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shiandtian

木虫 (小有名气)

[求助] 配位水上的氢是关于镜面对称的,看了审稿意见仍然加不好,求助各位虫友,成分感激 已有3人参与

以下是审稿意见:
Hydrogens of the coordinated water molecules O(1W) and O(2W). Refining hydrogens in close proximity to a heavy atom, especially on room-temperature data, is seldom successful, especially as both O lie on a mirror plane, so in the suggested models each H is disordered between two positions. Thus, some O-H bonds are almost pointing towards the lanthanide atom, with unrealistically short H...Ln contacts of 2.10-2.35 Ang (in one case in 4, as short as 1.76 Ang). Then, these hydrogens do not make a sensible network of hydrogen bonds, which is improbable when there are plenty of acceptors (O) nearby. My suggestions are shown in the attached file 7.res. Here, O(2W)  has its hydrogens related by the mirror plane, hence only one independent H with occupancy of 1. It forms a hydrogen bond with O(3W). Thus there is no hydrogen directed towards the metal. At O(1W), one H atom lies on the mirror plane (like the O itself) and forms H-bond with O(2W)(2-x, y, -z), related by twofold axis. The other H is disordered between two positions related by the mirror plane, and interacts with O(4A)(2-x,1-y,1-z). Note that the latter atom has occupancy of 0.5, which agrees well with the half-occupancy of the H. In this file, O(5W), O(6W) and O(7W) have increased occupancies, better fitting the electron density, so now there is 1.75 H2O per asymmetric unit, or 3.5 per formula unit, and the formula should be
        
_chemical_formula_moiety  ‘C23 H19 Er O10, 3.5(H2 O) '
_chemical_formula_sum            'C23 H26 Er O13.5'
_chemical_formula_weight          686.35
_exptl_absorpt_coefficient_mu     3.798
_exptl_crystal_density_diffrn     1.724
Structures 4 and 5 can be treated similarly.
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leaves922

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7楼: Originally posted by shiandtian at 2017-08-19 16:01:14
我还是不太懂,请问如何更改H的指向,非特殊位置与特殊位置指是什么?...

处在镜面上的都是特殊位置,H的位置自己要找合适的位置,然后定住不修

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9楼2017-08-19 16:19:25
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leaves922

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【答案】应助回帖

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感谢参与,应助指数 +1
shiandtian: 金币+2 2017-08-18 19:33:46
把水分子放进part -1试试,占据数10.5

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2楼2017-08-18 17:36:02
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shiandtian

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2楼: Originally posted by leaves922 at 2017-08-18 17:36:02
把水分子放进part -1试试,占据数10.5

试过了,不过还是出现了3个H,有一个还键连不上~
3楼2017-08-18 19:13:07
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shiandtian

木虫 (小有名气)

引用回帖:
2楼: Originally posted by leaves922 at 2017-08-18 17:36:02
把水分子放进part -1试试,占据数10.5

不好意思,记错了,‘把水分子放进part -1试试,占据数10.5’后,有两个H原子,但是它们和O1W不键连~DFIX 后,会出现3个H,有一个是对称位置的
4楼2017-08-19 09:39:44
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