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【分享】教你如何在CIF文件中表达氢键
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本来是回答4028...同学的问题的. 但那个主题不知道为何被删除了. 看其他人也老在问, 就在这里说一说. 问题一: 向ACta Cryst. C或E投稿, 需要产生氢键表, 该怎么办呢? 正确次序如下: 1. 先在.ins中加 HTAB (加在UNIT后面和FVAR之前的任何地方) 2. 从.lst中 查看可能的氢键, 一般会看到如下 Hydrogen bonds with H..A < r(A) + 2.000 Angstroms and D-H d(D-H) d(H..A) O19-H3 0.864 2.168 154.00 2.969 O4 [ -x, -y, -z ] O21-H6 0.857 1.949 144.74 2.695 O27 [ -x, -y, -z+1 ] 3. 在 .ins中, 加以下行 ACTA BOND $H HTAB HTAB O25 O21 EQIV $1 -x, -y, -z EQIV $2 -x, -y, 1-z HTAB O19 O4_$1 HTAB O21 O27_$2 (加在UNIT后面和FVAR之前的任何地方) 4. 精修n轮到收敛 5. 那么, 在.lst中 你会看到 Specified hydrogen bonds (with esds except fixed and riding H) D-H H...A D...A <(DHA) 0.90 2.34 3.151(8) 149.0 O25-H13...O21 0.86(2) 2.17(4) 2.969(8) 154(8) O19-H3...O4_$1 0.86(2) 1.95(6) 2.695(7) 145(8) O21-H6...O27_$2 5. 而在 .cif中, 你会看到以下信息. 注意一下 symmtry code的对应关系. 比如3556 表示 -x, -y, 1-z _symmetry_cell_setting monoclinic _symmetry_space_group_name_H-M P2(1)/n loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x+1/2, y+1/2, -z+1/2' '-x, -y, -z' 'x-1/2, -y-1/2, z-1/2' (这是P21/n空间群相对应的四个symmetry operations) loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA _geom_hbond_site_symmetry_A O25 H13 O21 0.90 2.34 3.151(8) 149.0 . O19 H3 O4 0.86(2) 2.17(4) 2.969(8) 154(8) 3 O21 H6 O27 0.86(2) 1.95(6) 2.695(7) 145(8) 3_556 问题二: 如何查看不常见的氢键?, 用别的程序算出来的氢键, 其acceptor的symmetry code对称码与shelx算的不一致怎么办? 象C-H...O这类氢键, Shelx好象不给计算, 至少是我不知道如何算. 那么怎么算呢? 方法一: 用Platon, 或者PWT中的Platon 其中有Calc H-bond或Calc all的命令 方法二: 用Material Studio可以检查, 但要把C设为donor 但是, 根据一些虫子的报道, Platon算出来的氢键, 其对称操作码会和XP和shelx 算出来的不一致. 这个, 据我查看, 好象是Platon计算时, 有时会把你的文件中的有些原子坐标做个平移.(是不是这个原因, 要请熟悉Platon的人说说). 而要注意的是, 有时候, XP中的symmetry code (用SYMM指令)和最终CIF中的 也会有所不同, 比如 P2(1)/n, 在XP中, 就把-x, -y, -z排在2, 而在cif中是在3. 我的看法, 如果你的结构是用Shelx或Shextl解的, 可以用Platon计算非常规氢键, 但不要相信platon所给的对称操作码, 因为platon做计算时可能把有些原子的坐标平移了. 这时候, 要回过头来用XP来查对正确的对称操作码. 比如我举的上述例子, 用Platon算的, 有个氢键是 O(21) --H(6) ..O(27) [ 2545.07] 0.86 1.95 2.6946 145 那你用XP打开.ins, fmol后, arad 0.2 2 2 O21 envi o21 你就会发现与O21距离是2.6946对应的O27的symmetry code是2556, symm 一下, 发现 2 对应的是-x, -y, -z 所以, O27的对称操作是-x, -y, 1-z 而要注意的是, 在CIF中, -x, -y, -z是排在第三个的, 所以O27的symmetry code 最后在CIF中应为3556. 所以, 关键是要明白symmetry code的含义. 然后要以CIF中的为准. 问题三: 对称操作的含义 关于对称操作码的含义, 举个例子: 比如 P21/n 这个空间群, 在CIF中有 _symmetry_cell_setting monoclinic _symmetry_space_group_name_H-M P2(1)/n loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x+1/2, y+1/2, -z+1/2' '-x, -y, -z' 'x-1/2, -y-1/2, z-1/2' 上面四个就是P21/n这个空间群对应的对称操作. 如果你有个氢键是: O21 H6 O27 0.86(2) 1.95(6) 2.695(7) 145(8) 3_556 就表明: O27的坐标是在 -x, -y, 1-z的位置. 其中3表示空间群P21/n的第三个对称操作, 即'-x, -y, -z' ; 也就是在_symmetry_equiv_pos_as_xyz 中排第三的那个操作. 而556表示在a, b ,c方向上的平移. 5不平移. 6是往正方向平移一个单胞, 即+1, 4是-1. 注意一下, 在.ins中, 对称操作数目对有心的空间群来说是减半的, 而且x, y, z这个操作也不会出现. 比如 上述P21/n, 在.ins中, 就只出现 0.5-X, 0.5+Y, 0.5-Z 具体举例如下: TITL NONE in P2(1)/n CELL 0.71073 1.0000 1.0000 1.0000 90.000 90.000 90.000 ZERR 1.00 0.0002 0.0002 0.0002 0.000 0.030 0.000 LATT 1 SYMM 0.5-X, 0.5+Y, 0.5-Z [ Last edited by xi2004 on 2009-7-31 at 09:15 ] |
