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请斑竹把我的20金币转给xi2004
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我请xi2004给我解释了一个结构,请斑竹把我的20金币转给xi2004, 谢谢! 个人觉得人家不容易,花这么多时间给我解释了这么多, 应该和大家分享,下面是我的文件和解释内容,供大家学习了.呵呵, 再次谢谢xi2004!!! ----------------------------------------------------------------------------------- 部分的CIF内容: data_I #================================================== # CHEMICAL DATA _audit_creation_method SHELXL-97 _chemical_name_systematic ; ? ; _chemical_name_common '5, 5'-dithiodisalicylic acid' _chemical_melting_point 523 _chemical_formula_moiety 'C14 H10 O6 S2' _chemical_formula_sum 'C14 H10 O6 S2' _chemical_formula_weight 338.34 loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source 'C' 'C' 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'H' 'H' 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'O' 'O' 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'S' 'S' 0.1246 0.1234 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' _symmetry_cell_setting Orthorhombic _symmetry_space_group_name_H-M P2(1)2(1)2(1) _symmetry_space_group_name_Hall P2ac2ab loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x+1/2, -y, z+1/2' '-x, y+1/2, -z+1/2' 'x+1/2, -y+1/2, -z' _cell_length_a 5.3065(6) _cell_length_b 11.1657(13) _cell_length_c 23.906(2) _cell_angle_alpha 90.00 _cell_angle_beta 90.00 _cell_angle_gamma 90.00 _cell_volume 1416.5(3) _cell_formula_units_Z 4 _cell_measurement_temperature 298(2) _cell_measurement_reflns_used 2489 _cell_measurement_theta_min 2.498 _cell_measurement_theta_max 25.478 _exptl_crystal_description needle _exptl_crystal_colour yellow _exptl_crystal_size_max 0.24 _exptl_crystal_size_mid 0.15 _exptl_crystal_size_min 0.14 _exptl_crystal_density_meas none _exptl_crystal_density_diffrn 1.587 _exptl_crystal_density_method 'not measured' _exptl_crystal_F_000 696 _exptl_absorpt_coefficient_mu 0.403 _exptl_absorpt_correction_type multi-scan _exptl_absorpt_correction_T_min 0.9095 _exptl_absorpt_correction_T_max 0.9458 _exptl_absorpt_process_details '(SADABS; Bruker, 1999)' #========================================================================== # EXPERIMENTAL DATA _exptl_special_details ; ? ; _diffrn_ambient_temperature 298(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\a _diffrn_radiation_source 'fine-focus sealed tube' _diffrn_radiation_monochromator graphite _diffrn_measurement_device_type 'CCD area detector' _diffrn_measurement_method 'phi and omega scans' _diffrn_detector_area_resol_mean ? _diffrn_standards_number 0 _diffrn_standards_interval_count 100 _diffrn_standards_interval_time ? _diffrn_standards_decay_% 0 _diffrn_reflns_number 6436 _diffrn_reflns_av_R_equivalents 0.0428 _diffrn_reflns_av_sigmaI/netI 0.0516 _diffrn_reflns_limit_h_min -6 _diffrn_reflns_limit_h_max 6 _diffrn_reflns_limit_k_min -13 _diffrn_reflns_limit_k_max 13 _diffrn_reflns_limit_l_min -28 _diffrn_reflns_limit_l_max 12 _diffrn_reflns_theta_min 1.70 _diffrn_reflns_theta_max 25.01 _diffrn_measured_fraction_theta_max 1.000 _diffrn_reflns_theta_full 25.01 _diffrn_measured_fraction_theta_full 1.000 _reflns_number_total 2502 _reflns_number_gt 2060 _reflns_threshold_expression >2sigma(I) _computing_data_collection 'Bruker SMART(Bruker, 2004)' _computing_cell_refinement 'Bruker SMART(Bruker, 2004)' _computing_data_reduction 'Bruker SAINT' _computing_structure_solution 'SHELXS-97 (Sheldrick, 1997a)' _computing_structure_refinement 'SHELXL-97 (Sheldrick, 1997b)' _computing_molecular_graphics 'Bruker SHELXTL(Sheldrick, 1997b)' _computing_publication_material 'Bruker SHELXTL' #========================================================================== # REFINEMENT DATA _refine_special_details ; Refinement of F^2^ against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F^2^, conventional R-factors R are based on F, with F set to zero for negative F^2^. The threshold expression of F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F^2^ are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. ; _refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_weighting_scheme calc _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.0345P)^2^+0.9647P] where P=(Fo^2^+2Fc^2^)/3' _atom_sites_solution_primary direct _atom_sites_solution_secondary difmap _atom_sites_solution_hydrogens geom _refine_ls_hydrogen_treatment constr _refine_ls_extinction_method none _refine_ls_extinction_coef ? _refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881' _refine_ls_abs_structure_Flack 0.49(13) _refine_ls_number_reflns 2502 _refine_ls_number_parameters 199 _refine_ls_number_restraints 0 _refine_ls_R_factor_all 0.0591 _refine_ls_R_factor_gt 0.0449 _refine_ls_wR_factor_ref 0.1028 _refine_ls_wR_factor_gt 0.0960 _refine_ls_goodness_of_fit_ref 1.082 _refine_ls_restrained_S_all 1.082 _refine_ls_shift/su_max 0.000 _refine_ls_shift/su_mean 0.000 _refine_diff_density_max 0.401 _refine_diff_density_min -0.283 _refine_diff_density_rms 0.057 ------------------------------------------------------------------------------------------------- Check出来的问题 1. REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 25.01 From the CIF: _reflns_number_total 2502 Count of symmetry unique reflns 1495 Completeness (_total/calc) 167.36% -------------------------------------------------------------------------------------------- xi2004关于这个问题的分析: 由于你这个晶体最重的元素是S, 所以绝对构型很难用反常散射来确定. 从修正结果看, flack parameter =0.49(13), falck值大,偏差也大,可以说绝对构型并没有确定, 或者你的化合物根本就是racemic. 所以我在你的CIF中加了 _chemical_absolute_configuration unk ,而把flack参数的两行给去掉了, 意思是说绝对构型无法确定. 这样处理, 那个alert G还在, 但编辑询问时是可以如上面回答的. 不过, 实际上, 如果绝对构型无法确定时, friedel pairs是应该被merged掉的, 就是说要在.ins中加merg 3, 这样一来, unique reflection的数目就要减少了, 而cif文件中关于flack parameter 的两行还是要删去, 仍然要加 _chemical_absolute_configuration unk 但这样一来unique reflection number/parameters 的比例就小了, 你那个omit -2 50 就要改成 omit -2 54才可以. 我认为这样处理才是对的. 不过, 目前, 我没有做merg 3,送给你的文件中, 只是做了上述第一部分的处理. 具体的, 要等编辑意见回来后, 照他说的来改为好. 综上所述, 1. 由于你的结构中重原子只是S, 不够重, 导致用反常散射来确定绝对构型困难. 所以要在CIF中加 _chemical_absolute_configuration unk 2.更麻烦的是, 这种情况, 编辑可能会要求你收全球的数据, 这样friedel pairs的数目和unique reflection的数目会达到1:1; flack参数的偏差可能会小一些, falck 参数会更可靠些, 或许能确定结构的绝对构型 3. 不论怎样处理, 那个alert G总会在的, 那个不要紧, 可以解释的. 4. 建议不要投ACTA了, 这种非心结构又没有重原子的会很麻烦. 实在要投,那可以先投出去, 听从编辑的意见来改就好. 但要做好收全球数据的准备. 以上供你参考. |
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