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信源：https://journals.iucr.org/c/services/cif/tips.html The importance of even routine crystal structure **yses is highlighted by Hui et al. [Acta Cryst. C70, 250–255] who say "structural `anomalies', even when first seen in flawed X-ray diffraction data sets obtained under non-ideal (but real world) conditions, carry important messages to anyone willing to listen. Outliers are sometimes truly `noise', but in select cases can be the invitation to discovery." | Hui等人[Acta Cryst. C70, 250–255]强调了即使是常规晶体结构分析的重要性。他们说，“结构‘反常’，即使是在非理想（但现实世界）条件下获得的有缺陷的X射线衍射数据集中首次看到的，也会向任何愿意倾听的人传递重要信息。反常有时确实是‘噪音’，但在某些情况下，可能是发现的邀请。” |
| The following suggestions are intended to help authors produce refinement results and a CIF in which the atoms of the structure, the atom naming and the lists of atomic coordinate and geometric parameters are organised in a logical way. While these matters are mostly cosmetic and do not change the scientific results, they are `good housekeeping' and allow any user of the resultant CIF and publication to easily find an entry and follow the structure description. These concepts require little effort to implement if most of them are attended to during the model building and refinement or at the latest prior to the final refinement. It is much easier to implement this in the instructions input to the refinement program (e.g. in the SHELXL .ins file) than by trying to edit the final CIF. If it is later discovered that another refinement is needed, there will be no need to have to edit the CIF all over again. | 以下建议旨在帮助作者生成精修结果和CIF，其中结构的原子、原子命名以及原子坐标和几何参数列表以逻辑方式组织。虽然这些内容大多是修饰性的，不会改变科学结果，但它们是“良好的内务管理”，并允许所得CIF和出版物的任何用户轻松找到条目并遵循结构描述。如果在模型构建和精修过程中或最晚在最终精修之前注意到这些概念中的大多数，则几乎不需要执行这些概念。在输入到精修程序的指令中（例如在SHELXL .ins文件中）实现这一点要比试图编辑最终的CIF容易得多。如果后来发现需要进行另一次精修，则无需重新编辑CIF。 |
| atom labels | 原子标签 | | The symmetry-unique atoms in the refinement model should be identified by unique labels composed of a number appended to the IUPAC chemical symbol without the use of parentheses (e.g. Zn1, C7 etc.). Chemical and crystallographic numbering should be in agreement wherever possible. Atom labels should be as simple and concise as possible and not contain superfluous characters, e.g. C2 is better than C02. In principle, there is no need to specify the O atom of a water molecule as OW or O5W; just any numbered O label, like O5, will do. Where there is just one atom of a given element, include the digit, i.e. it is preferable to use Zn1 rather than just Zn. | 精修模型中的对称唯一原子应通过由附加在IUPAC化学符号后的数字组成的唯一标签进行识别，而不使用括号（例如Zn1、C7等）。化学和晶体学编号应尽可能一致。原子标签应该尽可能简单简洁，不包含多余的字符，例如C2比C02好。原则上，不需要将水分子的O原子指定为OW或O5W；任何编号的O标记，如O5，都可以。当给定元素只有一个原子时，包括数字，即优选使用Zn1而是仅仅Zn。 |
| H-atom numbers should relate to the atom to which they are bonded, unless this leads to naming ambiguities; chemically ambiguous or complex labels such as HO1 (could mean holmium), H1N4, H1W2 etc., should be avoided. | 氢原子编号应该与它们所连接的原子有关，除非这会导致命名歧义；应避免化学模糊或复杂的标记，如HO1（可能表示钬）、H1N4、H1W2等。 |
| If a structure has more than one chemically identical entity in the asymmetric unit, it is sensible to label both using similar labels and in the same sequence. This might be C1A, C2A... and C1B, C2B... for two molecules, or to start the labels for the second molecule at the next decade, e.g. if one molecule has C1 through to C33, the second molecule could start at C41. | 如果一个结构在不对称单元中有不止一个化学上相同的实体，那么使用相似的标签和以相同的顺序进行标记是明智的。这可能是C1A、C2A……以及C1B、C2B……，对于两个分子，或者在下一个十开始第二个分子的标记，例如，如果一个分子具有C1到C33，则第二分子可以在C41开始。 |
