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wgfz1979

铜虫 (正式写手)

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虫号: 549156
注册: 2008-04-20
性别: GG
专业: 配位化学

[交流] 请斑竹把我的20金币转给xi2004

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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