Iodine salts of the pharmaceutical compound agomelatine: the effect of the symmetric H-bond on amide protonation
Skořepová, Eliška; Hušák, Michal; Ridvan, Luděk; Tkadlecová, Marcela; Havlíček, Jaroslav; Dušek, Michal; CrystEngComm 18 (2016) 4518–; doi:10.1039/C6CE00304D

data_7225044
_publ_section_title
;
 Iodine salts of the pharmaceutical compound agomelatine: the effect of
 the symmetric H-bond on amide protonation
;
_journal_issue                   24
_journal_name_full               CrystEngComm
_journal_page_first              4518
_journal_paper_doi               10.1039/C6CE00304D
_journal_volume                  18
_journal_year                    2016
_chemical_formula_moiety         'C15 H24 I1 N1 O5'
_chemical_formula_sum            'C15 H24 I N O5'
_chemical_formula_weight         425.26
_chemical_name_systematic        'agomelatine hydriodide trihydrate '
_chemical_properties_physical    'Air-sensitive, Oxygen-sensitive'
_space_group_IT_number           14
_symmetry_cell_setting           monoclinic
_symmetry_space_group_name_Hall  '-P 2ybc'
_symmetry_space_group_name_H-M   'P 1 21/c 1'
_atom_sites_solution_hydrogens   difmap
_atom_sites_solution_primary     other
_audit_update_record
;
2016-02-04 deposited with the CCDC.
2016-04-29 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 109.567(9)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   13.5939(11)
_cell_length_b                   7.2782(5)
_cell_length_c                   19.7522(16)
_cell_measurement_reflns_used    1814
_cell_measurement_temperature    301
_cell_measurement_theta_max      26
_cell_measurement_theta_min      4
_cell_volume                     1841.4(3)
_computing_cell_refinement       'CrysAlis, (Oxford Diffraction, 2002)'
_computing_data_collection       'SuperNova, (Oxford Diffraction, 2010)'
_computing_data_reduction        'CrysAlis, (Oxford Diffraction, 2002)'
_computing_molecular_graphics    'CAMERON (Watkin et al., 1996)'
_computing_publication_material  'CRYSTALS (Betteridge et al., 2003)'
_computing_structure_refinement  'CRYSTALS (Betteridge et al., 2003)'
_computing_structure_solution    'Superflip (Palatinus & Chapuis, 2007)'
_diffrn_ambient_pressure         100
_diffrn_ambient_temperature      301
_diffrn_measured_fraction_theta_full 0.994
_diffrn_measured_fraction_theta_max 0.853
_diffrn_measurement_device       Area
_diffrn_measurement_device_type  'Oxford Diffraction SuperNova'
_diffrn_measurement_method       \w
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.024
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -18
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -6
_diffrn_reflns_limit_l_max       25
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            7497
_diffrn_reflns_theta_full        26.061
_diffrn_reflns_theta_max         29.189
_diffrn_reflns_theta_min         3.107
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    1.759
_exptl_absorpt_correction_T_max  0.81
_exptl_absorpt_correction_T_min  0.75
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   'CrysAlis, (Oxford Diffraction, 2002)'
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.534
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       rod
_exptl_crystal_F_000             856
_exptl_crystal_recrystallization_method 'Re-crystallisation from solvent: '
_exptl_crystal_size_max          0.440
_exptl_crystal_size_mid          0.180
_exptl_crystal_size_min          0.120
_refine_diff_density_max         3.06
_refine_diff_density_min         -1.41
_refine_ls_extinction_method     None
_refine_ls_goodness_of_fit_ref   0.9748
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     199
_refine_ls_number_reflns         4236
_refine_ls_number_restraints     1
_refine_ls_R_factor_all          0.0793
_refine_ls_R_factor_gt           0.0565
_refine_ls_shift/su_max          0.0001950
_refine_ls_shift/su_mean         0.0000442
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
;
 Method= Modified Sheldrick 
 w=1/[\s^2^(F^2^) + ( 0.04P)^2^ + 7.06P] 
 ,where P=(max(Fo^2^,0) + 2Fc^2^)/3 
;
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_all         0.1356
_refine_ls_wR_factor_gt          0.1201
_refine_ls_wR_factor_ref         0.1356
_reflns_limit_h_max              16
_reflns_limit_h_min              -18
_reflns_limit_k_max              9
_reflns_limit_k_min              0
_reflns_limit_l_max              25
_reflns_limit_l_min              0
_reflns_number_gt                3042
_reflns_number_total             4236
_reflns_threshold_expression     I>2.0\s(I)
_oxford_diffrn_Wilson_B_factor   4.41
_oxford_diffrn_Wilson_scale      0.09
_oxford_refine_ls_r_factor_ref   0.0793
_oxford_refine_ls_scale          3.59(5)
_oxford_reflns_number_all        4236
_oxford_reflns_threshold_expression_ref I>-3.0\s(I)
_cod_data_source_file            c6ce00304d2.cif
_cod_data_source_block           1
_cod_depositor_comments
;
The following automatic conversions were performed:

'_atom_sites_solution_primary' value 'Other' changed to 'other'
according to
/usr/data/users/saulius/crontab/automatic-downloads/rss-feeds/RSC/lib/dictionaries/cif_core.dic
dictionary named 'cif_core.dic' version 2.4.2 from 2011-04-26.

Automatic conversion script
Id: cif_fix_values 4268 2015-11-12 08:31:59Z antanas 

 Adding full bibliography for 7225043--7225045.cif.
;
_cod_original_sg_symbol_H-M      'P 21/c '
_cod_original_formula_sum        'C15 H24 I1 N1 O5'
_cod_database_code               7225044
_iucr_refine_instruction_details_constraints
;
BLOCK SCALE X'S, U'S 
RIDE O   (  20,X'S) H   ( 201,X'S) H   ( 202,X'S) 
RIDE C   (   4,X'S) H   (  41,X'S) H   (  43,X'S) H   (  42,X'S) 
RIDE C   (   6,X'S) H   (  61,X'S) 
RIDE C   (   9,X'S) H   (  91,X'S) 
RIDE C   (  10,X'S) H   ( 101,X'S) 
RIDE C   (  11,X'S) H   ( 111,X'S) 
RIDE C   (  12,X'S) H   ( 121,X'S) 
RIDE C   (  13,X'S) H   ( 131,X'S) 
RIDE C   (  15,X'S) H   ( 152,X'S) H   ( 151,X'S) 
RIDE C   (  16,X'S) H   ( 161,X'S) H   ( 162,X'S) 
RIDE N   (  17,X'S) H   ( 171,X'S) 
RIDE O   (  19,X'S) H   ( 191,X'S) 
RIDE C   (  20,X'S) H   ( 203,X'S) H   ( 204,X'S) H   ( 205,X'S) 
RIDE O   (  21,X'S) H   ( 211,X'S) H   ( 212,X'S) 
RIDE O   (  22,X'S) H   ( 222,X'S) H   ( 221,X'S) 
END                                                                             
;
_iucr_refine_instruction_details_restraints
;
NO 
REM   HREST   START (DO NOT REMOVE THIS LINE) 
REM   HREST   END (DO NOT REMOVE THIS LINE) 
ANGLE 104.500000 , 1.000000 = H(222) TO O(22) TO H(221) 
DISTANCE 0.820000 , 0.001000 = O(22) TO H(222) 
DISTANCE 0.820000 , 0.0010000 = O(22) TO H(221) 
ANGLE 180.000000 , 1.000000 = I(1) TO H(222) TO O(22) 
END                                                                             
;