e.g. ~ 4 ångströms (bonds are roughly 1.5-2.5 Å). You can think of it like the waves fit nice and snugly between the atoms and "fill" the crystal and thereby give us information about where the "cavities"...

8

You raise an excellent question and the short answer is "yes, quantum chemistry calculations are intrinsically in vacuum". Approximate methods like semiempirical (AM1, PM6, PM7) and hybrid DFT methods (e.g., B3LYP) use experimental data, which often comes from crystal structures. For many years, single-crystal x-ray diffraction studies were the gold ...

6

I'll use quotes from B. Rupp, Biomolecular Crystallography (p. 7-8) to answer. Generally the structure is similar... Comparison of many nuclear magnetic resonance (NMR) solution structure ensembles with crystallographic structure has shown that the core structure of protein molecules remains unchanged compared with the solution state during ...

6

The description given in your question pretty much explains things. I would put it in slightly different words which may or may not help, which is that the x-ray photon induces a dipole moment in the atom (a field induced dipole) which then radiates and so the x-ray is scattered. This is pretty much what happens in scattering by visible photons and we must ...

6

Since there were no further suggestions, I decided to use the references from my comment in an answer, which, I believe, is element 99, einsteinium. Both single crystal x-ray diffraction (SCXRD) and powder x-ray diffraction (PXRD) have certain sample requirements/limitations: Mass/amount PXRD: lower limit is in micrograms region, ideally at least a couple ...

5

Explaining the diffraction of a photon off of a crystal lattice quantum mechanically is the same as finding what momenta can be transferred to the photon by the crystal lattice. The simplest way to model this, as Ivan noted, is to describe the momentum states of a particle in this kind of potential as these are the momenta which can be transferred to the ...

5

You should not really have assumed that the compound was tetragonal. If it was indeed tetragonal, then the peaks corresponding to the $(200)$ and $(020)$ planes would overlap. Instead, you can see that one occurs at $2\theta = 46.7^\circ$ and the other at $2\theta = 47.6^\circ$. The question may be considered a little misleading, but it does hint at this; it ...

4

It is possible to do crystal structure optimizations in Gaussian by adding translation vectors (DFT isn't as good with intermolecular reactions, but it will probably be a better approximation than optimizing without PBC, which is akin to a gas phase molecule). Whether or not solid behavior and gas behavior are similar will depend on the material, and the ...

4

In 3D you will see spots not cones from a single crystal. If you Google for "XRD spot pattern" images, you will probably find yourself enlightened about how many different shapes, and forms diffraction patterns can take. Debye-Scherrer rings are one special case which occurs when you have a diffraction pattern from a very fine powder. In such a powder ...

4

The reflection with $n=2,\;(h,k,l)=(1,0,0)$ is the same as $n=1,(h,k,l)=(2,0,0)$. Yes, I said "same", not "similar"; they are one thing, there are no "both". For this reason, you may just as well abandon using $n$ altogether. As for why the peak is so small compared to others you've seen, let me respectfully suggest that maybe you haven't seen all that many....

4

Not just in the '20s but up to the '90s at least, the d-spacings were estimated by hand measurements of diffractometer peaks or film lines and applying the Bragg formula. d-spacings were then ranked from the most intense down to the least intense. Starting with the 2 most intense d-spacing values - and allowing +/- 0.02 angstrom error margin to each - a ...

3

Structure determination by X-ray diffraction, regardless if powder diffraction, or single crystal diffraction analysis, is a spatial mapping of electron density. After solving a crystallographic structure (phase problem), the subsequent structure refinement includes steps to complete the crystallographic model, and to minimise the differences in the Fourier ...

3

I don't have much information on your particular system: are they nanocrystals? Are you expecting just one or two phases? Dozens of phases? Do you have a lot of amorphous material present? I have one publication you can look at which addresses a rather complicated sample with amorphous, nanocrystalline, and crystalline objects. It is (hopefully) overkill ...

3

You could use HyperSpy library for Python. Some examples of what you can do with it are available here.

