审稿意见240610-残留峰,溶剂掩膜

文摘   2024-06-10 00:03   北京  

【关键词】残留峰,溶剂掩膜。residuals,solvent mask

【审稿意见】

There are 4 structures in this paper. 
Please note esd’s for all bond lengths and angles noted in the MS.

Structure 1

Please use a reasonable PART concept when modeling a disorder. Various chemical entities should be easy to identify at a glance. Also, if PARTS aren't used, non-existing distances and angles will be reported in the cif file. Additionally, hydrogen atoms can be added at calculated positions.

These CheckCif A and B alerts are raised by this structure. This is for your information only - you may wish to address these issues before re-submitting your cif file to the CCDC.

097_ALERT_2_B Large Reported Max. (Positive) Residual Density 0.92 eA-3

201_ALERT_2_B Isotropic non-H Atoms in Main Residue(s) ....... 3 Report

The following cif items regarding the software used in this structure determination are missing:

_computing_data_collection

_computing_molecular_graphics

_computing_publication_material

_computing_publication_material

Please supply values for these items.

Structure 2

Looking at the residuals (see attached figures) there is something very strange. These effects can occur for a mixed crystal or if a twinned crystal was measured or if the data reduction went wrong or.... Please check carefully your diffraction data for twinning or try a new measurement or data reduction. What was the exposure time for this measurement? The diffraction data were very weak, maybe a better data set can be obtained. I cannot recommend this structure for publication until these effects have been eliminated or clarified.

If you wish to use a solvent mask, please also comment on the number and nature of the masked entities in the relevant fields of the CIF loops as well as provide a verbal note in _refine_special_details. Your assessment must be backed up by relevant independent data such as TGA. Please note that your final reported sum formula and subsequent items like F(000) etc must contain all entities present in your crystal, including those that have been solvent-masked.

The following cif items regarding the software used in this structure determination are missing:

_computing_data_collection

_computing_molecular_graphics

_computing_publication_material

_computing_publication_material

Please supply values for these items.

Structure 3

Why was a solvent mask applied? A (disordered) HCCl3 molecule can be refined easily, and a better R-value is obtained. Please do or explain why not.

The following cif items regarding the software used in this structure determination are missing:

_computing_data_collection

_computing_molecular_graphics

_computing_publication_material

_computing_publication_material

Please supply values for these items.

Structure 4

The cif item _computing_data_collection regarding the software used in this structure determination is missing. Please supply this value.

【分析回复】

文章中共有四个结构。正文中涉及到的键长和键角均需给出误差值。
对于结构1,审稿人指出在对无序进行精修时,请使用合理的PART概念。各种化学实体应易于一眼识别。此外,如果不使用PARTS,则cif文件中将报告不存在的键长和键角。此外,可以在计算的位置添加氢原子。
在checkcif报告中有些警告,需要解决或解释。cif中缺失一些项需要补充。
对于结构2,审稿人发现残余电子云密度图中有一些非常奇怪的东西。这可能是混晶、孪晶、数据还原有误或者其他一些原因造成的。请仔细检查衍射数据是否为孪晶,或者尝试新的测量或数据还原。这次测量的暴光时间是多少?本衍射数据非常微弱,也许可以获得更好的数据集。
如果希望使用溶剂掩膜,还请在CIF中的相关字段中描述掩膜实体的数量和种类,并在_refine_special_details中提供说明。相关描述必须通过热重等相关独立数据支持。请注意,您最终报告的总和公式和后续项目(如F(000)等)必种类须包含晶体中存在的所有实体,包括那些已被溶剂掩膜的实体。
结构3中审稿人认为不需要进行溶剂掩膜。无序的氯仿分子很容易精修,并获得更好的R值。
审稿人提的问题比较中肯,还比较好解决。对于结构1,只要将无序的部分正确放到不同的PART中即可,每个PART中键长和键角需要是合理的。如果PART错误,会出现一些过短或过长的键长,这时候需要对不合理的原子进行调整。
结构2中出现一些不大,但是位置很奇怪的残留峰。审稿人指出三种可能,混晶、孪晶、数据还原,只需要按照要求挨个排查即可。这个数据衍射很弱,最好重新测定数据。
对于溶剂掩膜的问题,这个是老生常谈了。需要在cif中准确描述掩蔽掉的溶剂个数和种类。而且还需要通过其他表征验证掩蔽掉的溶剂的信息。
对于结构3,只需要将氯仿分子找回来,按无序精修即可。
对于四个结构中cif缺失项只要找到相应信息填进去即可。对应的信息如下。
_computing_data_collection:数据收集用到的程序,一般为APEX或者CAP

_computing_molecular_graphics:结构画图用到的程序,一般为olex2,MERCURY,diamond等

_computing_publication_material:cif编辑用到的程序,一般为olex2

本公众号永远免费且无任何广告。

如需软件下载请去qq群。

如需交流可加公众号微信进微信群:dayouzidanjin

或者qq群:653906413

目前微信一群已满,有兴趣可加二群。

单晶X射线衍射结构测定
本公众号关注于单晶X射线衍射结构测定,包括单晶生长、上机测试,数据处理、结构粗解和精修等等。公益教学,永久无广告,永久免费。
 最新文章