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老实说我对这个没有研究. IUCR如是说: http://journals.iucr.org/services/cif/hbonds.html hydrogen-bond considerations Descriptions and discussion of weak and non-conventional hydrogen bonds (C-H...X, X-H...C and C-H...C) need not always parallel what is accepted for the stronger and more conventional types of hydrogen-bond interactions (X-H...X). The following may be noted: (1) The van der Waals criterion for a weak hydrogen bond can sometimes be unnecessarily restrictive. This criterion is without real scientific basis because hydrogen bonds and van der Waals interactions have different distance dependence characteristics. In practical terms this means that a short hydrogen bond formed by an activated C-H donor (chloroform, alkyne or more acidic C-H group) would usually be correctly identified. The problem arises for longer contacts formed by donors of moderate activity. Here, a more detailed look is often necessary and useful. In general, statements like `the contact is shorter than the van der Waals limit and is therefore a hydrogen bond' should be avoided. (2) Unlike strong hydrogen bonds, the weaker varieties are easily distorted by the crystal environment. Therefore, it is useful to discuss hydrogen-bond lengths and angles jointly. A longer C-H...O contact (D > 3.6 Å  may be acceptable as a hydrogen bond if the angle tends towards linearity ( > 150°). Very short C-H...O contacts (D < 3.2 Å with very bent angles (90-110°) should be viewed with some scepticism. In cases of doubt, angular considerations should take precedence over length considerations. (3) Unactivated methyl groups could pose special problems. These are known to sometimes form very short hydrogen-bond-like contacts (perhaps even tending to linearity) but these contacts are most likely repulsive and possibly even destabilising. This situation is, however, uncommon. Methyl groups also form genuine hydrogen bonds. In summary, the results of commonly used geometry programs should not be transferred directly and routinely into tables without adequate inspection of the molecular and crystal structure. Unqualified statements like `the structure is stabilized by C-H...O hydrogen bonds' should be avoided. The study of weak hydrogen bonds is still evolving. Factors like donor acidity, acceptor basicity, hydrogen-bond length, hydrogen-bond angle and possible co-operativity effects should be assessed (even if they are not commented upon explicitly in the paper). For further information, authors could refer to some of the following: (a) Desiraju, G. R. (1991). Acc. Chem. Res. 24, 270. (b) Desiraju, G. R. (1996). Acc. Chem. Res. 29, 441. (c) Steiner, T. (1996). Crystallogr. Rev. 6, 1. (d) Steiner, T. (1997). Chem. Commun. 727. (e) Desiraju, G. R. & Steiner, T. (1999). In The Weak Hydrogen Bond in Structural Chemistry and Biology, Oxford University Press. ----------------------- 再提供一些连接,你看后来告诉大家吧. http://d.wanfangdata.com.cn/NSTLQK_NSTL_QK3698391.aspx http://pubs.acs.org/doi/abs/10.1021/jp054123n http://cat.inist.fr/?aModele=afficheN&cpsidt=16470689 http://cat.inist.fr/?aModele=afficheN&cpsidt=10971303 http://www.kubinyi.de/dd-05.pdf http://citation.nstl.gov.cn/detail.jsp?internal_id=352036 Organometallics , 2006, 25 (24) : 5709-5723 http://www.sciencedirect.com/sci ... 77ffc2f09bce94c1478 |
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