Questions tagged [crystallography]
For questions concerning crystalline structures and their properties.
155
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Visualizing Crystal Structures [closed]
I would like to know if there are any free alternatives to VESTA for visualizing crystal structures.
Thanks
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1answer
68 views
What do sequence numbers in PDB files actually mean and why don't they match the sequence?
I am studying the 3D structure of the LDH from x-ray crystallographic imaging I was pointed to from Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry ...
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27 views
Appearance of drying hemoglobin-and-salt droplets
I initially posted these or similar images at the bio site because they looked to me like organic/mold contamination in a slide (low power) containing hemoglobin and salt. As the slide dried these ...
2
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1answer
52 views
How to identify 'water' mistakes in protein crystal structures: Are B-factors and occupancy good indicators?
When solving the structure of a protein from diffraction data (x-ray crystallography), it can sometimes be difficult know what should be modelled into small spheres of electron density that are not ...
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148 views
What determines the kind of Bravais lattice structure (body-centred cubic, hexagonal, etc) a transition metal shows?
With the exception of Zn, Hg, Cd and Mn transition metals most transition metals have only one kind of lattice structure at room temperature. Another trend I noticed was that Groups 3 and 4 have ...
5
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2answers
442 views
Why are there only 14 types of Bravais lattices and not 28 when there are 7 types of unit cells and each can have four variations?
As the title suggests, I can't understand why certain kinds of variations (like Face-centred or Body-centred) are restricted to certain types of unit cells. An orthorhombic unit cell has Primitive, ...
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1answer
161 views
How many 4th nearest neighbours are there in an hcp lattice?
My teacher told us that there are 18 4th nearest neighbors in an hcp lattice, at a distance of √3a . I have only been able to identify 12.
Can you help me find all the 4th nearest neighbors?
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24 views
What does “Average Width” mean in crystallography?
Mathematician G. Polya noted (the solution for Problem 8, Axes of a Cube) in his book How to Solve it:
... there are three kinds of axes:
(1) 4 axes, each through two opposite vertices ...
(2) 6 axes,...
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1answer
48 views
In crystallography, how does the real space R factor relate to the atomic B factor?
In assessing the quality of different parts of an atomic model derived from diffraction data, you can look at the real space R factor or at the atomic B factor. Do these give the same information or ...
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1answer
377 views
Radius ratio of octahedral interstitial site in BCC lithium
Problem
Determine the minimum radius of an atom that will just fit into (a) the tetrahedral interstitial site in FCC nickel and (b) the octahedral interstitial site in BCC lithium.
Solution
(a) For ...
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30 views
HCP and hexagonal primitive cell [duplicate]
There are 14 types of Bravais lattices one of them is hexagonal which is just present as primitive cell ie the basis are at its corners , now when I read about hexagonal closed packing I came to know ...
2
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1answer
218 views
Whats the difference between unit cell and motif?
The definition in my material is that motif and unit cells are both a repeating unit, but whereas motif is with respect to 2D lattice the unit cell is with respect to 3D lattice. But I can't find ...
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32 views
Debye–Waller factors for tin(IV) oxide
How I could find the bulk Debye–Waller factor for tetragonal rutile type $\ce{SnO2}$ at room temperature?
I have been doing some online digging with no luck. If anyone has a reference I could use that ...
4
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1answer
103 views
Getting an “index” of 7 for a set of powder diffraction data
I tried to index powder diffractogram from the following problem:
A metal (of density $\pu{0.862 g cm^-3})$ gives the following powder X-ray diffraction data $(\lambda = \pu{1.5418 Å}).$
$$2\theta \...
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0answers
36 views
Find the Linear Packing factor of FCC [-1 -2 1]
I have been trying to figure out this question, and essentially if I assume that the only atoms that the vector touches are the starting and ending atoms, then I get 0.58. I am trying to find a more ...
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2answers
130 views
$P 4_{2} 22$ tetragonal group choice of origin for symmetry of special projections
I was looking at the description of the tetragonal group $$P 4_{2} 2 2$$ (No 93 in the International Tables of Crystallography) and there is one aspect that I do not understand. Namely, what is the ...
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34 views
octahedral interstitial sites located entirely within a full hexagonal HCP unit cell at a height of $c/4$ up from the bottom of the unit cell
I have been trying to visualize and find the number of them for a while, through the image attached.
