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怎么精修晶体学占位，如何得到有意义的结果，个人的一些理解。

xujun16

2016/03/27

X射线衍射仪（XRD）

最近论坛很多精修占位的讨论，自己就这方面做一些讨论，有不足之处，敬请指出，以大家一起提高。
(1) introduction
Itis not recommended refining occupancy with near-neighbors in the periodic tableand more than 2 atoms at the same site by only X-ray diffraction method.*
Theprecision with which site-occupancies can be measured depends on the differencein scattering factors of the atoms involved. Therefore it is easy to distinguishscattering of disparate atomic number (such as Mg and Fe) but ordering of atomsthat are adjacent or near-neighbors in the periodic table (such as Al and Si).* If the disorder has three or more type of atomsat the same crystallographic site, the refinement may not lead to physicalmeaningful solution. The refinement of occupancy with near-neighbors could be done with anomalous scattering method. **
(2) General rule:
1) A gooddata is needed: for example, step scan (Cu, 0.02 degree), wide angle (as wideas the diffactometer can), long exposure time, 10s, etc. (dependent on theinstrument); Oneshould also be aware of the fluorescence background (if a compound contains Mn,Fe, Co, using Cu will produce the fluorescence background).
2) Figureof merit: R < 10%, CHI2 > 1. (Giving proper polarization correction is very important, since it corrects the diffraction intensity. http://bbs.instrument.com.cn/topic/6119833)
3) Thethermal displacement parameters should be in the meaningful range. For example, a Uvalue is about 0.005 - 0.025 Å² (B = 78 U). To get thethermal vibration parameters of a compound, one could search for literatures inorder to compare with one's own.
The behavior of thermal displacement parameters is the key informationfor solving disorder problems.
4) Donot refine both occupancy and thermal displacement parameters U or B, sincethey are highly correlated. For example, decreasing U has the same effect asincreasing occupancy.
(3) Example:
Belowtwo examples are given to illustrate how to find the problems and to solve them (two atoms atsame site):
1. Thefirst case shows that Li sits at position 0 0 0.5, full occupied, but Uiso isnegative.

Discussion:
Problem:
Uisois negative. It means that there should be more electrons in this site (more electronsare needed). Li alone does not offer enough electrons in this site.
How tosolve the problem:
In thiscase, we know this site should also have partial Ni. Therefore, it should look likexLi + (1-x)Ni where x is the occupancy.
i)first introduce Ni in this site. Then set the Uiso to value 0.015 (Why set0.015, two reasons: in this sample O shows U 0.022. Ni is heavier that O, settingU(Ni) = 0.015 or 0.010 is reasonable.). Again please look at literatures to get proper values.
ii) setConstraints, Li Ni, xyzU+-f. (how to do it, google it or check information on thisforum: http://bbs.instrument.com.cn/topic/5063558)
iii)Fix U, refine Occupancy.

Sigmais 0.001 which is good.
2. Thesecond case shows that two disordered sites, one site shows B = 1.81 (2), theother shows 0.98 (2).

Discussion:
Problem:
Theresults show that 2(c) site has much larger atomic displacement parameters thanidentical atoms in the 3(g) site. If these two sites have the same content, theB values should be same. Therefore, we expect that 2(c) site has too muchelectrons than it should.
Afterrefinement, the result shows that Sn does not exist in 2(c) site.
Thisexample is taken from book fundamentals of powder diffraction and structuralcharacterization of materials, chapter 16.
4 Conclusion
To refine occupancy, pleasecheck the thermal displacement parameters first. For inorganic compound, itshould be in the range U = 0.005 -0.025 Å². To get thethermal vibration parameters of a compound, one could search for literatures.

Reference:
* Quantitative characterization of site-occupancies in minerals, American Mineralogist, Volume 68, pages 287, 1983.
**Site Occupancies in the Battery Electrode Material LaNi3.55Mn0.4Al0.3Co0.75 as Determined by Multiwavelength Synchrotron Powder Diffraction, J. Appl. Cryst. (1998). 31, 327-332

相关话题

xujun16

第1楼2016/03/27

Site Occupancies in the Battery Electrode Material LaNi3.55Mn0.4Al0.3Co0.75 as Determined by Multiwavelength Synchrotron Powder Diffraction

J. Appl. Cryst. (1998). 31, 327-332
doi:10.1107/S0021889897010911

1

iangie

第2楼2016/04/08

应助达人

谢谢讨论，请问xujun对精修原子位置xyz有什么建议吗？

0

xujun16

第3楼2016/04/08

iangle兄，谢谢讨论。

如果在特殊位置，对称元素上，0， 0.25， 0.5，软件会限制精修。
除了这些情况，一般是同时与温度因子，或与占位同时精修。

0

598878157

第4楼2016/04/27

徐老师，您好！我在精修一个氢氧化物结构的时候发现，如果不加限制条件，H和O分别精修之后，发现H和O的间距变得很大，不能再成键了。请问，这种情况下，H和O需要怎样设置限定条件，才能精修得到比较理想的结果？谢谢您！

0

xujun16

第5楼2016/04/28

H和O需要怎样设置限定条件，才能精修得到比较理想的结果？
解释：
假设你是在做粉末衍射。
X射线和电子有效作用，从X射线得到的信息是电子密度图。通俗来讲，由于H原子只有一个电子，X射线对其不敏感，也就是说很难探测到其存在。另外，粉末衍射强度数据不精确。
所以X射线粉末衍射是无法探测H原子的。
单晶衍射对于小分子有机物，前提是没有无序，是可以看到H的。
如果你想看到准确的看到H原子位置，需要做中子衍射。
如何解决：
当然，如果你知道化合物结构，做理论加氢，并做结构限制（键长，键角）。是可行的。
如何做限制
利用化学知识（比如化学键理论，杂化理论）看看理论键长，键角。O - H 的话应该在 0.9 A 左右。
键角的话，去看看类似化合物。
如有不当之处，请大家指出。
598878157(598878157) 发表:徐老师，您好！我在精修一个氢氧化物结构的时候发现，如果不加限制条件，H和O分别精修之后，发现H和O的间距变得很大，不能再成键了。请问，这种情况下，H和O需要怎样设置限定条件，才能精修得到比较理想的结果？谢谢您！

0

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