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 ...


19

Boron is a covalent solid with high melting point, like diamond (though not quite), and hence its crystals are hard to make. Unlike diamond crystals, they are not nice and probably wouldn't make a great display. The table on http://periodictable.com/Properties/A/MolarVolume.v.log.html seems to corroborate your findings about boron molar volume being the ...


18

When we are talking about the prediction of materials, it is generally about the structure and corresponding free energy, not the crystallization process. That being said there are a huge number of inorganic materials that predicted to be stable yet no one has synthesized them. There are computational databases like Materials Project that contain ...


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 ...


15

Arguably, there are more such crystals than those which have been made. It is just that nobody bothered to write them all down, because hey, what's the point. A tiny minority of those theoretical crystals haven't been made for the reasons you envisioned, that is, because the conditions of crystallization are hard to achieve. Here by "conditions" we mean ...


11

To be precise, if in a close packed structure (ccp or fcc) there are $n$ atoms or ions then the number of octahedral voids and tetrahedral voids will be $n$ and $2n$ respectively. For example, there are 8 tetrahedral voids per unit cell of fcc structure $(Z_{\text{eff}}=4)$. If you divide the FCC unit cell into 8 small cubes then each small cube has 1 ...


10

Now, as I understand it, all processes proceed so as to maximize the "randomness" of its constituent particles. (Oversimplified version of the Second Law of Thermodynamics, yes, I know... just don't chew me out in the comments section...) Yes. True. This Law can easily be observed in, and verified by, natural processes. Sure. Still with you. Now the ...


10

Imagine an infantry unit of soldiers marching in file. Each of them may be quite irregular, but together they form a repeating pattern. And that's exactly what happens with protein molecules in a crystal. When we say that a protein is irregular, we mean it on a different level. Indeed, one molecule of our protein is irregular if we are talking about the ...


9

I've used Reduce before, which is excellent. I'm not sure what you mean by ' does not always seem to be giving the correct result', though? Perhaps you could file a bug report with the PyMOL team if you think there is a bug in h_add.


9

IFF I remember correctly... Sometimes you have to "move" the plane, in order to see where the axis crosses. Take example 7, if you look at the example plane, the one actually shown, it is (0 ∞ ∞) not very useful. The ones making the examples have "moved the planes" (not really, but it is a useful fiction) in order to get the plane into the unit cell so ...


8

1) Oxygen CAN form 3 or 4 bonds. The most common example is $\ce{H3O+}$ ion This form of bonding is critical to understand basic nature of ammonia solutions, so for exact description of it look that part of the book. 2)Boron also can form more than 3 bonds if at least one its partner provides an electron pair for bonding, not one electron. As a general ...


8

This is a crystallographer’s shorthand for a certain type of space group. You may have heard of the 14 Bravais lattices, e.g. cubic, monoclinic, orthorhombic. These lattices all assume perfect sphere’s at the corners of the elementary cell and potentially also in certain central positions (if the lattice is not a primitive one). In actual X-ray structure ...


8

Ivan basically gave a nice and clear example of what is going in. I’m going to offer a more in-depth explanation. If you were to consider possible crystal structures of just one type of atom, you can boil the possible structures down to a set of similar structures, the Bravais lattices. Only 14 of these exist with different constraints: i.e. the C-centred ...


8

From http://www.crystallography.net/cod/1000062.html one can see that Sn sits in the middle, without any displacement, and mimics the classic Rutile-type structure: I checked original Wikimedia image, and according to metadata CIF retrieved from The American Mineralogist Crystal Structure Database is no longer available. I also failed to discover this ...


8

From the first picture depicted, I would refrain from stating there are five HCl molecules per unit cell. One thing, while there is some choice in the definition of a unitcell (there are several definitions possible, even under the constrain "it should be the simplest and still complete representation possible"), lower multiplicities occur more often; and ...


8

A mole of neutrons in a neutron star would take up about $10^{-20}$ m$^3$. And in a black hole, they would be even smaller.


8

This statement is relevant for the initially [incorrectly] determined structure of $\ce{B2O3}$ by Berger [1, 2] who used powder x-ray diffraction data. You can still access the structure and visualize it in 3D (ICSD 24047), but it was shown later by several researchers and summarized in paper by Gurr et al. [3] that this structure has been erroneously ...


