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[求助]
结构空洞如何解释
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This is some information about oxygen atoms in this structure: Atom information Atom Type X Y Z Ueq Um Uvol ChemOccu R-bond R-VdW O5 O 0.716 0.280 0.234 0.049 0.045 0.041 1.000 0.66 1.52 O4W O 0.802 0.135 0.305 0.272 0.272 0.593 1.000 0.66 1.52 O1W O 0.372 0.020 0.713 0.159 0.142 0.225 1.000 0.66 1.52 O3W O 0.058 0.393 0.492 0.281 0.241 0.494 1.000 0.66 1.52 O6W O 0.224 0.960 0.467 0.540 0.540 1.660 1.000 0.66 1.52 O7W O 0.581 0.977 0.499 0.442 . 1.231 1.000 0.66 1.52 O5W O 0.596 0.852 0.407 0.266 0.266 0.575 1.000 0.66 1.52 O2W O 0.888 0.410 0.379 0.185 0.177 0.313 1.000 0.66 1.52 The first one is a fully occupied atom in the main molecule. The others are water molecules in the solvent sphere. The Ueq values of these can be expected to be larger than those in a molecule, but not *that* much larger. These water molecules are almost certainly not fully occupied, and some may not be present at all. Have you tried using SQUEEZE to determine the number of electrons that are present in the space currently occupied by these O atoms? These CheckCif A and B alerts are raised by this structure: 230_ALERT_2_B Hirshfeld Test Diff for C41 -- C42 .. 7.7 su 306_ALERT_2_B Isolated Oxygen Atom (H-atoms Missing ?) ....... O7W Check 417_ALERT_2_B Short Inter D-H..H-D H1WA .. H4WA .. 1.93 Ang. 420_ALERT_2_B D-H Without Acceptor O1W - H1WB ... Please Check 420_ALERT_2_B D-H Without Acceptor O2W - H2WB ... Please Check 420_ALERT_2_B D-H Without Acceptor O3W - H3WA ... Please Check 420_ALERT_2_B D-H Without Acceptor O4W - H4WB ... Please Check 420_ALERT_2_B D-H Without Acceptor O6W - H6WA ... Please Check 601_ALERT_2_B Structure Contains Solvent Accessible VOIDS of . 187 Ang3 The number of restraints is reported as 102, but no details about these restraints were given in the _refine_special_details section of the cif file. This information can also be provided by making use of the restraint CIF dictionary items. The Ueq values of the following atoms are extremely large(Ueq = > 0.15). Either the occupancy is set too high for these atom, or you might need to explore the possibility that these atoms are involve in some form of disorder: O1W O2W O3W O4W O5W O6W O7W. A large solvent accessible void is present in this structure. What is in there? Has SQUEEZE been used and its use not been reported? Please comment on this void and should you have used SQUEEZE, report this in the main paper, the SI and in the cif file. There should be a verbal description of what has been done including an estimate of the number and nature of 'squeezed out' entities in the _refine_special_details section of the cif file as well as the standard SQUEEZE cif output. |
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