I can't tell whether the c/4 part includes the octahedral site or not...how should I go about ...
5
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2answers
421 views
Why is the base-centered orthorhombic crystal lattice a unique crystal system?
I'm having difficulty understanding why the base-centered orthorhombic crystal system is a unique crystal system. When I draw two base-centered orthorhombic unit cells next to each other there appears ...
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253 views
Why is U the symbol for lattice energy?
I often see $U$ or even $\Delta U$ being the symbol for lattice energy. Why is that? Does it refer to internal energy?
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1answer
32 views
Miller Indices of Goldnanoparticles from Turkevich and Frens method
I need the miller indices of gold nanoparticles that were synthesized after the route of Turkevich and Frens. I during my research I found a lot of publications, but it looks like no one measured it ...
2
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1answer
1k views
Finding the atomic packing factor (APF) of Sodium Chloride and other FCC ionic compounds
For a piece of coursework I am doing, I need to calculate the atomic packing factor of some ionic compounds. I have had no formal teaching in this area, so what I know comes from information I have ...
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1answer
40 views
What is meant by "basis" in "... its basis in particles leads to a material comprising crystallites or grains tightly bound together, ..."?
I am currently studying Ultrasonic transducers – Materials and design for sensors, actuators and medical applications by Kentaro Nakamura. In chapter 1.2.1 Ferroelectricity, the author says the ...
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1answer
109 views
What is the precision of intensity data in XRD measurement?
I made some relative crystallinity measurements on a zeolite (crystalline aluminosilicate). Which is measured for a specific peak area and compared with a reference sample.
The XRD of powder patterns ...
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1answer
94 views
Can a crystal structure of a substance appear or disappear?
I read somewhere before that some substances no longer crystallize naturally in some specific structures, although it do that readily before. Instead, new structures that never happen before become ...
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Could someone advise me on sources for crystallography and surface sciences?
I'm a physicist learning crystallography and surface science on the side of my research and I came across the concepts: surface reconstruction in hexagonal materials, unit mesh of surfaces, etc.
I was ...
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53 views
Conventional unit cell for a hexagonal crystal system
The figure shows a unit cell of a hexagonal crystal system. Drawn in bold, is the unit cell. The lightly shaded one is a unit cell as well and has a six fold symmetry along an axis, hence is more ...
3
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2answers
370 views
Trouble understanding interplanar spacing using miller indices
We know that two parallel planes have the same Miller indices, this implies that we can have an infinite number of parallel planes close to one another all of which have the same Miller indices.
But ...
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1answer
140 views
How to differentiate hydrous and anhydrous compound? [closed]
For an experiment, my teacher gave me containers of hydrates and their corresponding anhydrous compounds, but I have a feeling that for one of the compounds she switched the hydrate and anhydrous ...
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2answers
165 views
If stirring negatively affects crystal purity, why is it so?
My Intellectual Expectations
Intuitively, I would expect strong stirring to improve crystal purity during the process of crystalization. My rationale is that strong stirring would increase contact ...
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1answer
55 views
The formation of ice crystals on/in frozen food that has been defrosted and then frozen again
I made a mistake. I put my ice cream in the refrigerator instead of the freezer and left it there for a night. I realized my folly the next day.
I put it in the freezer. When I took it out, I noticed ...
2
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0answers
107 views
What does the order of a class mean in a character table?
I am not from a chemistry background. I am trying to see how the symmetry operations affect the stiffness tensor which led me in the path of understanding character tables. I am looking at the ...
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3answers
574 views
Are crystallographic omit maps only used with molecular replacement?
(This is in the context of macromolecular X-ray crystallography.)
From Lamb et al. 2015:
Model bias is the result of how maps are calculated: because the
phase estimates [of the structure factor] for ...
8
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3answers
392 views
If you accumulate 100 identical spheres how many will end up on the surface?
So far I have asked this question in physics, engineering and math sections but have not gotten an answer in three years. If you have 100 identical spheres and group them into A sphere shape, how many ...
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1answer
72 views
Change of ionic packing upon crystals are pressurized
When rock salt crystal is pressurized, its FCC structure changes to BCC structure whereby coordination ratio changes from 6:6 to 8:8. At the same time packing efficiency of the crystal decreases from ...