7

For your first question, the original paper (J. Chem. Soc., Dalton Trans. 1984, 1349–1356) that described the geometry index $\tau_5$ defined it as an "index of trigonality". For example, they write for a compound with $\tau_5=0.48$ By this criterion, the irregular co-ordination geometry of $\ce{[Cu(bmdhp)(OH2)]2+}$ in the solid state is described as ...


7

The denominator signifies the number of cubes that are needed to completely encompass the whole point. For example, a corner point can be thought of as a center of 8 whole cubes, while a face centre is enclosed by 2 cubes and an edge center by 4. Hence, only 1/8 of a corner atom is in a specific unit cell and so on and so forth. Consequently, the total ...


7

Olex2 (free, available for Windows, MacOS, Linux) can also be used to add hydrogens to any structure with the similar to PyMOL's command hadd. Example: hemoglobin PDB without H-atoms loaded in Olex2: Executing hadd command adds hydrogens to all atoms where it is appropriate (taking hybridization into account), chemdraw assigns proper bonds order: ...


7

You can think of the body centered cubic lattice as two simple cubic lattice, one with points at coordinates $(ma,na,pa)$ where $m,n,p$ are integers, the other with points at $((m+(1/2))a,(n+(1/2))a,(p+(1/2))a)$. If you work out increasing distances for both omponent cubic lattices you get, in units of $a$: $\sqrt{0^2+0^2+1^2}=1$ $\sqrt{0^2+1^2+1^2}=\sqrt{...


7

With $\sqrt3\over2$ being that close to $1$, BCC packing is better not looked at in terms of coordination spheres. But if you insist... Say you are sitting in the center of a cell. Then: Your first neighbours are at the corners of the same cell. Second neighbours are at the centers of the nearest adjacent cells. Third neighbours: centers of the next ...


7

X-rays do not allow you to look at the material just like an microscope. You get the spacing information from the diffraction pattern of only crystalline materials and a lot of mathematics. On the other hand, atomic force microscopy may actually be able to tell you where one atomic layer starts and where it ends on a surface. For example, imagine a gold ...


6

Atoms on the corners, edges, and faces of a unit cell are shared by more than one unit cell. An atom on a face is shared by two unit cells $\implies$ half an atom belongs to each unit cell. An atom on the edge is shared by four unit cells and an atom on the corner is shared by eight unit cells What does this have to do with the equations? Well lets ...


6

$\ce{NaH}$ has a rock salt type structure meaning each edge has two $\ce{Na-H}$ bonds. When working out bond lengths in a unit cell, you assume the atoms are point charges (i.e. they take up no volume) and so you do not need to know the radius, only the unit cell parameter which as you have said is $\pu{488 pm}$. Since there are two bonds along each edge, ...


6

The image below gives some example of different rotation inversion operations. For the $\bar 6$ operation rotate by 60 degrees (black dot to open circle in the direction towards 3) then invert through the centre of coordinates to the opposite side. Inversion changes a point at (x, y, z) to (-x, -y, -z) thus, in the diagram point 1 becomes point 2 after the ...


5

I would like to say your answer is right, but the question is wrong. Remember that a lattice is "infinitely" repeated units in 3 dimensional space so you should be able to expand the unit cell in x, y and z axes, indefinitely. Now imagine your cubic lattice with an $\ce{Y}$ atom in just 1 (out of 8) corners. Expanding the unit cell in the x-axis will ...


5

This question is possibly a little broad- there are entire books dedicated to methods of structure determination and assignment of stereochemistry. The tl;dr answer is that there is no single method by which absolute stereochemisty can be assigned unambiguously, it depends on the nature of the natural product (terpene, polyketide, polypeptide, etc) and the ...


5

What you call a molecular structure is in reality an asymmetric unit. These two terms are not related, and in general are not interchangeable. The same way $\ce{Pb3O4}$ is not a molecular formula, but a formula unit. All pictures you presented are correct in terms that they do represent an asymmetric unit, but actually an IUCr-recommended asymmetric unit (...


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