3

It is possible to reconstruct molecular structure from powder X-ray data. It is called the Rietveld method: http://home.wxs.nl/~rietv025/ http://www.aps.anl.gov/Xray_Science_Division/Powder_Diffraction_Crystallography/ However, it requires high quality, high resolution data (meaning generally synchrothrone powder data), and it is an involved process which ...

3

What do you hope to achieve? It is possible to obtain accurate interatomic distances from powder data (here is an example, the structures of several alkali metal cyclopentadienides), but the method is non-routine, and the data-parameter ratio is low, which means that you cannot refine many parameters and must put much information in through appropiate ...

3

Does this help? The distance between planes will be less than the distance between atoms in many cases because the atoms don't have to stack directly on top of one another in each plane.

2

First of all, diffraction is best thought of in reciprocal space rather than from planes of atoms, but let me answer your question directly. You may not understand the meaning of a reflection index. If one imagines a simple cubic lattice made up of atoms of diameter a, then the lattice dimension of the cube is also a. The spacing between (100) planes is ...

2

There is a well-known exercise in the basic courses on quantum mechanics: calculate a wavefunction of a 1D system with a rectangular potential barrier in the middle. The results are then interpreted as scattering of a wave on the said barrier: some part of it gets reflected, and some penetrates (probably tunnels) the barrier and continues on its way. Well, ...

2

To answer the last part of your question the amplitude of the scatted x-ray is proportional to what is called the structure factor $F_{hkl}$ and the measured intensity to $|F_{hkl}|^2$. If the unit cell contains i atoms with a scattering factor of $f_i$ each of the atoms are at the coordinate $ax_i+by_i+cz_i$ within the unit cell of where a, b, c are the ...

2

Directions & sites are said to be crystallographically equivalent, because there are symmetry operators that relate them. So learn about simpler symmetry operations (proper axes, mirror planes, centres of inversion) or advanced ones (like screw axes, glide planes, etc.) learn how to recognize them in every-day's life. It may be helpful for ...

2

Best reason I can think of is that you're being given data in momentum space rather than position space. You can convert from "position-time" space, which is what we're comfortable with as humans, and describe the system in "momentum-energy" space, which is simpler from a physics point of view. Position is the reciprocal of momentum and energy is the ...

2

The definition of a substance that is "multi-phase" is that there is more than one distinct compound in it and the compounds form distinct regions in the substance with different properties. Examples make this clearer. Salt dissolved in water forms a uniform mixture: a salt solution. There is more than one compound there but they are perfectly mixed. ...

2

Reciprocal space One way to derive the formula is to use reciprocal space coordinates. The reciprocal space lattice has three unit cell vectors, a*, b* and c*. The diffraction vector d* is given by: $$d^* = h a^* + k b^* + h c^*$$ The d-spacing is given by the reciprocal length of d*. The relationship between direct space and reciprocal space unit cell ...

2

We know that the planes (h k l) are the planes which are perpendicular to the vector (h, k, l). Thus, their equations are: $$hx+ky+lz=D$$, in which D is a real number. But these planes have to pass through atoms of the crystal. So, $$D=na$$, where a is the lattice parameter and n is a natural number (e.g., 1, 2, 3, ...). So, the planes have the equation: ...

1

A metal phosphine complex, dichlorobis(triphenylphosphine)nickel(II) exists in two isomeric forms (blue and red) based on how you prepared it (Wikipedia). The blue isomer, which is paramagnetic can be prepared by treating hydrated nickel chloride ($\ce{NiCl2.6H2O}$) with triphenylphosphine in alcohols or glacial acetic acid. When allowed to crystallize from ...

1

You might have success with amorphous carbon sheets[1]. It's not cheap, but it's effective. It's the material used in the windows of the AMPIX cell[2] developed at Argonne. It does react at low potentials, though, so might not work for anode studies. Have you considered aluminum? It's crystalline, but cubic so there aren't very many peaks to worry about. ...

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