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1answer
76 views
Will these K-alum crystals combine into a "cohesive/well-glued" mass?
The attempt to make a single solid mass of K-alum, using over 125 grams of McCormick K-alum powder, has resulted, in less than 2 hours, in:
So besides the growth around the loop of the seed "...
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1answer
543 views
How do I find miller indices for a plane whose intercepts are fractions of the lattice constant?
[I'm talking with respect to cubic lattices alone.]
For instance, if a plane has $x,y,z$ intercepts $a/2,a/2,a/2$ (where $a$ is the lattice constant) the miller index would be $[2\space2\space2]$. The ...
4
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2answers
106 views
Is there a standard scholarly reference for lattice constants of crystals of the elements?
I need to discuss the lattice constants of bulk crystals of several metal and semiconductor elements. I can find plenty of tables and numbers that are probably "close enough" but for a paper ...
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42 views
Any open-source to animate 2D materials in 3D. (e.g. van der Waals heterostructures, 2D crystal layers etc.)
I want to model different 2D nano-structures, layered materials in 3D (animated version). Is there any open source where I can build these structures. Like this:
3
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1answer
64 views
Why should the scalar product of the components along two axes remain unchanged after transformation?
A couple of proofs from Chapter 2 of "Space Groups for Solid State Scientists" are giving me a hard time (see attached image).
So what I understand is:
"r" was the original ...
3
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3answers
2k views
Converting fractional coordinates into cartesian coordinates for crystallography
So let's say for a given molecule I have the volume of a unit cell, the shape of the unit cell (monoclinic, cubic, etc), the cell angles alpha, beta, and gamma, the cell lengths a,b, and c, and a list ...
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814 views
How to find bond lengths from .cif files of crystal structure
I am confused about how to calculate the bond lengths within a given structure given its .cif file. I have highlighted the bond of interest in the image below. The atom coordinates are shown in the ...
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38 views
What is meant by "rotation about an axis that passes through a lattice point"?
I am currently studying Introduction to Solid State Physics, 8th edition, by Charles Kittel. In the section Fundamental Types of Lattices of chapter 1, the author says the following:
Crystal lattices ...
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25 views
Crystmet or alternative metals/alloys/intermetallics powder diffraction database
Does anyone know what happened to Crystmet, the metals structure database? The website seems to have disappeared.
Is there any way to access the database or is there a recommended powder diffraction ...
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2answers
216 views
Sketching lattice points, primitive axes, primitive cell, and basis of atoms
I am currently studying Introduction to Solid State Physics, 8th edition, by Kittel. Chapter 1 provides the following figure and accompanying explanations:
It also says the following:
An ideal ...
2
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1answer
51 views
Free refined value in Rietveld
I have a question about Rietveld refinement
The author of this paper claimed that the free refined CN ligand is 1.081.
However, they does not show how they got that number. They stated it was based ...
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478 views
Why rutile structure have primitive unit cell instead of body centered?
In the literature (Wikipedia), I read that $\ce{MgH2}$ have a structure of rutile. Then, I looked at its space group which is $P4_2/mnm$. From this notation, I understood that it possesses a (...
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2k views
What are the limitations of the Born-Lande' equation?
The Born-Lande' equation is used to theoretically calculate the lattice energy, $\Delta U$, of ionic compounds. It is often cited as such in literature,
$$\Delta U = -\frac{k_Az_1z_2Me^2}{4 \pi \...
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1answer
856 views
Bonding and coordination of oxygen in a Ga2O3 crystal structure [duplicate]
I'm trying to find the crystal structure of gallium oxide ($\ce{Ga2O3}$). However, I find the images of the crystal structure in the peer-reviewed journals problematic.
First, I hop to the wikipedia ...
3
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1answer
114 views
Origin in a crystal
I am trying to understand the International Tables for Crystallography.
How can I identify the origin in the image on the left?
Without knowing the origin, I cannot identify the position of the ...
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26 views
How to Visualize the crystal planes of calcite?
I've been struggling to visualize the structure of calcite. Most papers say it grows in a rhombohedron capped by (104) faces. However, I don't see why it would do this when looking at it using ...