| Two isostructural compounds, even if one is in another report, should be labelled in the same way and the atomic coordinates of both structures defined using the same asymmetric units. This simplifies comparisons of geometry, coordination and packing parameters. The same applies for labelling of atoms in polymorphs. | 两种同构化合物，即使其中一种在另一份报告中，也应以相同的方式标记，并且两种结构的原子坐标应使用相同的不对称单元定义。这简化了几何、坐标和堆积参数的比较。这同样适用于多晶型物中原子的标记。 |
| atomic coordinates | 原子坐标 | | Atomic coordinates for molecular and the unique part of extended species should be supplied as connected sets, i.e. the entire species is shown as one connected entity if the CIF is displayed in PLATON with the NOMOVE option turned on (note that the NOMOVE default is on for a CIF, but off for a .res or .ins file). If this test displays the molecule as two or more disconnected fragments, one or more of these fragments needs to be moved to another symmetry-related position so that all fragments are connected. This can easily be achieved by reading the CIF into PLATON, turning NOMOVE off and then clicking the option to generate a new SHELXL .res file. PLATON automatically moves the atoms into a connected set with their centre of gravity within the principle unit cell. | 分子的原子坐标和扩展物种的唯一部分应作为连接集提供，即如果CIF显示在PLATON中，且NOMOVE选项处于打开状态，则整个物种显示为一个连接实体（注意，对于CIF，NOMOVE默认为打开状态，而对于.res或.ins文件，则为关闭状态）。如果该测试将分子显示为两个或多个断开的片段，则需要将这些片段中的一个或多个中的一个移动到另一个与对称性相关的位置，以便将所有片段连接起来。这可以通过将CIF读取到PLATON中，关闭NOMOVE，然后单击该选项生成新的SHELXL .res文件来轻松实现。PLATON自动将原子移动到一个连接的**中，其重心位于主晶胞内。 |
| Whenever structure geometry permits, it is good practice to choose the set of connected coordinates which specify the asymmetric unit to have their centre of gravity within the primary unit cell (see the above tip on using PLATON). | 只要结构几何结构允许，最好选择一组连接坐标，这些坐标指定不对称单元的重心位于主晶胞内（参见上面关于使用PLATON的提示）。 |
| In systems with hydrogen-bonded networks, it is helpful to choose the asymmetric unit so that the minimum number of symmetry operators is required to specify the hydrogen-bond network. Among other things, these concepts help simplify the labelling of packing diagrams. | 在具有氢键网络的系统中，选择不对称单元是有帮助的，这样就需要最小数量的对称算符来指定氢键网络。除其他外，这些概念有助于简化堆积图的标记。 |
| sorting of atoms | 原子排序 | | Before the final refinement, the list of atoms should be sorted into a logical sequence. As a consequence, the geometry lists in the CIF and any tables generated therefrom will then also be in a logical order. A reasonable sort order might be: (i) group atoms belonging to discrete components together (e.g. multiple molecules in the asymmetric unit, ions or solvent molecules), (ii) sort those groups of atoms into decreasing atomic weight and (iii) sort atoms of the same element into numerically increasing order. The exception to this is that H atoms in calculated positions should immediately follow their parent atom, rather than being sorted to the end of the list. | 在进行最终精修之前，原子列表应按逻辑顺序进行排序。因此，CIF中的几何参数列表以及由此生成的任何表也将按逻辑顺序排列。合理的排序顺序可能是：（i）将属于离散组分的原子分组在一起（例如，不对称单元中的多个分子、离子或溶剂分子），（ii）将这些原子分组按原子量递减的顺序排序，以及（iii）将同一元素的原子按数值递增的顺序排序。例外的是，处于计算位置的氢原子应立即跟随其母原子，而不是排序到列表的末尾。 |
| H-atom treatment | 氢原子处理 | | Authors should note the advice on H-atom treatment given in the SHELXL97 manual, section 4.6: `For most purposes it is preferable to calculate the hydrogen positions according to well-established geometrical criteria and then adopt a refinement procedure which ensures that a sensible geometry is retained'. While this is usually good practice, care must be taken not to assume that a particular site has a certain geometry when defining the H atoms. Allowing methyl groups to rotate is often better than assuming a staggered conformation (i.e. in SHELXL, the AFIX 137 instruction may be preferable to AFIX 33). Except for amides, NH and NH2 groups are not always planar (sp2 N), even when a pi-system is nearby; e.g. if there are two NH substituents on a phenyl ring, the ring cannot delocalise with the lone pair on both N atoms, so at least one of the groups will be pyramidal (sp3 N). | 作者应注意SHELXL97手册第4.6节中给出的关于氢原子处理的建议：“对于大多数目的，最好根据公认的几何标准计算氢位置，然后采用精修程序，确保保留合理的几何结构”。虽然这通常是一种很好的做法，但在定义氢原子时，必须注意不要假设特定的位点具有特定的几何形状。允许甲基旋转通常比假设交错构象更好（即，在SHELXL中，AFIX 137指令可能比AFIX 33更可取）。除了酰胺外，NH和NH2基团并不总是平面的（sp2 N），即使在附近有π体系时也是如此；例如，如果苯环上有两个NH取代基，则该环不能与两个N原子上的孤电子对离域，因此至少有一个基团是金字塔形的（sp3 N）。 |
| With good quality data, especially low-temperature data, it should be possible to locate and even freely refine H atoms on any heteroatom, at least in a test refinement, thus alleviating any risk of ambiguity about the H-atom positions on groups such as amines, hydroxy groups and water molecules. The free refinement of Uiso values for such H atoms can act as a further confirmation of the correct positioning. Plotting contoured difference maps, e.g. using the `ContourDif' option of PLATON and omitting the relevant H atoms (`OmitFromSFC' option), can also aid in confirming the correctness of the H-atom positions. | 有了高质量的数据，特别是低温数据，至少在测试精修中，应该可以定位甚至自由地精修任何杂原子上的氢原子，从而减轻胺、羟基和水分子等基团上氢原子位置不明确的风险。对这种氢原子的Uiso值的自由精修可以作为对正确定位的进一步确认。绘制轮廓差值图，例如使用PLATON的“ContourDif”选项并省略相关的氢原子（“OmitFromSFC”选项），也有助于确认氢原子位置的正确性。 |
| absolute structure | 绝对结构 | | It is no longer necessary to merge Friedel opposites for noncentrosymmetric structures in cases where the anomalous scattering power is too low to allow a definitive value of the Flack parameter to be obtained. With advances ongoing in this area, it is better to archive the Friedel-unmerged reflection file, so that future users of the data might be able to extract useful information from the Friedel pairs as techniques develop. Reporting the Hooft parameter (calculated by PLATON) or the Parson's parameter may also be useful (the latter is calculated in SHELXL2012 or later versions and reported in the CIF if more precise than the Flack parameter). | 在反常散射能力太低而无法获得Flack参数的确定值的情况下，不再需要合并非中心对称结构的Friedel反常散射点。随着这一领域的进展，最好将Friedel未合并的衍射文件归档，这样随着技术的发展，数据的未来用户可能能够从Friedel衍射对中提取有用的信息。报告Hooft参数（由PLATON计算）或Parson参数也可能有用（后者在SHELXL2012或更高版本中计算，如果比Flack参数更精确，则在CIF中报告）。 |
| extinction parameter | 消光参数 | | If the refined extinction parameter is less than three times its s.u. from zero, the value is meaningless and the parameter should not be included in the refinement. | 如果精修的消光参数偏离0且小于其标准不确定度的三倍，则该值没有意义，并且该参数不应包含在精修中。 |
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发表于 2025-3-16 07:33:15
